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Sample records for radiation-induced genomic instability

  1. DNA damage in cells exhibiting radiation-induced genomic instability

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    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesis that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.

  2. DNA damage in cells exhibiting radiation-induced genomic instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesismore » that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.« less

  3. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levelsmore » of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.« less

  4. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    SciTech Connect (OSTI)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levels of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.

  5. DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage

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    Marchetti, Francesco; Wyrobek, Andrew J.

    2009-01-18

    Exposure to ionizing radiation and other environmental agents can affect the genomic integrity of germ cells and induce adverse health effects in the progeny. Efficient DNA repair during gametogenesis and the early embryonic cycles after fertilization is critical for preventing transmission of DNA damage to the progeny and relies on maternal factors stored in the egg before fertilization. The ability of the maternal repair machinery to repair DNA damage in both parental genomes in the fertilizing egg is especially crucial for the fertilizing male genome that has not experienced a DNA repair-competent cellular environment for several weeks prior to fertilization. During the DNA repair-deficient period of spermatogenesis, DNA lesions may accumulate in sperm and be carried into the egg where, if not properly repaired, could result in the formation of heritable chromosomal aberrations or mutations and associated birth defects. Studies with female mice deficient in specific DNA repair genes have shown that: (i) cell cycle checkpoints are activated in the fertilized egg by DNA damage carried by the sperm; and (ii) the maternal genotype plays a major role in determining the efficiency of repairing genomic lesions in the fertilizing sperm and directly affect the risk for abnormal reproductive outcomes. There is also growing evidence that implicates DNA damage carried by the fertilizing gamete as a mediator of postfertilization processes that contribute to genomic instability in subsequent generations. Transgenerational genomic instability most likely involves epigenetic mechanisms or error-prone DNA repair processes in the early embryo. Maternal and embryonic DNA repair processes during the early phases of mammalian embryonic development can have far reaching consequences for the genomic integrity and health of subsequent generations.

  6. In situ quantification of genomic instability in breast cancer progression

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    Ortiz de Solorzano, Carlos; Chin, Koei; Gray, Joe W.; Lockett, Stephen J.

    2003-05-15

    Genomic instability is a hallmark of breast and other solid cancers. Presumably caused by critical telomere reduction, GI is responsible for providing the genetic diversity required in the multi-step progression of the disease. We have used multicolor fluorescence in situ hybridization and 3D image analysis to quantify genomic instability cell-by-cell in thick, intact tissue sections of normal breast epithelium, preneoplastic lesions (usual ductal hyperplasia), ductal carcinona is situ or invasive carcinoma of the breast. Our in situ-cell by cell-analysis of genomic instability shows an important increase of genomic instability in the transition from hyperplasia to in situ carcinoma, followed by a reduction of instability in invasive carcinoma. This pattern suggests that the transition from hyperplasia to in situ carcinoma corresponds to telomere crisis and invasive carcinoma is a consequence of telomerase reactivation afertelomere crisis.

  7. Radiation-induced instability of MnS precipitates and its possible consequences on irradiation-induced stress corrosion cracking of austenitic stainless steels

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    Chung, H.M.; Sanecki, J.E.; Garner, F.A.

    1996-12-01

    Irradiation-assisted stress corrosion cracking (IASCC) is a significant materials issue for the light water reactor (LWR) industry and may also pose a problem for fusion power reactors that will use water as coolant. A new metallurgical process is proposed that involves the radiation-induced release into solution of minor impurity elements not usually thought to participate in IASCC. MnS-type precipitates, which contain most of the sulfur in stainless steels, are thought to be unstable under irradiation. First, Mn transmutes strongly to Fe in thermalized neutron spectra. Second, cascade-induced disordering and the inverse Kirkendall effect operating at the incoherent interfaces of MnS precipitates are thought to act as a pump to export Mn from the precipitate into the alloy matrix. Both of these processes will most likely allow sulfur, which is known to exert a deleterious influence on intergranular cracking, to re-enter the matrix. To test this hypothesis, compositions of MnS-type precipitates contained in several unirradiated and irradiated heats of Type 304, 316, and 348 stainless steels (SSs) were analyzed by Auger electron spectroscopy. Evidence is presented that shows a progressive compositional modification of MnS precipitates as exposure to neutrons increases in boiling water reactors. As the fluence increases, the Mn level in MnS decreases, whereas the Fe level increases. The S level also decreases relative to the combined level of Mn and Fe. MnS precipitates were also found to be a reservoir of other deleterious impurities such as F and O which could be also released due to radiation-induced instability of the precipitates.

  8. Mechanisms of Low Dose Radio-Suppression of Genomic Instability

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    Engelward, Bevin P

    2009-09-16

    The major goal of this project is to contribute toward the elucidation of the impact of long term low dose radiation on genomic stability. We have created and characterized novel technologies for delivering long term low dose radiation to animals, and we have studied genomic stability by applying cutting edge molecular analysis technologies. Remarkably, we have found that a dose rate that is 300X higher than background radiation does not lead to any detectable genomic damage, nor is there any significant change in gene expression for genes pertinent to the DNA damage response. These results point to the critical importance of dose rate, rather than just total dose, when evaluating public health risks and when creating regulatory guidelines. In addition to these studies, we have also further developed a mouse model for quantifying cells that have undergone a large scale DNA sequence rearrangement via homologous recombination, and we have applied these mice in studies of both low dose radiation and space radiation. In addition to more traditional approaches for assessing genomic stability, we have also explored radiation and possible beneficial effects (adaptive response), long term effects (persistent effects) and effects on communication among cells (bystander effects), both in vitro and in vivo. In terms of the adaptive response, we have not observed any significant induction of an adaptive response following long term low dose radiation in vivo, delivered at 300X background. In terms of persistent and bystander effects, we have revealed evidence of a bystander effect in vivo and with researchers at and demonstrated for the first time the molecular mechanism by which cells remember radiation exposure. Understanding the underlying molecular mechanisms by which radiation can induce genomic instability is fundamental to our ability to assess the biological impact of low dose radiation. Finally, in a parallel set of studies we have explored the effects of heavy iron particle radiation on large scale sequence rearrangements and we have discovered tissue specific differences in sensitivity to homologous recombination. DOE support has given rise to critical new knowledge about the biological impact of low dose rate radiation and about the underlying mechanisms that govern genomic stability in response to radiation exposure. This work has spurred interest in radiation among MIT scientists, and has fostered ongoing research projects that will continue to contribute toward our understanding of the biological effects of low dose radiation exposure.

  9. Low Dose Radiation-Induced Genome and Epigenome Instability Symposium and Epigenetic Mechanisms, DNA Repair, and Chromatin Symposium at the EMS 2008 Annual Meeting - October 2008

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    Morgan, William F.; Kovalchuk, Olga; Dolinoy, Dana C.; Dubrova, Yuri E.; Coleman, Matthew A.; Schr, Primo; Pogribny, Igor; Hendzel, Michael

    2010-02-19

    The Low Dose Radiation Symposium thoughtfully addressed ionizing radiation non-mutational but transmissable alterations in surviving cells. Deregulation of epigenetic processes has been strongly implicated in carcinogenesis, and there is increasing realization that a significant fraction of non-targeted and adaptive mechanisms in response to ionizing radiation are likely to be epigenetic in nature. Much remains to be learned about how chromatin and epigenetic regulators affect responses to low doses of radiation, and how low dose radiation impacts other epigenetic processes. The Epigenetic Mechanisms Symposium focused on on epigenetic mechanisms and their interplay with DNA repair and chromatin changes. Addressing the fact that the most well understood mediators of epigenetic regulation are histone modifications and DNA methylation. Low levels of radiation can lead to changes in the methylation status of certain gene promoters and the expression of DNA methyltransferases, However, epigenetic regulation can also involve changes in higher order chromosome structure.

  10. Radiation-induced mechanical property changes in filled rubber...

    Office of Scientific and Technical Information (OSTI)

    Radiation-induced mechanical property changes in filled rubber Citation Details In-Document Search Title: Radiation-induced mechanical property changes in filled rubber Authors:...

  11. Radiation-induced mechanical property changes in filled rubber (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Radiation-induced mechanical property changes in filled rubber Citation Details In-Document Search Title: Radiation-induced mechanical property changes in filled rubber Authors: Maiti, A ; Weisgraber, T H ; Gee, R H ; Small, W ; Alviso, C T ; Chinn, S C ; Maxwell, R S Publication Date: 2011-04-15 OSTI Identifier: 1227007 Report Number(s): LLNL-JRNL-481283 DOE Contract Number: AC52-07NA27344 Resource Type: Journal Article Resource Relation: Journal Name: Physical

  12. Radiation-induced decomposition of explosives under extreme conditions

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    Giefers, Hubertus; Pravica, Michael; Yang, Wenge; Liermann, Peter

    2008-11-03

    We present high-pressure and high temperature studies of the synchrotron radiation-induced decomposition of powder secondary high explosives pentaerythritol tetranitrate (PETN) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) using white beam synchrotron radiation at the 16 BM-B and 16 BM-D sectors of the HP-CAT beamline at the Advanced Photon Source. The radiation-induced decomposition rate TATB showed dramatic slowing with pressure up to 26.6 GPa (the highest pressure studied), implying a positive activation volume of the activated complex. The decomposition rate of PETN varied little with pressure up to 15.7 GPa (the highest pressure studied). Diffraction line intensities were measured as a function of time using energy-dispersive methods. By measuring the decomposition rate as a function of pressure and temperature, kinetic and other constants associated with the decomposition reactions were extracted.

  13. Genome

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    Decoding dark matter in genes February 19, 2016 Decoding the Dark Matter of the Human Genome Both animal and human studies have shown that traits acquired by the parents, such as stress responses or the ability to store fat, can be passed on to their offspring. While DNA remains unaltered, what triggers these changes in phenotype is the activation or deactivation of genes--in other words, whether certain genes produce the proteins they code for...Possible future applications, for example,

  14. Measurements of prompt radiation induced conductivity in Teflon (PTFE).

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, E.

    2013-05-01

    We performed measurements of the prompt radiation induced conductivity (RIC) in thin samples of Teflon (PTFE) at the Little Mountain Medusa LINAC facility in Ogden, UT. Three mil (76.2 microns) samples were irradiated with a 0.5 %CE%BCs pulse of 20 MeV electrons, yielding dose rates of 1E9 to 1E11 rad/s. We applied variable potentials up to 2 kV across the samples and measured the prompt conduction current. Details of the experimental apparatus and analysis are reported in this report on prompt RIC in Teflon.

  15. Measurements of prompt radiation induced conductivity of Kapton.

    SciTech Connect (OSTI)

    Preston, Eric F.; Zarick, Thomas Andrew; Sheridan, Timothy J.; Hartman, E. Frederick; Stringer, Thomas Arthur

    2010-10-01

    We performed measurements of the prompt radiation induced conductivity in thin samples of Kapton (polyimide) at the Little Mountain Medusa LINAC facility in Ogden, UT. Three mil samples were irradiated with a 0.5 {mu}s pulse of 20 MeV electrons, yielding dose rates of 1E9 to 1E10 rad/s. We applied variable potentials up to 2 kV across the samples and measured the prompt conduction current. Analysis rendered prompt conductivity coefficients between 6E-17 and 2E-16 mhos/m per rad/s, depending on the dose rate and the pulse width.

  16. Collective instabilities

    SciTech Connect (OSTI)

    K.Y. Ng

    2003-08-25

    The lecture covers mainly Sections 2.VIII and 3.VII of the book ''Accelerator Physics'' by S.Y. Lee, plus mode-coupling instabilities and chromaticity-driven head-tail instability. Besides giving more detailed derivation of many equations, simple interpretations of many collective instabilities are included with the intention that the phenomena can be understood more easily without going into too much mathematics. The notations of Lee's book as well as the e{sup jwt} convention are followed.

  17. Measurements of prompt radiation induced conductivity of alumina and sapphire.

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, Eric F.

    2011-04-01

    We performed measurements of the prompt radiation induced conductivity in thin samples of Alumina and Sapphire at the Little Mountain Medusa LINAC facility in Ogden, UT. Five mil thick samples were irradiated with pulses of 20 MeV electrons, yielding dose rates of 1E7 to 1E9 rad/s. We applied variable potentials up to 1 kV across the samples and measured the prompt conduction current. Analysis rendered prompt conductivity coefficients between 1E10 and 1E9 mho/m/(rad/s), depending on the dose rate and the pulse width for Alumina and 1E7 to 6E7 mho/m/(rad/s) for Sapphire.

  18. Radiation-Induced Notch Signaling in Breast Cancer Stem Cells

    SciTech Connect (OSTI)

    Lagadec, Chann; Vlashi, Erina; Alhiyari, Yazeed; Phillips, Tiffany M.; Bochkur Dratver, Milana; Pajonk, Frank

    2013-11-01

    Purpose: To explore patterns of Notch receptor and ligand expression in response to radiation that could be crucial in defining optimal dosing schemes for ?-secretase inhibitors if combined with radiation. Methods and Materials: Using MCF-7 and T47D breast cancer cell lines, we used real-time reverse transcriptionpolymerase chain reaction to study the Notch pathway in response to radiation. Results: We show that Notch receptor and ligand expression during the first 48 hours after irradiation followed a complex radiation dosedependent pattern and was most pronounced in mammospheres, enriched for breast cancer stem cells. Additionally, radiation activated the Notch pathway. Treatment with a ?-secretase inhibitor prevented radiation-induced Notch family gene expression and led to a significant reduction in the size of the breast cancer stem cell pool. Conclusions: Our results indicate that, if combined with radiation, ?-secretase inhibitors may prevent up-regulation of Notch receptor and ligand family members and thus reduce the number of surviving breast cancer stem cells.

  19. The Contribution of Tissue Level Organization to Genomic Stability Following Low Dose/Low Dose Rate Gamma and Proton Irradiation

    SciTech Connect (OSTI)

    Cheryl G. Burrell, Ph.D.

    2012-05-14

    The formation of functional tissue units is necessary in maintaining homeostasis within living systems, with individual cells contributing to these functional units through their three-dimensional organization with integrin and adhesion proteins to form a complex extra-cellular matrix (ECM). This is of particular importance in those tissues susceptible to radiation-induced tumor formation, such as epithelial glands. The assembly of epithelial cells of the thyroid is critical to their normal receipt of, and response to, incoming signals. Traditional tissue culture and live animals present significant challenges to radiation exposure and continuous sampling, however, the production of bioreactor-engineered tissues aims to bridge this gap by improve capabilities in continuous sampling from the same functional tissue, thereby increasing the ability to extrapolate changes induced by radiation to animals and humans in vivo. Our study proposes that the level of tissue organization will affect the induction and persistence of low dose radiation-induced genomic instability. Rat thyroid cells, grown in vitro as 3D tissue analogs in bioreactors and as 2D flask grown cultures were exposed to acute low dose (1, 5, 10 and 200 cGy) gamma rays. To assess immediate (6 hours) and delayed (up to 30 days) responses post-irradiation, various biological endpoints were studied including cytogenetic analyses, apoptosis analysis and cell viability/cytotoxicity analyses. Data assessing caspase 3/7 activity levels show that, this activity varies with time post radiation and that, overall, 3D cultures display more genomic instability (as shown by the lower levels of apoptosis over time) when compared to the 2D cultures. Variation in cell viability levels were only observed at the intermediate and late time points post radiation. Extensive analysis of chromosomal aberrations will give further insight on the whether the level of tissue organization influences genomic instability patterns after low dose radiation exposure. Cells viability/cytotoxicity analysis data are currently being analyzed to determine how these endpoints are affected under our experimental conditions. The results from this study will be translatable to risk assessment for assigning limits to radiation workers, pre-dosing for more effective radiotherapy and the consequences of long duration space flight. The data from this study has been presented a various scientific meetings/workshops and a manuscript, containing the findings, is currently being prepared for publication. Due to unforeseen challenges in collecting the data and standardizing experimental procedures, the second and third aims have not been completed. However, attempts will be made, based on the availability of funds, to continue this project so that these aims can be satisfied.

  20. Stress-related phenomena in transient radiation-induced absorption in optical fibers

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    Looney, L.D.; Lyons, P.B.; Kelly, R.E.

    1988-01-01

    The optical properties of materials can be modified by exposure to radiation and research to investigate these radiation-induced phenomena has intensified over the last several decades. The advent of optical fiber technology and the many applications of optical fiber for information transmission have sharply increased the interest in these investigations. Optical fibers present a long optical transmission path and that path may traverse different adverse environments, including radiation areas. The long tranmission path provides increased potential for interactions between the optical information signal and the optical medium. 10 refs., 10 figs.

  1. Radiation-induced complications in prostate cancer patients treated with radiotherapy

    SciTech Connect (OSTI)

    Azuddin, A. Yusof; Rahman, I. Abdul; Mohamed, F.; Siah, N. J.; Saadc, M.; Ismail, F.

    2014-09-03

    The purpose of the study is to determine the relationship between radiation-induced complications with dosimetric and radiobiological parameters for prostate cancer patients that underwent the conformal radiotherapy treatment. 17 prostate cancer patients that have been treated with conformal radiotherapy were retrospectively analysed. The dosimetric data was retrieved in the form of dose-volume histogram (DVH) from Radiotherapy Treatment Planning System. The DVH was utilised to derived Normal Tissue Complication Probability (NTCP) in radiobiological data. Follow-up data from medical records were used to grade the occurrence of acute gastrointestinal (GI) and genitourinary (GU) complications using Radiation Therapy Oncology Group (RTOG) scoring system. The chi-square test was used to determine the relationship between radiation-induced complication with dosimetric and radiobiological parameters. 8 (47%) and 7 (41%) patients were having acute GI and GU complications respectively. The acute GI complication can be associated with V60{sub rectum}, rectal mean dose and NTCP{sub rectum} with p-value of 0.016, 0.038 and 0.049 respectively. There are no significant relationships of acute GU complication with dosimetric and radiobiological variables. Further study can be done by increase the sample size and follow up duration for deeper understanding of the factors that effecting the GU and GI complication in prostate cancer radiotherapy.

  2. Comparative study of microwave radiation-induced magnetoresistive oscillations induced by circularly- and linearly- polarized photo-excitation

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    Ye, Tianyu; Liu, Han -Chun; Wang, Zhuo; Wegscheider, W.; Mani, Ramesh G.

    2015-10-09

    A comparative study of the radiation-induced magnetoresistance oscillations in the high mobility GaAs/AlGaAs heterostructure two dimensional electron system (2DES) under linearly- and circularly- polarized microwave excitation indicates a profound difference in the response observed upon rotating the microwave launcher for the two cases, although circularly polarized microwave radiation induced magnetoresistance oscillations observed at low magnetic fields are similar to the oscillations observed with linearly polarized radiation. For the linearly polarized radiation, the magnetoresistive response is a strong sinusoidal function of the launcher rotation (or linear polarization) angle, θ. As a result, for circularly polarized radiation, the oscillatory magnetoresistive response is hardly sensitive to θ.

  3. Radiation induced leakage current and stress induced leakage current in ultra-thin gate oxides

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    Ceschia, M.; Paccagnella, A.; Cester, A.; Scarpa, A.; Ghidini, G.

    1998-12-01

    Low-field leakage current has been measured in thin oxides after exposure to ionizing radiation. This Radiation Induced Leakage Current (RILC) can be described as an inelastic tunneling process mediated by neutral traps in the oxide, with an energy loss of about 1 eV. The neutral trap distribution is influenced by the oxide field applied during irradiation, thus indicating that the precursors of the neutral defects are charged, likely being defects associated to trapped holes. The maximum leakage current is found under zero-field condition during irradiation, and it rapidly decreases as the field is enhanced, due to a displacement of the defect distribution across the oxide towards the cathodic interface. The RILC kinetics are linear with the cumulative dose, in contrast with the power law found on electrically stressed devices.

  4. Ionizing radiation induced leakage current on ultra-thin gate oxides

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    Scarpa, A.; Paccagnella, A.; Montera, F.; Ghibaudo, G.; Pananakakis, G.; Fuochi, P.G.

    1997-12-01

    MOS capacitors with a 4.4 nm thick gate oxide have been exposed to {gamma} radiation from a Co{sup 60} source. As a result, the authors have measured a stable leakage current at fields lower than those required for Fowler-Nordheim tunneling. This Radiation Induced Leakage Current (RILC) is similar to the usual Stress Induced Leakage Currents (SILC) observed after electrical stresses of MOS devices. They have verified that these two currents share the same dependence on the oxide field, and the RILC contribution can be normalized to an equivalent injected charge for Constant Current Stresses. They have also considered the dependence of the RILC from the cumulative radiation dose, and from the applied bias during irradiation, suggesting a correlation between RILC and the distribution of trapped holes and neutral levels in the oxide layer.

  5. Prompt radiation-induced conductivity in polyurethane foam and glass microballoons

    SciTech Connect (OSTI)

    Hartman, E. Frederick; Zarick, Thomas Andrew; Sheridan, Timothy J.; Preston, Eric F.

    2014-06-01

    We performed measurements and analyses of the prompt radiation-induced conductivity (RIC) in thin samples of polyurethane foam and glass microballoon foam at the Little Mountain Medusa LINAC facility in Ogden, UT. The RIC coefficient was non-linear with dose rate for polyurethane foam; however, typical values at 1E11 rad(si)/s dose rate was measured as 0.8E-11 mho/m/rad/s for 5 lb./cu ft. foam and 0.3E-11 mho/m/rad/s for 10 lb./cu ft. density polyurethane foam. For encapsulated glass microballoons (GMB) the RIC coefficient was approximately 1E-15 mho/m/rad/s and was not a strong function of dose rate.

  6. Radiation-Induced Decomposition of PETN and TATB under Extreme Conditions

    SciTech Connect (OSTI)

    Giefers, Hubertus; Pravica, Michael

    2008-11-03

    We conducted a series of experiments investigating decomposition of secondary explosives PETN and TATB at varying static pressures and temperatures using synchrotron radiation. As seen in our earlier work, the decomposition rate of TATB at ambient temperature slows systematically with increasing pressure up to at least 26 GPa but varies little with pressure in PETN at ambient temperature up to 15.7 GPa, yielding important information pertaining to the activation complex volume in both cases. We also investigated the radiation-induced decomposition rate as a function of temperature at ambient pressure and 26 GPa for TATB up to 403 K, observing that the decomposition rate increases with increasing temperature as expected. The activation energy for the TATB reaction at ambient temperature was experimentally determined to be 16 {+-} 3 kJ/mol.

  7. Repair of radiation-induced heat-labile sites is independent of DNA-PKcs, XRCC1 or PARP

    SciTech Connect (OSTI)

    Stenerlw, Bo; Karlsson, Karin H.; Radulescu, Irina; Rydberg, Bjorn; Stenerlow, Bo

    2008-04-29

    Ionizing radiation induces a variety of different DNA lesions: in addition to the most critical DNA damage, the DSB, numerous base alterations, SSBs and other modifications of the DNA double-helix are formed. When several non-DSB lesions are clustered within a short distance along DNA, or close to a DSB, they may interfere with the repair of DSBs and affect the measurement of DSB induction and repair. We have previously shown that a substantial fraction of DSBs measured by pulsed-field gel electrophoresis (PFGE) are in fact due to heat-labile sites (HLS) within clustered lesions, thus reflecting an artifact of preparation of genomic DNA at elevated temperature. To further characterize the influence of HLS on DSB induction and repair, four human cell lines (GM5758, GM7166, M059K, U-1810) with apparently normal DSB rejoining were tested for bi-phasic rejoining after gamma irradiation. When heat-released DSBs were excluded from the measurements the fraction of fast rejoining decreased to less than 50% of the total. However, neither the half-times of the fast (t{sub 1/2} = 7-8 min) or slow (t{sub 1/2} = 2.5 h) DSB rejoining were changed significantly. At t=0 the heat-released DSBs accounted for almost 40% of the DSBs, corresponding to 10 extra DSB/cell/Gy in the initial DSB yield. These heat-released DSBs were repaired within 60-90 min in all tested cells, including M059K cells treated with wortmannin or DNA-PKcs defect M059J cells. Furthermore, cells lacking XRCC1 or Poly(ADP-ribose) polymerase-1 (PARP-1) rejoined both total DSBs and heat-released DSBs similar to normal cells. In summary, the presence of heat-labile sites have a substantial impact on DSB induction yields and DSB rejoining rates measured by pulsed-field gel electrophoresis, and HLS repair is independent of DNA-PKcs, XRCC1 and PARP.

  8. Radiation-Induced Segregation and Phase Stability in Candidate Alloys for the Advanced Burner Reactor

    SciTech Connect (OSTI)

    Gary S. Was; Brian D. Wirth

    2011-05-29

    Major accomplishments of this project were the following: 1) Radiation induced depletion of Cr occurs in alloy D9, in agreement with that observed in austenitic alloys. 2) In F-M alloys, Cr enriches at PAG grain boundaries at low dose (<7 dpa) and at intermediate temperature (400C) and the magnitude of the enrichment decreases with temperature. 3) Cr enrichment decreases with dose, remaining enriched in alloy T91 up to 10 dpa, but changing to depletion above 3 dpa in HT9 and HCM12A. 4) Cr has a higher diffusivity than Fe by a vacancy mechanism and the corresponding atomic flux of Cr is larger than Fe in the opposite direction to the vacancy flux. 5) Cr concentration at grain boundaries decreases as a result of vacancy transport during electron or proton irradiation, consistent with Inverse Kirkendall models. 6) Inclusion of other point defect sinks into the KLMC simulation of vacancy-mediated diffusion only influences the results in the low temperature, recombination dominated regime, but does not change the conclusion that Cr depletes as a result of vacancy transport to the sink. 7) Cr segregation behavior is independent of Frenkel pair versus cascade production, as simulated for electron versus proton irradiation conditions, for the temperatures investigated. 8) The amount of Cr depletion at a simulated planar boundary with vacancy-mediated diffusion reaches an apparent saturation value by about 1 dpa, with the precise saturation concentration dependent on the ratio of Cr to Fe diffusivity. 9) Cr diffuses faster than Fe by an interstitial transport mechanism, and the corresponding atomic flux of Cr is much larger than Fe in the same direction as the interstitial flux. 10) Observed experimental and computational results show that the radiation induced segregation behavior of Cr is consistent with an Inverse Kirkendall mechanism.

  9. The Role of Platelet Factor 4 in Radiation-Induced Thrombocytopenia

    SciTech Connect (OSTI)

    Lambert, Michele P.; Xiao Liqing; Nguyen, Yvonne; Kowalska, M. Anna; Poncz, Mortimer

    2011-08-01

    Purpose: Factors affecting the severity of radiation-induced thrombocytopenia (RIT) are not well described. We address whether platelet factor 4 (PF4; a negative paracrine for megakaryopoiesis) affects platelet recovery postradiation. Methods and Materials: Using conditioned media from irradiated bone marrow (BM) cells from transgenic mice overexpressing human (h) PF4 (hPF4+), megakaryocyte colony formation was assessed in the presence of this conditioned media and PF4 blocking agents. In a model of radiation-induced thrombocytopenia, irradiated mice with varying PF4 expression levels were treated with anti-hPF4 and/or thrombopoietin (TPO), and platelet count recovery and survival were examined. Results: Conditioned media from irradiated BM from hPF4+ mice inhibited megakaryocyte colony formation, suggesting that PF4 is a negative paracrine released in RIT. Blocking with an anti-hPF4 antibody restored colony formation of BM grown in the presence of hPF4+ irradiated media, as did antibodies that block the megakaryocyte receptor for PF4, low-density lipoprotein receptor-related protein 1 (LRP1). Irradiated PF4 knockout mice had higher nadir platelet counts than irradiated hPF4+/knockout litter mates (651 vs. 328 x 106/mcL, p = 0.02) and recovered earlier (15 days vs. 22 days, respectively, p <0.02). When irradiated hPF4+ mice were treated with anti-hPF4 antibody and/or TPO, they showed less severe thrombocytopenia than untreated mice, with improved survival and time to platelet recovery, but no additive effect was seen. Conclusions: Our studies show that in RIT, damaged megakaryocytes release PF4 locally, inhibiting platelet recovery. Blocking PF4 enhances recovery while released PF4 from megakaryocytes limits TPO efficacy, potentially because of increased release of PF4 stimulated by TPO. The clinical value of blocking this negative paracrine pathway post-RIT remains to be determined.

  10. Mitigation and Treatment of Radiation-Induced Thoracic Injury With a Cyclooxygenase-2 Inhibitor, Celecoxib

    SciTech Connect (OSTI)

    Hunter, Nancy R.; Valdecanas, David [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Liao Zhongxing [Division of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Division of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Milas, Luka [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Thames, Howard D. [Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)] [Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mason, Kathy A., E-mail: kmason@mdanderson.org [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)

    2013-02-01

    Purpose: To test whether a cyclooxygenase-2 inhibitor (celecoxib) could reduce mortality resulting from radiation-induced pneumonitis. Methods and Materials: Celecoxib was given to mice twice daily for 40 consecutive days starting on the day of local thoracic irradiation (LTI) or 40 or 80 days later. C3Hf/KamLaw mice were observed for morbidity, and time to death was determined. Results were analyzed using the Cox proportional hazards model. Results: Timing of celecoxib relative to LTI determined efficacy. A significant reduction in time to death was achieved only when celecoxib was started 80 days after LTI, corresponding to the time when pneumonitis is expressed. For these mice the reduction in mortality was quantified as a hazard ratio for mortality of treated vs untreated of 0.36 (95% confidence interval [CI] 0.24-0.53), thus significantly less than 1.0. Correspondingly, the median lethal dose for treated mice (12.9 Gy; 95% CI 12.55-13.25 Gy) was significantly (P=.026) higher than for untreated mice (12.4 Gy; 95% CI 12.2-12.65 Gy). Conclusions: Celecoxib significantly reduced lung toxicity when administered months after LTI when the deleterious effects of radiation were expressed. The schedule-dependent reduction in fatal pneumonitis suggests that celecoxib could be clinically useful by reintroduction of treatment months after completion of radiation therapy. These findings may be important for designing clinical trials using cyclooxygenase-2 inhibitors to treat radiation-induced lung toxicity as a complement to concurrent radiation therapy of lung cancers.

  11. Radiation-induced refraction artifacts in the optical CT readout of polymer gel dosimeters

    SciTech Connect (OSTI)

    Campbell, Warren G.; Jirasek, Andrew; Wells, Derek M.

    2014-11-01

    Purpose: The objective of this work is to demonstrate imaging artifacts that can occur during the optical computed tomography (CT) scanning of polymer gel dosimeters due to radiation-induced refractive index (RI) changes in polyacrylamide gels. Methods: A 1 L cylindrical polyacrylamide gel dosimeter was irradiated with 3 3 cm{sup 2} square beams of 6 MV photons. A prototype fan-beam optical CT scanner was used to image the dosimeter. Investigative optical CT scans were performed to examine two types of rayline bending: (i) bending within the plane of the fan-beam and (ii) bending out the plane of the fan-beam. To address structured errors, an iterative SavitzkyGolay (ISG) filtering routine was designed to filter 2D projections in sinogram space. For comparison, 2D projections were alternatively filtered using an adaptive-mean (AM) filter. Results: In-plane rayline bending was most notably observed in optical CT projections where rays of the fan-beam confronted a sustained dose gradient that was perpendicular to their trajectory but within the fan-beam plane. These errors caused distinct streaking artifacts in image reconstructions due to the refraction of higher intensity rays toward more opaque regions of the dosimeter. Out-of-plane rayline bending was observed in slices of the dosimeter that featured dose gradients perpendicular to the plane of the fan-beam. These errors caused widespread, severe overestimations of dose in image reconstructions due to the higher-than-actual opacity that is perceived by the scanner when light is bent off of the detector array. The ISG filtering routine outperformed AM filtering for both in-plane and out-of-plane rayline errors caused by radiation-induced RI changes. For in-plane rayline errors, streaks in an irradiated region (>7 Gy) were as high as 49% for unfiltered data, 14% for AM, and 6% for ISG. For out-of-plane rayline errors, overestimations of dose in a low-dose region (?50 cGy) were as high as 13 Gy for unfiltered data, 10 Gy for AM, and 3.1 Gy for ISG. The ISG routine also addressed unrelated artifacts that previously needed to be manually removed in sinogram space. However, the ISG routine blurred reconstructions, causing losses in spatial resolution of ?5 mm in the plane of the fan-beam and ?8 mm perpendicular to the fan-beam. Conclusions: This paper reveals a new category of imaging artifacts that can affect the optical CT readout of polyacrylamide gel dosimeters. Investigative scans show that radiation-induced RI changes can cause significant rayline errors when rays confront a prolonged dose gradient that runs perpendicular to their trajectory. In fan-beam optical CT, these errors manifested in two ways: (1) distinct streaking artifacts caused by in-plane rayline bending and (2) severe overestimations of opacity caused by rays bending out of the fan-beam plane and missing the detector array. Although the ISG filtering routine mitigated these errors better than an adaptive-mean filtering routine, it caused unacceptable losses in spatial resolution.

  12. CDK1 enhances mitochondrial bioenergetics for radiation-induced DNA repair

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qin, Lili; Fan, Ming; Candas, Demet; Jiang, Guochun; Papadopoulos, Stelios; Tian, Lin; Woloschak, Gayle; Grdina, David J.; Li, Jian  Jian

    2015-12-06

    Nuclear DNA repair capacity is a critical determinant of cell fate under genotoxic stress conditions. DNA repair is a well-defined energy-consuming process. However, it is unclear how DNA repair is fueled and whether mitochondrial energy production contributes to nuclear DNA repair. Here, we report a dynamic enhancement of oxygen consumption and mitochondrial ATP generation in irradiated normal cells, paralleled with increased mitochondrial relocation of the cell-cycle kinase CDK1 and nuclear DNA repair. The basal and radiation-induced mitochondrial ATP generation is reduced significantly in cells harboring CDK1 phosphorylation-deficient mutant complex I subunits. Similarly, mitochondrial ATP generation and nuclear DNA repair aremore »also compromised severely in cells harboring mitochondrially targeted, kinase-deficient CDK1. These findings demonstrate a mechanism governing the communication between mitochondria and the nucleus by which CDK1 boosts mitochondrial bioenergetics to meet the increased cellular fuel demand for DNA repair and cell survival under genotoxic stress conditions.« less

  13. Comparative study of microwave radiation-induced magnetoresistive oscillations induced by circularly- and linearly- polarized photo-excitation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ye, Tianyu; Liu, Han -Chun; Wang, Zhuo; Wegscheider, W.; Mani, Ramesh G.

    2015-10-09

    A comparative study of the radiation-induced magnetoresistance oscillations in the high mobility GaAs/AlGaAs heterostructure two dimensional electron system (2DES) under linearly- and circularly- polarized microwave excitation indicates a profound difference in the response observed upon rotating the microwave launcher for the two cases, although circularly polarized microwave radiation induced magnetoresistance oscillations observed at low magnetic fields are similar to the oscillations observed with linearly polarized radiation. For the linearly polarized radiation, the magnetoresistive response is a strong sinusoidal function of the launcher rotation (or linear polarization) angle, θ. As a result, for circularly polarized radiation, the oscillatory magnetoresistive response ismore » hardly sensitive to θ.« less

  14. Proteomic-based mechanistic investigation of low-dose radiation-induced cellular responses/effects

    SciTech Connect (OSTI)

    Chen, Xian

    2013-10-23

    The goal of our project is to apply our unique systems investigation strategy to reveal the molecular mechanisms underlying the radiation induction and transmission of oxidative damage, adaptive response, and bystander effect at low-doses. Beginning with simple in vitro systems such as fibroblast or epithelial pure culture, our amino acid-coded mass tagging (AACT) comparative proteomic platform will be used to measure quantitatively proteomic changes at high- or low-dose level with respect to their endogenous damage levels respectively, in which a broad range of unique regulated proteins sensitive to low-dose IR will be distinguished. To zoom in how these regulated proteins interact with other in the form of networks in induction/transmission pathways, these regulated proteins will be selected as baits for making a series of fibroblast cell lines that stably express each of them. Using our newly developed method of ?dual-tagging? quantitative proteomics that integrate the capabilities of natural complex expression/formation, simple epitope affinity isolation (not through tandem affinity purification or TAP), and ?in-spectra? AACT quantitative measurements using mass spectrometry (MS), we will be able to distinguish systematically interacting proteins with each bait in real time. Further, in addition to both proteome-wide (global differentially expressed proteins) and pathway-scale (bait-specific) profiling information, we will perform a computational network analysis to elucidate a global pathway/mechanisms underlying cellular responses to real-time low-dose IR. Similarly, we will extend our scheme to investigate systematically those induction/transmission pathways occurring in a fibroblast-epithelial interacting model in which the bystander cell (fibroblast) monitor the IR damage to the target cell (epithelial cell). The results will provide the proteome base (molecular mechanisms/pathways for signaling) for the low dose radiation-induced essential tissue environment interactions, including cell-cell, extracellular matrix and extracellular paracrine interactions.

  15. Recovery From Radiation-induced Bone Marrow Damage by HSP25 Through Tie2 Signaling

    SciTech Connect (OSTI)

    Lee, Hae-June; Kwon, Hee-Chung; Chung, Hee-Yong; Lee, Yoon-Jin; Lee, Yun-Sil

    2012-09-01

    Purpose: Whole-body radiation therapy can cause severe injury to the hematopoietic system, and therefore it is necessary to identify a novel strategy for overcoming this injury. Methods and Materials: Mice were irradiated with 4.5 Gy after heat shock protein 25 (HSP25) gene transfer using an adenoviral vector. Then, peripheral blood cell counts, histopathological analysis, and Western blotting on bone marrow (BM) cells were performed. The interaction of HSP25 with Tie2 was investigated with mouse OP9 and human BM-derived mesenchymal stem cells to determine the mechanism of HSP25 in the hematopoietic system. Results: HSP25 transfer increased BM regeneration and reduced apoptosis following whole-body exposure to ionizing radiation (IR). The decrease in Tie2 protein expression that followed irradiation of the BM was blocked by HSP25 transfer, and Tie2-positive cells were more abundant among the BM cells of HSP25-transferred mice, even after IR exposure. Following systemic RNA interference of Tie2 before IR, HSP25-mediated radioprotective effects were partially blocked in both mice and cell line systems. Stability of Tie2 was increased by HSP25, a response mediated by the interaction of HSP25 with Tie2. IR-induced tyrosine phosphorylation of Tie2 was augmented by HSP25 overexpression; downstream events in the Tie2 signaling pathway, including phosphorylation of AKT and EKR1/2, were also activated. Conclusions: HSP25 protects against radiation-induced BM damage by interacting with and stabilizing Tie2. This may be a novel strategy for HSP25-mediated radioprotection in BM.

  16. Formation mechanisms of precursors of radiation-induced color centers during fabrication of silica optical fiber preform

    SciTech Connect (OSTI)

    Tomashuk, A. L.; Zabezhailov, M. O.

    2011-04-15

    Samples in the form of transverse slices of rods and optical fiber preforms made from the high-hydroxyl KU-1 and low-hydroxyl KS-4V silica by the plasma outside deposition (POD) method are {gamma}-irradiated to a dose of {approx}1 MGy (SiO{sub 2}). Next, the radial dependences of the radiation-induced nonbridging oxygen hole center (NBOHC) and E'-center (three-coordinated silicon) in the samples are constructed by measuring the amplitudes of their 4.8 and 5.8 eV absorption bands, respectively. Based on the analysis of these radial dependences and considering the temperature and duration of the preirradiation heat treatment of the rods and preforms at the POD-installation, we determine the ratio of the oscillator strengths of the above bands and the microscopic thermoinduced processes occurring during preform fabrication and producing precursors of the radiation-induced NBOHC and E'-center. These processes are found to be associated with the escape of either H{sub 2} or H{sub 2}O from neighboring hydroxyl groups, and, therefore, can occur in high-hydroxyl silica only. It is concluded that enhancement of the radiation resistance of high-hydroxyl silica optical fibers requires decreasing the temperature and duration of the preform fabrication process, in particular, changing from the POD-technology to the low-temperature plasmachemical vapor deposition (PCVD) or surface PCVD (SPCVD)-technology.

  17. Radiation-Induced Upregulation of Gene Expression From Adenoviral Vectors Mediated by DNA Damage Repair and Regulation

    SciTech Connect (OSTI)

    Nokisalmi, Petri; Rajecki, Maria; Pesonen, Sari; Escutenaire, Sophie; Soliymani, Rabah; Tenhunen, Mikko; Ahtiainen, Laura; Hemminki, Akseli

    2012-05-01

    Purpose: In the present study, we evaluated the combination of replication-deficient adenoviruses and radiotherapy in vitro. The purpose of the present study was to analyze the mechanism of radiation-mediated upregulation of adenoviral transgene expression. Methods and Materials: Adenoviral transgene expression (luciferase or green fluorescent protein) was studied with and without radiation in three cell lines: breast cancer M4A4-LM3, prostate cancer PC-3MM2, and lung cancer LNM35/enhanced green fluorescent protein. The effect of the radiation dose, modification of the viral capsid, and five different transgene promoters were studied. The cellular responses were studied using mass spectrometry and immunofluorescence analysis. Double strand break repair was modulated by inhibitors of heat shock protein 90, topoisomerase-I, and DNA protein kinase, and transgene expression was measured. Results: We found that a wide range of radiation doses increased adenoviral transgene expression regardless of the cell line, transgene, promoter, or viral capsid modification. Treatment with adenovirus, radiation, and double strand break repair inhibitors resulted in persistence of double strand breaks and subsequent increases in adenovirus transgene expression. Conclusions: Radiation-induced enhancement of adenoviral transgene expression is linked to DNA damage recognition and repair. Radiation induces a global cellular response that results in increased production of RNA and proteins, including adenoviral transgene products. This study provides a mechanistic rationale for combining radiation with adenoviral gene delivery.

  18. Amifostine, a radioprotectant agent, protects rat brain tissue lipids against ionizing radiation induced damage: An FTIR microspectroscopic imaging study

    SciTech Connect (OSTI)

    Cakmak G.; Miller L.; Zorlu, F.; Severcan, F.

    2012-03-03

    Amifostine is the only approved radioprotective agent by FDA for reducing the damaging effects of radiation on healthy tissues. In this study, the protective effect of amifostine against the damaging effects of ionizing radiation on the white matter (WM) and grey matter (GM) regions of the rat brain were investigated at molecular level. Sprague-Dawley rats, which were administered amifostine or not, were whole-body irradiated at a single dose of 800 cGy, decapitated after 24 h and the brain tissues of these rats were analyzed using Fourier transform infrared microspectroscopy (FTIRM). The results revealed that the total lipid content and CH{sub 2} groups of lipids decreased significantly and the carbonyl esters, olefinic=CH and CH{sub 3} groups of lipids increased significantly in the WM and GM after exposure to ionizing radiation, which could be interpreted as a result of lipid peroxidation. These changes were more prominent in the WM of the brain. The administration of amifostine before ionizing radiation inhibited the radiation-induced lipid peroxidation in the brain. In addition, this study indicated that FTIRM provides a novel approach for monitoring ionizing radiation induced-lipid peroxidation and obtaining different molecular ratio images can be used as biomarkers to detect lipid peroxidation in biological systems.

  19. Gravitational Instability of a Nonrotating Galaxy (Conference...

    Office of Scientific and Technical Information (OSTI)

    Title: Gravitational Instability of a Nonrotating Galaxy Gravitational instability of the distribution of stars in a galaxy is a well-known phenomenon in astrophysics. This report ...

  20. A physical model of the photo- and radiation-induced degradation of ytterbium-doped silica optical fibres

    SciTech Connect (OSTI)

    Mady, Franck Duchez, Jean-Bernard Mebrouk, Yasmine Benabdesselam, Mourad

    2014-10-21

    We propose a model to describe the photo- or/and the radiation-induced darkening of ytterbium-doped silica optical fibers. This model accounts for the well-established experimental features of photo-darkening. Degradation behaviors predicted for fibers pumped in harsh environments are also fully confirmed by experimental data reported in the work by Duchez et al. (this proceeding), which gives a detailed characterization of the interplay between the effects of the pump and those of a superimposed ionizing irradiation (actual operation conditions in space-based applications for instance). In particular, dependences of the darkening build-up on the pump power, the total ionizing dose and the dose rate are all correctly reproduced. The presented model is a sufficient one, including the minimal physical ingredients required to reproduce experimental features. Refinements could be proposed to improve, e.g., quantitative kinetics.

  1. Analysis of single-event upset of magnetic tunnel junction used in spintronic circuits caused by radiation-induced current

    SciTech Connect (OSTI)

    Sakimura, N.; Nebashi, R.; Sugibayashi, T.; Natsui, M.; Hanyu, T.; Ohno, H.

    2014-05-07

    This paper describes the possibility of a switching upset of a magnetic tunnel junction (MTJ) caused by a terrestrial radiation-induced single-event-upset (SEU) current in spintronic integrated circuits. The current waveforms were simulated by using a 3-D device simulator in a basic circuit including MTJs designed using 90-nm CMOS parameters and design rules. The waveforms have a 400 -μA peak and a 200-ps elapsed time when neutron particles with a linear energy transfer value of 14 MeV cm{sup 2}/mg enter the silicon surface. The authors also found that the SEU current may cause soft errors with a probability of more than 10{sup −12} per event, which was obtained by approximate solution of the ordinary differential equation of switching probability when the intrinsic critical current (I{sub C0}) became less than 30 μA.

  2. Reproductive Status at First Diagnosis Influences Risk of Radiation-Induced Second Primary Contralateral Breast Cancer in the WECARE Study

    SciTech Connect (OSTI)

    Brooks, Jennifer D.; Boice, John D.; Stovall, Marilyn; Reiner, Anne S.; Bernstein, Leslie; John, Esther M.; Lynch, Charles F.; Mellemkjaer, Lene; Knight, Julia A.; Thomas, Duncan C.; Haile, Robert W.; Smith, Susan A.; Capanu, Marinela; Bernstein, Jonine L.; Shore, Roy E.; Radiation Effects Research Foundation, Hiroshima

    2012-11-15

    Purpose: Our study examined whether reproductive and hormonal factors before, at the time of, or after radiation treatment for a first primary breast cancer modify the risk of radiation-induced second primary breast cancer. Methods and Materials: The Women's Environmental, Cancer and Radiation Epidemiology (WECARE) Study is a multicenter, population-based study of 708 women (cases) with asynchronous contralateral breast cancer (CBC) and 1399 women (controls) with unilateral breast cancer. Radiotherapy (RT) records, coupled with anthropomorphic phantom simulations, were used to estimate quadrant-specific radiation dose to the contralateral breast for each patient. Rate ratios (RR) and 95% confidence intervals (CI) were computed to assess the relationship between reproductive factors and risk of CBC. Results: Women who were nulliparous at diagnosis and exposed to {>=}1 Gy to the contralateral breast had a greater risk for CBC than did matched unexposed nulliparous women (RR = 2.2; 95% CI, 1.2-4.0). No increased risk was seen in RT-exposed parous women (RR = 1.1; 95% CI, 0.8-1.4). Women treated with RT who later became pregnant (8 cases and 9 controls) had a greater risk for CBC (RR = 6.0; 95% CI, 1.3-28.4) than unexposed women (4 cases and 7 controls) who also became pregnant. The association of radiation with risk of CBC did not vary by number of pregnancies, history of breastfeeding, or menopausal status at the time of first breast cancer diagnosis. Conclusion: Nulliparous women treated with RT were at an increased risk for CBC. Although based on small numbers, women who become pregnant after first diagnosis also seem to be at an increased risk for radiation-induced CBC.

  3. Coupling of Kelvin-Helmholtz instability and buoyancy instability in a thermally laminar plasma

    SciTech Connect (OSTI)

    Ren Haijun; Wu Zhengwei [CAS Key Laboratory of Basic Plasma Physics, University of Science and Technology of China, Hefei 230026 (China); Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon (Hong Kong); Cao Jintao; Dong Chao [CAS Key Laboratory of Basic Plasma Physics, University of Science and Technology of China, Hefei 230026 (China); Chu, Paul K. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon (Hong Kong)

    2011-02-15

    Thermal convective instability is investigated in a thermally stratified plasma in the presence of shear flow, which is known to give rise to the Kelvin-Helmholtz (KH) instability. We examine how the KH instability and magnetothermal instability (MTI) affect each other. Based on the sharp boundary model, the KH instability coupled with the MTI is studied. We present the growth rate and instability criteria. The shear flow is shown to significantly alter the critical condition for the occurrence of thermal convective instability.

  4. Final Technical Report - Mechanisms and pathways controlling genomic instability

    SciTech Connect (OSTI)

    Dynan, William S.

    2013-05-31

    This project used model organisms, the zebrafish and the Japanese medaka fish to investigate the effects of low-dose radiation exposure on the vertebrate embryo. Endpoints measured included apoptotic cell death, aging, and oxidative stress.

  5. the Adaptive Response, Genetic Haplo-Insufficiency and Genomic Instability

    SciTech Connect (OSTI)

    Geard, Charles R.

    2014-12-12

    The linear no-threshold (LNT) hypothesis is the driving force in the establishment of radiation protection standards. However, the scientific basis for linearity has been brought into question, particularly due to the concerns about induced radiation resistance as it pertains to oxidative stress. Specifically, we investigated the observation that tumor hypoxia is associated with malignant progression, increased metastases, chemo- and radioresistance and poor prognosis. Experiments were conducted with non-malignant 3T3/NIH cells and normal human lung fibroblasts (NHLF) that were subjected to ?-irradiation under the levels of oxygen resembling those in growing tumors, and related our data to the concentrations of dissolved oxygen (DO), which is a better indicator of the amounts of residual oxygen inside the cells cultured in the hypoxic or anoxic atmosphere. We found that at DO levels about 0.5 mg/L cells subjected to both short-term (17 hours) and prolonged (48-72 hours) hypoxia continued to proliferate, and that apoptotic events were decreased at the early hours of hypoxic treatment. We showed that the short-term hypoxia up-regulated p53-binding protein 1 (53BP1) and resulted in facilitated 53BP1 nuclear foci formation and disappearance, thus indicating the higher efficiency of DNA double strand breaks repair processes. The latter was confirmed by the lower micronuclei incidence in irradiated hypoxic cells.

  6. Genome Engineering

    SciTech Connect (OSTI)

    Voytas, Dan [University of Minnesota

    2014-03-20

    Dan Voytas, University of Minnesota, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif

  7. microRNA Alterations Driving Acute and Late Stages of Radiation-Induced Fibrosis in a Murine Skin Model

    SciTech Connect (OSTI)

    Simone, Brittany A.; Ly, David; Savage, Jason E.; Hewitt, Stephen M.; Dan, Tu D.; Ylaya, Kris; Shankavaram, Uma; Lim, Meng; Jin, Lianjin; Camphausen, Kevin; Mitchell, James B.; Simone, Nicole L.

    2014-09-01

    Purpose: Although ionizing radiation is critical in treating cancer, radiation-induced fibrosis (RIF) can have a devastating impact on patients' quality of life. The molecular changes leading to radiation-induced fibrosis must be elucidated so that novel treatments can be designed. Methods and Materials: To determine whether microRNAs (miRs) could be responsible for RIF, the fibrotic process was induced in the right hind legs of 9-week old CH3 mice by a single-fraction dose of irradiation to 35Gy, and the left leg served as an unirradiated control. Fibrosis was quantified by measurements of leg length compared with control leg length. By 120days after irradiation, the irradiated legs were 20% (P=.013) shorter on average than were the control legs. Results: Tissue analysis was done on muscle, skin, and subcutaneous tissue from irradiated and control legs. Fibrosis was noted on both gross and histologic examination by use of a pentachrome stain. Microarrays were performed at various times after irradiation, including 7days, 14days, 50days, 90days, and 120days after irradiation. miR-15a, miR-21, miR-30a, and miR-34a were the miRs with the most significant alteration by array with miR-34a, proving most significant on confirmation by reverse transcriptase polymerase chain reaction, c-Met, a known effector of fibrosis and downstream molecule of miR-34a, was evaluated by use of 2cell lines: HCT116 and 1522. The cell lines were exposed to various stressors to induce miR changes, specifically ionizing radiation. Additionally, invitro transfections with pre-miRs and anti-miRs confirmed the relationship of miR-34a and c-Met. Conclusions: Our data demonstrate an inverse relationship with miR-34a and c-Met; the upregulation of miR-34a in RIF causes inhibition of c-Met production. miRs may play a role in RIF; in particular, miR-34a should be investigated as a potential target to prevent or treat this devastating side effect of irradiation.

  8. Stellar explosions, instabilities, and turbulence

    SciTech Connect (OSTI)

    Drake, R. P.; Kuranz, C. C.; Miles, A. R.; Muthsam, H. J.; Plewa, T.

    2009-04-15

    It has become very clear that the evolution of structure during supernovae is centrally dependent on the pre-existing structure in the star. Modeling of the pre-existing structure has advanced significantly, leading to improved understanding and to a physically based assessment of the structure that will be present when a star explodes. It remains an open question whether low-mode asymmetries in the explosion process can produce the observed effects or whether the explosion mechanism somehow produces jets of material. In any event, the workhorse processes that produce structure in an exploding star are blast-wave driven instabilities. Laboratory experiments have explored these blast-wave-driven instabilities and specifically their dependence on initial conditions. Theoretical work has shown that the relative importance of Richtmyer-Meshkov and Rayleigh-Taylor instabilities varies with the initial conditions and does so in ways that can make sense of a range of astrophysical observations.

  9. The radiation induced chemistry of uranyl cation in aqueous carbonate bicarbonate solutions as followed by NMR spectroscopy

    SciTech Connect (OSTI)

    McNamara, Bruce K.; Snow, Lanee A.; Soderquist, Chuck Z.; Sinkov, Sergei I.; Cho, Herman M.; Friese, Judah I.

    2006-05-01

    Alpha radiation induced formation of hydrogen peroxide in carbonate ?bicarbonate media was followed by 13C NMR using dissolved [233UO2(13CO3)3]4- as the alpha source (Dalpha= 12.1 Gy/hr). Between the pH region between 5.9 and 11.6 hydrogen peroxide causes a varied speciation of the uranyl carbonates that is a function of the uranium, carbonate and the hydrogen peroxide concentrations. It is shown that the speciation of the peroxy carbonates (or other species) formed in solution by titration with hydrogen peroxide are common to those formed by hydrogen peroxide generated by radiolysis. The radiolysis experiment was carried out above pH = 9.96 to minimize the loss of 13CO2 over a 2800 hr period. Radiolytic generation of hydrogen peroxide was followed by formation of a uranyl peroxy carbonate complex and complex formation accelerated for about 1200 hours. Complex formation was observed to terminate at a concentration between 1x10-4 and 5x10-4 M. It is assumed that either a steady state H2O2 production rate was established in solution or that some limiting feature of the experiment was responsible for slowing the yield of product.

  10. Ab Initio and Kinetic Rate Theory Modeling of 316SS with Oversized Solute Additions on Radiation-Induced Segregation

    SciTech Connect (OSTI)

    Hackett, Micah J.; Was, Gary S.

    2008-07-01

    Deleterious effects of radiation in nuclear reactor systems cause material degradation and the potential for component failure. Radiation damage is fundamentally due to freely migrating point defects produced in collision cascades. A reduction in the freely migrating point defect population should, then, reduce radiation damage and increase component lifetime. The addition of oversized solute atoms such as Zr or Hf to 316SS, a common structural material in reactors, is expected to reduce point defect population through a trapping mechanism that enhances recombination. The mechanism, however, requires a strong binding energy between the oversized solute atom and vacancies in order for the mechanism to significantly reduce the defect population. Experimental measurements of this binding energy are unavailable, but can be determined with atomistic calculations. Ab initio methods are used here to determine binding energies and atomic volumes of either Hf or Zr oversized solutes with vacancies in a face-centered cubic Fe matrix. The binding energies are then used to parameterize a kinetic rate-theory model, which is used here to calculate radiation-induced segregation (RIS). The calculated values of RIS are then compared to experimental measurements to benchmark the calculations and offer insight into the proposed point defect trapping mechanism. (author)

  11. A Systems Genetic Approach to Identify Low Dose Radiation-Induced Lymphoma Susceptibility/DOE2013FinalReport

    SciTech Connect (OSTI)

    Balmain, Allan; Song, Ihn Young

    2013-05-15

    The ultimate goal of this project is to identify the combinations of genetic variants that confer an individual's susceptibility to the effects of low dose (0.1 Gy) gamma-radiation, in particular with regard to tumor development. In contrast to the known effects of high dose radiation in cancer induction, the responses to low dose radiation (defined as 0.1 Gy or less) are much less well understood, and have been proposed to involve a protective anti-tumor effect in some in vivo scientific models. These conflicting results confound attempts to develop predictive models of the risk of exposure to low dose radiation, particularly when combined with the strong effects of inherited genetic variants on both radiation effects and cancer susceptibility. We have used a ??Systems Genetics approach in mice that combines genetic background analysis with responses to low and high dose radiation, in order to develop insights that will allow us to reconcile these disparate observations. Using this comprehensive approach we have analyzed normal tissue gene expression (in this case the skin and thymus), together with the changes that take place in this gene expression architecture a) in response to low or high- dose radiation and b) during tumor development. Additionally, we have demonstrated that using our expression analysis approach in our genetically heterogeneous/defined radiation-induced tumor mouse models can uniquely identify genes and pathways relevant to human T-ALL, and uncover interactions between common genetic variants of genes which may lead to tumor susceptibility.

  12. Effects of Adenovirus-Mediated Delivery of the Human Hepatocyte Growth Factor Gene in Experimental Radiation-Induced Heart Disease

    SciTech Connect (OSTI)

    Hu Shunying; Chen Yundai; Li Libing; Chen Jinlong; Wu Bin; Zhou, Xiao; Zhi Guang; Li Qingfang; Wang Rongliang; Duan Haifeng; Guo Zikuan; Yang Yuefeng; Xiao Fengjun; Wang Hua; Wang Lisheng

    2009-12-01

    Purpose: Irradiation to the heart may lead to late cardiovascular complications. The purpose of this study was to investigate whether adenovirus-mediated delivery of the human hepatocyte growth factor gene could reduce post-irradiation damage of the rat heart and improve heart function. Methods and Materials: Twenty rats received single-dose irradiation of 20 Gy gamma ray locally to the heart and were randomized into two groups. Two weeks after irradiation, these two groups of rats received Ad-HGF or mock adenovirus vector intramyocardial injection, respectively. Another 10 rats served as sham-irradiated controls. At post-irradiation Day 120, myocardial perfusion was tested by myocardial contrast echocardiography with contrast agent injected intravenously. At post-irradiation Day 180, cardiac function was assessed using the Langendorff technique with an isolated working heart model, after which heart samples were collected for histological evaluation. Results: Myocardial blood flow was significantly improved in HGF-treated animals as measured by myocardial contrast echocardiography at post-irradiation Day 120 . At post-irradiation Day 180, cardiac function was significantly improved in the HGF group compared with mock vector group, as measured by left ventricular peak systolic pressure (58.80 +- 9.01 vs. 41.94 +- 6.65 mm Hg, p < 0.05), the maximum dP/dt (5634 +- 1303 vs. 1667 +- 304 mm Hg/s, p < 0.01), and the minimum dP/dt (3477 +- 1084 vs. 1566 +- 499 mm Hg/s, p < 0.05). Picrosirius red staining analysis also revealed a significant reduction of fibrosis in the HGF group. Conclusion: Based on the study findings, hepatocyte growth factor gene transfer can attenuate radiation-induced cardiac injury and can preserve cardiac function.

  13. Chemical chaperones reduce ionizing radiation-induced endoplasmic reticulum stress and cell death in IEC-6 cells

    SciTech Connect (OSTI)

    Lee, Eun Sang; Lee, Hae-June; Lee, Yoon-Jin; Jeong, Jae-Hoon; Kang, Seongman; Lim, Young-Bin

    2014-07-25

    Highlights: UPR activation precedes caspase activation in irradiated IEC-6 cells. Chemical ER stress inducers radiosensitize IEC-6 cells. siRNAs that targeted ER stress responses ameliorate IR-induced cell death. Chemical chaperons prevent cell death in irradiated IEC-6 cells. - Abstract: Radiotherapy, which is one of the most effective approaches to the treatment of various cancers, plays an important role in malignant cell eradication in the pelvic area and abdomen. However, it also generates some degree of intestinal injury. Apoptosis in the intestinal epithelium is the primary pathological factor that initiates radiation-induced intestinal injury, but the mechanism by which ionizing radiation (IR) induces apoptosis in the intestinal epithelium is not clearly understood. Recently, IR has been shown to induce endoplasmic reticulum (ER) stress, thereby activating the unfolded protein response (UPR) signaling pathway in intestinal epithelial cells. However, the consequences of the IR-induced activation of the UPR signaling pathway on radiosensitivity in intestinal epithelial cells remain to be determined. In this study, we investigated the role of ER stress responses in IR-induced intestinal epithelial cell death. We show that chemical ER stress inducers, such as tunicamycin or thapsigargin, enhanced IR-induced caspase 3 activation and DNA fragmentation in intestinal epithelial cells. Knockdown of Xbp1 or Atf6 with small interfering RNA inhibited IR-induced caspase 3 activation. Treatment with chemical chaperones prevented ER stress and subsequent apoptosis in IR-exposed intestinal epithelial cells. Our results suggest a pro-apoptotic role of ER stress in IR-exposed intestinal epithelial cells. Furthermore, inhibiting ER stress may be an effective strategy to prevent IR-induced intestinal injury.

  14. Combustion instability modeling and analysis

    SciTech Connect (OSTI)

    Santoro, R.J.; Yang, V.; Santavicca, D.A.; Sheppard, E.J.

    1995-12-31

    It is well known that the two key elements for achieving low emissions and high performance in a gas turbine combustor are to simultaneously establish (1) a lean combustion zone for maintaining low NO{sub x} emissions and (2) rapid mixing for good ignition and flame stability. However, these requirements, when coupled with the short combustor lengths used to limit the residence time for NO formation typical of advanced gas turbine combustors, can lead to problems regarding unburned hydrocarbons (UHC) and carbon monoxide (CO) emissions, as well as the occurrence of combustion instabilities. The concurrent development of suitable analytical and numerical models that are validated with experimental studies is important for achieving this objective. A major benefit of the present research will be to provide for the first time an experimentally verified model of emissions and performance of gas turbine combustors. The present study represents a coordinated effort between industry, government and academia to investigate gas turbine combustion dynamics. Specific study areas include development of advanced diagnostics, definition of controlling phenomena, advancement of analytical and numerical modeling capabilities, and assessment of the current status of our ability to apply these tools to practical gas turbine combustors. The present work involves four tasks which address, respectively, (1) the development of a fiber-optic probe for fuel-air ratio measurements, (2) the study of combustion instability using laser-based diagnostics in a high pressure, high temperature flow reactor, (3) the development of analytical and numerical modeling capabilities for describing combustion instability which will be validated against experimental data, and (4) the preparation of a literature survey and establishment of a data base on practical experience with combustion instability.

  15. Radiation-Induced Rib Fractures After Hypofractionated Stereotactic Body Radiation Therapy: Risk Factors and Dose-Volume Relationship

    SciTech Connect (OSTI)

    Asai, Kaori [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Shioyama, Yoshiyuki, E-mail: shioyama@radiol.med.kyushu-u.ac.jp [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Nakamura, Katsumasa; Sasaki, Tomonari; Ohga, Saiji; Nonoshita, Takeshi [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Yoshitake, Tadamasa [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Heavy Particle Therapy and Radiation Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Ohnishi, Kayoko [Department of Radiology, National Center for Global Health and Medicine, Tokyo (Japan)] [Department of Radiology, National Center for Global Health and Medicine, Tokyo (Japan); Terashima, Kotaro; Matsumoto, Keiji [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Hirata, Hideki [Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan); Honda, Hiroshi [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)] [Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)

    2012-11-01

    Purpose: The purpose of this study was to clarify the incidence, the clinical risk factors, and the dose-volume relationship of radiation-induced rib fracture (RIRF) after hypofractionated stereotactic body radiation therapy (SBRT). Methods and Materials: One hundred sixteen patients treated with SBRT for primary or metastatic lung cancer at our institution, with at least 6 months of follow-up and no previous overlapping radiation exposure, were included in this study. To determine the clinical risk factors associated with RIRF, correlations between the incidence of RIRF and the variables, including age, sex, diagnosis, gross tumor volume diameter, rib-tumor distance, and use of steroid administration, were analyzed. Dose-volume histogram analysis was also conducted. Regarding the maximum dose, V10, V20, V30, and V40 of the rib, and the incidences of RIRF were compared between the two groups divided by the cutoff value determined by the receiver operating characteristic curves. Results: One hundred sixteen patients and 374 ribs met the inclusion criteria. Among the 116 patients, 28 patients (46 ribs) experienced RIRF. The estimated incidence of rib fracture was 37.7% at 3 years. Limited distance from the rib to the tumor (<2.0 cm) was the only significant risk factor for RIRF (p = 0.0001). Among the dosimetric parameters used for receiver operating characteristic analysis, the maximum dose showed the highest area under the curve. The 3-year estimated risk of RIRF and the determined cutoff value were 45.8% vs. 1.4% (maximum dose, {>=}42.4 Gy or less), 51.6% vs. 2.0% (V40, {>=}0.29 cm{sup 3} or less), 45.8% vs. 2.2% (V30, {>=}1.35 cm{sup 3} or less), 42.0% vs. 8.5% (V20, {>=}3.62 cm{sup 3} or less), or 25.9% vs. 10.5% (V10, {>=}5.03 cm{sup 3} or less). Conclusions: The incidence of RIRF after hypofractionated SBRT is relatively high. The maximum dose and high-dose volume are strongly correlated with RIRF.

  16. Normal Tissue Complication Probability Modeling of Radiation-Induced Hypothyroidism After Head-and-Neck Radiation Therapy

    SciTech Connect (OSTI)

    Bakhshandeh, Mohsen; Hashemi, Bijan; Mahdavi, Seied Rabi Mehdi; Nikoofar, Alireza; Vasheghani, Maryam; Kazemnejad, Anoshirvan

    2013-02-01

    Purpose: To determine the dose-response relationship of the thyroid for radiation-induced hypothyroidism in head-and-neck radiation therapy, according to 6 normal tissue complication probability models, and to find the best-fit parameters of the models. Methods and Materials: Sixty-five patients treated with primary or postoperative radiation therapy for various cancers in the head-and-neck region were prospectively evaluated. Patient serum samples (tri-iodothyronine, thyroxine, thyroid-stimulating hormone [TSH], free tri-iodothyronine, and free thyroxine) were measured before and at regular time intervals until 1 year after the completion of radiation therapy. Dose-volume histograms (DVHs) of the patients' thyroid gland were derived from their computed tomography (CT)-based treatment planning data. Hypothyroidism was defined as increased TSH (subclinical hypothyroidism) or increased TSH in combination with decreased free thyroxine and thyroxine (clinical hypothyroidism). Thyroid DVHs were converted to 2 Gy/fraction equivalent doses using the linear-quadratic formula with {alpha}/{beta} = 3 Gy. The evaluated models included the following: Lyman with the DVH reduced to the equivalent uniform dose (EUD), known as LEUD; Logit-EUD; mean dose; relative seriality; individual critical volume; and population critical volume models. The parameters of the models were obtained by fitting the patients' data using a maximum likelihood analysis method. The goodness of fit of the models was determined by the 2-sample Kolmogorov-Smirnov test. Ranking of the models was made according to Akaike's information criterion. Results: Twenty-nine patients (44.6%) experienced hypothyroidism. None of the models was rejected according to the evaluation of the goodness of fit. The mean dose model was ranked as the best model on the basis of its Akaike's information criterion value. The D{sub 50} estimated from the models was approximately 44 Gy. Conclusions: The implemented normal tissue complication probability models showed a parallel architecture for the thyroid. The mean dose model can be used as the best model to describe the dose-response relationship for hypothyroidism complication.

  17. Structural changes caused by radiation-induced reduction and radiolysis: the effect of X-ray absorbed dose in a fungal multicopper oxidase

    SciTech Connect (OSTI)

    De la Mora, Eugenio; Lovett, Janet E.; Blanford, Christopher F.; Garman, Elspeth F.; Valderrama, Brenda; Rudino-Pinera, Enrique

    2012-05-01

    Radiation-induced reduction, radiolysis of copper sites and the effect of pH value together with the concomitant geometrical distortions of the active centres were analysed in several fungal (C. gallica) laccase structures collected at cryotemperature. This study emphasizes the importance of careful interpretation when the crystallographic structure of a metalloprotein is described. X-ray radiation induces two main effects at metal centres contained in protein crystals: radiation-induced reduction and radiolysis and a resulting decrease in metal occupancy. In blue multicopper oxidases (BMCOs), the geometry of the active centres and the metal-to-ligand distances change depending on the oxidation states of the Cu atoms, suggesting that these alterations are catalytically relevant to the binding, activation and reduction of O{sub 2}. In this work, the X-ray-determined three-dimensional structure of laccase from the basidiomycete Coriolopsis gallica (Cg L), a high catalytic potential BMCO, is described. By combining spectroscopic techniques (UVVis, EPR and XAS) and X-ray crystallography, structural changes at and around the active copper centres were related to pH and absorbed X-ray dose (energy deposited per unit mass). Depletion of two of the four active Cu atoms as well as low occupancies of the remaining Cu atoms, together with different conformations of the metal centres, were observed at both acidic pH and high absorbed dose, correlating with more reduced states of the active coppers. These observations provide additional evidence to support the role of flexibility of copper sites during O{sub 2} reduction. This study supports previous observations indicating that interpretations regarding redox state and metal coordination need to take radiation effects explicitly into account.

  18. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Instability and Lou Gehrig's Disease Protein Instability and Lou Gehrig's Disease Print Wednesday, 25 March 2015 00:00 A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called

  19. Solid-state polymerization of acrylamide and its derivatives complexed with some Lewis acids. II. Radiation-induced in-source polymerization

    SciTech Connect (OSTI)

    Zurakowska-Orszagh, J.; Mirowski, K.; Chajewski, A.

    1982-07-01

    Radiation-induced solid-state polymerizations of complexes of N-tert-butylacrylamide, N-tert-amylacrylamide, and N-tert-hexylacrylamide with zinc chloride and zinc bromide have been studied. An accelerating effect of temperature and an inhibiting effect of oxygen on the polymerization process were observed. The activation energies have been established. The influence of monomer structure as well as the halide used on the polymerization rate have been discussed and some regularities have been pointed out. The polymers obtained show good solubilities in common solvents, which proves that they are not crosslinked.

  20. Two-Beam Instability in Electron Cooling

    SciTech Connect (OSTI)

    Burov, Alexey V.; /Fermilab

    2006-04-01

    The drift motion of cooling electrons makes them able to respond to transverse perturbations of a cooled ion beam. This response may lead to dipole or quadrupole transverse instabilities at specific longitudinal wave numbers. While the dipole instabilities can be suppressed by a combination of the Landau damping, machine impedance, and the active damper, the quadrupole and higher order modes can lead to either emittance growth, or a lifetime degradation, or both. The growth rates of these instabilities are strongly determined by the machine x-y coupling. Thus, tuning out of the coupling resonance and/or reduction of the machine coupling can be an efficient remedy for these instabilities.

  1. First Results From the Electron Hose Instability Studies in FACET...

    Office of Scientific and Technical Information (OSTI)

    the Electron Hose Instability Studies in FACET Citation Details In-Document Search Title: First Results From the Electron Hose Instability Studies in FACET You are accessing a...

  2. A Linear Theory of Microwave Instability in Electron Storage...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: A Linear Theory of Microwave Instability in Electron Storage Rings Citation Details In-Document Search Title: A Linear Theory of Microwave Instability in Electron...

  3. Summary of workshop session F on electron-cloud instabilities...

    Office of Scientific and Technical Information (OSTI)

    Conference: Summary of workshop session F on electron-cloud instabilities Citation Details In-Document Search Title: Summary of workshop session F on electron-cloud instabilities ...

  4. Baroclinic instability in stellar radiation zones

    SciTech Connect (OSTI)

    Kitchatinov, L. L.

    2014-03-20

    Surfaces of constant pressure and constant density do not coincide in differentially rotating stars. Stellar radiation zones with baroclinic stratification can be unstable. Instabilities in radiation zones are of crucial importance for angular momentum transport, mixing of chemical species, and, possibly, for magnetic field generation. This paper performs linear analysis of baroclinic instability in differentially rotating stars. Linear stability equations are formulated for differential rotation of arbitrary shape and then solved numerically for rotation nonuniform in radius. As the differential rotation increases, r- and g-modes of initially stable global oscillations transform smoothly into growing modes of baroclinic instability. The instability can therefore be interpreted as stability loss to r- and g-modes excitation. Regions of stellar parameters where r- or g-modes are preferentially excited are defined. Baroclinic instability onsets at a very small differential rotation of below 1%. The characteristic time of instability growth is about 1000 rotation periods. Growing disturbances possess kinetic helicity. Magnetic field generation by the turbulence resulting from baroclinic instability in differentially rotating radiation zones is therefore possible.

  5. Taylor Instability of Incompressible Liquids

    DOE R&D Accomplishments [OSTI]

    Fermi, E.; von Neumann, J.

    1955-11-01

    A discussion is presented in simplified form of the problem of the growth of an initial ripple on the surface of an incompressible liquid in the presence of an acceleration, g, directed from the outside into the liquid. The model is that of a heavy liquid occupying at t = 0 the half space above the plane z = 0, and a rectangular wave profile is assumed. The theory is found to represent correctly one feature of experimental results, namely the fact that the half wave of the heavy liquid into the vacuum becomes rapidly narrower while the half wave pushing into the heavy liquid becomes more and more blunt. The theory fails to account for the experimental results according to which the front of the wave pushing into the heavy liquid moves with constant velocity. The case of instability at the boundary of 2 fluids of different densities is also explored. Similar results are obtained except that the acceleration of the heavy liquid into the light liquid is reduced.

  6. SciFri AM: Mountain 04: Label-free Raman spectroscopy of single tumour cells detects early radiation-induced glycogen synthesis associated with increased radiation resistance

    SciTech Connect (OSTI)

    Matthews, Q; Lum, JJ; Isabelle, M; Harder, S; Jirasek, A; Brolo, AG

    2014-08-15

    Purpose: To use label-free Raman spectroscopy (RS) for early treatment monitoring of tumour cell radioresistance. Methods: Three human tumour cell lines, two radioresistant (H460, SF{sub 2} = 0.57 and MCF7, SF{sub 2} = 0.70) and one radiosensitive (LNCaP, SF{sub 2} = 0.36), were irradiated with single fractions of 2, 4, 6, 8 or 10 Gy. In additional experiments, H460 and MCF7 cells were irradiated under co-treatment with the anti-diabetic drug metformin, a known radiosensitizing agent. Treated and control cultures were analyzed with RS daily for 3 days post-treatment. Single-cell Raman spectra were acquired from 20 live cells per sample, and experiments were repeated in triplicate. The combined data sets were analyzed with principal component analysis using standard algorithms. Cells from each culture were also subjected to standard assays for viability, proliferation, cell cycle, and radiation clonogenic survival. Results: The radioresistant cells (H460, MCF7) exhibited a RS molecular radiation response signature, detectable as early as 1 day post-treatment, of which radiation-induced glycogen synthesis is a significant contributor. The radiosensitive cells (LNCaP) exhibited negligible glycogen synthesis. Co-treatment with metformin in MCF7 cells blocked glycogen synthesis, reduced viability and proliferation, and increased radiosensitivity. Conversely, metformin co-treatment in H460 cells did not produce these same effects; importantly, both radiation-induced synthesis of glycogen and radiosensitivity were unaffected. Conclusions: Label-free RS can detect early glycogen synthesis post-irradiation, a previously undocumented metabolic mechanism associated with tumour cell radioresistance that can be targeted to increase radiosensitivity. RS monitoring of intratumoral glycogen may provide new opportunities for personalized combined modality radiotherapy treatments.

  7. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  8. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  9. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  10. Protein Instability and Lou Gehrig's Disease

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Instability and Lou Gehrig's Disease Print A new study links protein instability with the progression of a lethal degenerative disease: amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. Using several biophysical techniques as well as small-angle x-ray scattering (SAXS) at the Advanced Light Source, researchers focused on the effects of mutations to a gene coding for a protein called superoxide dismutase (SOD). The study provides evidence that those proteins linked

  11. Frequency Instability Problems in North American Interconnections

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Frequency Instability Problems in North American Interconnections May 1, 2011 DOE/NETL-2011/1473 Frequency Instability Problems in North American Interconnections Disclaimer This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness

  12. SUPERSONIC SHEAR INSTABILITIES IN ASTROPHYSICAL BOUNDARY LAYERS

    SciTech Connect (OSTI)

    Belyaev, Mikhail A.; Rafikov, Roman R., E-mail: rrr@astro.princeton.edu [Department of Astrophysical Sciences, Princeton University, Ivy Lane, Princeton, NJ 08540 (United States)

    2012-06-20

    Disk accretion onto weakly magnetized astrophysical objects often proceeds via a boundary layer (BL) that forms near the object's surface, in which the rotation speed of the accreted gas changes rapidly. Here, we study the initial stages of formation for such a BL around a white dwarf or a young star by examining the hydrodynamical shear instabilities that may initiate mixing and momentum transport between the two fluids of different densities moving supersonically with respect to each other. We find that an initially laminar BL is unstable to two different kinds of instabilities. One is an instability of a supersonic vortex sheet (implying a discontinuous initial profile of the angular speed of the gas) in the presence of gravity, which we find to have a growth rate of order (but less than) the orbital frequency. The other is a sonic instability of a finite width, supersonic shear layer, which is similar to the Papaloizou-Pringle instability. It has a growth rate proportional to the shear inside the transition layer, which is of order the orbital frequency times the ratio of stellar radius to the BL thickness. For a BL that is thin compared to the radius of the star, the shear rate is much larger than the orbital frequency. Thus, we conclude that sonic instabilities play a dominant role in the initial stages of nonmagnetic BL formation and give rise to very fast mixing between disk gas and stellar fluid in the supersonic regime.

  13. Bernstein instability driven by thermal ring distribution

    SciTech Connect (OSTI)

    Yoon, Peter H.; Hadi, Fazal; Qamar, Anisa

    2014-07-15

    The classic Bernstein waves may be intimately related to banded emissions detected in laboratory plasmas, terrestrial, and other planetary magnetospheres. However, the customary discussion of the Bernstein wave is based upon isotropic thermal velocity distribution function. In order to understand how such waves can be excited, one needs an emission mechanism, i.e., an instability. In non-relativistic collision-less plasmas, the only known Bernstein wave instability is that associated with a cold perpendicular velocity ring distribution function. However, cold ring distribution is highly idealized. The present Brief Communication generalizes the cold ring distribution model to include thermal spread, so that the Bernstein-ring instability is described by a more realistic electron distribution function, with which the stabilization by thermal spread associated with the ring distribution is demonstrated. The present findings imply that the excitation of Bernstein waves requires a sufficiently high perpendicular velocity gradient associated with the electron distribution function.

  14. Plasma Instabilities in Heavy Ion Collisions

    SciTech Connect (OSTI)

    Attems, M.; Rebhan, A.; Strickland, M.

    2011-05-23

    Non-Abelian plasma instabilities play a crucial role in the nonequilibrium dynamics of a weakly coupled quark-gluon plasma. The Chromo-Weibel instabilities have been proposed as a possible mechanism for the fast apparent thermalization of the quark-gluon plasma and have been extensively studied in stationary anisotropic plasmas using the so-called hard-loop approximation. The generalization to the hard-expanding-loop (HEL) formalism allows the (numerical) calculation of the time evolution of gluonic mean fields in the more realistic dynamical case of anisotropic expansion.

  15. Genome Science/Technologies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Genome Science/Technologies Los Alamos using cutting-edge sequencing, finishing, and analysis, impact valuable genomic data. Srinivas Iyer Bioscience Group Leader Email Get Expertise David Bruce Bioscience Deputy Group Leader Email Momchilo Vuyisich Scientist Email Rebecca McDonald Bioscience Communications Email State-of-the art technology and extensive genomics expertise Protein research Read caption + Los Alamos National Laboratory graduate student, Patricia Langan, changes the

  16. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology Genomics and Systems Biology Los Alamos scientists perform research in functional genomics and structural genomics, and applications for such work cover diverse fields such as energy, agriculture, and environmental cleanup. Contact Us Babetta Marrone Biofuels Program Manager Email Cheryl Kuske DOE BER Biological System Science Division Program Manager Email Kirsten McCabe Emerging Threats Program Manager Email Rebecca McDonald Bioscience Communications Email "We

  17. The human genome project

    SciTech Connect (OSTI)

    Yager, T.D.; Zewert, T.E.; Hood, L.E. )

    1994-04-01

    The Human Genome Project (HGP) is a coordinated worldwide effort to precisely map the human genome and the genomes of selected model organisms. The first explicit proposal for this project dates from 1985 although its foundations (both conceptual and technological) can be traced back many years in genetics, molecular biology, and biotechnology. The HGP has matured rapidly and is producing results of great significance.

  18. Simulation of E-Cloud Driven Instability And Its Attenuation...

    Office of Scientific and Technical Information (OSTI)

    Instability And Its Attenuation Using a Feedback System in the CERN SPS Citation Details In-Document Search Title: Simulation of E-Cloud Driven Instability And Its Attenuation ...

  19. Simulation of E-Cloud Driven Instability And Its Attenuation...

    Office of Scientific and Technical Information (OSTI)

    of E-Cloud Driven Instability And Its Attenuation Using a Feedback System in the CERN SPS Citation Details In-Document Search Title: Simulation of E-Cloud Driven Instability...

  20. Current-Driven Filament Instabilities in Relativistic Plasmas. Final report

    SciTech Connect (OSTI)

    Chuang Ren

    2013-02-13

    This grant has supported a study of some fundamental problems in current- and flow-driven instabilities in plasmas and their applications in inertial confinement fusion (ICF) and astrophysics. It addressed current-driven instabilities and their roles in fast ignition, and flow-driven instabilities and their applications in astrophysics.

  1. The potential benefits of nicaraven to protect against radiation-induced injury in hematopoietic stem/progenitor cells with relative low dose exposures

    SciTech Connect (OSTI)

    Ali, Haytham; Galal, Omima; Urata, Yoshishige; Goto, Shinji; Guo, Chang-Ying; Luo, Lan; Abdelrahim, Eman; Ono, Yusuke; Mostafa, Emtethal; Li, Tao-Sheng

    2014-09-26

    Highlights: Nicaraven mitigated the radiation-induced reduction of c-kit{sup +} stem cells. Nicaraven enhanced the function of hematopoietic stem/progenitor cells. Complex mechanisms involved in the protection of nicaraven to radiation injury. - Abstract: Nicaraven, a hydroxyl radical-specific scavenger has been demonstrated to attenuate radiation injury in hematopoietic stem cells with 5 Gy ?-ray exposures. We explored the effect and related mechanisms of nicaraven for protecting radiation injury induced by sequential exposures to a relatively lower dose ?-ray. C57BL/6 mice were given nicaraven or placebo within 30 min before exposure to 50 mGy ?-ray daily for 30 days in sequences (cumulative dose of 1.5 Gy). Mice were victimized 24 h after the last radiation exposure, and the number, function and oxidative stress of hematopoietic stem cells were quantitatively estimated. We also compared the gene expression in these purified stem cells from mice received nicaraven and placebo treatment. Nicaraven increased the number of c-kit{sup +} stem/progenitor cells in bone marrow and peripheral blood, with a recovery rate around 6090% of age-matched non-irradiated healthy mice. The potency of colony forming from hematopoietic stem/progenitor cells as indicator of function was completely protected with nicaraven treatment. Furthermore, nicaraven treatment changed the expression of many genes associated to DNA repair, inflammatory response, and immunomodulation in c-kit{sup +} stem/progenitor cells. Nicaraven effectively protected against damages of hematopoietic stem/progenitor cells induced by sequential exposures to a relatively low dose radiation, via complex mechanisms.

  2. SNP in TXNRD2 Associated With Radiation-Induced Fibrosis: A Study of Genetic Variation in Reactive Oxygen Species Metabolism and Signaling

    SciTech Connect (OSTI)

    Edvardsen, Hege; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Landmark-Hyvik, Hege; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Reinertsen, Kristin V.; Zhao, Xi; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Grenaker-Alns, Grethe Irene; Nebdal, Daniel; Syvnen, Ann-Christine; Rdningen, Olaug; Alsner, Jan; Overgaard, Jens; Borresen-Dale, Anne-Lise; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo ; Foss, Sophie D.; National Resource Centre for Late Effects after Cancer Treatment, OUS Radiumhospitalet, Oslo ; Kristensen, Vessela N.; K. G. Jebsen Breast cancer centre, Institute for Clinical Medicine, University of Oslo, Oslo; Department of Clinical Molecular Biology , Division of Medicine, Ahus University Hospital

    2013-07-15

    Purpose: The aim of the study was to identify noninvasive markers of treatment-induced side effects. Reactive oxygen species (ROS) are generated after irradiation, and genetic variation in genes related to ROS metabolism might influence the level of radiation-induced adverse effects (AEs). Methods and Materials: 92 breast cancer (BC) survivors previously treated with hypofractionated radiation therapy were assessed for the AEs subcutaneous atrophy and fibrosis, costal fractures, lung fibrosis, pleural thickening, and telangiectasias (median follow-up time 17.1 years). Single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed for association to AE grade. SNPs associated with subcutaneous fibrosis were validated in an independent BC survivor material (n=283). The influence of the studied genetic variation on messenger ribonucleic acid (mRNA) expression level of 18 genes previously associated with fibrosis was assessed in fibroblast cell lines from BC patients. Results: Subcutaneous fibrosis and atrophy had the highest correlation (r=0.76) of all assessed AEs. The nonsynonymous SNP rs1139793 in TXNRD2 was associated with grade of subcutaneous fibrosis, the reference T-allele being more prevalent in the group experiencing severe levels of fibrosis. This was confirmed in another sample cohort of 283 BC survivors, and rs1139793 was found significantly associated with mRNA expression level of TXNRD2 in blood. Genetic variation in 24 ROS-related genes, including EGFR, CENPE, APEX1, and GSTP1, was associated with mRNA expression of 14 genes previously linked to fibrosis (P?.005). Conclusion: Development of subcutaneous fibrosis can be associated with genetic variation in the mitochondrial enzyme TXNRD2, critically involved in removal of ROS, and maintenance of the intracellular redox balance.

  3. Ultraviolet radiation induced discharge laser

    DOE Patents [OSTI]

    Gilson, Verle A. (Livermore, CA); Schriever, Richard L. (Livermore, CA); Shearer, James W. (Livermore, CA)

    1978-01-01

    An ultraviolet radiation source associated with a suitable cathode-anode electrode structure, disposed in a gas-filled cavity of a high pressure pulsed laser, such as a transverse electric atmosphere (TEA) laser, to achieve free electron production in the gas by photoelectric interaction between ultraviolet radiation and the cathode prior to the gas-exciting cathode-to-anode electrical discharge, thereby providing volume ionization of the gas. The ultraviolet radiation is produced by a light source or by a spark discharge.

  4. Radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.; Shearin-Jones, P.; Oryhon, J.

    1996-12-31

    In the process of identifying genes that are differentially regulated in cells exposed to ultraviolet radiation (UV), we identified a transcript that was repressed following the exposure of cells to a combination of UV and salicylate, a known inhibitor of NF-kappaB. Sequencing this band determined that it has identify to lactate dehydrogenase, and Northern blots confirmed the initial expression pattern. Analysis of the sequence of the LDH 5` region established the presence of NF-kappaB, Sp1, and two Ap-2 elements; two partial AP- 1; one partial RE, and two halves of E-UV elements were also found. Electromobility shift assays were then performed for the AP-1, NF- kappaB, and E-UV elements. These experiments revealed that binding to NF-kappaB was induced by UV but repressed with salicylic acid; UV did not affect AP-1 binding, but salicylic acid inhibited it alone or following UV exposure; and E-UV binding was repressed by UV, and salicylic acid had little effect. Since the binding of no single element correlated with the expression pattern of LDH, it is likely that multiple elements govern UV/salicylate-mediated expression.

  5. Radiation-induced lung injury

    SciTech Connect (OSTI)

    Rosiello, R.A.; Merrill, W.W. )

    1990-03-01

    The use of radiation therapy is limited by the occurrence of the potentially fatal clinical syndromes of radiation pneumonitis and fibrosis. Radiation pneumonitis usually becomes clinically apparent from 2 to 6 months after completion of radiation therapy. It is characterized by fever, cough, dyspnea, and alveolar infiltrates on chest roentgenogram and may be difficult to differentiate from infection or recurrent malignancy. The pathogenesis is uncertain, but appears to involve both direct lung tissue toxicity and an inflammatory response. The syndrome may resolve spontaneously or may progress to respiratory failure. Corticosteroids may be effective therapy if started early in the course of the disease. The time course for the development of radiation fibrosis is later than that for radiation pneumonitis. It is usually present by 1 year following irradiation, but may not become clinically apparent until 2 years after radiation therapy. It is characterized by the insidious onset of dyspnea on exertion. It most often is mild, but can progress to chronic respiratory failure. There is no known successful treatment for this condition. 51 references.

  6. Simulation of Weibel Instability for LWFA and PWFA Electron Beams

    SciTech Connect (OSTI)

    Allen, B.; Muggli, P.; Feng, B.; Katsouleas, T.; Huang, C.; Yakimenko, V.; Maksimchuk, A.

    2009-01-22

    Weibel instability is of central importance for relativistic beams both in laboratory, ex. fast-igniter concept for inertial confinement fusion, and astrophysical, ex. cosmic jets, plasmas. Simulations, using QuickPIC, of an intense and monoenergetic beam propagating through a plasma were conducted for experimental setups with Laser Wakefield and RF accelerators and show the appearance of Weibel instability (or current instability). The appearance of the instability is investigated as a function of beam parameters (density, spot size and bunch length) and plasma parameters (plasma density and length of plasma). We present preliminary simulation results that show that the instability should be observable for the RF accelerator experiment.

  7. Beam instability studies for the SSC

    SciTech Connect (OSTI)

    Chou, W.

    1994-09-01

    Beam instability studies of the Superconducting Super Collider (SSC) during the period 1989--1993 are briefly reviewed in this paper. Various topics are covered: single bunch and multi-bunch, single beam and beam-beam, parasitic heating and active feedback, etc. Although the SSC will not be built, many of the results obtained from these studies remain as useful references to the accelerator community.

  8. Coherent instabilities of a relativistic bunched beam

    SciTech Connect (OSTI)

    Chao, A.W.

    1982-06-01

    A charge-particle beam contained in an accelerator vacuum chamber interacts electromagnetically with its environment to create a wake field. This field than acts back on the beam, perturbing the particle motion. If the beam intensity is high enough, this beam-environment interaction may lead to an instability and to subsequent beam loss. The beam and its environment form a dynamical system, and it is this system that will be studied. 84 references.

  9. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology LANL leads the world in computational finishing of microbial genomes Read caption + In 2013, Los Alamos scientist Richard Sayre and his team genetically modified the organisms to harvest light more efficiently for maximum production. Overview of Research and Highlights Researchers at Los Alamos National Laboratory are using their renowned expertise in genomics, computation, and experimental biology as the foundation of a dynamic systems biology capability. Systems

  10. Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  11. Genomics Division Home

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the most primitive soil microbe represent a watershed opportunity for biology. The Genomics Division is taking advantage of this wealth of new information. While it is well...

  12. Genome Science/Technologies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    intra-genomic species heterogeneity and cell-to-cell interactions. He also loves volleyball, running, eating, sketching, shopping, and chillin' with a good movie. Cheryl...

  13. Human Genome: DOE Origins

    Office of Scientific and Technical Information (OSTI)

    of the Department of Energy; DOE Technical Report; 1988 Mapping and Sequencing the Human Genome; DOE Technical Report; 1988 Understanding our Genetic Inheritance: The U.S....

  14. The Future of Microbial Genomics

    SciTech Connect (OSTI)

    Kyrpides, Nikos [Genome Biology group at the DOE Joint Genome Institute

    2010-06-02

    Nikos Kyrpides, head of the Genome Biology group at the DOE Joint Genome Institute discusses current challenges in the field of microbial genomics on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  15. Linear plasmoid instability of thin current sheets with shear flow

    SciTech Connect (OSTI)

    Ni Lei; Germaschewski, Kai; Huang Yimin; Sullivan, Brian P.; Yang Hongang; Bhattacharjee, Amitava

    2010-05-15

    This paper presents linear analytical and numerical studies of plasmoid instabilities in the presence of shear flow in high-Lundquist-number plasmas. Analysis demonstrates that the stability problem becomes essentially two dimensional as the stabilizing effects of shear flow become more prominent. Scaling results are presented for the two-dimensional instabilities. An approximate criterion is given for the critical aspect ratio of thin current sheets at which the plasmoid instability is triggered.

  16. Pair instability supernovae of very massive population III stars (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Pair instability supernovae of very massive population III stars Citation Details In-Document Search Title: Pair instability supernovae of very massive population III stars Numerical studies of primordial star formation suggest that the first stars in the universe may have been very massive. Stellar models indicate that non-rotating Population III stars with initial masses of 140-260 M {sub ☉} die as highly energetic pair-instability supernovae. We present new

  17. SciTech Connect: genomics

    Office of Scientific and Technical Information (OSTI)

    genomics Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: genomics Semantic Semantic Term Title: Full Text: Bibliographic Data: Creator Author:...

  18. Two-stream instability with time-dependent drift velocity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qin, Hong; Davidson, Ronald C.

    2014-06-26

    The classical two-stream instability driven by a constant relative drift velocity between two plasma components is extended to the case with time-dependent drift velocity. A solution method is developed to rigorously define and calculate the instability growth rate for linear perturbations relative to the time-dependent unperturbed two-stream motions. The stability diagrams for the oscillating two-stream instability are presented over a large region of parameter space. It is shown that the growth rate for the classical two-stream instability can be significantly reduced by adding an oscillatory component to the relative drift velocity.

  19. Pair instability supernovae of very massive population III stars...

    Office of Scientific and Technical Information (OSTI)

    In red supergiant progenitors, the amplitudes of these instabilities are sufficient to mix the supernova ejecta. less Authors: Chen, Ke-Jung ; Woosley, Stan 1 ; Heger, ...

  20. Teasing Out the Nature of Structural Instabilities in Ceramic...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Instabilities in Ceramic Compounds MARCH 12, 2013 Bookmark and Share The simple perovskite structure of EuTiO3 illustrated above shows the essential competing structural...

  1. Density-shear instability in electron magneto-hydrodynamics

    SciTech Connect (OSTI)

    Wood, T. S. Hollerbach, R.; Lyutikov, M.

    2014-05-15

    We discuss a novel instability in inertia-less electron magneto-hydrodynamics (EMHD), which arises from a combination of electron velocity shear and electron density gradients. The unstable modes have a lengthscale longer than the transverse density scale, and a growth-rate of the order of the inverse Hall timescale. We suggest that this density-shear instability may be of importance in magnetic reconnection regions on scales smaller than the ion skin depth, and in neutron star crusts. We demonstrate that the so-called Hall drift instability, previously argued to be relevant in neutron star crusts, is a resistive tearing instability rather than an instability of the Hall term itself. We argue that the density-shear instability is of greater significance in neutron stars than the tearing instability, because it generally has a faster growth-rate and is less sensitive to geometry and boundary conditions. We prove that, for uniform electron density, EMHD is at least as stable as regular, incompressible MHD, in the sense that any field configuration that is stable in MHD is also stable in EMHD. We present a connection between the density-shear instability in EMHD and the magneto-buoyancy instability in anelastic MHD.

  2. Electrohydrodynamic instabilities in thin liquid trilayer films

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Roberts, Scott A.; Kumar, Satish

    2010-12-09

    Experiments by Dickey and Leach show that novel pillar shapes can be generated from electrohydrodynamic instabilities at the interfaces of thin polymer/polymer/air trilayer films. In this paper, we use linear stability analysis to investigate the effect of free charge and ac electric fields on the stability of trilayer systems. Our work is also motivated by our recent theoretical study which demonstrates how ac electric fields can be used to increase control over the pillar formation process in thin liquid bilayer films. For perfect dielectric films, the effect of an AC electric field can be understood by considering an equivalent DCmore » field. Leaky dielectric films yield pillar configurations that are drastically different from perfect dielectric films, and AC fields can be used to control the location of free charge within the trilayer system. This can alter the pillar instability modes and generate smaller diameter pillars when conductivities are mismatched. The results presented may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.« less

  3. Electrohydrodynamic instabilities in thin liquid trilayer films

    SciTech Connect (OSTI)

    Roberts, Scott A.; Kumar, Satish

    2010-01-01

    Experiments by Dickey and Leach show that novel pillar shapes can be generated from electrohydrodynamic instabilities at the interfaces of thin polymer/polymer/air trilayer films. In this paper, we use linear stability analysis to investigate the effect of free charge and ac electric fields on the stability of trilayer systems. Our work is also motivated by our recent theoretical study which demonstrates how ac electric fields can be used to increase control over the pillar formation process in thin liquid bilayer films. For perfect dielectric films, the effect of an AC electric field can be understood by considering an equivalent DC field. Leaky dielectric films yield pillar configurations that are drastically different from perfect dielectric films, and AC fields can be used to control the location of free charge within the trilayer system. This can alter the pillar instability modes and generate smaller diameter pillars when conductivities are mismatched. The results presented here may be of interest for the creation of complex topographical patterns on polymer coatings and in microelectronics.

  4. Criterion for thermo-plastic shear instability

    SciTech Connect (OSTI)

    Burns, T.J.; Grady, D.E.; Costin, L.S.

    1981-01-01

    Dynamic torsional Kolsky (split-Hopkinson) bar experiments on thin-walled tubes of 1018 cold-rolled and 1020 hot-rolled steel are modeled using a deformation plasticity theory which incorporates a specific constitutive model for the shear stress in terms of strain, strain-rate, and temperature into a system of differential equations. The exact time-dependent homogeneous flow solution of the equations is found and used to derive a special case of a generally accepted instability criterion. For given material parameters, this criterion predicts a critical strain at which a homogeneous deformation can bifuricate into a localized deformation, i.e., a shear band, at constant strain-rate. Stability diagrams of strain-rate vs. strain can be constructed for the two types of steel using the criterion. The Kolsky bar data is shown to be consistent with this analysis, and an explanation for the instability criterion is given which assumes that small perturbations on the non-steady homogeneous flow are isentropic to first order.

  5. Eukaryotic Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    From the JGI webportal users can choose Eukaryotic genomes from a photo list, access the JGI FTP directories to download data files, use the Tree of Life navigation tool, or choose a genome and go directly to a website specific to that one genome. The individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.

  6. Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  7. Genomic library construction

    DOE Patents [OSTI]

    Church, George M.; Zhang, Kun

    2011-07-26

    Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions and methods for constructing a genomic library from a single cell are also provided.

  8. Genomic definition of species

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  9. Pair instability supernovae of very massive population III stars

    SciTech Connect (OSTI)

    Chen, Ke-Jung; Woosley, Stan; Heger, Alexander; Almgren, Ann; Whalen, Daniel J.

    2014-09-01

    Numerical studies of primordial star formation suggest that the first stars in the universe may have been very massive. Stellar models indicate that non-rotating Population III stars with initial masses of 140-260 M {sub ?} die as highly energetic pair-instability supernovae. We present new two-dimensional simulations of primordial pair-instability supernovae done with the CASTRO code. Our simulations begin at earlier times than previous multidimensional models, at the onset of core contraction, to capture any dynamical instabilities that may be seeded by core contraction and explosive burning. Such instabilities could enhance explosive yields by mixing hot ash with fuel, thereby accelerating nuclear burning, and affect the spectra of the supernova by dredging up heavy elements from greater depths in the star at early times. Our grid of models includes both blue supergiants and red supergiants over the range in progenitor mass expected for these events. We find that fluid instabilities driven by oxygen and helium burning arise at the upper and lower boundaries of the oxygen shell ?20-100 s after core bounce. Instabilities driven by burning freeze out after the SN shock exits the helium core. As the shock later propagates through the hydrogen envelope, a strong reverse shock forms that drives the growth of Rayleigh-Taylor instabilities. In red supergiant progenitors, the amplitudes of these instabilities are sufficient to mix the supernova ejecta.

  10. Integrative Genomics Building

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Integrative Genomics Building Community Berkeley Global Campus Environmental Documents Tours Community Programs Friends of Berkeley Lab ⇒ Navigate Section Community Berkeley Global Campus Environmental Documents Tours Community Programs Friends of Berkeley Lab Project Description The Integrative Genomics Building (IGB) is proposed to be an approximately 77,000 gsf, four-story research and office building constructed in the former Bevatron area - a fully developed site in the geographic

  11. Indeterminacy and instability in Petschek reconnection

    SciTech Connect (OSTI)

    Forbes, Terry G.; Priest, Eric R.; Seaton, Daniel B.; Litvinenko, Yuri E.

    2013-05-15

    We explain two puzzling aspects of Petschek's model for fast reconnection. One is its failure to occur in plasma simulations with uniform resistivity. The other is its inability to provide anything more than an upper limit for the reconnection rate. We have found that previously published analytical solutions based on Petschek's model are structurally unstable if the electrical resistivity is uniform. The structural instability is associated with the presence of an essential singularity at the X-line that is unphysical. By requiring that such a singularity does not exist, we obtain a formula that predicts a specific rate of reconnection. For uniform resistivity, reconnection can only occur at the slow, Sweet-Parker rate. For nonuniform resistivity, reconnection can occur at a much faster rate provided that the resistivity profile is not too flat near the X-line. If this condition is satisfied, then the scale length of the nonuniformity determines the reconnection rate.

  12. Revenue instability induced by conservation rates

    SciTech Connect (OSTI)

    Chesnutt, T.W.; McSpadden, C.; Christianson, J.

    1996-01-01

    The shift toward conservation rate structures, although they may provide better incentives to use scarce water wisely, changes who pays what and can increase the variability of future revenue streams to the water agency. Though the definition of the correct rate structure varies by community, the managerial strategies necessary to cope with the uncertainty brought about by conservation rate structures apply universally. Revenue instability directly increases water supplier`s borrowing costs and adds indirect costs in the form of more complicated planning to provide for a reliable future water supply. This article describes an empirical study using data from two water agencies that have adopted conservation rate structures. The article proposes ways quantitative tools may be used to (1) measure and cope with added uncertainty and (2) make explicit the magnitude of trade-offs between revenue stability, equity, and the provision of incentives for efficient use of water resources.

  13. Probing instabilities in arc plasma devices using binary gas mixtures

    SciTech Connect (OSTI)

    Ghorui, S.; Vysohlid, M.; Heberlein, J. V. R.; Pfender, E.

    2007-07-15

    This paper presents an experimental approach to identify the sources of instabilities in arc plasma devices. The phenomena of demixing in arcs have been utilized to explore the characteristics of different instabilities. Problems in explaining the observed behavior with our current understanding of the phenomena are discussed. Hydrogen is used as a secondary gas with argon as the primary plasma gas for this study. Results indicate that the observed behavior such as steady, takeover, and restrike modes of instabilities in arcs may essentially originate from the thin boundary layer over the anode wall primarily at the location of the anodic arc root. The bulk core flow apparently does not play any significant role in such instabilities. Arc currents rather than flow rates control the behavior of the instabilities in frequency space. Bifurcation of the system behavior and evidence for the existence of quadratic zones in flow space of binary gas mixtures separating steady and unsteady behavior are discussed.

  14. The density gradient effect on quantum Weibel instability

    SciTech Connect (OSTI)

    Mahdavi, M. Khodadadi Azadboni, F.

    2015-03-15

    The Weibel instability plays an important role in stopping the hot electrons and energy deposition mechanism in the fast ignition of inertial fusion process. In this paper, the effects of the density gradient and degeneracy on Weibel instability growth rate are investigated. Calculations show that decreasing the density degenerate in the plasma corona, near the relativistic electron beam emitting region by 8.5% leads to a 92% reduction in the degeneracy parameter and about 90% reduction in Weibel instability growth rate. Also, decreasing the degenerate density near the fuel core by 8.5% leads to 1% reduction in the degeneracy parameter and about 8.5% reduction in Weibel instability growth rate. The Weibel instability growth rate shrinks to zero and the deposition condition of relativistic electron beam energy can be shifted to the fuel core for a suitable ignition by increasing the degeneracy parameter in the first layer of plasma corona.

  15. Modulational instability of electromagnetic waves in a collisional quantum magnetoplasma

    SciTech Connect (OSTI)

    Niknam, A. R.; Rastbood, E.; Bafandeh, F.; Khorashadizadeh, S. M.

    2014-04-15

    The modulational instability of right-hand circularly polarized electromagnetic electron cyclotron (CPEM-EC) wave in a magnetized quantum plasma is studied taking into account the collisional effects. Employing quantum hydrodynamic and nonlinear Schrdinger equations, the dispersion relation of modulated CPEM-EC wave in a collisional plasma has been derived. It is found that this wave is unstable in such a plasma system and the growth rate of the associated instability depends on various parameters such as electron Fermi temperature, plasma number density, collision frequency, and modulation wavenumber. It is shown that while the increase of collision frequency leads to increase of the growth rate of instability, especially at large wavenumber limit, the increase of plasma number density results in more stable modulated CPEM-EC wave. It is also found that in contrast to collisionless plasma in which modulational instability is restricted to small wavenumbers, in collisional plasma, the interval of instability occurrence can be extended to a large domain.

  16. Electron-ion hybrid instability experiment upgrades to the Auburn Linear Experiment for Instability Studies

    SciTech Connect (OSTI)

    DuBois, A. M.; Arnold, I.; Thomas, E. Jr.; Tejero, E.; Amatucci, W. E.

    2013-04-15

    The Auburn Linear EXperiment for Instability Studies (ALEXIS) is a laboratory plasma physics experiment used to study spatially inhomogeneous flows in a magnetized cylindrical plasma column that are driven by crossed electric (E) and magnetic (B) fields. ALEXIS was recently upgraded to include a small, secondary plasma source for a new dual source, interpenetrating plasma experiment. Using two plasma sources allows for highly localized electric fields to be made at the boundary of the two plasmas, inducing strong E Multiplication-Sign B velocity shear in the plasma, which can give rise to a regime of instabilities that have not previously been studied in ALEXIS. The dual plasma configuration makes it possible to have independent control over the velocity shear and the density gradient. This paper discusses the recent addition of the secondary plasma source to ALEXIS, as well as the plasma diagnostics used to measure electric fields and electron densities.

  17. Feedback techniques and SPS Ecloud instabilities - design estimates

    SciTech Connect (OSTI)

    Fox,J.D.; Mastorides, T.; Ndabashimiye, G.; Rivetta, C.; Van Winkle, D.; Byrd, J.; Vay, J-L.; Hofle, W.; Rumolo, G.; de Maria, R.

    2009-05-04

    The SPS at high intensities exhibits transverse single-bunch instabilities with signatures consistent with an Ecloud driven instability. While the SPS has a coupled-bunch transverse feedback system, control of Ecloud driven motion requires a much wider control bandwidth capable of sensing and controlling motion within each bunched beam. This paper draws beam dynamics data from the measurements and simulations of this SPS instability, and estimates system requirements for a feedback system with 2-4 GS/sec. sampling rates to damp Ecloud-driven transverse motion in the SPS at intensities desired for high-current LHC operation.

  18. Two-dimensional simulations of pulsational pair-instability supernovae

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Two-dimensional simulations of pulsational pair-instability supernovae Citation Details In-Document Search Title: Two-dimensional simulations of pulsational pair-instability supernovae Massive stars that end their lives with helium cores in the range of 35-65 M {sub ☉} are known to produce repeated thermonuclear outbursts due to a recurring pair-instability. In some of these events, solar masses of material are ejected in repeated outbursts of several ×

  19. Berkeley Quantitative Genome Browser

    Energy Science and Technology Software Center (OSTI)

    2008-02-29

    The Berkeley Quantitative Genome Browser provides graphical browsing functionality for genomic data organized, at a minimum, by sequence and position. While supporting the annotation browsing features typical of many other genomic browsers, additional emphasis is placed on viewing and utilizing quantitative data. Data may be read from GFF, SGR, FASTA or any column delimited format. Once the data has been read into the browser's buffer, it may be searched. filtered or subjected to mathematical transformation.more » The browser also supplies some graphical design manipulation functionality geared towards preparing figures for presentations or publication. A plug-in mechanism enables development outside the core functionality that adds more advanced or esoteric analysis capabilities. BBrowse's development and distribution is open-source and has been built to run on Linux, OSX and MS Windows operating systems.« less

  20. MHD Ballooning Instability in the Plasma Sheet

    SciTech Connect (OSTI)

    C.Z. Cheng; S. Zaharia

    2003-10-20

    Based on the ideal-MHD model the stability of ballooning modes is investigated by employing realistic 3D magnetospheric equilibria, in particular for the substorm growth phase. Previous MHD ballooning stability calculations making use of approximations on the plasma compressibility can give rise to erroneous conclusions. Our results show that without making approximations on the plasma compressibility the MHD ballooning modes are unstable for the entire plasma sheet where beta (sub)eq is greater than or equal to 1, and the most unstable modes are located in the strong cross-tail current sheet region in the near-Earth plasma sheet, which maps to the initial brightening location of the breakup arc in the ionosphere. However, the MHD beq threshold is too low in comparison with observations by AMPTE/CCE at X = -(8 - 9)R(sub)E, which show that a low-frequency instability is excited only when beq increases over 50. The difficulty is mitigated by considering the kinetic effects of ion gyrorad ii and trapped electron dynamics, which can greatly increase the stabilizing effects of field line tension and thus enhance the beta(sub)eq threshold [Cheng and Lui, 1998]. The consequence is to reduce the equatorial region of the unstable ballooning modes to the strong cross-tail current sheet region where the free energy associated with the plasma pressure gradient and magnetic field curvature is maximum.

  1. Microbial Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    As of March 2008, The Joint Genome Institute has released 296 Prokaryotic microbial sites, with 216 in finished status.

  2. Human Genome: DOE Origins

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DOE Origins Resources with Additional Information Charles DeLisi Charles DeLisi The genesis of the Department of Energy (DOE) human genome project took place when "Charles DeLisi ... conceived of a concerted effort to sequence the human genome under the aegis of the ... DOE. ... In 1985, DeLisi took the reins of DOE's Office of Health and Environmental Research [OHER], the program that supported most Biology in the Department. The origins of DOE's biology program traced to the Manhattan

  3. Ordinary mode instability associated with thermal ring distribution

    SciTech Connect (OSTI)

    Hadi, F.; Qamar, A.; Yoon, P. H.

    2015-02-15

    The purely growing ordinary (O) mode instability driven by excessive parallel temperature anisotropy has recently received renewed attention owing to its potential applicability to the solar wind plasma. Previous studies of O mode instability have assumed either bi-Maxwellian or counter-streaming velocity distributions. For solar wind plasma trapped in magnetic mirror-like geometry such as magnetic clouds or in the vicinity of the Earth's collisionless bow shock environment, however, the velocity distribution function may possess a loss-cone feature. The O-mode instability in such a case may be excited for cyclotron harmonics as well as the purely growing branch. The present paper investigates the O-mode instability for plasmas characterized by the parallel Maxwellian distribution and perpendicular thermal ring velocity distribution in order to understand the general stability characteristics.

  4. Kink instability suppression with stochastic cooling pickup and kicker

    SciTech Connect (OSTI)

    Hao Y.; Blaskiewicz, M.; Litvinenko, V.N.; Ptitsyn, V.

    2012-05-20

    The kink instability is one of the major beam dynamics issues of the linac-ring based electron ion collider. This head-tail type instability arises from the oscillation of the electron beam inside the opposing ion beam. It must be suppressed to achieve the desired luminosity. There are various ways to suppress the instability, such as tuning the chromaticity in the ion ring or by a dedicated feedback system of the electron beam position at IP, etc. However, each method has its own limitation. In this paper, we will discuss an alternative opportunity of suppressing the kink instability of the proposed eRHIC at BNL using the existing pickup-kicker system of the stochastic cooling system in RHIC.

  5. The role of phase instabilities in the early material response...

    Office of Scientific and Technical Information (OSTI)

    The role of phase instabilities in the early material response during laser-induced breakdown in bulk fused silica Citation Details In-Document Search Title: The role of phase...

  6. When linear stability does not exclude nonlinear instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kevrekidis, P. G.; Pelinovsky, D. E.; Saxena, A.

    2015-05-29

    We describe a mechanism that results in the nonlinear instability of stationary states even in the case where the stationary states are linearly stable. In this study, this instability is due to the nonlinearity-induced coupling of the linearization’s internal modes of negative energy with the continuous spectrum. In a broad class of nonlinear Schrödinger equations considered, the presence of such internal modes guarantees the nonlinear instability of the stationary states in the evolution dynamics. To corroborate this idea, we explore three prototypical case examples: (a) an antisymmetric soliton in a double-well potential, (b) a twisted localized mode in a one-dimensionalmore » lattice with cubic nonlinearity, and (c) a discrete vortex in a two-dimensional saturable lattice. In all cases, we observe a weak nonlinear instability, despite the linear stability of the respective states.« less

  7. A Linear Theory of Microwave Instability in Electron Storage...

    Office of Scientific and Technical Information (OSTI)

    Title: A Linear Theory of Microwave Instability in Electron Storage Rings The well-known ... in an analysis of this stability that are associated with the potential-well distortion. ...

  8. Growth of filaments and saturation of the filamentation instability

    SciTech Connect (OSTI)

    Gedalin, M.; Medvedev, M.; Spitkovsky, A.; Krasnoselskikh, V.; Vaivads, A.; Perri, S.

    2010-03-15

    The filamentation instability of counterstreaming beams is a nonresonant hydrodynamic-type instability whose growth rate is a smooth function of the wavelength (scale). As a result, perturbations with all unstable wavelengths develop, and the growth saturates due to the saturation of available current. For a given scale, the magnetic field at saturation is proportional to the scale. As a result, the instability develops in a nearly linear regime, where the unstable modes stop growing as soon as the saturation of the corresponding wavelength is reached. At each moment there exists a dominant scale of the magnetic field which is the scale that reached saturation at this particular time. The smaller scales do not disappear and can be easily distinguished in the current structure. The overall growth of the instability stops when the loss of the streaming ion energy because of deceleration is comparable to the initial ion energy.

  9. Microturbulence in DIII-D tokamak pedestal. I. Electrostatic instabilities

    SciTech Connect (OSTI)

    Fulton, D. P.; Holod, I.; Lin, Z.; Xiao, Y.

    2014-04-15

    Gyrokinetic simulations of electrostatic driftwave instabilities in a tokamak edge have been carried out to study the turbulent transport in the pedestal of an H-mode plasma. The simulations use annulus geometry and focus on two radial regions of a DIII-D experiment: the pedestal top with a mild pressure gradient and the middle of the pedestal with a steep pressure gradient. A reactive trapped electron instability with a typical ballooning mode structure is excited by trapped electrons in the pedestal top. In the middle of the pedestal, the electrostatic instability exhibits an unusual mode structure, which peaks at the poloidal angle ?=?/2. The simulations find that this unusual mode structure is due to the steep pressure gradients in the pedestal but not due to the particular DIII-D magnetic geometry. Realistic DIII-D geometry appears to have a stabilizing effect on the instability when compared to a simple circular tokamak geometry.

  10. Influence of flavor oscillations on neutrino beam instabilities

    SciTech Connect (OSTI)

    Mendona, J. T.; Haas, F.; Bret, A.

    2014-09-15

    We consider the collective neutrino plasma interactions and study the electron plasma instabilities produced by a nearly mono-energetic neutrino beam in a plasma. We describe the mutual interaction between neutrino flavor oscillations and electron plasma waves. We show that the neutrino flavor oscillations are not only perturbed by electron plasmas waves but also contribute to the dispersion relation and the growth rates of neutrino beam instabilities.

  11. Instability and Anharmonicity in Plutonium Thermo-physical Properties

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Instability and Anharmonicity in Plutonium Thermo-physical Properties Citation Details In-Document Search Title: Instability and Anharmonicity in Plutonium Thermo-physical Properties Authors: Freibert, Franz J [1] ; Mitchell, Jeremy N. [1] ; Saleh, Tarik A. [1] ; Migliori, Albert [1] + Show Author Affiliations Los Alamos National Laboratory Publication Date: 2012-07-10 OSTI Identifier: 1053884 Report Number(s): LA-UR-12-22830 DOE Contract Number: AC52-06NA25396

  12. Linear theory of microwave instability in electron storage rings (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Linear theory of microwave instability in electron storage rings Citation Details In-Document Search Title: Linear theory of microwave instability in electron storage rings Authors: Cai, Yunhai Publication Date: 2011-06-14 OSTI Identifier: 1099585 Type: Published Article Journal Name: Physical Review Special Topics - Accelerators and Beams Additional Journal Information: Journal Volume: 14; Journal Issue: 6; Journal ID: ISSN 1098-4402 Publisher: American Physical

  13. Suppression of Rayleigh Taylor instability in strongly coupled plasmas

    SciTech Connect (OSTI)

    Das, Amita; Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar 382428 (India)

    2014-06-15

    The Rayleigh Taylor instability in a strongly coupled plasma medium has been investigated using the equations of generalized hydrodynamics. It is demonstrated that the visco-elasticity of the strongly coupled medium due to strong inter particle correlations leads to a suppression of the Rayleigh Taylor instability unless certain threshold conditions are met. The relevance of these results to experiments on laser compression of matter to high densities including those related to inertial confinement fusion using lasers has also been shown.

  14. Surface Plasmon Instability Leading to Emission of Radiation. (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Surface Plasmon Instability Leading to Emission of Radiation. Citation Details In-Document Search Title: Surface Plasmon Instability Leading to Emission of Radiation. Abstract not provided. Authors: Gumbs, Godfrey ; Iurov, Andrii ; Huang, Danhong ; Pan, Wei Publication Date: 2014-11-01 OSTI Identifier: 1184587 Report Number(s): SAND2014-19499J 541018 DOE Contract Number: AC04-94AL85000 Resource Type: Journal Article Resource Relation: Journal Name: Physical Review

  15. Decay instability of a whistler in a plasma

    SciTech Connect (OSTI)

    Tewari, D.P.; Sharma, R.R.

    1981-08-01

    The parametric instabilities of a high power whistler in a high-density plasma possess large growth rates when the scattered sideband is an electrostatic lower hybrid mode. The efficient channels of decay include oscillating two stream instability, nonlinear Landau damping, and resonant decay involving ion acoustic and ion cyclotron modes. The processes of nonlinear scattering i.e., the ones possessing whistler sidebands are relatively less significant.

  16. Finite-size instabilities in nuclear energy density functionals

    SciTech Connect (OSTI)

    Hellemans, V.; Heenen, P.-H.; Bender, M.

    2012-10-20

    The systematic lack of convergence of self-consistent mean-field calculations with certain parameterizations of the Skyrme energy density functional has been attributed to the appearance of finite-size instabilities. In this contribution, we investigate what happens at the instability associated with the C{sub 0}{sup {Delta}s}s{sub 0} Dot-Operator {Delta}s{sub 0} term in a high-spin state of the superdeformed band in {sup 194}Hg.

  17. Pair-instability supernovae in the local universe

    SciTech Connect (OSTI)

    Whalen, Daniel J. [Zentrum fr Astronomie, Institut fr Theoretische Astrophysik, Universitt Heidelberg, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Smidt, Joseph [CCS-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Heger, Alexander [Monash Centre for Astrophysics, Monash University, Victoria 3800 (Australia); Hirschi, Raphael [Astrophysics Group, EPSAM, University of Keele, Lennard-Jones Labs, Keele ST5 5BG (United Kingdom); Yusof, Norhasliza [Department of Physics, University of Malaysia, 50603 Kuala Lampur (Malaysia); Even, Wesley; Fryer, Chris L. [T-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Stiavelli, Massimo [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Chen, Ke-Jung [Department of Astronomy and Astrophysics, UCSC, Santa Cruz, CA 95064 (United States); Joggerst, Candace C. [XTD-3, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2014-12-10

    The discovery of 150-300 M {sub ?} stars in the Local Group and pair-instability supernova candidates at low redshifts has excited interest in this exotic explosion mechanism. Realistic light curves for pair-instability supernovae at near-solar metallicities are key to identifying and properly interpreting these events as more are found. We have modeled pair-instability supernovae of 150-500 M {sub ?} Z ? 0.1-0.4 Z {sub ?} stars. These stars lose up to 80% of their mass to strong line-driven winds and explode as bare He cores. We find that their light curves and spectra are quite different from those of Population III pair-instability explosions, which therefore cannot be used as templates for low-redshift events. Although non-zero metallicity pair-instability supernovae are generally dimmer than their Population III counterparts, in some cases they will be bright enough to be detected at the earliest epochs at which they can occur, the formation of the first galaxies at z ? 10-15. Others can masquerade as dim, short duration supernovae that are only visible in the local universe and that under the right conditions could be hidden in a wide variety of supernova classes. We also report for the first time that some pair-instability explosions can create black holes with masses of ?100 M {sub ?}.

  18. LOCAL RADIATION MAGNETOHYDRODYNAMIC INSTABILITIES IN MAGNETICALLY STRATIFIED MEDIA

    SciTech Connect (OSTI)

    Tao, Ted; Blaes, Omer

    2011-11-20

    We study local radiation magnetohydrodynamic instabilities in static, optically thick, vertically stratified media with constant flux mean opacity. We include the effects of vertical gradients in a horizontal background magnetic field. Assuming rapid radiative diffusion, we use the zero gas pressure limit as an entry point for investigating the coupling between the photon bubble instability and the Parker instability. Apart from factors that depend on wavenumber orientation, the Parker instability exists for wavelengths longer than a characteristic wavelength {lambda}{sub tran}, while photon bubbles exist for wavelengths shorter than {lambda}{sub tran}. The growth rate in the Parker regime is independent of the orientation of the horizontal component of the wavenumber when radiative diffusion is rapid, but the range of Parker-like wavenumbers is extended if there exists strong horizontal shear between field lines (i.e., horizontal wavenumber perpendicular to the magnetic field). Finite gas pressure introduces an additional short-wavelength limit to the Parker-like behavior, and also limits the growth rate of the photon bubble instability to a constant value at short wavelengths. We also consider the effects of differential rotation with accretion disk applications in mind. Our results may explain why photon bubbles have not yet been observed in recent stratified shearing box accretion disk simulations. Photon bubbles may physically exist in simulations with high radiation to gas pressure ratios, but higher spatial resolution will be needed to resolve the asymptotically growing unstable wavelengths.

  19. Filamentation instability of nonextensive current-driven plasma in the ion acoustic frequency range

    SciTech Connect (OSTI)

    Khorashadizadeh, S. M. Rastbood, E.; Niknam, A. R.

    2014-12-15

    The filamentation and ion acoustic instabilities of nonextensive current-driven plasma in the ion acoustic frequency range have been studied using the Lorentz transformation formulas. Based on the kinetic theory, the possibility of filamentation instability and its growth rate as well as the ion acoustic instability have been investigated. The results of the research show that the possibility and growth rate of these instabilities are significantly dependent on the electron nonextensive parameter and drift velocity. Besides, the increase of electrons nonextensive parameter and drift velocity lead to the increase of the growth rates of both instabilities. In addition, the wavelength region in which the filamentation instability occurs is more stretched in the presence of higher values of drift velocity and nonextensive parameter. Finally, the results of filamentation and ion acoustic instabilities have been compared and the conditions for filamentation instability to be dominant mode of instability have been presented.

  20. Collisionless shock experiments with lasers and observation of Weibel instabilities

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Park, H. -S.; Huntington, C. M.; Fiuza, F.; Drake, R. P.; Froula, D. H.; Gregori, G.; Koenig, M.; Kugland, N. L.; Kuranz, C. C.; Lamb, D. Q.; et al

    2015-05-13

    Astrophysical collisionless shocks are common in the universe, occurring in supernova remnants, gamma ray bursts, and protostellar jets. They appear in colliding plasma flows when the mean free path for ion-ion collisions is much larger than the system size. It is believed that such shocks could be mediated via the electromagnetic Weibel instability in astrophysical environments without preexisting magnetic fields. Here, we present laboratory experiments using high-power lasers and investigate the dynamics of high-Mach-number collisionless shock formation in two interpenetrating plasma streams. Our recent proton-probe experiments on Omega show the characteristic filamentary structures of the Weibel instability that are electromagneticmore » in nature with an inferred magnetization level as high as ~1% These results imply that electromagnetic instabilities are significant in the interaction of astrophysical conditions.« less

  1. Impedances and collective instabilities of the Tevatron at Run II

    SciTech Connect (OSTI)

    Ng, King-Yuen, FERMI

    1998-09-01

    The longitudinal and transverse coupling impedances of the Tevatron vacuum chamber are estimated and summed up. The resistive-wall impedances of the beam pipe and the laminations in the Lambertson magnets dominate below {approximately} 50 MHz. Then come the inductive parts of the bellows and BPM`s. The longitudinal and transverse collective instabilities, for both single bunch and multi bunches, are studied using Run II parameters. As expected the transverse coupled-bunch instability driven by the resistive-wall impedance is the most severe collective instability. However, it can be damped by a transverse damper designed for the correction of injection offsets. The power of such a damper has been studied.

  2. Collisionless shock experiments with lasers and observation of Weibel instabilities

    SciTech Connect (OSTI)

    Park, H. -S.; Huntington, C. M.; Fiuza, F.; Drake, R. P.; Froula, D. H.; Gregori, G.; Koenig, M.; Kugland, N. L.; Kuranz, C. C.; Lamb, D. Q.; Levy, M. C.; Li, C. K.; Meinecke, J.; Morita, T.; Petrasso, R. D.; Pollock, B. B.; Remington, B. A.; Rinderknecht, H. G.; Rosenberg, M.; Ross, J. S.; Ryutov, D. D.; Sakawa, Y.; Spitkovsky, A.; Takabe, H.; Turnbull, D. P.; Tzeferacos, P.; Weber, S. V.; Zylstra, A. B.

    2015-05-13

    Astrophysical collisionless shocks are common in the universe, occurring in supernova remnants, gamma ray bursts, and protostellar jets. They appear in colliding plasma flows when the mean free path for ion-ion collisions is much larger than the system size. It is believed that such shocks could be mediated via the electromagnetic Weibel instability in astrophysical environments without preexisting magnetic fields. Here, we present laboratory experiments using high-power lasers and investigate the dynamics of high-Mach-number collisionless shock formation in two interpenetrating plasma streams. Our recent proton-probe experiments on Omega show the characteristic filamentary structures of the Weibel instability that are electromagnetic in nature with an inferred magnetization level as high as ~1% These results imply that electromagnetic instabilities are significant in the interaction of astrophysical conditions.

  3. DOE Science Showcase - Genomics | OSTI, US Dept of Energy, Office...

    Office of Scientific and Technical Information (OSTI)

    DOE Genomics Research Information on OSTI.gov In the OSTI Collections: Genomics, Dr. William Watson DOE and Human Genome Research, Mary Schorn Human Genome Research: DOE Origins, ...

  4. Gauge theories on hyperbolic spaces and dual wormhole instabilities

    SciTech Connect (OSTI)

    Buchel, Alex

    2004-09-15

    We study supergravity duals of strongly coupled four-dimensional gauge theories formulated on compact quotients of hyperbolic spaces. The resulting background geometries are represented by Euclidean wormholes, which complicate establishing the precise gauge theory/string theory correspondence dictionary. These backgrounds suffer from the nonperturbative instabilities arising from the D3D3-bar pair-production in the background four-form potential. We discuss conditions for suppressing this Schwingerlike instability. We find that Euclidean wormholes arising in this construction develop a naked singularity before they can be stabilized.

  5. Nuclear-Coupled Flow Instabilities and Their Effects on Dryout

    SciTech Connect (OSTI)

    M. Ishii; X. Sunn; S. Kuran

    2004-09-27

    Nuclear-coupled flow/power oscillations in boiling water reactors (BWRs) are investigated experimentally and analytically. A detailed literature survey is performed to identify and classify instabilities in two-phase flow systems. The classification and the identification of the leading physical mechanisms of the two-phase flow instabilities are important to propose appropriate analytical models and scaling criteria for simulation. For the purpose of scaling and the analysis of the nonlinear aspects of the coupled flow/power oscillations, an extensive analytical modeling strategy is developed and used to derive both frequency and time domain analysis tools.

  6. First Results From the Electron Hose Instability Studies in FACET

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Results From the Electron Hose Instability Studies in FACET Citation Details In-Document Search Title: First Results From the Electron Hose Instability Studies in FACET Authors: Adli, E. ; /Oslo U. ; Corde, S. ; England, R.J. ; Frederico, J. ; Gessner, S.J. ; Li, S. ; Wu, Z. ; Hogan, M.J. ; Litos, M.D. ; /SLAC ; An, W. ; Clayton, C.E. ; Marsh, K.A. ; Lu, W. ; Mori, W.B. ; Joshi, C. ; Vafaei-Najafabadi, N. ; /UCLA ; Muggli, P. more »; /Munich, Max Planck Inst.

  7. Acoustic stabilization of electric arc instabilities in nontransferred plasma torches

    SciTech Connect (OSTI)

    Rat, V.; Coudert, J. F.

    2010-03-08

    Electric arc instabilities in dc plasma torches lead to nonhomogeneous treatments of nanosized solid particles or liquids injected within thermal plasma jets. This paper shows that an additional acoustic resonator mounted on the cathode cavity allows reaching a significant damping of these instabilities, particularly the Helmholtz mode of arc oscillations. The acoustic resonator is coupled with the Helmholtz resonator of the plasma torch limiting the amplitude of arc voltage variations. It is also highlighted that this damping is dependent on friction effects in the acoustic resonator.

  8. The general relativistic instability supernova of a supermassive population

    Office of Scientific and Technical Information (OSTI)

    III star (Journal Article) | SciTech Connect The general relativistic instability supernova of a supermassive population III star Citation Details In-Document Search Title: The general relativistic instability supernova of a supermassive population III star The formation of supermassive Population III stars with masses ≳10,000 M{sub ☉} in primeval galaxies in strong ultraviolet backgrounds at z ∼ 15 may be the most viable pathway to the formation of supermassive black holes by z ∼ 7.

  9. Human Genome Program Image Gallery (from genomics.energy.gov)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    This collection contains approximately 240 images from the genome programs of DOE's Office of Science. The images are divided into galleries related to biofuels research, systems biology, and basic genomics. Each image has a title, a basic citation, and a credit or source. Most of the images are original graphics created by the Genome Management Information System (GMIS). GMIS images are recognizable by their credit line. Permission to use these graphics is not needed, but please credit the U.S. Department of Energy Genome Programs and provide the website http://genomics.energy.gov. Other images were provided by third parties and not created by the U.S. Department of Energy. Users must contact the person listed in the credit line before using those images. The high-resolution images can be downloaded.

  10. FARLEY-BUNEMAN INSTABILITY IN THE SOLAR CHROMOSPHERE

    SciTech Connect (OSTI)

    Gogoberidze, G.; Voitenko, Y.; Poedts, S.; Goossens, M.

    2009-11-20

    The Farley-Buneman instability (FBI) is studied in the partially ionized plasma of the solar chromosphere taking into account the finite magnetization of the ions and Coulomb collisions. We obtain the threshold value for the relative velocity between ions and electrons necessary for the instability to develop. It is shown that Coulomb collisions play a destabilizing role in the sense that they enable the instability even in the regions where the ion magnetization is larger than unity. By applying these results to chromospheric conditions, we show that the FBI cannot be responsible for the quasi-steady heating of the solar chromosphere. However, we do not exclude the instability development locally in the presence of strong cross-field currents and/or strong small-scale magnetic fields. In such cases, FBI should produce locally small-scale, approx0.1-3 m, density irregularities in the solar chromosphere. These irregularities can cause scintillations of radio waves with similar wave lengths and provide a tool for remote chromospheric sensing.

  11. Alfvnic instabilities driven by runaways in fusion plasmas

    SciTech Connect (OSTI)

    Flp, T.; Newton, S.

    2014-08-15

    Runaway particles can be produced in plasmas with large electric fields. Here, we address the possibility that such runaway ions and electrons excite Alfvnic instabilities. The magnetic perturbation induced by these modes can enhance the loss of runaways. This may have important implications for the runaway electron beam formation in tokamak disruptions.

  12. Heavy-fermion instability in double-degenerate plasmas

    SciTech Connect (OSTI)

    Akbari-Moghanjoughi, M.

    2012-07-15

    In this work, we study the propagations of normal frequency modes for quantum hydrodynamic waves in the linear limit and introduce a new kind of instability in a double-degenerate plasma. Three different regimes, namely, low, intermediate, and high magnetic field strengths are considered which span the applicability of the work to a wide variety of environments. Distinct behavior is observed for different regimes, for instance, in the laboratory-scale field regime no frequency-mode instability occurs unlike those of intermediate and high magnetic-field strength regimes. It is also found that the instability of this kind is due to the heavy-fermions which appear below a critical effective-mass parameter ({mu}{sub cr}={radical}(3)) and that the responses of the two (lower and upper frequency) modes to fractional effective-mass change in different effective-mass parameter ranges (below and above the critical value) are quite opposite to each other. It is shown that the heavy-fermion instability due to extremely high magnetic field such as that encountered for a neutron-star crust can lead to confinement of stable propagations in both lower and upper frequency modes to the magnetic poles. Current study can have important implications for linear wave dynamics in both laboratory and astrophysical environments possessing high magnetic fields.

  13. Combustion instabilities in sudden expansion oxy-fuel flames

    SciTech Connect (OSTI)

    Ditaranto, Mario; Hals, Joergen

    2006-08-15

    An experimental study on combustion instability is presented with focus on oxy-fuel type combustion. Oxidants composed of CO{sub 2}/O{sub 2} and methane are the reactants flowing through a premixer-combustor system. The reaction starts downstream a symmetric sudden expansion and is at the origin of different instability patterns depending on oxygen concentration and Reynolds number. The analysis has been conducted through measurement of pressure, CH* chemiluminescence, and velocity. As far as stability is concerned, oxy-fuel combustion with oxygen concentration similar to that found in air combustion cannot be sustained, but requires at least 30% oxygen to perform in a comparable manner. Under these conditions and for the sudden expansion configuration used in this study, the instability is at low frequency and low amplitude, controlled by the flame length inside the combustion chamber. Above a threshold concentration in oxygen dependent on equivalence ratio, the flame becomes organized and concentrated in the near field. Strong thermoacoustic instability is then triggered at characteristic acoustic modes of the system. Different modes can be triggered depending on the ratio of flame speed to inlet velocity, but for all types of instability encountered, the heat release and pressure fluctuations are linked by a variation in mass-flow rate. An acoustic model of the system coupled with a time-lag-based flame model made it possible to elucidate the acoustic mode selection in the system as a function of laminar flame speed and Reynolds number. The overall work brings elements of reflection concerning the potential risk of strong pressure oscillations in future gas turbine combustors for oxy-fuel gas cycles. (author)

  14. Filamentation instability of current-driven dust ion-acoustic waves in a collisional dusty plasma

    SciTech Connect (OSTI)

    Niknam, A. R. [Laser and Plasma Research Institute, Shahid Beheshti University, G.C., Tehran 19839-63113 (Iran, Islamic Republic of); Haghtalab, T.; Khorashadizadeh, S. M. [Physics Department, Birjand University, Birjand 97179-63384 (Iran, Islamic Republic of)

    2011-11-15

    A theoretical investigation has been made of the dust ion-acoustic filamentation instability in an unmagnetized current-driven dusty plasma by using the Lorentz transformation formulas. The effect of collision between the charged particles with neutrals and their thermal motion on this instability is considered. Developing the filamentation instability of the current-driven dust ion-acoustic wave allows us to determine the period and the establishment time of the filamentation structure and threshold for instability development.

  15. Genome patent fight erupts

    SciTech Connect (OSTI)

    Roberts, L.

    1991-10-11

    At a Congressional briefing while describing a new project to sequence partially every gene active in the human brain, it was made known that the National Institutes of Health was planning to file patent applications on 1,000 of these sequences a month. The scheme has engendered a firestorm of criticism from genome scientists and project officials alike. The critics argue that these sequences probably can't be patented in the first place - and even if they can, they shouldn't be. The plan would undercut patent protection for those who labor long and hard at the real task of elucidating the function of the proteins encoded by the genes, thereby driving industry away from developing inventions based on that work.

  16. Immortalization of normal human mammary epithelial cells in two steps by direct targeting of senescence barriers does not require gross genomic alterations

    SciTech Connect (OSTI)

    Garbe, James C.; Vrba, Lukas; Sputova, Klara; Fuchs, Laura; Novak, Petr; Brothman, Arthur R.; Jackson, Mark; Chin, Koei; LaBarge, Mark A.; Watts, George; Futscher, Bernard W.; Stampfer, Martha R.

    2014-10-29

    Telomerase reactivation and immortalization are critical for human carcinoma progression. However, little is known about the mechanisms controlling this crucial step, due in part to the paucity of experimentally tractable model systems that can examine human epithelial cell immortalization as it might occur in vivo. We achieved efficient non-clonal immortalization of normal human mammary epithelial cells (HMEC) by directly targeting the 2 main senescence barriers encountered by cultured HMEC. The stress-associated stasis barrier was bypassed using shRNA to p16INK4; replicative senescence due to critically shortened telomeres was bypassed in post-stasis HMEC by c-MYC transduction. Thus, 2 pathologically relevant oncogenic agents are sufficient to immortally transform normal HMEC. The resultant non-clonal immortalized lines exhibited normal karyotypes. Most human carcinomas contain genomically unstable cells, with widespread instability first observed in vivo in pre-malignant stages; in vitro, instability is seen as finite cells with critically shortened telomeres approach replicative senescence. Our results support our hypotheses that: (1) telomere-dysfunction induced genomic instability in pre-malignant finite cells may generate the errors required for telomerase reactivation and immortalization, as well as many additional passenger errors carried forward into resulting carcinomas; (2) genomic instability during cancer progression is needed to generate errors that overcome tumor suppressive barriers, but not required per se; bypassing the senescence barriers by direct targeting eliminated a need for genomic errors to generate immortalization. Achieving efficient HMEC immortalization, in the absence of passenger genomic errors, should facilitate examination of telomerase regulation during human carcinoma progression, and exploration of agents that could prevent immortalization.

  17. Immortalization of normal human mammary epithelial cells in two steps by direct targeting of senescence barriers does not require gross genomic alterations

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Garbe, James C.; Vrba, Lukas; Sputova, Klara; Fuchs, Laura; Novak, Petr; Brothman, Arthur R.; Jackson, Mark; Chin, Koei; LaBarge, Mark A.; Watts, George; et al

    2014-10-29

    Telomerase reactivation and immortalization are critical for human carcinoma progression. However, little is known about the mechanisms controlling this crucial step, due in part to the paucity of experimentally tractable model systems that can examine human epithelial cell immortalization as it might occur in vivo. We achieved efficient non-clonal immortalization of normal human mammary epithelial cells (HMEC) by directly targeting the 2 main senescence barriers encountered by cultured HMEC. The stress-associated stasis barrier was bypassed using shRNA to p16INK4; replicative senescence due to critically shortened telomeres was bypassed in post-stasis HMEC by c-MYC transduction. Thus, 2 pathologically relevant oncogenic agentsmore » are sufficient to immortally transform normal HMEC. The resultant non-clonal immortalized lines exhibited normal karyotypes. Most human carcinomas contain genomically unstable cells, with widespread instability first observed in vivo in pre-malignant stages; in vitro, instability is seen as finite cells with critically shortened telomeres approach replicative senescence. Our results support our hypotheses that: (1) telomere-dysfunction induced genomic instability in pre-malignant finite cells may generate the errors required for telomerase reactivation and immortalization, as well as many additional “passenger” errors carried forward into resulting carcinomas; (2) genomic instability during cancer progression is needed to generate errors that overcome tumor suppressive barriers, but not required per se; bypassing the senescence barriers by direct targeting eliminated a need for genomic errors to generate immortalization. Achieving efficient HMEC immortalization, in the absence of “passenger” genomic errors, should facilitate examination of telomerase regulation during human carcinoma progression, and exploration of agents that could prevent immortalization.« less

  18. Whose genome is it, anyway?

    SciTech Connect (OSTI)

    Marshall, E.

    1996-09-27

    The genome program has issued guidelines to ensure that sequencing is done on DNA from diverse sources who have given informed consent and are anonymous. Most current sources don`t meet those criteria. It may be the first question every nonexpert asks on learning about the Human Genome Project: Whose genome are we studying, anyway? It sounds naive, says one government scientist-so naive, in fact, that {open_quotes}we chuckle as we explain that we aren`t sequencing anyone`s genome in particular; we`re sequencing a representative genome{close_quotes} made up of a mosaic of DNA from a variety of anonymous sources. And Bruce Birren, a clone-maker now at the Massachusetts Institute of Technology`s (MIT`s) Whitehead Center for Genome Research says: {open_quotes}We spent many years pooh-poohing the question{close_quotes} of whose genome would be stored in the database. But now that labs have begun working on large stretches of human DNA-aiming to identify all 3 billion base pairs in the genetic code-the question no longer seems to laughable. To the distress of program managers in Bethesda, Maryland, the initial sources of DNA are not as diverse or as anonymous as they had assumed.

  19. The genome of Eucalyptus grandis

    SciTech Connect (OSTI)

    Myburg, Alexander A; Grattapaglia, Dario; Tuskan, Gerald A; Yang, Xiaohan; Priya, Ranjan; Tschaplinski, Timothy J; Ye, Chuyu; Li, Ting

    2014-01-01

    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  20. Human genome. 1993 Program report

    SciTech Connect (OSTI)

    Not Available

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  1. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  2. Mechanisms of radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.

    1996-10-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.

  3. Mitigation of radiation induced surface contamination

    DOE Patents [OSTI]

    Klebanoff, Leonard E. (Dublin, CA); Stulen, Richard H. (Livermore, CA)

    2003-01-01

    A process for mitigating or eliminating contamination and/or degradation of surfaces having common, adventitious atmospheric contaminants adsorbed thereon and exposed to radiation. A gas or a mixture of gases is introduced into the environment of a surface(s) to be protected. The choice of the gaseous species to be introduced (typically a hydrocarbon gas, water vapor, or oxygen or mixtures thereof) is dependent upon the contaminant as well as the ability of the gaseous species to bind to the surface to be protected. When the surface and associated bound species are exposed to radiation reactive species are formed that react with surface contaminants such as carbon or oxide films to form volatile products (e.g., CO, CO.sub.2) which desorb from the surface.

  4. Excitation of flow instabilities due to nonlinear scale invariance

    SciTech Connect (OSTI)

    Prasad Datta, Dhurjati; Sen, Sudip

    2014-05-15

    A novel route to instabilities and turbulence in fluid and plasma flows is presented in kinetic Vlasov-Maxwell model. New kind of flow instabilities is shown to arise due to the availability of new kinetic energy sources which are absent in conventional treatments. The present approach is based on a scale invariant nonlinear analytic formalism developed to address irregular motions on a chaotic attractor or in turbulence in a more coherent manner. We have studied two specific applications of this turbulence generating mechanism. The warm plasma Langmuir wave dispersion relation is shown to become unstable in the presence of these multifractal measures. In the second application, these multifractal measures are shown to induce naturally non-Gaussian, i.e., a stretched, Gaussian distribution and anomalous transport for tracer particles from the turbulent advection-diffusion transport equation in a Vlasov plasma flow.

  5. Stabilization of beam-weibel instability by equilibrium density ripples

    SciTech Connect (OSTI)

    Mishra, S. K. Kaw, Predhiman; Das, A.; Sengupta, S.; Ravindra Kumar, G.

    2014-01-15

    In this paper, we present an approach to achieve suppression/complete stabilization of the transverse electromagnetic beam Weibel instability in counter streaming electron beams by modifying the background plasma with an equilibrium density ripple, shorter than the skin depth; this weakening is more pronounced when thermal effects are included. On the basis of a linear two stream fluid model, it is shown that the growth rate of transverse electromagnetic instabilities can be reduced to zero value provided certain threshold values for ripple parameters are exceeded. We point out the relevance of the work to recent experimental investigations on sustained (long length) collimation of fast electron beams and integral beam transport for laser induced fast ignition schemes, where beam divergence is suppressed with the assistance of carbon nano-tubes.

  6. Collaborative Research: Instability and transport of laser beam in plasma

    SciTech Connect (OSTI)

    Rose, Harvey Arnold; Lushnikov, Pavel

    2014-11-18

    Our goal was to determine the onset of laser light scattering due to plasma wave instabilities. Such scatter is usually regarded as deleterious since laser beam strength is thereby diminished. While this kind of laser-plasma-instability (LPI) has long been understood for the case of coherent laser light, the theory of LPI onset for a laser beam with degraded coherence is recent. Such a laser beam fills plasma with a mottled intensity distribution, which has large fluctuations. The key question is: do the exceptionally large fluctuations control LPI onset or is it controlled by the relatively quiescent background laser intensity? We have answered this question. This is significant because LPI onset power in the former case is typically small compared to that of the latter. In addition, if large laser intensity fluctuations control LPI onset, then nonlinear effects become significant for less powerful laser beams than otherwise estimated.

  7. Instability-driven electromagnetic fields in coronal plasmas

    SciTech Connect (OSTI)

    Manuel, M. J.-E.; Li, C. K.; Sguin, F. H.; Sinenian, N.; Frenje, J. A.; Casey, D. T.; Petrasso, R. D.; Hager, J. D.; Betti, R.; Hu, S. X.; Delettrez, J.; Meyerhofer, D. D.

    2013-05-15

    Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. Sguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser-irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of ?210 ?m throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature and density profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.

  8. Instability-driven electromagnetic fields in coronal plasmas

    SciTech Connect (OSTI)

    Manuel, M. J.-E.; Li, C. K.; Seguin, F. H.; Sinenian, N.; Frenje, J. A.; Casey, D. T.; Petrasso, R. D.; Hager, J. D.; Betti, R.; Hu, S. X.; Delettrez, J.; Meyerhofer, D. D.

    2013-04-15

    Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. S#2;eguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of #2;210 lm throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature and density profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.

  9. Instability-driven electromagnetic fields in coronal plasmas

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Manuel, M. J.-E.; Li, C. K.; Seguin, F. H.; Sinenian, N.; Frenje, J. A.; Casey, D. T.; Petrasso, R. D.; Hager, J. D.; Betti, R.; Hu, S. X.; et al

    2013-04-15

    Filamentary electromagnetic fields previously observed in the coronae of laser-driven spherical targets [F. H. S#2;eguin et al., Phys. Plasma. 19, 012701 (2012)] have been further investigated in laser irradiated plastic foils. Face-on proton-radiography provides an axial view of these filaments and shows coherent cellular structure regardless of initial foil-surface conditions. The observed cellular fields are shown to have an approximately constant scale size of #2;210 lm throughout the plasma evolution. A discussion of possible field-generation mechanisms is provided and it is demonstrated that the likely source of the cellular field structure is the magnetothermal instability. Using predicted temperature and densitymore » profiles, the fastest growing modes of this instability were found to be slowly varying in time and consistent with the observed cellular size.« less

  10. Theory and calculations of synchrotron instabilities and feedback-mechanism

    SciTech Connect (OSTI)

    Meijssen, T.E.M.

    1981-08-12

    The properties of the phenomenon synchrotron radiation are given with general theory on the basic processes and betatron and synchrotron oscillations. A more extended theoretical view at transverse instabilities and the influence of a damping feedback system are discussed. The longitudinal case is covered. For the calculations on the longitudinal case with M equally spaced pointbunches, with N electrons each, in the storage ring, the parasitic modes of the radio-frequency cavity were measured. A description of this is given. The values of damping rates of the longitudinal feedback system found, are as expected, but too low to damp the longitudinal instabilities calculated. This might be caused by the input data. The calculated growth rates are very sensitive to changes in frequency and width of the parasitic modes, which were measured under conditions differing slightly from the operating conditions.

  11. Transposable Elements and Genetic Instabilities in Crop Plants

    DOE R&D Accomplishments [OSTI]

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  12. Genomic Aspects of Research Involving Polyploid Plants

    SciTech Connect (OSTI)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  13. CURVATURE-DRIFT INSTABILITY FAILS TO GENERATE PULSAR RADIO EMISSION

    SciTech Connect (OSTI)

    Kaganovich, Alexander; Lyubarsky, Yuri

    2010-10-01

    The curvature-drift instability has long been considered as a viable mechanism for pulsar radio emission. We reconsidered this mechanism by finding an explicit solution describing the propagation of short electromagnetic waves in a plasma flow along curved magnetic field lines. We show that even though the waves could be amplified, the amplification factor remains very close to unity; therefore, this mechanism is unable to generate high brightness temperature emission from initial weak fluctuations.

  14. Gradient instabilities of electromagnetic waves in Hall thruster plasma

    SciTech Connect (OSTI)

    Tomilin, Dmitry

    2013-04-15

    This paper presents a linear analysis of gradient plasma instabilities in Hall thrusters. The study obtains and analyzes the dispersion equation of high-frequency electromagnetic waves based on the two-fluid model of a cold plasma. The regions of parameters corresponding to unstable high frequency modes are determined and the dependence of the increments and intrinsic frequencies on plasma parameters is obtained. The obtained results agree with those of previously published studies.

  15. 'Catch and Suppress' Control of Instabilities in High Performance

    Office of Science (SC) Website

    Fusion Plasmas | U.S. DOE Office of Science (SC) 'Catch and Suppress' Control of Instabilities in High Performance Fusion Plasmas Fusion Energy Sciences (FES) FES Home About Research Facilities Science Highlights Benefits of FES Funding Opportunities Fusion Energy Sciences Advisory Committee (FESAC) Community Resources Contact Information Fusion Energy Sciences U.S. Department of Energy SC-24/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-4941 F: (301)

  16. Dissolving the mineral calcite: Reaction front instability | Argonne

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    National Laboratory calcite: Reaction front instability Share Topic Programs Chemical sciences & engineering Synchrotron radiation X-ray imaging & holography Using the X-ray Reflection Interfacial Microscope powered by the Advanced Photon Source, researchers can both watch and drive the nanoscale changes of the surface of a calcite mineral as it dissolves in real-time. In this image, researchers observe distortions in the reaction front (the boundary between the blue and red regions)

  17. The role of the magnetorotational instability in the sun

    SciTech Connect (OSTI)

    Kagan, Daniel; Wheeler, J. Craig E-mail: wheel@astro.as.utexas.edu

    2014-05-20

    We calculate growth rates for nonaxisymmetric instabilities including the magnetorotational instability (MRI) throughout the Sun. We first derive a dispersion relation for nonaxisymmetric instability including the effects of shear, convective buoyancy, and three diffusivities (thermal conductivity, resistivity, and viscosity). We then use a solar model evolved with the stellar evolution code MESA and angular velocity profiles determined by Global Oscillations Network Group helioseismology to determine the unstable modes present at each location in the Sun and the associated growth rates. The overall instability has unstable modes throughout the convection zone and also slightly below it at middle and high latitudes. It contains three classes of modes: large-scale hydrodynamic convective modes, large-scale hydrodynamic shear modes, and small-scale magnetohydrodynamic shear modes, which may be properly called MRI modes. While large-scale convective modes are the most rapidly growing modes in most of the convective zone, MRI modes are important in both stably stratified and convectively unstable locations near the tachocline at colatitudes ? < 53. Nonaxisymmetric MRI modes grow faster than the corresponding axisymmetric modes; for some poloidal magnetic fields, the nonaxisymmetric MRI growth rates are similar to the angular rotation frequency ?, while axisymmetric modes are stabilized. We briefly discuss the saturation of the field produced by MRI modes, finding that the implied field at the base of the convective zone in the Sun is comparable to that derived based on dynamos active in the tachocline and that the saturation of field resulting from the MRI may be of importance even in the upper convection zone.

  18. Three dimensional electromagnetic wavepackets in a plasma: Spatiotemporal modulational instability

    SciTech Connect (OSTI)

    Borhanian, J.; Hosseini Faradonbe, F.

    2014-04-15

    The nonlinear interaction of an intense electromagnetic beam with relativistic collisionless unmagnetized plasma is investigated by invoking the reductive perturbation technique, resting on the model of three-dimensional nonlinear Schrdinger (NLS) equation with cubic nonlinearity which incorporates the effects of self-focusing, self-phase modulation, and diffraction on wave propagation. Relying on the derived NLS equation, the occurrence of spatiotemporal modulational instability is investigated in detail.

  19. Viscous Rayleigh-Taylor instability in spherical geometry

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mikaelian, Karnig O.

    2016-02-08

    We consider viscous fluids in spherical geometry, a lighter fluid supporting a heavier one. Chandrasekhar [Q. J. Mech. Appl. Math. 8, 1 (1955)] analyzed this unstable configuration providing the equations needed to find, numerically, the exact growth rates for the ensuing Rayleigh-Taylor instability. He also derived an analytic but approximate solution. We point out a weakness in his approximate dispersion relation (DR) and offer one that is to some extent improved.

  20. On the interface instability during rapid evaporation in microgravity

    SciTech Connect (OSTI)

    Juric, D.

    1997-05-01

    The rapid evaporation of a superheated liquid (vapor explosion) under microgravity conditions is studied by direct numerical simulation. The time-dependent Navier-Stokes and energy equations coupled to the interface dynamics are solved using a two-dimensional finite-difference/front-tracking method. Large interface deformations, topology change, latent heat, surface tension and unequal material properties between the liquid and vapor phases are included in the simulations. A comparison of numerical results to the exact solution of a one-dimensional test problem shows excellent agreement. For the two-dimensional rapid evaporation problem, the vapor volume growth rate and unstable interface dynamics are studied for increasing levels of initial liquid superheat. As the superheat is increased the liquid-vapor interface experiences increasingly unstable energetic growth. These results indicate that heat transfer plays a very important role in the instability mechanism leading to vapor explosions. It is suggested that the Mullins-Sekerka instability could play a role in the instability initiation mechanism.

  1. The Weibel instability in a strongly coupled plasma

    SciTech Connect (OSTI)

    Mahdavi, M. Khanzadeh, H.

    2014-06-15

    In this paper, the growth rate of the Weibel instability is calculated for an energetic relativistic electron beam penetrated into a strongly coupled plasma, where the collision effects of background electron-ion scattering play an important role in equations. In order to calculate the growth rate of the Weibel instability, two different models of anisotropic distribution function are used. First, the distribution of the plasma and beam electrons considered as similar forms of bi-Maxwellian distribution. Second, the distribution functions of the plasma electrons and the beam electrons follows bi-Maxwellian and delta-like distributions, respectively. The obtained results show that the collision effect decreases the growth rate in two models. When the distribution function of electrons beam is in bi-Maxwellian form, the instability growth rate is greater than where the distribution function of beam electrons is in delta-like form, because, the anisotropic temperature for bi-Maxwellian distribution function in velocity space is greater than the delta-like distribution function.

  2. GIANT PLANET FORMATION BY DISK INSTABILITY IN LOW MASS DISKS?

    SciTech Connect (OSTI)

    Boss, Alan P.

    2010-12-20

    Forming giant planets by disk instability requires a gaseous disk that is massive enough to become gravitationally unstable and able to cool fast enough for self-gravitating clumps to form and survive. Models with simplified disk cooling have shown the critical importance of the ratio of the cooling to the orbital timescales. Uncertainties about the proper value of this ratio can be sidestepped by including radiative transfer. Three-dimensional radiative hydrodynamics models of a disk with a mass of 0.043 M{sub sun} from 4 to 20 AU in orbit around a 1 M{sub sun} protostar show that disk instabilities are considerably less successful in producing self-gravitating clumps than in a disk with twice this mass. The results are sensitive to the assumed initial outer disk (T{sub o}) temperatures. Models with T{sub o} = 20 K are able to form a single self-gravitating clump, whereas models with T{sub o} = 25 K form clumps that are not quite self-gravitating. These models imply that disk instability requires a disk with a mass of at least {approx}0.043 M{sub sun} inside 20 AU in order to form giant planets around solar-mass protostars with realistic disk cooling rates and outer-disk temperatures. Lower mass disks around solar-mass protostars must rely upon core accretion to form inner giant planets.

  3. Rayleigh-Taylor instabilities with sheared magnetic fields

    SciTech Connect (OSTI)

    Ruderman, M. S. [Solar Physics and Space Plasma Research Centre (SP2RC), University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH (United Kingdom); Terradas, J.; Ballester, J. L. [Departament de Fsica, Universitat de les Illes Balears, E-07122 Palma de Mallorca (Spain)

    2014-04-20

    Magnetic Rayleigh-Taylor (MRT) instabilities may play a relevant role in many astrophysical problems. In this work the effect of magnetic shear on the growth rate of the MRT instability is investigated. The eigenmodes of an interface and a slab model under the presence of gravity are analytically calculated assuming that the orientation of the magnetic field changes in the equilibrium, i.e., there is magnetic shear. We solve the linearized magnetohydrodynamic equations in the incompressible regime. We find that the growth rate is bounded under the presence of magnetic shear. We have derived simple analytical expressions for the maximum growth rate, corresponding to the most unstable mode of the system. These expressions provide the explicit dependence of the growth rate on the various equilibrium parameters. For small angles the growth time is linearly proportional to the shear angle, and in this regime the single interface problem and the slab problem tend to the same result. On the contrary, in the limit of large angles and for the interface problem the growth time is essentially independent of the shear angle. In this regime we have also been able to calculate an approximate expression for the growth time for the slab configuration. Magnetic shear can have a strong effect on the growth rates of the instability. As an application of the results found in this paper we have indirectly determined the shear angle in solar prominence threads using their lifetimes and the estimation of the Alfvn speed of the structure.

  4. Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs

    SciTech Connect (OSTI)

    Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-09

    Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes.Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 and ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome,relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats,which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at many but not all inversion endpoints. There is likely nosingle mechanism responsible for the remarkable number of alterations inthis genome, but both repeats and tRNAs are clearly associated with theserearrangements. Land plant chloroplast genomes are highly conserved instructure, gene order and content. The chloroplast genomes of ferns, thegymnosperm Ginkgo, and most angiosperms are nearly collinear, reflectingthe gene order in lineages that diverged from lycopsids and the ancestralchloroplast gene order over 350 million years ago (Raubeson and Jansen,1992). Although earlier mapping studies identified a number of taxa inwhich several rearrangements have occurred (reviewed in Raubeson andJansen, 2005), an extraordinary number of chloroplast genome alterationsare concentrated in several families in the angiosperm order Asterales(sensu APGII, Bremer et al., 2003). Gene mapping studies ofrepresentatives of the Campanulaceae (Cosner, 1993; Cosner et al.,1997,2004) and Lobeliaceae (Knox et al., 1993; Knox and Palmer, 1999)identified large inversions, contraction and expansion of the invertedrepeat regions, and several insertions and deletions in the cpDNAs ofthese closely related taxa. Detailed restriction site and gene mapping ofthe chloroplast genome of Trachelium caeruleum (Campanulaceae) identifiedseven to ten large inversions, families of repeats associated withrearrangements, possible transpositions, and even the disruption ofoperons (Cosner et al., 1997). Seventeen other members of theCampanulaceae were mapped and exhibit many additional rearrangements(Cosner et al., 2004). What happened in this lineage that made itsusceptible to so many chloroplast genome rearrangements? How do normallyvery conserved chloroplast genomes change? The cause of rearrangements inthis group is unclear based on the limited resolution available withmapping techniques. Several mechanisms have been proposed to explain howrearrangements occur: recombination between repeats, transposition, ortemporary instability due to loss of the inverted repeat (Raubeson andJansen, 2005). Sequencing whole chloroplast genomes within theCampanulaceae offers a unique opportunity to examine both the extent andmechanisms of rearrangements within a phylogenetic framework.We reporthere the first complete chloroplast genome sequence of a member of theCampanulaceae, Trachelium caeruleum. This work will serve as a benchmarkfor subsequent, comparative sequencing and analysis of other members ofthis family and close relatives, with the goal of further understandingchloroplast genome evolution. We confirmed features previously identifiedthrough mapping, and discovered many additional structural changes,i

  5. The mouse genome informatics and the mouse genome database

    SciTech Connect (OSTI)

    Maltais, L.J.; Blackburn, R.E.; Bradt, D.W.

    1994-09-01

    The Mouse Genome Database (MGD) is a centralized, comprehensive database of the mouse genome that includes genetic mapping data, comparative mapping data, gene descriptions, mutant phenotype descriptions, strains and allelic polymorphism data, inbred strain characteristics, physical mapping data, and molecular probes and clones data. Data in MGD are obtained from the published literature and by electronic transfer from laboratories working on large backcross panels of mice. MGD provides tools that enable the user to search the database, retrieve data, generate reports, analyze data, annotate records, and build genetic maps. The Encyclopedia of the Mouse Genome provides a graphic user interface to mouse genome data. It consists of software tools including: LinkMap, a graphic display of genetic linkage maps with the ability to magnify regions of high locus density: CytoMap, a graphic display of cytogenetic maps showing banded chromosomes with cytogenetic locations of genes and chromosomal aberrations; CATS, a catalog searching tool for text retrieval of mouse locus descriptions. These software tools provide access to the following data sets: Chromosome Committee Reports, MIT Genome Center data, GBASE reports, Mouse Locus Catalog (MLC), and Mouse Cytogenetic Mapping Data. The MGD is available to the scientific community through the World Wide Web (WWW) and Gopher. In addition GBASE can be accessed via the Internet.

  6. GOLD: The Genomes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

    Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

    The basic tables in the GOLD database that can be browsed or searched include the following information:

    • Gold Stamp ID
    • Organism name
    • Domain
    • Links to information sources
    • Size and link to a map, when available
    • Chromosome number, Plas number, and GC content
    • A link for downloading the actual genome data
    • Institution that did the sequencing
    • Funding source
    • Database where information resides
    • Publication status and information

    (Specialized Interface)

  7. Transforming Growth Factor ?-1 (TGF-?1) Is a Serum Biomarker of Radiation Induced Fibrosis in Patients Treated With Intracavitary Accelerated Partial Breast Irradiation: Preliminary Results of a Prospective Study

    SciTech Connect (OSTI)

    Boothe, Dustin L.; Coplowitz, Shana; Greenwood, Eleni; Barney, Christian L.; Christos, Paul J.; Parashar, Bhupesh; Nori, Dattatreyudu; Chao, K. S. Clifford; Wernicke, A. Gabriella

    2013-12-01

    Purpose: To examine a relationship between serum transforming growth factor ? -1 (TGF-?1) values and radiation-induced fibrosis (RIF). Methods and Materials: We conducted a prospective analysis of the development of RIF in 39 women with American Joint Committee on Cancer stage 0-I breast cancer treated with lumpectomy and accelerated partial breast irradiation via intracavitary brachytherapy (IBAPBI). An enzyme-linked immunoassay (Quantikine, R and D, Minneapolis, MN) was used to measure serum TGF-?1 before surgery, before IBAPBI, and during IBAPBI. Blood samples for TGF-?1 were also collected from 15 healthy, nontreated women (controls). The previously validated tissue compliance meter (TCM) was used to objectively assess RIF. Results: The median time to follow-up for 39 patients was 44 months (range, 5-59 months). RIF was graded by the TCM scale as 0, 1, 2, and 3 in 5 of 20 patients (25%), 6 of 20 patients (30%), 5 of 20 patients (25%), and 4 of 20 patients (20%), respectively. The mean serum TGF-?1 values were significantly higher in patients before surgery than in disease-free controls, as follows: all cancer patients (30,201 5889 pg/mL, P=.02); patients with any type of RIF (32,273 5016 pg/mL, P<.0001); and women with moderate to severe RIF (34,462 4713 pg/mL, P<0.0001). Patients with moderate to severe RIF had significantly elevated TGF-?1 levels when compared with those with none to mild RIF before surgery (P=.0014) during IBAPBI (P?0001), and the elevation persisted at 6 months (P?.001), 12 months (P?.001), 18 months (P?.001), and 24 months (P=.12). A receiver operating characteristic (ROC) curve of TGF-?1 values predicting moderate to severe RIF was generated with an area under the curve (AUC){sub ROC} of 0.867 (95% confidence interval 0.700-1.000). The TGF-?1 threshold cutoff was determined to be 31,000 pg/mL, with associated sensitivity and specificity of 77.8% and 90.0%, respectively. Conclusions: TGF-?1 levels correlate with the development of moderate to severe RIF. The pre-IBAPBI mean TGF-?1 levels can serve as an early biomarker for the development of moderate to severe RIF after IBAPBI.

  8. Expanding genomics of mycorrhizal symbiosis

    SciTech Connect (OSTI)

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.

  9. Expanding genomics of mycorrhizal symbiosis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolvemore » through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.« less

  10. Human Genome Education Program

    SciTech Connect (OSTI)

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field testing result from this analysis will contribute to the final revisions of each unit during the second-year of this grant.

  11. Reconnection and interchange instability in the near magnetotail

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Birn, Joachim; Liu, Yi -Hsin; Daughton, William; Hesse, Michael; Schindler, Karl

    2015-07-16

    This paper provides insights into the possible coupling between reconnection and interchange/ballooning in the magnetotail related to substorms and flow bursts. The results presented are largely based on recent simulations of magnetotail dynamics, exploring onset and progression of reconnection. 2.5-dimensional particle-in-cell (PIC) simulations with different tail deformation demonstrate a clear boundary between stable and unstable cases depending on the amount of deformation, explored up to the real proton/electron mass ratio. The evolution prior to onset, as well as the evolution of stable cases, are governed by the conservation of integral flux tube entropy S as imposed in ideal MHD, maintainingmore » a monotonic increase with distance downtail. This suggests that ballooning instability in the tail should not be expected prior to the onset of tearing and reconnection. 3-D MHD simulations confirm this conclusion, showing no indication of ballooning prior to reconnection, if the initial state is ballooning stable. The simulation also shows that, after imposing resistivity necessary to initiate reconnection, the reconnection rate and energy release initially remain slow. However, when S becomes reduced from plasmoid ejection and lobe reconnection, forming a negative slope in S as a function of distance from Earth, the reconnection rate and energy release increase drastically. The latter condition has been shown to be necessary for ballooning/interchange instability, and the cross-tail structures that develop subsequently in the MHD simulation are consistent with such modes. The simulations support a concept in which tail activity is initiated by tearing instability but significantly enhanced by the interaction with ballooning/interchange enabled by plasmoid loss and lobe reconnection.« less

  12. Microsatellite instability is rare in sporadic ovarian cancer

    SciTech Connect (OSTI)

    Chen, S.S.; Han, H.; Schwartz, P.E.

    1994-09-01

    Microsatellite instability was first demonstrated to be a common underlying mechanism in hereditary nonpolyposis colorectal cancer (HNPCC) and has recently been implicated in the development of several other human cancers. Although numerous genetic changes have been documented in ovarian cancer, their molecular bases are poorly understood. In investigating the molecular genetics of ovarian cancer, we analyzed twelve short tandem repeats that were amplified by PCR from DNA of 48 tumors and their corresponding lymphocyte samples. All of the 48 cases studied have no noticeable family history and, of them, 42 are epithelial (benign/borderline, 5; grade I, 4; GII, 4; GIII, 29) and 6 are nonepithelial. A microsatellite instability has been shown to be inversely correlated with the occurrence of allelic losses, half of those cases chosen have a fractional allele loss of {le}15 (median = .18 of 50 tumors tested for 86 loci from every chromosomal arm). The loci examined included eight dinucleotide repeats (D2S123, D9S104, D10S197, D11S904, D16S408, D16S421, D17S250, and D17S579), two trinucleotide repeats (DM and AR) and two tetranucleotide repeats (DXS981 and VWF). Despite the fact that HNPCC phenotype includes ovarian cancer and that microsatellite instability has been shown in one ovarian cancer from an HNPCC family, the allele sizes of 12 loci were found to be identical in all paired tumor and normal samples we studied except for one tumor at a single locus. The band shift displayed on polyacrylamide gel representing an additional allele of VWF was only observed in one grade III tumor. Our results are thus a strong indication that the alteration of microsatellite repeats may not play a major role in the development of sporadic ovarian cancer.

  13. Non-modal analysis of the diocotron instability: Cylindrical geometry

    SciTech Connect (OSTI)

    Mikhailenko, V. V.; Lee, Hae June; Mikhailenko, V. S.; Azarenkov, N. A.

    2013-04-15

    The temporal evolution of the linear diocotron instability of the cylindrical annular plasma column is investigated by employing the extension of the shearing modes methodology to the cylindrical geometry. It was obtained that the spatial time-dependent distortion of the electron density initial perturbations by shear flows leads to the non-modal evolution of the potential, which was referred to as the manifestation of the continuous spectrum. The evolution process leads toward the convergence to the phase-locking configuration of the mutually growing normal modes.

  14. NUMERICAL STUDY OF THE VISHNIAC INSTABILITY IN SUPERNOVA REMNANTS

    SciTech Connect (OSTI)

    Michaut, C.; Cavet, C.; Bouquet, S. E.; Roy, F.; Nguyen, H. C.

    2012-11-10

    The Vishniac instability is thought to explain the complex structure of radiative supernova remnants in their Pressure-Driven Thin Shell (PDTS) phase after a blast wave (BW) has propagated from a central explosion. In this paper, the propagation of the BW and the evolution of the PDTS stage are studied numerically with the two-dimensional (2D) code HYDRO-MUSCL for a finite-thickness shell expanding in the interstellar medium (ISM). Special attention is paid to the adiabatic index, {gamma}, and three distinct values are taken for the cavity ({gamma}{sub 1}), the shell ({gamma}{sub 2}), and the ISM ({gamma}{sub 3}) with the condition {gamma}{sub 2} < {gamma}{sub 1}, {gamma}{sub 3}. This low value of {gamma}{sub 2} accounts for the high density in the shell achieved by a strong radiative cooling. Once the spherical background flow is obtained, the evolution of a 2D-axisymmetric perturbation is computed from the linear to the nonlinear regime. The overstable mechanism, previously demonstrated theoretically by E. T. Vishniac in 1983, is recovered numerically in the linear stage and is expected to produce and enhance anisotropies and clumps on the shock front, leading to the disruption of the shell in the nonlinear phase. The period of the increasing oscillations and the growth rate of the instability are derived from several points of view (the position of the perturbed shock front, mass fluxes along the shell, and density maps), and the most unstable mode differing from the value given by Vishniac is computed. In addition, the influence of several parameters (the Mach number, amplitude and wavelength of the perturbation, and adiabatic index) is examined and for wavelengths that are large enough compared to the shell thickness, the same conclusion arises: in the late stage of the evolution of the radiative supernova remnant, the instability is dampened and the angular initial deformation of the shock front is smoothed while the mass density becomes uniform with the angle. As a result, our model shows that the supernova remnant returns to a stable evolution and the Vishniac instability does not lead to the fragmentation of the shock as predicted by the theory.

  15. PPPL successfully tests system for mitigating instabilities called

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    "ELMs" | Princeton Plasma Physics Lab PPPL successfully tests system for mitigating instabilities called "ELMs" By John Greenwald September 29, 2014 Tweet Widget Google Plus One Share on Facebook Close-up view of the high-speed propellor inside the injector. (Photo by Elle Starkman/Princeton Office of Communications ) Close-up view of the high-speed propellor inside the injector. PPPL has successfully tested a Laboratory-designed device to be used to diminish the size of

  16. PPPL successfully tests system for mitigating instabilities called

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    "ELMs" | Princeton Plasma Physics Lab PPPL successfully tests system for mitigating instabilities called "ELMs" By John Greenwald September 29, 2014 Tweet Widget Google Plus One Share on Facebook Close-up view of the high-speed propellor inside the injector. (Photo by Elle Starkman/Princeton Office of Communications ) Close-up view of the high-speed propellor inside the injector. PPPL has successfully tested a Laboratory-designed device to be used to diminish the size of

  17. Reconnection and interchange instability in the near magnetotail

    Office of Scientific and Technical Information (OSTI)

    Birn etal. Earth, Planets and Space (2015) 67:110 DOI 10.1186/S40623-015-0282-3 0 Earth, Planets and Space a SpringerOpen Journal LETTER Open Access Reconnection and interchange instability in the near magnetotail CrossMark Joachim Birn* 1'2*, Yi-Hsin Liu3, William Daughton4, Michael Hesse5 and Karl Schindler6 Abstract This paper provides insights into the possible coupling between reconnection and interchange/ballooning in the magnetotail related to substorms and flow bursts. The results

  18. Analysis of beam loss induced abort kicker instability

    SciTech Connect (OSTI)

    Zhang W.; Sandberg, J.; Ahrens, L.; Fischer, W.; Hahn, H.; Mi, J.; Pai, C.; Tan, Y.

    2012-05-20

    Through more than a decade of operation, we have noticed the phenomena of beam loss induced kicker instability in the RHIC beam abort systems. In this study, we analyze the short term beam loss before abort kicker pre-fire events and operation conditions before capacitor failures. Beam loss has caused capacitor failures and elevated radiation level concentrated at failed end of capacitor has been observed. We are interested in beam loss induced radiation and heat dissipation in large oil filled capacitors and beam triggered thyratron conduction. We hope the analysis result would lead to better protection of the abort systems and improved stability of the RHIC operation.

  19. Equilibrium magnetohydrodynamic flows of liquid metals in magnetorotational instability experiments

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fluid Mech. (2010), vol. 644, pp. 257-280. c Cambridge University Press 2010 doi:10.1017/S0022112009992394 257 Equilibrium magnetohydrodynamic flows of liquid metals in magnetorotational instability experiments I. V. K H A L Z O V 1 †, A. I. S M O L Y A K O V 2 A N D V. I. I L G I S O N I S 3 1 Center for Magnetic Self-Organization, University of Wisconsin, 1150 University Avenue, Madison, WI 53706, USA 2 University of Saskatchewan, 116 Science Place, Saskatoon, Saskatchewan, S7N5E2, Canada 3

  20. Suppression of energetic particle driven instabilities with HHFW heating

    SciTech Connect (OSTI)

    Fredrickson, E. D.; Taylor, G.; Bertelli, N.; Darrow, D. S.; Gorelenkov, N.; Kramer, G.; Liu, D.; Crocker, N. A.; Kubota, S.; White, R.

    2015-01-01

    In plasmas in the National Spherical Torus Experiment (NSTX) [Ono et al., Nucl. Fusion 40 (2000) 557] heated with neutral beams, the beam ions typically excite Energetic Particle Modes (EPMs or fishbones), and Toroidal, Global or Compressional Alfvn Eigenmodes (TAE, GAE, CAE). These modes can redistribute the energetic beam ions, altering the beam driven current profile and the plasma heating profile, or they may affect electron thermal transport or cause losses of the beam ions. In this paper we present experimental results where these instabilities, driven by the super-thermal beam ions, are suppressed with the application of High Harmonic Fast Wave heating.

  1. Kelvin-Helmholtz instability in a strongly coupled dusty plasma medium

    SciTech Connect (OSTI)

    Tiwari, Sanat Kumar; Das, Amita; Patel, Bhavesh G. [Institute for Plasma Research, Bhat, Gandhinagar 382 428 (India); Angom, Dilip [Physical Research Laboratory, Ahmedabad 380 009 (India); Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar 382 428 (India); Physical Research Laboratory, Ahmedabad 380 009 (India)

    2012-07-15

    The Kelvin-Helmholtz (KH) instability in the context of strongly coupled dusty plasma medium has been investigated. In particular, the role of transverse shear and the compressional acoustic modes in both the linear and nonlinear regimes of the KH instability has been studied. It is observed that in addition to the conventional nonlocal KH instability, there exists a local instability in the strong coupling case. The interplay of the KH mode with this local instability shows up in the simulations as an interesting phenomenon of recurrence in the nonlinear regime. Thus, a cyclic KH instability process is observed to occur. These cyclic events are associated with bursts of activity in terms of transverse and compressional wave generation in the medium.

  2. Enhancer Identification through Comparative Genomics

    SciTech Connect (OSTI)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  3. Hosing Instability of the Drive Electron Beam in the E157 Plasma...

    Office of Scientific and Technical Information (OSTI)

    If the beam is tilted, then it will undergo transverse oscillations inside of the plasma. These oscillations can grow exponentially via an instability know as the electron hose ...

  4. Electromagnetic drift instabilities in high-beta plasma under conditions of a field reversed configuration

    SciTech Connect (OSTI)

    Chirkov, A. Yu.; Khvesyuk, V. I.

    2010-01-15

    Electromagnetic drift instabilities are studied in the conditions of a field reversed configuration (FRC). Dispersion equation is based on the set of Vlasov-Maxwell equations taking into account nonadiabatic responses both of ions and electrons. Considered drift instabilities are caused by density and temperature gradients. It is assumed that magnetic field of the FRC is purely poloidal. Two kinds of magnetic field nonuniformity are considered: (i) perpendicular gradient due to high beta values (beta is the plasma pressure/magnetic pressure) and (ii) curvature of magnetic lines. There is low frequency drift instability existing for high-beta regimes. Modes of such instability can propagate transversally to the unperturbed magnetic field lines.

  5. Simulation of E-Cloud Driven Instability And Its Attenuation Using a

    Office of Scientific and Technical Information (OSTI)

    Feedback System in the CERN SPS (Conference) | SciTech Connect Simulation of E-Cloud Driven Instability And Its Attenuation Using a Feedback System in the CERN SPS Citation Details In-Document Search Title: Simulation of E-Cloud Driven Instability And Its Attenuation Using a Feedback System in the CERN SPS Electron clouds have been shown to trigger fast growing instabilities on proton beams circulating in the SPS, and a feedback system to control the instabilities is under active

  6. Simulations and model of the nonlinear Richtmyer–Meshkov instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dimonte, Guy; Ramaprabhu, P.

    2010-01-21

    The nonlinear evolution of the Richtmyer-Meshkov (RM) instability is investigated using numerical simulations with the FLASH code in two-dimensions (2D). The purpose of the simulations is to develop an empiricial nonlinear model of the RM instability that is applicable to inertial confinement fusion (ICF) and ejecta formation, namely, at large Atwood number A and scaled initial amplitude kho (k ≡ wavenumber) of the perturbation. The FLASH code is first validated with a variety of RM experiments that evolve well into the nonlinear regime. They reveal that bubbles stagnate when they grow by an increment of 2/k and that spikes acceleratemore » for A > 0.5 due to higher harmonics that focus them. These results are then compared with a variety of nonlinear models that are based on potential flow. We find that the models agree with simulations for moderate values of A < 0.9 and kho< 1, but not for the larger values that characterize ICF and ejecta formation. We thus develop a new nonlinear empirical model that captures the simulation results consistent with potential flow for a broader range of A and kho. Our hope is that such empirical models concisely capture the RM simulations and inspire more rigorous solutions.« less

  7. Four-photon homoclinic instabilities in nonlinear highly birefringent media

    SciTech Connect (OSTI)

    De Angelis, C.; Santagiustina, M. ); Trillo, S. )

    1995-01-01

    We investigate the nonlinear dynamics of a nonconventional (i.e., pumped by a mixed-mode wave) modulational instability in a highly birefringent nonlinear dispersive medium. We find that the depleted regime of propagation beyond the linearized stage can be described analytically in a proper region of the parameter space. In this case the governing coupled nonlinear Schroedinger equations, which are not integrable, are reduced to an integrable one-dimensional nonlinear oscillator that rules the propagation of the pump wave and a single sideband pair. This approach permits us to predict the existence of stable and unstable manifolds of time-periodic solutions of the coupled nonlinear Schroedinger equations. The nonlinear dynamics governed by these equations mimics the period-doubling instabilities associated with the homoclinic separatrices in the reduced phase space. Moreover, our approach is also capable of describing the onset of spatial chaos that occurs when the parameter values are such that the additional degree of freedom represented by the conjugated sidebands becomes effective.

  8. Study on the Mechanical Instability of MICE Coupling Magnets

    SciTech Connect (OSTI)

    Wang, Li; Pan, Heng; Gou, Xing Long; Wu, Hong; Zheng, Shi Xian; Green, Michael A

    2011-05-04

    The superconducting coupling solenoid magnet is one of the key equipment in the Muon Ionization Cooling Experiment (MICE). The coil has an inner radius of 750 mm, length of 281 mm and thickness of 104 mm at room temperature. The peak induction in the coil is about 7.3 T with a full current of 210 A. The mechanical disturbances which might cause the instability of the impregnated superconducting magnet involve the frictional motion between conductors and the cracking of impregnated materials. In this paper, the mechanical instability of the superconducting coupling magnet was studied. This paper presents the numerical calculation results of the minimum quench energy (MQE) of the coupling magnet, as well as the dissipated strain energy in the stress concentration region when the epoxy cracks and the frictional energy caused by 'stick-slip' of the conductor based on the bending theory of beam happens. Slip planes are used in the coupling coil and the frictional energy due to 'slow slip' at the interface of the slip planes was also investigated. The dissipated energy was compared with MQE, and the results show that the cracking of epoxy resin in the region of shear stress concentration is the main factor for premature quench of the coil.

  9. Effects of plasma {beta} on the plasmoid instability

    SciTech Connect (OSTI)

    Ni Lei; Ziegler, Udo; Huang Yimin; Lin Jun; Mei Zhixing

    2012-07-15

    The effects of the initial upstream plasma {beta} on the plasmoid instability are studied via two-dimensional resistive magnetohydrodynamic simulations. For cases with nonuniform {beta} dependent initial plasma mass density and uniform temperature, our numerical results indicate that the critical Lundquist number for onset of the plasmoid instability depends on the initial plasma {beta}. The critical Lundquist number is approximately 2000-3000 for {beta}=50 and is 8000-10 000 for {beta}=0.2. The higher the {beta}, the smaller the critical Lundquist number is. Similar to previous studies of high-{beta} systems, the average reconnection rate in low {beta} systems is found to become weakly dependent on the Lundquist number in the plasmoid-unstable regime. However, the average reconnection rate, normalized to the asymptotic value of upstream BV{sub A}, is lower in a low {beta} system than that in a high {beta} system. The magnetic energy spectral index, which characterizes fragmentation of the reconnection layer, is approximately two and is insensitive to {beta} in the high-Lunquist number regime. It is also found that the magnetic reconnection rate becomes similar for different {beta} cases, if the initial force-balance is provided by temperature gradient instead of density gradient. Therefore, it is concluded that the {beta}-dependence mentioned above may be largely attributed to the density variation.

  10. Plasmoid instability in high-Lundquist-number magnetic reconnection

    SciTech Connect (OSTI)

    Huang, Yi-Min; Bhattacharjee, A.

    2013-05-15

    Our understanding of magnetic reconnection in resistive magnetohydrodynamics has gone through a fundamental change in recent years. The conventional wisdom is that magnetic reconnection mediated by resistivity is slow in laminar high Lundquist (S) plasmas, constrained by the scaling of the reconnection rate predicted by Sweet-Parker theory. However, recent studies have shown that when S exceeds a critical value ?10{sup 4}, the Sweet-Parker current sheet is unstable to a super-Alfvnic plasmoid instability, with a linear growth rate that scales as S{sup 1/4}. In the fully developed statistical steady state of two-dimensional resistive magnetohydrodynamic simulations, the normalized average reconnection rate is approximately 0.01, nearly independent of S, and the distribution function f(?) of plasmoid magnetic flux ? follows a power law f(?)??{sup ?1}. When Hall effects are included, the plasmoid instability may trigger onset of Hall reconnection even when the conventional criterion for onset is not satisfied. The rich variety of possible reconnection dynamics is organized in the framework of a phase diagram.

  11. Two-dimensional simulations of pulsational pair-instability supernovae

    SciTech Connect (OSTI)

    Chen, Ke-Jung; Woosley, Stan [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Heger, Alexander [Monash Centre for Astrophysics, Monash University, Melbourne, Victoria 3800 (Australia); Almgren, Ann [Center for Computational Sciences and Engineering, Lawrence Berkeley National Lab, Berkeley, CA 94720 (United States); Whalen, Daniel J., E-mail: kchen@ucolick.org [T-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2014-09-01

    Massive stars that end their lives with helium cores in the range of 35-65 M {sub ?} are known to produce repeated thermonuclear outbursts due to a recurring pair-instability. In some of these events, solar masses of material are ejected in repeated outbursts of several 10{sup 50} erg each. Collisions between these shells can sometimes produce very luminous transients that are visible from the edge of the observable universe. Previous one-dimensional (1D) studies of these events produce thin, high-density shells as one ejection plows into another. Here, in the first multi-dimensional simulations of these collisions, we show that the development of a Rayleigh-Taylor instability truncates the growth of the high-density spike and drives mixing between the shells. The progenitor is a 110 M {sub ?} solar-metallicity star that was shown in earlier work to produce a superluminous supernova. The light curve of this more realistic model has a peak luminosity and duration that are similar to those of 1D models but a structure that is smoother.

  12. Nature of the wiggle instability of galactic spiral shocks

    SciTech Connect (OSTI)

    Kim, Woong-Tae; Kim, Yonghwi; Kim, Jeong-Gyu, E-mail: wkim@astro.snu.ac.kr, E-mail: kimyh@astro.snu.ac.kr, E-mail: jgkim@astro.snu.ac.kr [Center for the Exploration of the Origin of the Universe (CEOU), Astronomy Program, Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2014-07-01

    Gas in disk galaxies interacts nonlinearly with an underlying stellar spiral potential to form galactic spiral shocks. While numerical simulations typically show that spiral shocks are unstable to wiggle instability (WI) even in the absence of magnetic fields and self-gravity, its physical nature has remained uncertain. To clarify the mechanism behind the WI, we conduct a normal-mode linear stability analysis and nonlinear simulations assuming that the disk is isothermal and infinitesimally thin. We find that the WI is physical, originating from the generation of potential vorticity at a deformed shock front, rather than Kelvin-Helmholtz instabilities as previously thought. Since gas in galaxy rotation periodically passes through the shocks multiple times, the potential vorticity can accumulate successively, setting up a normal mode that grows exponentially with time. Eigenfunctions of the WI decay exponentially downstream from the shock front. Both shock compression of acoustic waves and a discontinuity of shear across the shock stabilize the WI. The wavelength and growth time of the WI depend on the arm strength quite sensitively. When the stellar-arm forcing is moderate at 5%, the wavelength of the most unstable mode is about 0.07 times the arm-to-arm spacing, with the growth rate comparable to the orbital angular frequency, which is found to be in good agreement with the results of numerical simulations.

  13. Strategies and tools for whole genome alignments

    SciTech Connect (OSTI)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  14. Joint Genome Institute's Automation Approach and History

    SciTech Connect (OSTI)

    Roberts, Simon

    2006-07-05

    Department of Energy/Joint Genome Institute (DOE/JGI) collaborates with DOE national laboratories and community users, to advance genome science in support of the DOE missions of clean bio-energy, carbon cycling, and bioremediation.

  15. GDB - Human Genome Database final report

    SciTech Connect (OSTI)

    Talbot, C. Conover, Jr.

    2002-01-08

    This is the DOE final report for the GDB, Human Genome Database, project at the Johns Hopkins University.

  16. Genome informatics: Requirements and challenges

    SciTech Connect (OSTI)

    Robbins, R.J.

    1993-12-31

    Informatics of some kind will play a role in every aspect of the Human Genome Project (HGP); data acquisition, data analysis, data exchange, data publication, and data visualization. What are the real requirements and challenges? The primary requirement is clear thinking and the main challenge is design. If good design is lacking, the price will be failure of genome informatics and ultimately failure of the genome project itself. Scientists need good designs to deliver the tools necessary for acquiring and analyzing DNA sequences. As these tools become more efficient, they will need new tools for comparative genomic analyses. To make the tools work, the scientists will need to address and solve nomenclature issues that are essential, if also tedious. They must devise systems that will scale gracefully with the increasing flow of data. The scientists must be able to move data easily from one system to another, with no loss of content. As scientists, they will have failed in their responsibility to share results, should repeating experiments ever become preferable to searching the literature. Their databases must become a new kind of scientific literature and the scientists must develop ways to make electronic data publishing as routine as traditional journal publishing. Ultimately, they must build systems so advanced that they are virtually invisible. In summary, the HGP can be considered the most ambitious, most audacious information-management project ever undertaken. In the HGP, computers will not merely serve as tools for cataloging existing knowledge. Rather, they will serve as instruments, helping to create new knowledge by changing the way the scientists see the biological world. Computers will allow them to see genomes, just as radio telescopes let them see quasars and electron microscopes let them see viruses.

  17. Validation of model based active control of combustion instability

    SciTech Connect (OSTI)

    Fleifil, M.; Ghoneim, Z.; Ghoniem, A.F.

    1998-07-01

    The demand for efficient, company and clean combustion systems have spurred research into the fundamental mechanisms governing their performance and means of interactively changing their performance characteristics. Thermoacoustic instability which is frequently observed in combustion systems with high power density, when burning close to the lean flammability limit, or using exhaust gas recirculation to meet more stringent emissions regulations, etc. Its occurrence and/or means to mitigate them passively lead to performance degradation such as reduced combustion efficiency, high local heat transfer rates, increase in the mixture equivalence ratio or system failure due to structural damage. This paper reports on their study of the origin of thermoacoustic instability, its dependence on system parameters and the means of actively controlling it. The authors have developed an analytical model of thermoacoustic instability in premixed combustors. The model combines a heat release dynamics model constructed using the kinematics of a premixed flame stabilized behind a perforated plate with the linearized conservation equations governing the system acoustics. This formulation allows model based controller design. In order to test the performance of the analytical model, a numerical solution of the partial differential equations governing the system has been carried out using the principle of harmonic separation and focusing on the dominant unstable mode. This leads to a system of ODEs governing the thermofluid variables. Analytical predictions of the frequency and growth ate of the unstable mode are shown to be in good agreement with the numerical simulations as well s with those obtained using experimental identification techniques when applied to a laboratory combustor. The authors use these results to confirm the validity of the assumptions used in formulating the analytical model. A controller based on the minimization of a cost function using the LQR technique has been designed using the analytical model and implemented on a bench top laboratory combustor. The authors show that the controller is capable of suppressing the pressure oscillations in the combustor with a settling time much shorter than what had been attained before and without exciting secondary peaks.

  18. The ecoresponsive genome of Daphnia pulex

    SciTech Connect (OSTI)

    Colbourne, John K.; Pfrender, Michael E.; Gilbert, Donald; Thomas, W. Kelley; Tucker, Abraham; Oakley, Todd H.; Tokishita, Shinichi; Aerts, Andrea; Arnold, Georg J.; Basu, Malay Kumar; Bauer, Darren J.; Caceres, Carla E.; Carmel, Liran; Casola, Claudio; Choi, Jeong-Hyeon; Detter, John C.; Dong, Qunfeng; Dusheyko, Serge; Eads, Brian D.; Frohlich, Thomas; Geiler-Samerotte, Kerry A.; Gerlach, Daniel; Hatcher, Phil; Jogdeo, Sanjuro; Krijgsveld, Jeroen; Kriventseva, Evgenia V; Kltz, Dietmar; Laforsch, Christian; Lindquist, Erika; Lopez, Jacqueline; Manak, Robert; Muller, Jean; Pangilinan, Jasmyn; Patwardhan, Rupali P.; Pitluck, Samuel; Pritham, Ellen J.; Rechtsteiner, Andreas; Rho, Mina; Rogozin, Igor B.; Sakarya, Onur; Salamov, Asaf; Schaack, Sarah; Shapiro, Harris; Shiga, Yasuhiro; Skalitzky, Courtney; Smith, Zachary; Souvorov, Alexander; Sung, Way; Tang, Zuojian; Tsuchiya, Dai; Tu, Hank; Vos, Harmjan; Wang, Mei; Wolf, Yuri I.; Yamagata, Hideo; Yamada, Takuji; Ye, Yuzhen; Shaw, Joseph R.; Andrews, Justen; Crease, Teresa J.; Tang, Haixu; Lucas, Susan M.; Robertson, Hugh M.; Bork, Peer; Koonin, Eugene V.; Zdobnov, Evgeny M.; Grigoriev, Igor V.; Lynch, Michael; Boore, Jeffrey L.

    2011-02-04

    This document provides supporting material related to the sequencing of the ecoresponsive genome of Daphnia pulex. This material includes information on materials and methods and supporting text, as well as supplemental figures, tables, and references. The coverage of materials and methods addresses genome sequence, assembly, and mapping to chromosomes, gene inventory, attributes of a compact genome, the origin and preservation of Daphnia pulex genes, implications of Daphnia's genome structure, evolutionary diversification of duplicated genes, functional significance of expanded gene families, and ecoresponsive genes. Supporting text covers chromosome studies, gene homology among Daphnia genomes, micro-RNA and transposable elements and the 46 Daphnia pulex opsins. 36 figures, 50 tables, 183 references.

  19. Suppression of energetic particle driven instabilities with HHFW heating

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Fredrickson, E. D.; Taylor, G.; Bertelli, N.; Darrow, D. S.; Gorelenkov, N.; Kramer, G.; Liu, D.; Crocker, N. A.; Kubota, S.; White, R.

    2015-01-01

    In plasmas in the National Spherical Torus Experiment (NSTX) [Ono et al., Nucl. Fusion 40 (2000) 557] heated with neutral beams, the beam ions typically excite Energetic Particle Modes (EPMs or fishbones), and Toroidal, Global or Compressional Alfvén Eigenmodes (TAE, GAE, CAE). These modes can redistribute the energetic beam ions, altering the beam driven current profile and the plasma heating profile, or they may affect electron thermal transport or cause losses of the beam ions. In this paper we present experimental results where these instabilities, driven by the super-thermal beam ions, are suppressed with the application of High Harmonic Fastmore » Wave heating.« less

  20. Instability of black hole formation in gravitational collapse

    SciTech Connect (OSTI)

    Joshi, Pankaj S.; Malafarina, Daniele

    2011-01-15

    We consider here the classic scenario given by Oppenheimer, Snyder, and Datt, for the gravitational collapse of a massive matter cloud, and examine its stability under the introduction of small tangential stresses. We show, by offering an explicit class of physically valid tangential stress perturbations, that an introduction of tangential pressure, however small, can qualitatively change the final fate of collapse from a black hole final state to a naked singularity. This shows instability of black hole formation in collapse and sheds important light on the nature of cosmic censorship hypothesis and its possible formulations. The key effect of these perturbations is to alter the trapped surface formation pattern within the collapsing cloud and the apparent horizon structure. This allows the singularity to be visible, and implications are discussed.

  1. The cylindrical magnetic Rayleigh-Taylor instability for viscous fluids

    SciTech Connect (OSTI)

    Chambers, K.; Forbes, L. K.

    2012-10-15

    This paper considers a cylindrical Rayleigh-Taylor instability, in which a heavy fluid surrounds a light fluid, and gravity is directed radially inwards. A massive object is located at the centre of the light fluid, and it behaves like a line dipole both for fluid flow and magnetic field strength. The initially circular interface between the two conducting fluids evolves into plumes, dependent on the magnetic and fluid dipole strengths and the nature of the initial disturbance to the interface. A spectral method is presented to solve the time-dependent interface shapes, and results are presented and discussed. Bipolar solutions are possible, and these are of particular relevance to astrophysics. The solutions obtained resemble structures of some HII regions and nebulae.

  2. MAGNETOHYDRODYNAMIC TURBULENCE POWERED BY MAGNETOROTATIONAL INSTABILITY IN NASCENT PROTONEUTRON STARS

    SciTech Connect (OSTI)

    Masada, Youhei [Department of Computational Science, Kobe University, Kobe 657-8501 (Japan); Takiwaki, Tomoya [Division of Theoretical Astronomy, National Astronomical Observatory of Japan, Tokyo 181-8588 (Japan); Kotake, Kei, E-mail: ymasada@harbor.kobe-u.ac.jp [Faculty of Science, Department of Applied Physics, Fukuoka University, Fukuoka 814-0180 (Japan)

    2015-01-01

    Magnetorotational instability (MRI) in a convectively stable layer around the neutrinosphere is simulated by a three-dimensional model of a supernova core. To resolve MRI-unstable modes, a thin layer approximation considering only the radial global stratification is adopted. Our intriguing finding is that the convectively stable layer around the neutrinosphere becomes fully turbulent due to the MRI and its nonlinear penetration into the strongly stratified MRI-stable region. The intensity of the MRI-driven turbulence increases with magnetic flux threading the core, but is limited by the free energy stored in the differential rotation. The turbulent neutrinosphere is a natural consequence of rotating core-collapse and could exert a positive impact on the supernova mechanism.

  3. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  4. THE ROLE OF THE MAGNETOROTATIONAL INSTABILITY IN MASSIVE STARS

    SciTech Connect (OSTI)

    Wheeler, J. Craig; Kagan, Daniel; Chatzopoulos, Emmanouil

    2015-01-20

    The magnetorotational instability (MRI) is key to physics in accretion disks and is widely considered to play some role in massive star core collapse. Models of rotating massive stars naturally develop very strong shear at composition boundaries, a necessary condition for MRI instability, and the MRI is subject to triply diffusive destabilizing effects in radiative regions. We have used the MESA stellar evolution code to compute magnetic effects due to the Spruit-Tayler (ST) mechanism and the MRI, separately and together, in a sample of massive star models. We find that the MRI can be active in the later stages of massive star evolution, leading to mixing effects that are not captured in models that neglect the MRI. The MRI and related magnetorotational effects can move models of given zero-age main sequence mass across ''boundaries'' from degenerate CO cores to degenerate O/Ne/Mg cores and from degenerate O/Ne/Mg cores to iron cores, thus affecting the final evolution and the physics of core collapse. The MRI acting alone can slow the rotation of the inner core in general agreement with the observed ''initial'' rotation rates of pulsars. The MRI analysis suggests that localized fields ?10{sup 12} G may exist at the boundary of the iron core. With both the ST and MRI mechanisms active in the 20 M {sub ?} model, we find that the helium shell mixes entirely out into the envelope. Enhanced mixing could yield a population of yellow or even blue supergiant supernova progenitors that would not be standard SN IIP.

  5. Insights from Human/Mouse genome comparisons

    SciTech Connect (OSTI)

    Pennacchio, Len A.

    2003-03-30

    Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish (Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestry of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.

  6. On the marginal instability threshold condition of the aperiodic ordinary mode

    SciTech Connect (OSTI)

    Schlickeiser, R.; Yoon, P. H.

    2014-07-15

    The purely growing ordinary (O) mode instability has recently received renewed attention owing to its potential applicability to the solar wind plasma. Here, an analytical marginal instability condition is derived for counter-streaming bi-Maxwellian plasma particle distribution functions. The derived marginal instability condition as a function of the temperature anisotropy and plasma beta agrees remarkably well with the numerically determined instability condition. The existence of a new instability domain of the O-mode at small plasma beta values is confirmed with the leading A??{sub ?}{sup ?1}-dependence, if the counter-stream parameter P{sub e} exceeds a critical value. At small plasma beta values at large enough counter-stream parameter, the O-mode also operates for temperature anisotropies A?=?T{sub ?}/T{sub ?}?>?1 even larger than unity, as the parallel counter-stream free energy exceeds the perpendicular bi-Maxwellian free energy.

  7. Structural Genomics of Protein Phosphatases

    SciTech Connect (OSTI)

    Almo,S.; Bonanno, J.; Sauder, J.; Emtage, S.; Dilorenzo, T.; Malashkevich, V.; Wasserman, S.; Swaminathan, S.; Eswaramoorthy, S.; et al

    2007-01-01

    The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.

  8. 11th Annual Energy Department Joint Genome Institute Genomics of Energy &

    Energy Savers [EERE]

    Environment Meeting | Department of Energy 11th Annual Energy Department Joint Genome Institute Genomics of Energy & Environment Meeting 11th Annual Energy Department Joint Genome Institute Genomics of Energy & Environment Meeting March 21, 2016 9:00AM PDT to March 25, 2016 4:00PM PDT Marriott Hotel 2355 North Main Street Walnut Creek, California 94596 The 11th Annual Energy Department (DOE) Joint Genome Institute Genomics of Energy & Environment Meeting will be held March 21-25,

  9. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

    Grimwood, Jane: Schmutz, Jeremy, J.: Myers, Richard, M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the JGI has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  10. Fueling the Future with Fungal Genomes

    SciTech Connect (OSTI)

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

  11. Cassava Genomics: can genomic technology benefit smallholder farmers in Africa? (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Rounsley, Steve

    2014-03-20

    Steve Rounsley of the University of Arizona speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  12. Observation of Rayleigh-Taylor-instability evolution in a plasma with magnetic and viscous effects

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Adams, Colin S.; Moser, Auna L.; Hsu, Scott C.

    2015-11-06

    We present time-resolved observations of Rayleigh-Taylor-instability (RTI) evolution at the interface between an unmagnetized plasma jet colliding with a stagnated, magnetized plasma. The observed instability growth time (~10μs) is consistent with the estimated linear RTI growth rate calculated using experimentally inferred values of density (~1014cm–3) and deceleration (~109 m/s2). The observed mode wavelength (≳1 cm) nearly doubles within a linear growth time. Furthermore, theoretical estimates of magnetic and viscous stabilization and idealized magnetohydrodynamic simulations including a physical viscosity model both suggest that the observed instability evolution is subject to magnetic and/or viscous effects.

  13. Linear study of Rayleigh-Taylor instability in a diffusive quantum plasma

    SciTech Connect (OSTI)

    Momeni, Mahdi

    2013-08-15

    The linear Rayleigh-Taylor (RT) instability in an incompressible quantum plasma is investigated on the basis of quantum magnetohydrodynamic model. It is shown that the occurrence of RT instability depends on density-temperature inhomogeneity (characteristic lengths) on one hand, and the system layer size on the other. It is also observed that the combined effects of external magnetic field, diffusivity, and quantum pressure significantly modify the dispersion properties of system in both the parallel and perpendicular directions. For any case, the imaginary and real parts of dispersion relation are presented and the possibility and conditions for the instability growth rate are discussed.

  14. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Genome Engineering with TAL Effector Nucleases Print Tuesday, 24 April 2012 09:48 Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such as the correction of gene sequences in patients suffering from genetic diseases, the modification or insertion of genes in plants, and the generation of unique cell lines for treatment of diseases such as cancer. GE

  15. Chapter 27 -- Breast Cancer Genomics, Section VI, Pathology and Biological Markers of Invasive Breast Cancer

    SciTech Connect (OSTI)

    Spellman, Paul T.; Heiser, Laura; Gray, Joe W.

    2009-06-18

    Breast cancer is predominantly a disease of the genome with cancers arising and progressing through accumulation of aberrations that alter the genome - by changing DNA sequence, copy number, and structure in ways that that contribute to diverse aspects of cancer pathophysiology. Classic examples of genomic events that contribute to breast cancer pathophysiology include inherited mutations in BRCA1, BRCA2, TP53, and CHK2 that contribute to the initiation of breast cancer, amplification of ERBB2 (formerly HER2) and mutations of elements of the PI3-kinase pathway that activate aspects of epidermal growth factor receptor (EGFR) signaling and deletion of CDKN2A/B that contributes to cell cycle deregulation and genome instability. It is now apparent that accumulation of these aberrations is a time-dependent process that accelerates with age. Although American women living to an age of 85 have a 1 in 8 chance of developing breast cancer, the incidence of cancer in women younger than 30 years is uncommon. This is consistent with a multistep cancer progression model whereby mutation and selection drive the tumor's development, analogous to traditional Darwinian evolution. In the case of cancer, the driving events are changes in sequence, copy number, and structure of DNA and alterations in chromatin structure or other epigenetic marks. Our understanding of the genetic, genomic, and epigenomic events that influence the development and progression of breast cancer is increasing at a remarkable rate through application of powerful analysis tools that enable genome-wide analysis of DNA sequence and structure, copy number, allelic loss, and epigenomic modification. Application of these techniques to elucidation of the nature and timing of these events is enriching our understanding of mechanisms that increase breast cancer susceptibility, enable tumor initiation and progression to metastatic disease, and determine therapeutic response or resistance. These studies also reveal the molecular differences between cancer and normal that may be exploited to therapeutic benefit or that provide targets for molecular assays that may enable early cancer detection, and predict individual disease progression or response to treatment. This chapter reviews current and future directions in genome analysis and summarizes studies that provide insights into breast cancer pathophysiology or that suggest strategies to improve breast cancer management.

  16. Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome

    SciTech Connect (OSTI)

    Pennacchio, Len A.; Baroukh, Nadine; Rubin, Edward M.

    2003-05-15

    Deciphering the genetic code embedded within the human genome remains a significant challenge despite the human genome consortium's recent success at defining its linear sequence (Lander et al. 2001; Venter et al. 2001). While useful strategies exist to identify a large percentage of protein encoding regions, efforts to accurately define functional sequences in the remaining {approx}97 percent of the genome lag. Our primary interest has been to utilize the evolutionary relationship and the universal nature of genomic sequence information in vertebrates to reveal functional elements in the human genome. This has been achieved through the combined use of vertebrate comparative genomics to pinpoint highly conserved sequences as candidates for biological activity and transgenic mouse studies to address the functionality of defined human DNA fragments. Accordingly, we describe strategies and insights into functional sequences in the human genome through the use of comparative genomics coupled wit h functional studies in the mouse.

  17. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Zimmer, Carl [New York Times

    2013-01-22

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  18. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Zimmer, Carl [New York Times] [New York Times

    2012-03-20

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  19. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Ambrust, Ginger

    2011-04-25

    Ginger Armbrust from the University of Washington spoke about diatom genomics on March 26, 2009 at the DOE JGI User Meeting

  20. Metagenomics, metatranscriptomics and single cell genomics reveal...

    Office of Scientific and Technical Information (OSTI)

    and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill Citation Details In-Document Search Title: Metagenomics, metatranscriptomics and...

  1. History of the DOE Human Genome Program

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of the DOE Human Genome Program The following history is taken from the U.S. Department of Energy 1991-91 Human Genome Program Report (June 1992). This is an archived item. A brief history of the U.S. Department of Energy (DOE) Human Genome Program will be useful in a discussion of the objectives of the DOE program as well as those of the collaborative U.S. Human Genome Project. The Office of Health and Environmental Research (OHER) of DOE and its predecessor agencies--the Atomic Energy

  2. Synthetic Genomics Inc | Open Energy Information

    Open Energy Info (EERE)

    search Name: Synthetic Genomics Inc. Place: La Jolla, California Sector: Hydro, Hydrogen, Renewable Energy Product: California-based company planning to create new types of...

  3. Astronomy Particle Physics Light Sources Genomics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 - 2 Astronomy Particle Physics Light Sources Genomics Climate * Big Data Software - Broad ecosystem of capabilities and technologies - Research and evaluate - Customize and...

  4. Today, DOE's Joint Genome Institute (a

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in forms of kidney disease, prostate and colorectal cancer, leukemia, hypertension, diabetes, and atherosclerosis. The JGI's DNA Production Genomics Facility is one of the most...

  5. 11th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting

    Broader source: Energy.gov [DOE]

    The 11th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting will be held March 21–25, 2016 in Walnut Creek, California. The meeting will gather together experts and researchers working in energy and environmental genomics and synthetic biology, and it will have a special focus on the work done at the DOE Joint Genome Institute. Bioenergy Technologies Office Technology Manager Daniel Fishman will be in attendance.

  6. Magnetic reconnection mediated by hyper-resistive plasmoid instability

    SciTech Connect (OSTI)

    Huang, Yi-Min; Bhattacharjee, A.; Forbes, Terry G.

    2013-08-15

    Magnetic reconnection mediated by the hyper-resistive plasmoid instability is studied with both linear analysis and nonlinear simulations. The linear growth rate is found to scale as S{sub H}{sup 1/6} with respect to the hyper-resistive Lundquist number S{sub H}?L{sup 3}V{sub A}/?{sub H}, where L is the system size, V{sub A} is the Alfvn velocity, and ?{sub H} is the hyper-resistivity. In the nonlinear regime, reconnection rate becomes nearly independent of S{sub H}, the number of plasmoids scales as S{sub H}{sup 1/2}, and the secondary current sheet length and width both scale as S{sub H}{sup ?1/2}. These scalings are consistent with a heuristic argument assuming secondary current sheets are close to marginal stability. The distribution of plasmoids as a function of the enclosed flux ? is found to obey a ?{sup ?1} power law over an extended range, followed by a rapid fall off for large plasmoids. These results are compared with those from resistive magnetohydrodynamic studies.

  7. Neutrino flavor instabilities in a time-dependent supernova model

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Abbar, Sajad; Duan, Huaiyu

    2015-10-19

    In this study, a dense neutrino medium such as that inside a core-collapse supernova can experience collective flavor conversion or oscillations because of the neutral-current weak interaction among the neutrinos. This phenomenon has been studied in a restricted, stationary supernova model which possesses the (spatial) spherical symmetry about the center of the supernova and the (directional) axial symmetry around the radial direction. Recently it has been shown that these spatial and directional symmetries can be broken spontaneously by collective neutrino oscillations. In this letter we analyze the neutrino flavor instabilities in a time-dependent supernova model. Our results show that collectivemore »neutrino oscillations start at approximately the same radius in both the stationary and time-dependent supernova models unless there exist very rapid variations in local physical conditions on timescales of a few microseconds or shorter. Our results also suggest that collective neutrino oscillations can vary rapidly with time in the regimes where they do occur which need to be studied in time-dependent supernova models.« less

  8. Physical interpretation of Jeans instability in quantum plasmas

    SciTech Connect (OSTI)

    Akbari-Moghanjoughi, M.

    2014-08-15

    In this paper, we use the quantum hydrodynamics and its hydrostatic limit to investigate the newly posed problem of Jeans instability in quantum plasmas from a different point of view in connection with the well-known Chandrasekhar mass-limit on highly collapsed degenerate stellar configurations. It is shown that the hydrodynamic stability of a spherically symmetric uniform quantum plasma with a given fixed mass is achieved by increase in its mass-density or decrease in the radius under the action of gravity. It is also remarked that for masses beyond the limiting Jeans-mass, the plasma becomes completely unstable and the gravitational collapse would proceed forever. This limiting mass is found to depend strongly on the composition of the quantum plasma and the atomic-number of the constituent ions, where it is observed that heavier elements rather destabilize the quantum plasma hydrodynamically. It is also shown that the Chandrasekhar mass-limit for white dwarf stars can be directly obtained from the hydrostatic limit of our model.

  9. Fast reconnection in high-Lundquist-number plasmas due to the plasmoid Instability

    SciTech Connect (OSTI)

    Bhattacharjee, A.; Huang Yimin; Yang, H.; Rogers, B.

    2009-11-15

    Thin current sheets in systems of large size that exceed a critical value of the Lundquist number are unstable to a super-Alfvenic tearing instability, referred to hereafter as the plasmoid instability. The scaling of the growth rate of the most rapidly growing plasmoid instability with respect to the Lundquist number is shown to follow from the classical dispersion relation for tearing modes. As a result of this instability, the system realizes a nonlinear reconnection rate that appears to be weakly dependent on the Lundquist number, and larger than the Sweet-Parker rate by nearly an order of magnitude (for the range of Lundquist numbers considered). This regime of fast reconnection is realizable in a dynamic and highly unstable thin current sheet, without requiring the current sheet to be turbulent.

  10. Investigation of the Rayleigh-Taylor and Richtmyer-Meshkov instabilities

    SciTech Connect (OSTI)

    Riccardo Bonazza, Mark Anderson, Jason Oakley

    2006-11-03

    The present research program is centered on the experimental and numerical study of two instabilities that develop at the interface between two different fluids when the interface experiences an impulsive or a constant acceleration. The instabilities, called the Richtmyer-Meshkov and Rayleigh-Taylor instability, respectively, adversely affect target implosion in experiments aimed at the achievement of nuclear fusion by inertial confinement by causing the nuclear fuel contained in a target and the shell material to mix, leading to contamination of the fuel, yield reduction or no ignition at all. The laboratory experiments summarized in this report include shock tube experiments to study a shock-accelerated bubble and a shock-accelerated 2-D sinusoidal interface; and experiments based on the use of magnetorheological fluids for the study of the Rayleigh-Taylor instability. Computational experiments based on the shock tube experimental conditions are also reported.

  11. Electromagnetic fluctuation spectrum associated with the drift Alfven-cyclotron instability

    SciTech Connect (OSTI)

    Rha, Kicheol; Ryu, Chang-Mo; Yoon, Peter H.

    2012-07-15

    The present paper investigates the electromagnetic fluctuation spectrum associated with the drift Alfven-cyclotron instability by means of a two-dimensional particle-in-cell simulation, which may be plausibly associated with a current disruption event. The current disruption event shows localized high-amplitude electromagnetic fluctuations. In recent theories, these fluctuation characteristics are shown to correspond to the drift Alfven-cyclotron instability. A simulation is carried out to clarify this instability. The simulation shows that the drift Alfven-cyclotron instabilities are excited in two frequency regimes, a relatively low frequency mode propagating in a quasi-perpendicular direction while the second high-frequency branch propagating in a predominantly parallel propagation direction, consistent with observations as well as with a recent theory.

  12. On an instability exhibited by the ballistic-diffusive heat conduction model of Xu and Hu

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Christov, I. C.; Jordan, P. M.

    2013-11-13

    We show that the constitutive relation for the thermal flux proposed by Xu & Hu (2011) admits an unconditional instability. We also highlight the difference between mathematical models containing delay and those that include relaxation effects.

  13. Bulk viscosity in a hyperonic star and r-mode instability

    SciTech Connect (OSTI)

    Jha, T. K.; Mishra, H.; Sreekanth, V.

    2010-08-15

    We consider a rotating neutron star with the presence of hyperons in its core. We use an equation of state in an effective chiral model within the relativistic mean-field approximation. We calculate the hyperonic bulk viscosity coefficient caused by nonleptonic weak interactions. By estimating the damping time scales of the dissipative processes, we investigate its role in the suppression of gravitationally driven instabilities in the r mode. We observe that r-mode instability remains very significant for hyperon core temperatures of around 10{sup 8} K, which results in a comparatively larger instability window. We find that such instability can reduce the angular velocity of the rapidly rotating star considerably up to {approx}0.04{Omega}{sub K}, with {Omega}{sub K} as the Keplerian angular velocity.

  14. Functional Insights from Structural Genomics

    SciTech Connect (OSTI)

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  15. Hosing Instability of the Drive Electron Beam in the E157 Plasma-Wakefield

    Office of Scientific and Technical Information (OSTI)

    Acceleration Experiment at the Stanford Linear Accelerator (Technical Report) | SciTech Connect Technical Report: Hosing Instability of the Drive Electron Beam in the E157 Plasma-Wakefield Acceleration Experiment at the Stanford Linear Accelerator Citation Details In-Document Search Title: Hosing Instability of the Drive Electron Beam in the E157 Plasma-Wakefield Acceleration Experiment at the Stanford Linear Accelerator In the plasma-wakefield experiment at SLAC, known as E157, an

  16. Microbunching-Instability-Induced Sidebands in a Seeded Free-Electron Laser

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Journal Article: Microbunching-Instability-Induced Sidebands in a Seeded Free-Electron Laser Citation Details In-Document Search Title: Microbunching-Instability-Induced Sidebands in a Seeded Free-Electron Laser Authors: Zhang, Zhen ; /SLAC /Tsinghua U., Beijing, Dept. Eng. Phys. ; Lindberg, Ryan ; /ANL, APS ; Fawley, William M. ; Huang, Zhirong ; Krzywinski, Jacek ; Lutman, Alberto ; Marcus, Gabriel ; Marinelli, Agostino ; /SLAC Publication Date:

  17. Simulation of filamentation instability of a current-carrying plasma by particle in cell method

    SciTech Connect (OSTI)

    Niknam, A. R.; Mostafavi, P. S.; Komaizi, D.; Salahshoor, M. [Laser-Plasma Research Institute, Shahid Beheshti University, G. C., Tehran 19839-63113 (Iran, Islamic Republic of)

    2012-08-15

    The nonlinear dynamics of filamentation instability in a weakly ionized current-carrying plasma in the diffusion frequency region is studied using particle in cell simulation. The effects of electron thermal motion and ion-neutral collision on the evolution of this instability in the nonlinear stage of the filaments coalescence are discussed. It is found that the coalescence of the current filaments is enhanced by increasing the temperature and is delayed by increasing the collision frequency.

  18. A Linear Theory of Microwave Instability in Electron Storage Rings (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Journal Article: A Linear Theory of Microwave Instability in Electron Storage Rings Citation Details In-Document Search Title: A Linear Theory of Microwave Instability in Electron Storage Rings The well-known Haissinski distribution provides a stable equilibrium of longitudinal beam distribution in electron storage rings below a threshold current. Yet, how to accurately determine this threshold, above which the Haissinski distribution becomes unstable, is not

  19. Nonlinear heat-release/acoustic model for thermoacoustic instability in lean premixed combustors

    SciTech Connect (OSTI)

    Peracchio, A.A.; Proscia, W.M.

    1999-07-01

    Lean premixed combustors, such as those used in industrial gas turbines to achieve low emissions, are often susceptible to thermoacoustic combustion instabilities, which manifest themselves as pressure and heat release oscillations in the combustor. These oscillations can result in increased noise and decreased durability due to vibration and flame motion. A physically based nonlinear parametric model has been developed that captures this instability. It describes the coupling of combustor acoustics with the rate of heat release. The model represents this coupling by accounting for the effect of acoustic pressure fluctuations on the varying fuel/air ratio being delivered to the flame, causing a fluctuating heat release due to both fuel air ratio variations and flame front oscillations. If the phasing of the fluctuating heat release and pressure are proper, an instability results that grows into a limit cycle. The nonlinear nature of the model predicts the onset of the instability and additionally captures the resulting limit cycle. Tests of a lean premixed nozzle at engine scale and engine operating conditions in the UTRC single nozzle rig, conducted under DARPA contract, exhibited instabilities. Parameters from the model were adjusted so that analytical results were consistent with relevant experimental data from this test. The parametric model captures the limit cycle behavior over a range of mean fuel air ratios, showing the instability amplitude (pressure and heat release) to increase and limit cycle frequency to decrease as mean fuel air ratio is reduced.

  20. Rayleigh-Taylor-Instability Evolution in Colliding-Plasma-Jet Experiments with Magnetic and Viscous Stabilization

    SciTech Connect (OSTI)

    Adams, Colin Stuart

    2015-01-15

    The Rayleigh-Taylor instability causes mixing in plasmas throughout the universe, from micron-scale plasmas in inertial confinement fusion implosions to parsec-scale supernova remnants. The evolution of this interchange instability in a plasma is influenced by the presence of viscosity and magnetic fields, both of which have the potential to stabilize short-wavelength modes. Very few experimental observations of Rayleigh-Taylor growth in plasmas with stabilizing mechanisms are reported in the literature, and those that are reported are in sub-millimeter scale plasmas that are difficult to diagnose. Experimental observations in well-characterized plasmas are important for validation of computational models used to make design predictions for inertial confinement fusion efforts. This dissertation presents observations of instability growth during the interaction between a high Mach-number, initially un-magnetized plasma jet and a stagnated, magnetized plasma. A multi-frame fast camera captures Rayleigh-Taylor-instability growth while interferometry, spectroscopy, photodiode, and magnetic probe diagnostics are employed to estimate plasma parameters in the vicinity of the collision. As the instability grows, an evolution to longer mode wavelength is observed. Comparisons of experimental data with idealized magnetohydrodynamic simulations including a physical viscosity model suggest that the observed instability evolution is consistent with both magnetic and viscous stabilization. These data provide the opportunity to benchmark computational models used in astrophysics and fusion research.

  1. VERTICAL STRUCTURE AND CORONAL POWER OF ACCRETION DISKS POWERED BY MAGNETOROTATIONAL-INSTABILITY TURBULENCE

    SciTech Connect (OSTI)

    Uzdensky, Dmitri A.

    2013-10-01

    In this paper, we consider two outstanding intertwined problems in modern high-energy astrophysics: (1) the vertical-thermal structure of an optically thick accretion disk heated by the dissipation of magnetohydrodynamic turbulence driven by the magnetorotational instability (MRI), and (2) determining the fraction of the accretion power released in the corona above the disk. For simplicity, we consider a gas-pressure-dominated disk and assume a constant opacity. We argue that the local turbulent dissipation rate due to the disruption of the MRI channel flows by secondary parasitic instabilities should be uniform across most of the disk, almost up to the disk photosphere. We then obtain a self-consistent analytical solution for the vertical thermal structure of the disk, governed by the balance between the heating by MRI turbulence and the cooling by radiative diffusion. Next, we argue that the coronal power fraction is determined by the competition between the Parker instability, viewed as a parasitic instability feeding off of MRI channel flows, and other parasitic instabilities. We show that the Parker instability inevitably becomes important near the disk surface, leading to a certain lower limit on the coronal power. While most of the analysis in this paper focuses on the case of a disk threaded by an externally imposed vertical magnetic field, we also discuss the zero net flux case, in which the magnetic field is produced by the MRI dynamo itself, and show that most of our arguments and conclusions should be valid in this case as well.

  2. On the Numerical Dispersion of Electromagnetic Particle-In-Cell Code : Finite Grid Instability

    SciTech Connect (OSTI)

    Meyers, Michael David; Huang, Chengkun; Zeng, Yong; Yi, Sunghwan; Albright, Brian James

    2014-07-15

    The Particle-In-Cell (PIC) method is widely used in relativistic particle beam and laser plasma modeling. However, the PIC method exhibits numerical instabilities that can render unphysical simulation results or even destroy the simulation. For electromagnetic relativistic beam and plasma modeling, the most relevant numerical instabilities are the finite grid instability and the numerical Cherenkov instability. We review the numerical dispersion relation of the electromagnetic PIC algorithm to analyze the origin of these instabilities. We rigorously derive the faithful 3D numerical dispersion of the PIC algorithm, and then specialize to the Yee FDTD scheme. In particular, we account for the manner in which the PIC algorithm updates and samples the fields and distribution function. Temporal and spatial phase factors from solving Maxwell's equations on the Yee grid with the leapfrog scheme are also explicitly accounted for. Numerical solutions to the electrostatic-like modes in the 1D dispersion relation for a cold drifting plasma are obtained for parameters of interest. In the succeeding analysis, we investigate how the finite grid instability arises from the interaction of the numerical 1D modes admitted in the system and their aliases. The most significant interaction is due critically to the correct representation of the operators in the dispersion relation. We obtain a simple analytic expression for the peak growth rate due to this interaction.

  3. THE EFFECT OF NONLINEAR LANDAU DAMPING ON ULTRARELATIVISTIC BEAM PLASMA INSTABILITIES

    SciTech Connect (OSTI)

    Chang, Philip; Lamberts, Astrid; Broderick, Avery E.; Shalaby, Mohamad; Pfrommer, Christoph; Puchwein, Ewald

    2014-12-20

    Very high energy gamma-rays from extragalactic sources produce pairs from the extragalactic background light, yielding an electron-positron pair beam. This pair beam is unstable to various plasma instabilities, especially the ''oblique'' instability, which can be the dominant cooling mechanism for the beam. However, recently, it has been claimed that nonlinear Landau damping renders it physically irrelevant by reducing the effective damping rate to a low level. Here we show with numerical calculations that the effective damping rate is 8 10{sup 4} the growth rate of the linear instability, which is sufficient for the ''oblique'' instability to be the dominant cooling mechanism of these pair beams. In particular, we show that previous estimates of this rate ignored the exponential cutoff in the scattering amplitude at large wave numbers and assumed that the damping of scattered waves entirely depends on collisions, ignoring collisionless processes. We find that the total wave energy eventually grows to approximate equipartition with the beam by increasingly depositing energy into long-wavelength modes. As we have not included the effect of nonlinear wave-wave interactions on these long-wavelength modes, this scenario represents the ''worst case'' scenario for the oblique instability. As it continues to drain energy from the beam at a faster rate than other processes, we conclude that the ''oblique'' instability is sufficiently strong to make it the physically dominant cooling mechanism for high-energy pair beams in the intergalactic medium.

  4. Genome Structure Gallery from the Mycobacterium Tuberculosis Structual Genomics Consortium

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The TB Structural Genomics Consortium works with the structures of proteins from M. tuberculosis, analyzing these structures in the context of functional information that currently exists and that the Consortium generates. The database of linked structural and functional information constructed from this project will form a lasting basis for understanding M. tuberculosis pathogenesis and for structure-based drug design. The Consortium's structural and functional information is publicly available. The Structures Gallery makes more than 650 total structures available by PDB identifier. Some of these are not consortium targets, but all are viewable in 3D color and can be manipulated in various ways by Jmol, an open-source Java viewer for chemical structures in 3D from http://www.jmol.org/

  5. Quality Scores for 32,000 Genomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Land, Miriam L; Hyatt, Philip Douglas; Jun, Se Ran; Kora, Guruprasad H; Hauser, Loren John; Ussery, David W

    2014-01-01

    More than 80% of the microbial genomes in GenBank are of draft quality (12,553 draft vs. 2,679 finished, as of October, 2013). We examined the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases and assigned quality scores for more than 30,000 prokaryotic genome sequences. Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 120 conserved genes in prokaryotes. Most (~87.6%) of the genomes had quality scores of 0.8 ormore » better and can be safely used for standard comparative genomics analysis, although only 6.1% of the genomes had a perfect quality score. We find that about 2.9% of the genomes had a score below 0.6 and probably have too low a quality to yield reliable analysis. This score corresponds to more than 1000 contigs. Comparison of the codon usage across 15,000 quality genomes found that anti-codons beginning with an A (codons ending with a U ) are almost non-existent, with the exception of one arginine codon (CGU).« less

  6. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L; Uehling, Jessie K; Payen, Thibaut; Plett, Jonathan

    2014-01-01

    The last 10 years have seen the cost of sequencing complete genomes decrease at an incredible speed. This has led to an increase in the number of genomes sequenced in all the fungal tree of life as well as a wide variety of plant genomes. The increase in sequencing has permitted us to study the evolution of organisms on a genomic scale. A number of talks during the conference discussed the importance of transposable elements (TEs) that are present in almost all species of fungi. These TEs represent an especially large percentage of genomic space in fungi that interact with plants. Thierry Rouxel (INRA, Nancy, France) showed the link between speciation in the Leptosphaeria complex and the expansion of TE families. For example in the Leptosphaeria complex, one species associated with oilseed rape has experienced a recent and massive burst of movement by a few TE families. The alterations caused by these TEs took place in discrete regions of the genome leading to shuffling of the genomic landscape and the appearance of genes specific to the species, such as effectors useful for the interactions with a particular plant (Rouxel et al., 2011). Other presentations showed the importance of TEs in affecting genome organization. For example, in Amanita different species appear to have been invaded by different TE families (Veneault-Fourrey & Martin, 2011).

  7. Uses of antimicrobial genes from microbial genome

    DOE Patents [OSTI]

    Sorek, Rotem; Rubin, Edward M.

    2013-08-20

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

  8. The domains of instability for the pulsating PG1159 stars.

    SciTech Connect (OSTI)

    Quirion, P.-O.; Fontaine, Gilles.; Brassard, Pierre; Herwig, F. H.

    2004-01-01

    The fact that we find pulsating and nonpulsating stars mixed together in the PG 1159 region of the log g - T{sub eff} diagram has been a long standing puzzle. The poor understanding of the driving mechanism in those stars has been the reason why it has taken so long to address properly this problem. Following the work of Saio (1996) and Gautschy (1997) based on the OPAL opacities, Quirion, Fontaine, & Brassard (2004) recently showed that we are now able to understand and reproduce the ranges of observed periods in the pulsating PG 1159 stars in terms of the original {kappa}-mechanism associated with the partial ionization of the K-shell electrons of C and O which, along with He, make up the composition of the envelope of those stars. Contrary to others, those three studies agree in that no composition gradients are needed between the atmospheric layers and the driving region. Furthermore, the cohabitation of pulsating and nonpulsating PG 1159 stars is naturally explained in terms of a dispersion in atmospheric parameters and in terms of a variation in surface composition from star to star. In particular, the most He-rich stars tend to be stable. We go beyond the findings discussed by Quirion et al. (2004) in this paper, and present the results of additional calculations aimed at describing better the role of the chemical composition (in particular the role of metallicity) as well as that of the stellar mass on the boundaries of the instability domain in the log g - T{sub eff} plane.

  9. Implications of structural genomics target selection strategies: Pfam5000,

    Office of Scientific and Technical Information (OSTI)

    whole genome, and random approaches (Journal Article) | SciTech Connect Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches Citation Details In-Document Search Title: Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary

  10. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

    SciTech Connect (OSTI)

    Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

    2011-04-29

    In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

  11. Genomic definition of species. Revision 2

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  12. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  13. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  14. Electrolyte Genome Could Be Battery Game-Changer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Electrolyte Genome Could Be Battery Game-Changer Electrolyte Genome Could Be Battery Game-Changer The Materials Project screens molecules to accelerate electrolyte discovery April...

  15. 2013 Progress Report -- DOE Joint Genome Institute (Program Document...

    Office of Scientific and Technical Information (OSTI)

    Program Document: 2013 Progress Report -- DOE Joint Genome Institute Citation Details In-Document Search Title: 2013 Progress Report -- DOE Joint Genome Institute In October 2012, ...

  16. Using Genomics to Dissect Seed Development (JGI Seventh Annual...

    Office of Scientific and Technical Information (OSTI)

    Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting) Citation Details In-Document Search Title: Using...

  17. Next Generation Sequencing at the University of Chicago Genomics...

    Office of Scientific and Technical Information (OSTI)

    The University of Chicago Genomics Core provides University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation ...

  18. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  19. Achievements of structural genomics (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Conference: Achievements of structural genomics Citation Details In-Document Search Title: Achievements of structural genomics You are accessing a document from the Department...

  20. Achievements of structural genomics (Journal Article) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Achievements of structural genomics Citation Details In-Document Search Title: Achievements of structural genomics You are accessing a document from the...

  1. Structural Genomics of Minimal Organisms: Pipeline and Results...

    Office of Scientific and Technical Information (OSTI)

    Book: Structural Genomics of Minimal Organisms: Pipeline and Results Citation Details In-Document Search Title: Structural Genomics of Minimal Organisms: Pipeline and Results The ...

  2. Fueling Future with Algal Genomics (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing...

  3. Using Genomics to Dissect Seed Development (JGI Seventh Annual...

    Office of Scientific and Technical Information (OSTI)

    Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting) Citation Details In-Document Search Title: Using Genomics to Dissect Seed...

  4. A PARALLEL-PROPAGATING ALFVENIC ION-BEAM INSTABILITY IN THE HIGH-BETA SOLAR WIND

    SciTech Connect (OSTI)

    Verscharen, Daniel; Bourouaine, Sofiane; Chandran, Benjamin D. G.; Maruca, Bennett A. E-mail: s.bourouaine@unh.edu E-mail: bmaruca@ssl.berkeley.edu

    2013-08-10

    We investigate the conditions under which parallel-propagating Alfven/ion-cyclotron waves are driven unstable by an isotropic (T{sub {alpha}} = T{sub Parallel-To {alpha}}) population of alpha particles drifting parallel to the magnetic field at an average speed U{sub {alpha}} with respect to the protons. We derive an approximate analytic condition for the minimum value of U{sub {alpha}} needed to excite this instability and refine this result using numerical solutions to the hot-plasma dispersion relation. When the alpha-particle number density is {approx_equal} 5% of the proton number density and the two species have similar thermal speeds, the instability requires that {beta}{sub p} {approx}> 1, where {beta}{sub p} is the ratio of the proton pressure to the magnetic pressure. For 1 {approx}< {beta}{sub p} {approx}< 12, the minimum U{sub {alpha}} needed to excite this instability ranges from 0.7v{sub A} to 0.9v{sub A}, where v{sub A} is the Alfven speed. This threshold is smaller than the threshold of {approx_equal} 1.2v{sub A} for the parallel magnetosonic instability, which was previously thought to have the lowest threshold of the alpha-particle beam instabilities at {beta}{sub p} {approx}> 0.5. We discuss the role of the parallel Alfvenic drift instability for the evolution of the alpha-particle drift speed in the solar wind. We also analyze measurements from the Wind spacecraft's Faraday cups and show that the U{sub {alpha}} values measured in solar-wind streams with T{sub {alpha}} Almost-Equal-To T{sub Parallel-To {alpha}} are approximately bounded from above by the threshold of the parallel Alfvenic instability.

  5. Genome Sequence of the Palaeopolyploid soybean

    SciTech Connect (OSTI)

    Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; Ma, Jianxin; Mitros, Therese; Nelson, William; Hyten, David L.; Song, Qijian; Thelen, Jay J.; Cheng, Jianlin; Xu, Dong; Hellsten, Uffe; May, Gregory D.; Yu, Yeisoo; Sakura, Tetsuya; Umezawa, Taishi; Bhattacharyya, Madan K.; Sandhu, Devinder; Valliyodan, Babu; Lindquist, Erika; Peto, Myron; Grant, David; Shu, Shengqiang; Goodstein, David; Barry, Kerrie; Futrell-Griggs, Montona; Abernathy, Brian; Du, Jianchang; Tian, Zhixi; Zhu, Liucun; Gill, Navdeep; Joshi, Trupti; Libault, Marc; Sethuraman, Anand; Zhang, Xue-Cheng; Shinozaki, Kazuo; Nguyen, Henry T.; Wing, Rod A.; Cregan, Perry; Specht, James; Grimwood, Jane; Rokhsar, Dan; Stacey, Gary; Shoemaker, Randy C.; Jackson, Scott A.

    2009-08-03

    Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70percent more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78percent of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75percent of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

  6. Genome Sequence Databases (Overview): Sequencing and Assembly

    SciTech Connect (OSTI)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  7. Annotation of the Clostridium Acetobutylicum Genome

    SciTech Connect (OSTI)

    Daly, M. J.

    2004-06-09

    The genome sequence of the solvent producing bacterium Clostridium acetobutylicum ATCC824, has been determined by the shotgun approach. The genome consists of a 3.94 Mb chromosome and a 192 kb megaplasmid that contains the majority of genes responsible for solvent production. Comparison of C. acetobutylicum to Bacillus subtilis reveals significant local conservation of gene order, which has not been seen in comparisons of other genomes with similar, or, in some cases, closer, phylogenetic proximity. This conservation allows the prediction of many previously undetected operons in both bacteria.

  8. Progress in indirect and direct-drive planar experiments on hydrodynamic instabilities at the ablation front

    SciTech Connect (OSTI)

    Casner, A. Masse, L.; Huser, G.; Galmiche, D.; Liberatore, S.; Riazuelo, G.; Delorme, B.; Martinez, D.; Remington, B.; Smalyuk, V. A.; Igumenshchev, I.; Michel, D. T.; Froula, D.; Seka, W.; Goncharov, V. N.; Olazabal-Loumé, M.; Nicolaï, Ph.; Breil, J.; Tikhonchuk, V. T.; Fujioka, S.; and others

    2014-12-15

    Understanding and mitigating hydrodynamic instabilities and the fuel mix are the key elements for achieving ignition in Inertial Confinement Fusion. Cryogenic indirect-drive implosions on the National Ignition Facility have evidenced that the ablative Rayleigh-Taylor Instability (RTI) is a driver of the hot spot mix. This motivates the switch to a more flexible higher adiabat implosion design [O. A. Hurricane et al., Phys. Plasmas 21, 056313 (2014)]. The shell instability is also the main candidate for performance degradation in low-adiabat direct drive cryogenic implosions [Goncharov et al., Phys. Plasmas 21, 056315 (2014)]. This paper reviews recent results acquired in planar experiments performed on the OMEGA laser facility and devoted to the modeling and mitigation of hydrodynamic instabilities at the ablation front. In application to the indirect-drive scheme, we describe results obtained with a specific ablator composition such as the laminated ablator or a graded-dopant emulator. In application to the direct drive scheme, we discuss experiments devoted to the study of laser imprinted perturbations with special phase plates. The simulations of the Richtmyer-Meshkov phase reversal during the shock transit phase are challenging, and of crucial interest because this phase sets the seed of the RTI growth. Recent works were dedicated to increasing the accuracy of measurements of the phase inversion. We conclude by presenting a novel imprint mitigation mechanism based on the use of underdense foams. The foams induce laser smoothing by parametric instabilities thus reducing the laser imprint on the CH foil.

  9. LIMITS ON ALPHA PARTICLE TEMPERATURE ANISOTROPY AND DIFFERENTIAL FLOW FROM KINETIC INSTABILITIES: SOLAR WIND OBSERVATIONS

    SciTech Connect (OSTI)

    Bourouaine, Sofiane; Verscharen, Daniel; Chandran, Benjamin D. G.; Maruca, Bennett A.; Kasper, Justin C.

    2013-11-01

    Previous studies have shown that the observed temperature anisotropies of protons and alpha particles in the solar wind are constrained by theoretical thresholds for pressure and anisotropy driven instabilities such as the Alfvn/ion-cyclotron (A/IC) and fast-magnetosonic/whistler (FM/W) instabilities. In this Letter, we use a long period of in situ measurements provided by the Wind spacecraft's Faraday cups to investigate the combined constraint on the alpha proton differential flow velocity and the alpha particle temperature anisotropy due to A/IC and FM/W instabilities. We show that the majority of the data are constrained to lie within the region of parameter space in which A/IC and FM/W waves are either stable or have extremely low growth rates. In the minority of observed cases in which the growth rate of the A/IC (FM/W) instability is comparatively large, we find relatively higher values of T {sub ?}/T {sub p} (T {sub ??}/T {sub ?p}) when the alpha proton differential flow velocity is small, where T {sub ?} and T {sub p} (T {sub ??} and T {sub ?p}) are the perpendicular (parallel) temperatures of alpha particles and protons. We conjecture that this observed feature might arise from preferential alpha particle heating which can drive the alpha particles beyond the instability thresholds.

  10. On the dispersion relation of the transit time instability in inverted fireballs

    SciTech Connect (OSTI)

    Gruenwald, J.

    2014-08-15

    Recently discovered inverted fireballs are non-linear plasma phenomena, which are formed in hollow grid anodes with high transparency in an existing background plasma. If a sufficiently large potential is applied, accelerated electrons from the bulk start to oscillate through the grid. Experimental investigations have shown that they produce different types of plasma instabilities. One of those oscillations is a transit time instability which originates from strong electron beams that travel through the inverted fireball. This type of instability is similar to vircator reflex oscillations and produces radio frequency waves. Hence, it is suitable to convert DC signals into signals oscillating in the MHz range. This paper analyses the dispersion relation of the transit time instability for three different plasma regimes. The regimes can be divided into a collision less regime, a regime with high collisionality and one in between those former two. It is demonstrated that the plasma properties of the surrounding background plasma have a strong influence on the behavior of the instability itself.

  11. Experiments and theory on parametric instabilities excited in HF heating experiments at HAARP

    SciTech Connect (OSTI)

    Kuo, Spencer; Snyder, Arnold; Lee, M. C.

    2014-06-15

    Parametric instabilities excited by O-mode HF heater and the induced ionospheric modification were explored via HAARP digisonde operated in a fast mode. The impact of excited Langmuir waves and upper hybrid waves on the ionosphere are manifested by bumps in the virtual spread, which expand the ionogram echoes upward as much as 140?km and the downward range spread of the sounding echoes, which exceeds 50?km over a significant frequency range. The theory of parametric instabilities is presented. The theory identifies the ionogram bump located between the 3.2?MHz heater frequency and the upper hybrid resonance frequency and the bump below the upper hybrid resonance frequency to be associated with the Langmuir and upper hybrid instabilities, respectively. The Langmuir bump is located close to the upper hybrid resonance frequency, rather than to the heater frequency, consistent with the theory. Each bump in the virtual height spread of the ionogram is similar to the cusp occurring in daytime ionograms at the E-F2 layer transition, indicating that there is a small ledge in the density profile similar to E-F2 layer transitions. The experimental results also show that the strong impact of the upper hybrid instability on the ionosphere can suppress the Langmuir instability.

  12. The Methanosarcina barkeri genome: comparative analysis withMethanosarcina

    Office of Scientific and Technical Information (OSTI)

    acetivorans and Methanosarcina mazei reveals extensiverearrangement within methanosarcinal genomes (Journal Article) | SciTech Connect Journal Article: The Methanosarcina barkeri genome: comparative analysis withMethanosarcina acetivorans and Methanosarcina mazei reveals extensiverearrangement within methanosarcinal genomes Citation Details In-Document Search Title: The Methanosarcina barkeri genome: comparative analysis withMethanosarcina acetivorans and Methanosarcina mazei reveals

  13. Prokaryotic Genomes from Microbes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche, Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    To describe the potential functions of genes, MicrobesOnline includes protein family analyses (from InterPro and COG), metabolic maps (from KEGG), links to research papers (from UniProt and PubMed), and operon predictions for every genome. To examine each gene's evolutionary history, MicrobesOnline includes precomputed phylogenetic trees for all the gene families. It displays gene trees with genomic context or it compares the gene tree to the species tree. The tools provided with MicrobesOnline allow users to: compute customized motifs, sequence alignments, and phylogenetic trees change expression patterns in metabolic maps annotate genes in various ways The database contains more than 430 genomes. A browse tree tool and a genome browser are available, along with specialized search capabilities. (Specialized Interface)

  14. Genomic definition of species. Revision 1

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Dramanac, R.

    1992-06-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called (species) genome. The definition of species based on chromosomes, genes, or genome common to its member organisms has been implied or mentioned in passing numerous times. Some population biologists think that members of species have similar ``homeostatic genotypes,`` which are to a degree resistant to mutation or environmental change in the production of a basic phenotype.

  15. Phytozome System for Comparative Plant Genomics

    Energy Science and Technology Software Center (OSTI)

    2011-09-27

    Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the UC Berkeley Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release 7.0, Phytozome providesmore » access to twenty-five sequenced and annotated green plant genomes which have been clustered into gene families at eleven evolutionarily significant nodes., Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are lyper-linked and searchable.« less

  16. Webinar December 2: Materials Genome Initiative

    Broader source: Energy.gov [DOE]

    The Energy Department will present a live webinar entitled "Materials Genome Initiative" on Tuesday, December 2, from 12:00 to 1:00 p.m. Eastern Standard Time.

  17. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M.

    1992-12-31

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  18. Justice and the Human Genome Project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M.

    1992-01-01

    Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

  19. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such as...

  20. Comparative Genomics Analysis and Phenotypic Characterization...

    Office of Scientific and Technical Information (OSTI)

    of electron acceptors for respiration is due to the large number of c-type cytochrome genes present in the genome of Shewanella strains. More recently the dissimilatory metal...

  1. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such...

  2. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOE’s Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  3. Facilities and Equipment for Genomics/Comparative Functional Genomics at New York University

    SciTech Connect (OSTI)

    Lennie, Peter

    2006-06-29

    This award was for partial support for the renovation of space to house research laboratories and moveable scientific equipment for genomics/functional geonomics at New York University.

  4. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOEs Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  5. Stories of Discovery & Innovation: From Human Genome to Materials "Genome"

    Office of Science (SC) Website

    | U.S. DOE Office of Science (SC) From Human Genome to Materials "Genome" Energy Frontier Research Centers (EFRCs) EFRCs Home Centers Research Science Highlights News & Events EFRC News EFRC Events DOE Announcements Publications History Contact BES Home 07.09.14 Stories of Discovery & Innovation: From Human Genome to Materials "Genome" Print Text Size: A A A Subscribe FeedbackShare Page Government initiative seeks to speed the pace of materials discovery and

  6. Accelerating Biofuel Feedstock Crop Improvement with Miscanthus Genomics (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Swaminathan, Kankshita

    2014-03-20

    Kankshita Swaminathan of the Energy Biosciences Institute speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  7. The Human Genome Diversity Project

    SciTech Connect (OSTI)

    Cavalli-Sforza, L.

    1994-12-31

    The Human Genome Diversity Project (HGD Project) is an international anthropology project that seeks to study the genetic richness of the entire human species. This kind of genetic information can add a unique thread to the tapestry knowledge of humanity. Culture, environment, history, and other factors are often more important, but humanity`s genetic heritage, when analyzed with recent technology, brings another type of evidence for understanding species` past and present. The Project will deepen the understanding of this genetic richness and show both humanity`s diversity and its deep and underlying unity. The HGD Project is still largely in its planning stages, seeking the best ways to reach its goals. The continuing discussions of the Project, throughout the world, should improve the plans for the Project and their implementation. The Project is as global as humanity itself; its implementation will require the kinds of partnerships among different nations and cultures that make the involvement of UNESCO and other international organizations particularly appropriate. The author will briefly discuss the Project`s history, describe the Project, set out the core principles of the Project, and demonstrate how the Project will help combat the scourge of racism.

  8. Standards for a new genomic era

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Standards for new genomic era Standards for a new genomic era A team of geneticists has recently proposed a set of standards designed to elucidate the quality of publicly available genetic sequencing information. October 21, 2009 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and new materials. Los

  9. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such as the correction of gene sequences in patients suffering from genetic diseases, the modification or insertion of genes in plants, and the generation of unique cell lines for treatment of diseases such as cancer. GE requires the development of molecular tools that can search out and bind to one

  10. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such as the correction of gene sequences in patients suffering from genetic diseases, the modification or insertion of genes in plants, and the generation of unique cell lines for treatment of diseases such as cancer. GE requires the development of molecular tools that can search out and bind to one

  11. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such as the correction of gene sequences in patients suffering from genetic diseases, the modification or insertion of genes in plants, and the generation of unique cell lines for treatment of diseases such as cancer. GE requires the development of molecular tools that can search out and bind to one

  12. Genome Engineering with TAL Effector Nucleases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Engineering with TAL Effector Nucleases Print Genome engineering (GE), an emerging discipline in which a DNA sequence is altered at a single position, has a wide variety of potential uses, such as the correction of gene sequences in patients suffering from genetic diseases, the modification or insertion of genes in plants, and the generation of unique cell lines for treatment of diseases such as cancer. GE requires the development of molecular tools that can search out and bind to one

  13. Materials Genome Initiative | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Emerging Technologies » Materials Genome Initiative Materials Genome Initiative Credit: The White House Credit: The White House Lead Performers: -- National Renewable Energy Laboratory - Golden, CO -- Lawrence Berkeley National Laboratory - Berkeley, CA Project Term: October 2014 to July 2015 Project Background The development of new higher performing materials for buildings and building systems will be a key element of making the high-efficiency, high-performing buildings of the future. The

  14. Lattice coupling to electronic and magnetic instabilities in high magnetic fields

    SciTech Connect (OSTI)

    Thompson, J.D.; Graf, T.; Hundley, M.; Neumeier, J. [Los Alamos National Lab., NM (United States); Lacerda, A. [National High Magnetic Field Lab., Tallahassee, FL (United States); Lawrence, J. [California Univ., Irvine, CA (United States); Phillips, N. [California Univ., Berkeley, CA (United States)

    1996-04-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project focused on understanding electronic and magnetic instabilities in broad classes of materials in which the instabilities are coupled to the underlying crystallographic structure. Explaining these properties of materials poses outstanding theoretical and experimental challenges that are at the forefront of materials science/condensed matter physics. Very high magnetic fields available at the Los Alamos National High Magnetic Field Laboratory (NHMFL) are a key parameter in helping to provide this understanding. We have developed new experimental capabilities (thermal- expansion/magnetostriction, uniaxial stress and high-field heat capacity) needed to characterize how structure couples to the instabilities.

  15. Observation of Rayleigh-Taylor-instability evolution in a plasma with magnetic and viscous effects

    SciTech Connect (OSTI)

    Adams, Colin S.; Moser, Auna L.; Hsu, Scott C.

    2015-11-06

    We present time-resolved observations of Rayleigh-Taylor-instability (RTI) evolution at the interface between an unmagnetized plasma jet colliding with a stagnated, magnetized plasma. The observed instability growth time (~10μs) is consistent with the estimated linear RTI growth rate calculated using experimentally inferred values of density (~1014cm–3) and deceleration (~109 m/s2). The observed mode wavelength (≳1 cm) nearly doubles within a linear growth time. Furthermore, theoretical estimates of magnetic and viscous stabilization and idealized magnetohydrodynamic simulations including a physical viscosity model both suggest that the observed instability evolution is subject to magnetic and/or viscous effects.

  16. Ion finite Larmor radius effects on the interchange instability in an open system

    SciTech Connect (OSTI)

    Katanuma, I.; Sato, S.; Okuyama, Y.; Kato, S.; Kubota, R. [Plasma Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577 (Japan)] [Plasma Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577 (Japan)

    2013-11-15

    A particle simulation of an interchange instability was performed by taking into account the ion finite Larmor radius (FLR) effects. It is found that the interchange instability with large FLR grows in two phases, that is, linearly growing phase and the nonlinear phase subsequent to the linear phase, where the instability grows exponentially in both phases. The linear growth rates observed in the simulation agree well with the theoretical calculation. The effects of FLR are usually taken in the fluid simulation through the gyroviscosity, the effects of which are verified in the particle simulation with large FLR regime. The gyroviscous cancellation phenomenon observed in the particle simulation causes the drifts in the direction of ion diamagnetic drifts.

  17. In-silico investigation of Rayleigh instability in ultra-thin copper nanowire in premelting regime

    SciTech Connect (OSTI)

    Dutta, Amlan; Chatterjee, Swastika; Raychaudhuri, A. K.; Moitra, Amitava; Saha-Dasgupta, T.

    2014-06-28

    Motivated by the recent experimental reports, we explore the formation of Rayleigh-like instability in metallic nanowires during the solid state annealing, a concept originally introduced for liquid columns. Our molecular dynamics study using realistic interatomic potential reveals instability induced pattern formation at temperatures even below the melting temperature of the wire, in accordance with the experimental observations. We find that this is driven by the surface diffusion, which causes plastic slips in the system initiating necking in the nanowire. We further find the surface dominated mass-transport is of subdiffusive nature with time exponent less than unity. Our study provides an atomistic perspective of the instability formation in nanostructured solid phase.

  18. Computational and experimental studies of hydrodynamic instabilities and turbulent mixing (Review of NVIIEF efforts)

    SciTech Connect (OSTI)

    Andronov, V.A.; Zhidov, I.G.; Meskov, E.E.; Nevmerzhitskii, N.V.; Nikiforov, V.V.; Razin, A.N.; Rogatchev, V.G.; Tolshmyakov, A.I.; Yanilkin, Yu.V.

    1995-02-01

    This report describes an extensive program of investigations conducted at Arzamas-16 in Russia over the past several decades. The focus of the work is on material interface instability and the mixing of two materials. Part 1 of the report discusses analytical and computational studies of hydrodynamic instabilities and turbulent mixing. The EGAK codes are described and results are illustrated for several types of unstable flow. Semiempirical turbulence transport equations are derived for the mixing of two materials, and their capabilities are illustrated for several examples. Part 2 discusses the experimental studies that have been performed to investigate instabilities and turbulent mixing. Shock-tube and jelly techniques are described in considerable detail. Results are presented for many circumstances and configurations.

  19. Rayleigh-Taylor Instability within Sediment Layers Due to Gas Retention: Preliminary Theory and Experiments

    SciTech Connect (OSTI)

    Gauglitz, Phillip A.; Wells, Beric E.; Buchmiller, William C.; Rassat, Scot D.

    2013-03-21

    In Hanford underground waste storage tanks, a typical waste configuration is settled beds of waste particles beneath liquid layers. The settled beds are typically composed of layers, and these layers can have different physical and chemical properties. One postulated configuration within the settled bed is a less-dense layer beneath a more-dense layer. The different densities can be a result of different gas retention in the layers or different degrees of settling and compaction in the layers. This configuration can experience a Rayleigh-Taylor (RT) instability where the less dense lower layer rises into the upper layer. Previous studies of gas retention and release have not considered potential buoyant motion within a settle bed of solids. The purpose of this report is to provide a review of RT instabilities, discuss predictions of RT behavior for sediment layers, and summarize preliminary experimental observations of RT instabilities in simulant experiments.

  20. The effect of degeneracy parameter on Weibel instability in dense plasma

    SciTech Connect (OSTI)

    Mahdavi, M.; Khodadadi Azadboni, F.; Young Researchers Club, Sari Branch, Islamic Azad University, P.O. Box 48161-194 Sari

    2013-12-15

    In this paper, the role of degeneracy parameter, in both directions parallel and perpendicular with propagation direction of the laser beam in plasma, on the growth rate of Weibel instability, is studied. Calculations show that with the temperature anisotropy, ? = T{sub ?}/T{sub ?} = 0.2 and a 0.75 times reduction of the degeneracy parameter, the increased rate of the the Weibel instability growth rate is 72%. The degeneracy required for minimal growth rate in interaction laser plasma with a density of 1.2 10{sup 32}m{sup ?3}, is larger than 3. The reduction of temperature and the degeneracy parameter of plasma in parallel direction will also increase growth rate about 30% more than incrossing degeneracy parameter in transverse direction. With the minimum pressure costs of cold compression, subsequent degeneracy parameters, and the minimum value of electron quiver energy, we can expect growth rate of Weibel instability order 0.01.

  1. The effect of density gradient on the growth rate of relativistic Weibel instability

    SciTech Connect (OSTI)

    Mahdavi, M.; Khodadadi Azadboni, F.

    2014-02-15

    In this paper, the effect of density gradient on the Weibel instability growth rate is investigated. The density perturbations in the near corona fuel, where temperature anisotropy, ?, is larger than the critical temperature anisotropy, ?{sub c}, (??>??{sub c}), enhances the growth rate of Weibel instability due to the sidebands coupled with the electron oscillatory velocity. But for ???2. The analysis shows that relativistic effects and density gradient tend to stabilize the Weibel instability. The growth rate can be reduced by 88% by reducing ? by a factor of 100 and increasing relativistic parameter by a factor of 3.

  2. Marginal instability threshold condition of the aperiodic ordinary mode in equal-mass plasmas

    SciTech Connect (OSTI)

    Vafin, S.; Schlickeiser, R.; Yoon, P. H.

    2014-10-15

    The purely growing ordinary (O) mode instability for counter-streaming bi-Maxwellian plasma particle distribution functions has recently received renewed attention due to its importance for the solar wind plasma. Here, the analytical marginal instability condition is derived for magnetized plasmas consisting of equal-mass charged particles, distributed in counter-streams with equal temperatures. The equal-mass composition assumption enormously facilitates the theoretical analysis due to the equality of the values of the electron and positron (positive and negative ion) plasma and gyrofrequencies. The existence of a new instability domain of the O-mode at small plasma beta values is confirmed, when the parallel counter-stream free energy exceeds the perpendicular bi-Maxwellian free energy.

  3. Catastrophe versus instability for the eruption of a toroidal solar magnetic flux rope

    SciTech Connect (OSTI)

    Kliem, B.; Lin, J.; Forbes, T. G.; Priest, E. R.; Trk, T.

    2014-07-01

    The onset of a solar eruption is formulated here as either a magnetic catastrophe or as an instability. Both start with the same equation of force balance governing the underlying equilibria. Using a toroidal flux rope in an external bipolar or quadrupolar field as a model for the current-carrying flux, we demonstrate the occurrence of a fold catastrophe by loss of equilibrium for several representative evolutionary sequences in the stable domain of parameter space. We verify that this catastrophe and the torus instability occur at the same point; they are thus equivalent descriptions for the onset condition of solar eruptions.

  4. Parametric instability of plasmas produced by linearly polarized microwave pulsed fields

    SciTech Connect (OSTI)

    Shokri, B.; Ghorbanalilu, M.

    2005-04-15

    After analyzing the interaction of an intense linearly polarized microwave, field weaker than atomic field, with a dilute gas, the production of a plasma is studied. It is shown that the electron distribution function obtained is nonequilibrium and anisotropic. By considering the interaction of the high-frequency electric field with the produced plasma the dispersion relation of oscillations in the produced plasma is obtained. The parametric instability is studied for the produced plasma when instability frequency is higher than ion plasma frequency. Calculations show that the harmonic generation takes place in the produced plasma.

  5. Suppression of n=1 Tilt Instability by Magnetic Shaping Coils in Rotamak Plasmas

    SciTech Connect (OSTI)

    Yang, X.; Petrov, Y.; Huang, T. S.

    2009-06-26

    Measurements from the array of Mirnov magnetic coils provide the first evidence for n=1 tilt and radial shift instabilities in a 40 ms field-reversed configuration (FRC) driven by rotating magnetic field. External plasma-shaping magnetic coils are utilized to suppress the n=1 instability modes. It is demonstrated that by energizing the middle shaping coil with 250-500 A current, the tilt mode is completely suppressed when a doublet FRC with an internal figure-of-eight separatrix is formed.

  6. Laser parametric instability experiments of a 3ω, 15 kJ, 6-ns laser

    Office of Scientific and Technical Information (OSTI)

    pulse in gas-filled hohlraums at the Ligne d'Intégration Laser facility (Journal Article) | SciTech Connect Laser parametric instability experiments of a 3ω, 15 kJ, 6-ns laser pulse in gas-filled hohlraums at the Ligne d'Intégration Laser facility Citation Details In-Document Search Title: Laser parametric instability experiments of a 3ω, 15 kJ, 6-ns laser pulse in gas-filled hohlraums at the Ligne d'Intégration Laser facility Experimental investigation of stimulated Raman (SRS) and

  7. Role of phase instabilities in the early response of bulk fused silica

    Office of Scientific and Technical Information (OSTI)

    during laser-induced breakdown (Journal Article) | SciTech Connect Role of phase instabilities in the early response of bulk fused silica during laser-induced breakdown Citation Details In-Document Search Title: Role of phase instabilities in the early response of bulk fused silica during laser-induced breakdown Authors: DeMange, P. ; Negres, R. A. ; Raman, R. N. ; Colvin, J. D. ; Demos, S. G. Publication Date: 2011-08-17 OSTI Identifier: 1100571 Type: Publisher's Accepted Manuscript Journal

  8. The role of phase instabilities in the early material response during

    Office of Scientific and Technical Information (OSTI)

    laser-induced breakdown in bulk fused silica (Journal Article) | SciTech Connect role of phase instabilities in the early material response during laser-induced breakdown in bulk fused silica Citation Details In-Document Search Title: The role of phase instabilities in the early material response during laser-induced breakdown in bulk fused silica Authors: Demange, P ; Negres, R A ; Raman, R N ; Colvin, J D ; Demos, S G Publication Date: 2011-05-24 OSTI Identifier: 1122206 Report Number(s):

  9. Integrated Microbial Genomes (IMG) System from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov. [Abstract from The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions; Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova and Nikos C. Kyrpides; Nucleic Acids Research, 2008, Vol. 36. (Database Issue) See also the companion system, Integrated Microbial Genomes with Microbiome Samples.

  10. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    SciTech Connect (OSTI)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  11. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping errormore » rates low, as well as offering unique data visualization options.« less

  12. Genomic Sequence or Signature Tags (GSTs) from the Genome Group at Brookhaven National Laboratory (BNL)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; Van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K.

    Genomic Signature Tags (GSTs) are the products of a method we have developed for identifying and quantitatively analyzing genomic DNAs. The DNA is initially fragmented with a type II restriction enzyme. An oligonucleotide adaptor containing a recognition site for MmeI, a type IIS restriction enzyme, is then used to release 21-bp tags from fixed positions in the DNA relative to the sites recognized by the fragmenting enzyme. These tags are PCR-amplified, purified, concatenated and then cloned and sequenced. The tag sequences and abundances are used to create a high resolution GST sequence profile of the genomic DNA. [Quoted from Genomic Signature Tags (GSTs): A System for Profiling Genomic DNA, Dunn, John J.; McCorkle, Sean R.; Praissman, Laura A.; Hind, Geoffrey; Van der Lelie, Daniel; Bahou, Wadie F.; Gnatenko, Dmitri V.; Krause, Maureen K., Revised 9/13/2002

  13. Multi-dimensional instability of obliquely propagating ion acoustic solitary waves in electron-positron-ion superthermal magnetoplasmas

    SciTech Connect (OSTI)

    EL-Shamy, E. F.

    2014-08-15

    The solitary structures of multidimensional ion-acoustic solitary waves (IASWs) have been considered in magnetoplasmas consisting of electron-positron-ion with high-energy (superthermal) electrons and positrons are investigated. Using a reductive perturbation method, a nonlinear Zakharov-Kuznetsov equation is derived. The multi-dimensional instability of obliquely propagating (with respect to the external magnetic field) IASWs has been studied by the small-k (long wavelength plane wave) expansion perturbation method. The instability condition and the growth rate of the instability have been derived. It is shown that the instability criterion and their growth rate depend on the parameter measuring the superthermality, the ion gyrofrequency, the unperturbed positrons-to-ions density ratio, the direction cosine, and the ion-to-electron temperature ratio. Clearly, the study of our model under consideration is helpful for explaining the propagation and the instability of IASWs in space observations of magnetoplasmas with superthermal electrons and positrons.

  14. To Know Ourselves: The U.S. Department of Energy and The Human Genome Project

    DOE R&D Accomplishments [OSTI]

    1996-07-01

    The Genome Project and its various aspects: why the DOE?; introducing the human genome; exploring the genomic landscape; beyond biology; and ethical, legal, and social implications.

  15. VISTA - computational tools for comparative genomics

    SciTech Connect (OSTI)

    Frazer, Kelly A.; Pachter, Lior; Poliakov, Alexander; Rubin,Edward M.; Dubchak, Inna

    2004-01-01

    Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/VISTA/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, submit their own sequences of interest to several VISTA servers for various types of comparative analysis, and obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kilobase (kb) interval on human chromosome 5 that encodes for the kinesin family member3A (KIF3A) protein.

  16. Onset of fast reconnection in Hall magnetohydrodynamics mediated by the plasmoid instability

    SciTech Connect (OSTI)

    Huang Yimin; Bhattacharjee, A.; Sullivan, Brian P.

    2011-07-15

    The role of a super-Alfvenic plasmoid instability in the onset of fast reconnection is studied by means of the largest Hall magnetohydrodynamics simulations to date, with system sizes up to 10{sup 4} ion skin depths (d{sub i}). It is demonstrated that the plasmoid instability can facilitate the onset of rapid Hall reconnection, in a regime where the onset would otherwise be inaccessible because the Sweet-Parker width is significantly above d{sub i}. However, the topology of Hall reconnection is not inevitably a single stable X-point. There exists an intermediate regime where the single X-point topology itself exhibits instability, causing the system to alternate between a single X-point geometry and an extended current sheet with multiple X-points produced by the plasmoid instability. Through a series of simulations with various system sizes relative to d{sub i}, it is shown that system size affects the accessibility of the intermediate regime. The larger the system size is, the easier it is to realize the intermediate regime. Although our Hall magnetohydrodynamics (MHD) model lacks many important physical effects included in fully kinetic models, the fact that a single X-point geometry is not inevitable raises the interesting possibility for the first time that Hall MHD simulations may have the potential to realize reconnection with geometrical features similar to those seen in fully kinetic simulations, namely, extended current sheets and plasmoid formation.

  17. The multi-species Farley-Buneman instability in the solar chromosphere

    SciTech Connect (OSTI)

    Madsen, Chad A.; Dimant, Yakov S.; Oppenheim, Meers M.; Fontenla, Juan M.

    2014-03-10

    Empirical models of the solar chromosphere show intense electron heating immediately above its temperature minimum. Mechanisms such as resistive dissipation and shock waves appear insufficient to account for the persistence and uniformity of this heating as inferred from both UV lines and continuum measurements. This paper further develops the theory of the Farley-Buneman instability (FBI) which could contribute substantially to this heating. It expands upon the single-ion theory presented by Fontenla by developing a multiple-ion-species approach that better models the diverse, metal-dominated ion plasma of the solar chromosphere. This analysis generates a linear dispersion relationship that predicts the critical electron drift velocity needed to trigger the instability. Using careful estimates of collision frequencies and a one-dimensional, semi-empirical model of the chromosphere, this new theory predicts that the instability may be triggered by velocities as low as 4 km s{sup -1}, well below the neutral acoustic speed. In the Earth's ionosphere, the FBI occurs frequently in situations where the instability trigger speed significantly exceeds the neutral acoustic speed. From this, we expect neutral flows rising from the photosphere to have enough energy to easily create electric fields and electron Hall drifts with sufficient amplitude to make the FBI common in the chromosphere. If so, this process will provide a mechanism to convert neutral flow and turbulence energy into electron thermal energy in the quiet Sun.

  18. On the nature of local instabilities in rotating galactic coronae and cool cores of galaxy clusters

    SciTech Connect (OSTI)

    Nipoti, Carlo; Posti, Lorenzo

    2014-09-01

    A long-standing question is whether radiative cooling can lead to local condensation of cold gas in the hot atmospheres of galaxies and galaxy clusters. We address this problem by studying the nature of local instabilities in rotating, stratified, weakly magnetized, optically thin plasmas in the presence of radiative cooling and anisotropic thermal conduction. For both axisymmetric and nonaxisymmetric linear perturbations, we provide general equations which can be applied locally to specific systems to establish whether they are unstable and, in case of instability, to determine the kind of evolution (monotonically growing or overstable) and the growth rates of the unstable modes. We present results for models of rotating plasmas representative of Milky-Way-like galaxy coronae and cool-cores of galaxy clusters. We show that the unstable modes arise from a combination of thermal, magnetothermal, magnetorotational, and heat-flux-driven buoyancy instabilities. Local condensation of cold clouds tends to be hampered in cluster cool cores, while it is possible under certain conditions in rotating galactic coronae. If the magnetic field is sufficiently weak, then the magnetorotational instability is dominant even in these pressure-supported systems.

  19. Kink instability evidenced by analyzing the leg rotation of a filament

    SciTech Connect (OSTI)

    Yan, X. L.; Xue, Z. K.; Ma, L.; Kong, D. F.; Qu, Z. Q.; Liu, J. H.; Li, Z.

    2014-02-20

    Kink instability is a possible mechanism for solar filament eruption. However, it is very difficult to directly measure the twist of the solar filament from observation. In this paper, we measured the twist of a solar filament by analyzing its leg rotation. An inverse S-shaped filament in the active region NOAA 11485 was observed by the Atmospheric Imaging Assembly of the Solar Dynamics Observatory on 2012 May 22. During its eruption, the leg of the filament exhibited a significant rotation motion. The 304 images were used to uncurl the circles, the centers of which are the axis of the filament's leg. The result shows that the leg of the filament rotated up to about 510 (about 2.83?) around the axis of the filament within 23 minutes. The maximal rotation speed reached 100 degrees/minute (about 379.9 km s{sup 1} at radius 18''), which is the fastest rotation speed reported. We also calculated the decay index along the polarity inversion line in this active region and found that the decline of the overlying field with height is not fast enough to trigger the torus instability. According to the kink instability condition, this indicates that the kink instability is the trigger mechanism for the solar filament eruption.

  20. Numerical study of self modulation instability of 1 nC electron bunch at ATF

    SciTech Connect (OSTI)

    Fang Yun; Mori, Warren; Muggli, Patric

    2012-12-21

    The development of self-modulation instability (SMI) is investigated numerically for the 1 nC electron bunch available at Accelerator Test Facility (ATF) of Brookhaven National Laboratory (BNL). Possible experiment based on the simulation results is proposed. All the simulations are performed with the 2D-cylindrically symmetric particle-in-cell code.

  1. Physical mapping of complex genomes

    DOE Patents [OSTI]

    Evans, G.A.

    1993-06-15

    A method for the simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts in the pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert in the common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed.

  2. Physical mapping of complex genomes

    DOE Patents [OSTI]

    Evans, Glen A. (Encinitas, CA)

    1993-01-01

    Method for simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts int he pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert int he common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed. In other preferred embodiments, the cosmid clones are arranged in a three dimensional matrix, pooled and compared in threes according to intersecting planes of the three dimensional matrix. Arrangements corresponding to geometries of higher dimensions may also be prepared and used to simultaneously identify overlapping clones in highly complex libraries with relatively few hybridization reactions.

  3. Sequencing and comparing whole mitochondrial genomes ofanimals

    SciTech Connect (OSTI)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  4. Genomic Evolution of the Ascomycete Yeasts

    SciTech Connect (OSTI)

    Riley, Robert; Haridas, Sajeet; Salamov, Asaf; Boundy-Mills, Kyria; Goker, Markus; Hittinger, Chris; Klenk, Hans-Peter; Lopes, Mariana; Meir-Kolthoff, Jan P.; Rokas, Antonis; Rosa, Carlos; Scheuner, Carmen; Soares, Marco; Stielow, Benjamin; Wisecaver, Jennifer H.; Wolfe, Ken; Blackwell, Meredith; Kurtzman, Cletus; Grigoriev, Igor; Jeffries, Thomas

    2015-03-16

    Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and a tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.

  5. Justice and the human genome project

    SciTech Connect (OSTI)

    Murphy, T.F.; Lappe, M.A.

    1995-04-01

    This book is a collection of nine essays originally presented at a conference entitled {open_quotes}Justice and the Human Genome{close_quotes} held in Chicago in late 1991. The goal of the articles in this collection is to explore questions of justice raised by developments in genomic research and by applications of genetic knowledge and technology. The Human Genome Project (HGP) is used as a starting point for exploring these questions, but, as Marc Lappe recognizes, the database generated by HGP research will have implications far beyond the medical applications frequently used to justify this research effort. Thus, the book`s contributors consider questions of justice in relation to screening and testing for various predispositions, conditions, and diseases and gene therapy but also examine testing for other characteristics, forensic uses of genetic information, issues associated with DNA banks, and (hypothetical) genetic enhancement possibilities.

  6. Enabling Graph Appliance for Genome Assembly

    SciTech Connect (OSTI)

    Singh, Rina; Graves, Jeffrey A; Lee, Sangkeun; Sukumar, Sreenivas R; Shankar, Mallikarjun

    2015-01-01

    In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to store and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.

  7. Multiple Whole Genome Alignments Without a Reference Organism

    SciTech Connect (OSTI)

    Dubchak, Inna; Poliakov, Alexander; Kislyuk, Andrey; Brudno, Michael

    2009-01-16

    Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.

  8. Genomic Data and Annotation from the SEED

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  9. Genomic Data and Annotation from the SEED

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The projects subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  10. Genome-Facilitated Analyses of Geomicrobial Processes

    SciTech Connect (OSTI)

    Kenneth H. Nealson

    2012-05-02

    This project had the goal(s) of understanding the mechanism(s) of extracellular electron transport (EET) in the microbe Shewanella oneidensis MR-1, and a number of other strains and species in the genus Shewanella. The major accomplishments included sequencing, annotation, and analysis of more than 20 Shewanella genomes. The comparative genomics enabled the beginning of a systems biology approach to this genus. Another major contribution involved the study of gene regulation, primarily in the model organism, MR-1. As part of this work, we took advantage of special facilities at the DOE: e.g., the synchrotron radiation facility at ANL, where we successfully used this system for elemental characterization of single cells in different metabolic states (1). We began work with purified enzymes, and identification of partially purified enzymes, leading to initial characterization of several of the 42 c-type cytochromes from MR-1 (2). As the genome became annotated, we began experiments on transcriptome analysis under different conditions of growth, the first step towards systems biology (3,4). Conductive appendages of Shewanella, called bacterial nanowires were identified and characterized during this work (5, 11, 20,21). For the first time, it was possible to measure the electron transfer rate between single cells and a solid substrate (20), a rate that has been confirmed by several other laboratories. We also showed that MR-1 cells preferentially attach to cells at a given charge, and are not attracted, or even repelled by other charges. The interaction with the charged surfaces begins with a stimulation of motility (called electrokinesis), and eventually leads to attachment and growth. One of the things that genomics allows is the comparative analysis of the various Shewanella strains, which led to several important insights. First, while the genomes predicted that none of the strains looked like they should be able to degrade N-acetyl glucosamine (NAG), the monomer that makes up chitin, virtually all of the strains were in fact capable. This led to the discovery of a great many new genes involved with chitin and NAG metabolism (7). In a similar vein, a detailed study of the sugar utilization pathway revealed a major new insight into the regulation of sugar metabolism in this genus (19). Systems Biology and Comparative Genomics of the shewanellae: Several publications were put together describing the use of comparative genomics for analyses of the group Shewanella, and these were a logical culmination of our genomic-driven research (10,15,18). Eight graduate students received their Ph.D. degrees doing part of the work described here, and four postdoctoral fellows were supported. In addition, approximately 20 undergraduates took part in projects during the grant period.

  11. Characterization of the role of Fhit in maintenance of genomic integrity following low dose radiation, in vivo and in vitro

    SciTech Connect (OSTI)

    Ya Wang

    2010-05-31

    The major goal of this study is to determine the effects of the Fhit pathway on low dose ({le} 0.1 Gy) ionizing radiation (IR)-induced genetic instability. Reduction of Fhit protein expression is observed in most solid tumors particularly in those tumors resulting from exposure to environmental carcinogens. Therefore, characterization of the role of the Fhit-dependent pathway in preventing low dose IR-induced genetic instability will provide useful parameters for evaluating the low dose IR-induced risk of mutagenesis and carcinogenesis. We pursued 3 specific aims to study our hypothesis that the Fhit-dependent pathways maintain genomic integrity through adjusting checkpoint response and repair genes expression following low dose IR. Aim 1: Determine whether Fhit interaction with RPA is necessary for Fhit to affect the cellular response to low dose IR. We combined the approaches of in vitro (GST pull-down and site-directed mutagenesis) and in vivo (observing the co-localization and immunoprecipitation of Fhit and RPA in Fhit knock out mouse cells transfected with mutant Fhit which has lost ability to interact with RPA in vitro). Aim 2: Determine the role of genes whose expression is affected by Fhit in low dose irradiated cells. We analyzed the distinct signature of gene expression in low dose irradiated Fhit-/- cells compared with Fhit+/+ cells by combining microarray, gene transfection and siRNA approaches. Aim 3: Determine the role of Fhit in genetic susceptibility to low dose IR in vivo. We compared the gene mutation frequency and the fragile site stability in the cells isolated from the Fhit+/+ and Fhit-/- mice at 1.5 years following low dose IR. These results determine the role of the Fhit-dependent pathway in maintaining genomic integrity in vitro and in vivo, which provide a basis for choosing surrogate markers in the Fhit-dependent pathway to evaluate low dose IR-induced risk of mutagenesis and carcinogenesis.

  12. Characterization of the role of Fhit in maintenance of genomic integrity following low dose radiation, in vivo and in vitro

    SciTech Connect (OSTI)

    Wang, Ya

    2010-05-14

    The major goal of this study is to determine the effects of the Fhit pathway on low dose (< 0.1 Gy) ionizing radiation (IR)-induced genetic instability. Reduction of Fhit protein expression is observed in most solid tumors particularly in those tumors resulting from exposure to environmental carcinogens. Therefore, characterization of the role of the Fhit-dependent pathway in preventing low dose IR-induced genetic instability will provide useful parameters for evaluating the low dose IR-induced risk of mutagenesis and carcinogenesis. We pursued 3 specific aims to study our hypothesis that the Fhit-dependent pathways maintain genomic integrity through adjusting checkpoint response and repair genes expression following low dose IR. Aim 1: Determine whether Fhit interaction with RPA is necessary for Fhit to affect the cellular response to low dose IR. We combined the approaches of in vitro (GST pull-down and site-directed mutagenesis) and in vivo (observing the co-localization and immunoprecipitation of Fhit and RPA in Fhit knock out mouse cells transfected with mutant Fhit which has lost ability to interact with RPA in vitro). Aim 2: Determine the role of genes whose expression is affected by Fhit in low dose irradiated cells. We analyzed the distinct signature of gene expression in low dose irradiated Fhit-/- cells compared with Fhit+/+ cells by combining microarray, gene transfection and siRNA approaches. Aim 3: Determine the role of Fhit in genetic susceptibility to low dose IR in vivo. We compared the gene mutation frequency and the fragile site stability in the cells isolated from the Fhit+/+ and Fhit-/- mice at 1.5 years following low dose IR. These results determine the role of the Fhit-dependent pathway in maintaining genomic integrity in vitro and in vivo, which provide a basis for choosing surrogate markers in the Fhit-dependent pathway to evaluate low dose IR-induced risk of mutagenesis and carcinogenesis.

  13. Introduction to Using NERSC for the Joint Genome Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NERSC Introduction to Using NERSC for the Joint Genome Institute May 2, 2011 jgi logo sm NERSC Training Event 1:00-5:00 p.m. PDT May 2, 2011 Joint Genome Institute, 2800 Mitchell...

  14. MycoCosm, an Integrated Fungal Genomics Resource (Conference...

    Office of Scientific and Technical Information (OSTI)

    In-Document Search Title: MycoCosm, an Integrated Fungal Genomics Resource MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in...

  15. The Human Genome Initiative of the Department of Energy

    DOE R&D Accomplishments [OSTI]

    1988-01-01

    The structural characterization of genes and elucidation of their encoded functions have become a cornerstone of modern health research, biology and biotechnology. A genome program is an organized effort to locate and identify the functions of all the genes of an organism. Beginning with the DOE-sponsored, 1986 human genome workshop at Santa Fe, the value of broadly organized efforts supporting total genome characterization became a subject of intensive study. There is now national recognition that benefits will rapidly accrue from an effective scientific infrastructure for total genome research. In the US genome research is now receiving dedicated funds. Several other nations are implementing genome programs. Supportive infrastructure is being improved through both national and international cooperation. The Human Genome Initiative of the Department of Energy (DOE) is a focused program of Resource and Technology Development, with objectives of speeding and bringing economies to the national human genome effort. This report relates the origins and progress of the Initiative.

  16. Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)

    SciTech Connect (OSTI)

    Yasawong, Montri; Teshima, Hazuki; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Sikorski, Johannes; Pukall, Rudiger; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. FCTO Projects and the Materials Genome Initiative | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    FCTO Projects and the Materials Genome Initiative FCTO Projects and the Materials Genome Initiative Download presentation slides from the DOE Fuel Cell Technologies Office webinar "Materials Genome Initiative" held on December 2, 2014. PDF icon FCTO Projects and the Materials Genome Initiative Webinar Slides More Documents & Publications Vehicle Technologies Office Merit Review 2015: Lightweight Materials Overview High Througput Combinatorial Techniques in Hydrogen Storage

  18. Next Generation Sequencing at the University of Chicago Genomics Core

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Next Generation Sequencing at the University of Chicago Genomics Core Citation Details In-Document Search Title: Next Generation Sequencing at the University of Chicago Genomics Core The University of Chicago Genomics Core provides University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation sequencing, Sanger sequencing / genotyping and micro-arrays (gene expression, genotyping, and methylation).

  19. Electrolyte Genome Could Be Battery Game-Changer

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Electrolyte Genome Could Be Battery Game-Changer Electrolyte Genome Could Be Battery Game-Changer The Materials Project screens molecules to accelerate electrolyte discovery April 15, 2015 Julie Chao, JHChao@lbl.gov, +1 510 486 6491 Persson Electrolyte Genome 628x465 Berkeley Lab scientist Kristin Persson (right) and her Electrolyte Genome team, Nav Nidhi Rajput and Xiaohui Qu. (Roy Kaltschmidt, Berkeley Lab) A new breakthrough battery-one that has significantly higher energy, lasts longer, and

  20. Global Alignment System for Large Genomic Sequencing

    Energy Science and Technology Software Center (OSTI)

    2002-03-01

    AVID is a global alignment system tailored for the alignment of large genomic sequences up to megabases in length. Features include the possibility of one sequence being in draft form, fast alignment, robustness and accuracy. The method is an anchor based alignment using maximal matches derived from suffix trees.

  1. Comparative Analysis of Genome Sequences with VISTA

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Dubchak, Inna

    VISTA is a comprehensive suite of programs and databases developed by and hosted at the Genomics Division of Lawrence Berkeley National Laboratory. They provide information and tools designed to facilitate comparative analysis of genomic sequences. Users have two ways to interact with the suite of applications at the VISTA portal. They can submit their own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. A key menu option is the Enhancer Browser and Database at http://enhancer.lbl.gov/. The VISTA Enhancer Browser is a central resource for experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates. The results of this enhancer screen are provided through this publicly available website. The browser also features relevant results by external contributors and a large collection of additional genome-wide conserved noncoding elements which are candidate enhancer sequences. The LBL developers invite external groups to submit computational predictions of developmental enhancers. As of 10/19/2009 the database contains information on 1109 in vivo tested elements - 508 elements with enhancer activity.

  2. Rapid genome resequencing of an atoxigenic strain of Aspergillus

    Office of Scientific and Technical Information (OSTI)

    de Barcelona, Bellaterra, Catalonia (Spain) 59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks fungal genomics; gene regulatory networks In...

  3. Genomic Science | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Genomic Science Biological and Environmental Research (BER) BER Home About Research Biological Systems Science Division (BSSD) Genomic Science DOE Bioenergy Research Centers Bioimaging Technology DOE Joint Genome Institute Structural Biology Radiochemistry & Imaging Instrumentation Radiobiology: Low Dose Radiation Research DOE Human Subjects Protection Program Climate and Environmental Sciences Division (CESD) Research Abstracts Searchable Archive of BER Highlights External link Facilities

  4. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Rieseberg, Loren [University of British Columbia

    2013-01-15

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  5. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    FitzGerald, Michael [Broad Institute

    2013-02-12

    Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  6. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    ScienceCinema (OSTI)

    Goldberg, Robert [UCLA

    2013-01-22

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  7. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    SciTech Connect (OSTI)

    Goldberg, Robert [UCLA] [UCLA

    2012-03-21

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  8. Entering the Era of Mega-genomics ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory] [Cold Spring Harbor Laboratory

    2012-03-21

    Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  9. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Rieseberg, Loren [University of British Columbia] [University of British Columbia

    2012-03-21

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  10. Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Bermingham, Eldredge

    2013-03-27

    Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  11. Entering the Era of Mega-genomics ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory

    2013-01-15

    Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  12. Kinetic simulations and reduced modeling of longitudinal sideband instabilities in non-linear electron plasma waves

    SciTech Connect (OSTI)

    Brunner, S. Hausammann, L.; Berger, R. L. Cohen, B. I.; Valeo, E. J.

    2014-10-15

    Kinetic Vlasov simulations of one-dimensional finite amplitude Electron Plasma Waves are performed in a multi-wavelength long system. A systematic study of the most unstable linear sideband mode, in particular its growth rate ? and quasi- wavenumber ?k, is carried out by scanning the amplitude and wavenumber of the initial wave. Simulation results are successfully compared against numerical and analytical solutions to the reduced model by Kruer et al. [Phys. Rev. Lett. 23, 838 (1969)] for the Trapped Particle Instability (TPI). A model recently suggested by Dodin et al. [Phys. Rev. Lett. 110, 215006 (2013)], which in addition to the TPI accounts for the so-called Negative Mass Instability because of a more detailed representation of the trapped particle dynamics, is also studied and compared with simulations.

  13. Kinetic simulations and reduced modeling of longitudinal sideband instabilities in non-linear electron plasma waves

    SciTech Connect (OSTI)

    Brunner, S.; Berger, R. L.; Cohen, B. I.; Hausammann, L.; Valeo, E. J.

    2014-10-01

    Kinetic Vlasov simulations of one-dimensional finite amplitude Electron Plasma Waves are performed in a multi-wavelength long system. A systematic study of the most unstable linear sideband mode, in particular its growth rate ? and quasi- wavenumber ?k, is carried out by scanning the amplitude and wavenumber of the initial wave. Simulation results are successfully compared against numerical and analytical solutions to the reduced model by Kruer et al. [Phys. Rev. Lett. 23, 838 (1969)] for the Trapped Particle Instability (TPI). A model recently suggested by Dodin et al. [Phys. Rev. Lett. 110, 215006 (2013)], which in addition to the TPI accounts for the so-called Negative Mass Instability because of a more detailed representation of the trapped particle dynamics, is also studied and compared with simulations.

  14. A solution to Rayleigh-Taylor instabilities. Bubbles, spikes, and their scalings

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mikaelian, Karnig O.

    2014-05-12

    A fluid that pushes on and accelerates a heavier fluid, small perturbations at their interface grows with time and lead. to turbulent mixing. The same instability, known as the Rayleigh-Taylor instability, operates when a heavy fluid is supported by a lighter fluid in a gravitational field. Moreover, it has a particularly deleterious effect on inertial-confinement-fusion implosions and is known to operate over 18 orders of magnitude in dimension. We propose analytic expressions for the bubble and spike amplitudes and mixing widths in the linear, nonlinear, and turbulent regimes. They cover arbitrary density ratios and accelerations that are constant or changingmore » relatively slowly with time. Here, we discuss their scalings and compare them with simulations and experiments.« less

  15. Recent studies of the electron cloud induced beam instability at the Los Alamos PSR

    SciTech Connect (OSTI)

    Macek, Robert James; McCrady, Rodney C; Rybarcyk, Lawrence J; Zaugg, Thomas J

    2010-10-06

    Recent beam studies have focused on two aspects of the observed e-p instability at the Los Alamos Proton Storage Ring (PSR). Most recently it has been observed that a stable beam with the standard production bunch width (290 ns injected beam bunch width) will become e-p unstable when the bunch width is shortened to 200 ns or less. This was not the case years earlier when the ring RF operated at the exact 72.000 sub harmonic of the Linac bunch frequency. Experimental characteristics and possible explanations of this recent ''short pulse instability phenomenon'' will be presented. Other beam studies have focused on electron cloud generation, trapping and ejection from quadrupoles and are the focus of another talk. (auth)

  16. Simulation of Current Filamentation Instability for an Accelerator Beam in a Capillary Plasma

    SciTech Connect (OSTI)

    Allen, Brian; Seyedi, Ashkan; Muggli, Patric; Martins, Joana; Silva, Luis O.; Huang Chengkun; Mori, Warren

    2010-11-04

    Current Filamentation Instability (CFI) is of central importance for the propagation of relativistic electron beams in plasmas. It could play an important role in the generation of magnetic fields and of radiation in the after-glow of gamma ray bursts as well as in hot electrons energy transport in the fast-igniter inertial confinement fusion concept. Using the particle-in-cell code QuickPIC, simulations of the electron beam at the Brookhaven National Laboratory--Accelerator Test Facility, BNL-ATF, propagating in a cm-long plasma were conducted. Simulation results show that with beam and plasma parameters achievable at the BNL-ATF, the CFI should be observed within 2 cm of plasma. Simulation results are presented for an experiment currently underway at BNL-ATF and possible diagnostics for characterizing the instability are discussed.

  17. An optical beam frequency reference with 10{sup -14} range frequency instability

    SciTech Connect (OSTI)

    McFerran, J. J.; Hartnett, J. G.; Luiten, A. N. [School of Physics, University of Western Australia, 35 Stirling Highway, Crawley, 6009 Western Australia (Australia)

    2009-07-20

    The authors report on a thermal beam optical frequency reference with a fractional frequency instability of 9.2x10{sup -14} at 1 s reducing to 2.0x10{sup -14} at 64 s before slowly rising. The {sup 1}S{sub 0}{r_reversible}{sup 3}P{sub 1} intercombination line in neutral {sup 40}Ca is used as a frequency discriminator. A diode laser at 423 nm probes the ground state population after a Ramsey-Borde sequence of 657 nm light-field interactions on the atoms. The measured fractional frequency instability is an order of magnitude improvement on previously reported thermal beam optical clocks. The photon shot-noise of the read-out produces a limiting square root {lambda}-variance of 7x10{sup -14}/{radical}({tau})

  18. MHD instabilities and their control in high-beta plasmas in KSTAR

    SciTech Connect (OSTI)

    In, Yongkyoon

    2013-02-06

    We established 3 specific tasks as follows: Task 1 - Investigate the MHD activity during the current ramp-up phase with shaped plasmas; Task 2 - Develop a theoretical model that may show the hollowness dependent instability; Task 3 - Explore the beta-limiting instabilities. To address each task, FAR-TECH actively participated in the 2012 KSTAR run-campaign, which helped us make productive progress. Specifically, the shaping dependence of MHD activity during current ramp-up phase was investigated using dedicated run-time in KSTAR (October 4 and 9, 2012), which was also attempted to address the hollowness of temperature (or pressure) profiles. Also, a performance-limiting disruption, which occurred in a relatively high intermediate beta plasma (shot 7110) in KSTAR ({beta}{sub N} ~ 1.7), was studied, and the preliminary analysis shows that the disruption might not be stability-limited but likely density-limited.

  19. Short-wavelength plasma turbulence and temperature anisotropy instabilities: Recent computational progress

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gary, S. Peter

    2015-04-06

    Plasma turbulence consists of an ensemble of enhanced, broadband electromagnetic fluctuations, typically driven by multi-wave interactions which transfer energy in wavevector space via non- linear cascade processes. In addition, temperature anisotropy instabilities in collisionless plasmas are driven by quasi-linear wave–particle interactions which transfer particle kinetic energy to field fluctuation energy; the resulting enhanced fluctuations are typically narrowband in wavevector magnitude and direction. Whatever their sources, short-wavelength fluctuations are those at which charged particle kinetic, that is, velocity-space, properties are important; these are generally wavelengths of the order of or shorter than the ion inertial length or the thermal ion gyroradius.more » The purpose of this review is to summarize and interpret recent computational results concerning short-wavelength plasma turbulence, short-wavelength temperature anisotropy instabilities and relationships between the two phenomena.« less

  20. Photo-instability of CdSe/ZnS quantum dots in poly(methylmethacrylate) film

    SciTech Connect (OSTI)

    Zhang, Hongyi; Liu, Yu; Ye, Xiaoling; Chen, Yonghai

    2013-12-28

    The photo-instability of CdSe/ZnS quantum dots (QDs) has been studied under varied conditions. We discussed the main features of the evolution of photoluminescence (PL) intensity and energy at different laser powers, which showed critical dependences on the environment. The PL red shift in a vacuum showed strong temperature dependence, from which we concluded that the thermal activation energy for trapping states of the charge carriers was about 14.7 meV. Furthermore, the PL spectra showed asymmetric evolution during the laser irradiation, for which two possible explanations were discussed. Those results provided a comprehensive picture for the photo-instability of the colloidal QDs under different conditions.

  1. Method and apparatus for detecting combustion instability in continuous combustion systems

    DOE Patents [OSTI]

    Benson, Kelly J.; Thornton, Jimmy D.; Richards, George A.; Straub, Douglas L.

    2006-08-29

    An apparatus and method to sense the onset of combustion stability is presented. An electrode is positioned in a turbine combustion chamber such that the electrode is exposed to gases in the combustion chamber. A control module applies a voltage potential to the electrode and detects a combustion ionization signal and determines if there is an oscillation in the combustion ionization signal indicative of the occurrence of combustion stability or the onset of combustion instability. A second electrode held in a coplanar but spaced apart manner by an insulating member from the electrode provides a combustion ionization signal to the control module when the first electrode fails. The control module broadcasts a notice if the parameters indicate the combustion process is at the onset of combustion instability or broadcasts an alarm signal if the parameters indicate the combustion process is unstable.

  2. Kinetic theory of the electron bounce instability in two dimensional current sheetsFull electromagnetic treatment

    SciTech Connect (OSTI)

    Tur, A.; Fruit, G.; Louarn, P.

    2014-03-15

    In the general context of understanding the possible destabilization of a current sheet with applications to magnetospheric substorms or solar flares, a kinetic model is proposed for studying the resonant interaction between electromagnetic fluctuations and trapped bouncing electrons in a 2D current sheet. Tur et al. [A. Tur et al., Phys. Plasmas 17, 102905 (2010)] and Fruit et al. [G. Fruit et al., Phys. Plasmas 20, 022113 (2013)] already used this model to investigate the possibilities of electrostatic instabilities. Here, the model is completed for full electromagnetic perturbations. Starting with a modified Harris sheet as equilibrium state, the linearized gyrokinetic Vlasov equation is solved for electromagnetic fluctuations with period of the order of the electron bounce period. The particle motion is restricted to its first Fourier component along the magnetic field and this allows the complete time integration of the non local perturbed distribution functions. The dispersion relation for electromagnetic modes is finally obtained through the quasineutrality condition and the Ampere's law for the current density. It is found that for mildly strechted current, undamped modes oscillate at typical electron bounce frequency with wavelength of the order of the plasma sheet half thickness. As the stretching of the plasma sheet becomes more intense, the frequency of these normal modes decreases and beyond a certain threshold in ??=?B{sub z}/B{sub lobes}, the mode becomes explosive with typical growth rate of a few tens of seconds. The free energy contained in the bouncing motion of the electrons may trigger an electromagnetic instability able to disrupt the cross-tail current in a few seconds. This new instabilityelectromagnetic electron-bounce instabilitymay explain fast and global scale destabilization of current sheets as required to describe substorm phenomena.

  3. PPPL extends system for suppressing instabilities to long-pulse experiments

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    on KSTAR | Princeton Plasma Physics Lab PPPL extends system for suppressing instabilities to long-pulse experiments on KSTAR By John Greenwald March 18, 2014 Tweet Widget Google Plus One Share on Facebook A look into the microwave launcher showing the steering mirrors that guide the beam into the plasma. (Photo by PPPL) A look into the microwave launcher showing the steering mirrors that guide the beam into the plasma. PPPL collaborations have been instrumental in developing a system to

  4. PPPL extends system for suppressing instabilities to long-pulse experiments

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    on KSTAR | Princeton Plasma Physics Lab PPPL extends system for suppressing instabilities to long-pulse experiments on KSTAR By John Greenwald March 19, 2014 Tweet Widget Google Plus One Share on Facebook A look into the microwave launcher showing the steering mirrors that guide the beam into the plasma. (Photo by PPPL) A look into the microwave launcher showing the steering mirrors that guide the beam into the plasma. PPPL collaborations have been instrumental in developing a system to

  5. Computational study of the shock driven instability of a multiphase particle-gas system

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    None, None

    2016-02-01

    This paper considers the interaction of a shock wave with a multiphase particle-gas system which creates an instability somewhat similar to the Richtmyer-Meshkov instability but with a larger parameter space. Because this parameter space is large, we only present an introductory survey of the effects of many of these parameters. We highlight the effects of particle-gas coupling, incident shock strength, particle size, effective system density differences, and multiple particle relaxation time effects. We focus on dilute flows with mass loading up to 40% and do not attempt to cover all parametric combinations. Instead, we vary one parameter at a timemore » leaving additional parametric combinations for future work. The simulations are run with the Ares code, developed at Lawrence Livermore National Laboratory, which uses a multiphase particulate transport method to model two-way momentum and energy coupling. A brief validation of these models is presented and coupling effects are explored. It is shown that even for small particles, on the order of 1μm, multi-phase coupling effects are important and diminish the circulation deposition on the interface by up to 25%. These coupling effects are shown to create large temperature deviations from the dusty gas approximation, up to 20% greater, especially at higher shock strengths. It is also found that for a multiphase instability, the vortex sheet deposited at the interface separates into two sheets. In conclusion, depending on the particle and particle-gas Atwood numbers, the instability may be suppressed or enhanced by the interactions of these two vortex sheets.« less

  6. Mitigation of thermoacoustic instability utilizing steady air injection near the flame anchoring zone

    SciTech Connect (OSTI)

    Murat Altay, H.; Hudgins, Duane E.; Speth, Raymond L.; Annaswamy, Anuradha M.; Ghoniem, Ahmed F.

    2010-04-15

    The objective of this work is to investigate the effectiveness of steady air injection near the flame anchoring zone in suppressing thermoacoustic instabilities driven by flame-vortex interaction mechanism. We perform a systematic experimental study which involves using two different configurations of air injection in an atmospheric pressure backward-facing step combustor. The first configuration utilizes a row of micro-diameter holes allowing for air injection in the cross-stream direction just upstream of the step. The second configuration utilizes an array of micro-diameter holes located on the face of the step, allowing for air injection in the streamwise direction. The effects of each of these configurations are analyzed to determine which one is more effective in suppressing thermoacoustic instabilities at different operating conditions. The tests are conducted while varying the equivalence ratio and the inlet temperature. The secondary air temperature is always the same as the inlet temperature. We used pure propane or propane/hydrogen mixtures as fuels. Combustion dynamics are explored through simultaneous pressure and heat release-rate measurements, and high-speed video images. When the equivalence ratio of the reactant mixture is high, it causes the flame to flashback towards the inlet channel. When air is injected in the cross-stream direction, the flame anchors slightly upstream of the step, which suppresses the instability. When air is injected in the streamwise direction near the edge of step, thermoacoustic instability could be eliminated at an optimum secondary air flow rate, which depends on the operating conditions. When effective, the streamwise air injection prevents the shedding of an unsteady vortex, thus eliminating the flame-vortex interaction mechanism and resulting in a compact, stable flame to form near the step. (author)

  7. Radiation-induced mechanical property changes in filled rubber...

    Office of Scientific and Technical Information (OSTI)

    Authors: Maiti, A ; Weisgraber, T H ; Gee, R H ; Small, W ; Alviso, C T ; Chinn, S C ; Maxwell, R S Publication Date: 2011-04-15 OSTI Identifier: 1227007 Report Number(s):...

  8. Radiation-induced decomposition of PETN and TATB under pressure

    SciTech Connect (OSTI)

    Giefers, Hubertus; Pravica, Michael; Liermann, Hanns-Peter; Yang, Wenge

    2008-10-02

    We have investigated decomposition of PETN and TATB induced by white synchrotron X-ray radiation in a diamond anvil cell at ambient temperature and two pressures, nearly ambient and about 6 GPa. The decomposition rate of TATB decreases significantly when it is pressurized to 5.9 GPa. The measurements were highly reproducible and allowed us to obtain decomposition rates and the order parameters of the reactions.

  9. Effect of MPG on radiation-induced odontogenic tissue metaplasia

    SciTech Connect (OSTI)

    Geist, J.R.; Kafrawy, A.H.; Shupe, R.E.

    1988-01-01

    This investigation monitored the effect of 2-mercaptopropionylglycine (MPG) in reducing radiation damage to the tooth-forming tissues. Fifty rats were exposed to x-ray doses of between 3 and 19 Gy directed toward the maxillary incisor germinal centers. Half of the animals were given an injection of MPG before irradiation, while the other rats were injected with saline solution. Administration of MPG did not significantly reduce the frequency of dentinal niche formation relative to the control teeth. The average lengths and percentage depths of the apicoincisal niches were statistically smaller in the groups treated with MPG. Although statistically significant, the mild protective effect of MPG was not clinically important because damage to the irradiated teeth was still extensive.

  10. Radiation-induced mechanical property changes in filled rubber (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect In a recent paper we exposed a filled elastomer to controlled radiation dosages and explored changes in its cross-link density and molecular weight distribution between network junctions [A. Maiti et al., Phys. Rev. E 83, 031802 (2011)]. Here we report mechanical response measurements when the material is exposed to radiation while being under finite nonzero strain. We observe interesting hysteretic behavior and material softening representative of the Mullins

  11. Radiation-induced mechanical property changes in filled rubber...

    Office of Scientific and Technical Information (OSTI)

    Publication Date: 2011-06-15 OSTI Identifier: 21554517 Resource Type: Journal Article Resource Relation: Journal Name: Physical Review. E, Statistical, Nonlinear, and Soft Matter ...

  12. Radiation-induced grafting of sulfonates on polyethylene

    SciTech Connect (OSTI)

    Shkolnik, S.; Behar, D.

    1982-06-01

    Indirect methods for introducing sulfonate groups into polyethylene, using the preirradiation technique, were studied. One of the methods involved graft polymerization of 2,3-epoxypropylacrylate into polyethylene followed by sulfonation of the epoxy ring with bisulfite. The hydroxy sulfonate thus obtained was unstable in an acid or base environment and hydrolyzed at the esteric bond. The second method involved hydrophylization of the polyethylene by forming a pregraft of polyacrylic acid or polyvinyl alcohol, followed by preirradiation grafting with sodium styrene sulfonate or, less successfully, with sodium vinyl sulfonate. The sulfonates thus obtained were resistant to acids and bases. The acid capacity, water absorption, and water permeability of the grafted films were determined.

  13. Dynamic instabilities in spark-ignited combustion engines with high exhaust gas recirculation

    SciTech Connect (OSTI)

    Daw, C Stuart; FINNEY, Charles E A

    2011-01-01

    We propose a cycle-resolved dynamic model for combustion instabilities in spark-ignition engines operating with high levels of exhaust gas recirculation (EGR). High EGR is important for increasing fuel efficiency and implementing advanced low-emission combustion modes such as homogenous charge compression ignition (HCCI). We account for the complex combustion response to cycle-to-cycle feedback by utilizing a global probability distribution that describes the pre-spark state of in-cylinder fuel mixing. The proposed model does a good job of simulating combustion instabilities observed in both lean-fueling engine experiments and in experiments where nitrogen dilution is used to simulate some of the combustion inhibition of EGR. When used to simulate high internal EGR operation, the model exhibits a range of global bifurcations and chaos that appear to be very robust. We use the model to show that it should be possible to reduce high EGR combustion instabilities by switching from internal to external EGR. We also explain why it might be helpful to deliberately stratify the fuel in the pre-spark gas mixture. It might be possible to extend the simple approach used in this model to other chemical reaction systems with spatial inhomogeneity.

  14. Impact of Fuel Interchangeability on dynamic Instabilities in Gas Turbine Engines

    SciTech Connect (OSTI)

    Ferguson, D.H.; Straub, D.L.; Richards, G.A.; Robey, E.H.

    2007-03-01

    Modern, low NOx emitting gas turbines typically utilize lean pre-mixed (LPM) combustion as a means of achieving target emissions goals. As stable combustion in LPM systems is somewhat intolerant to changes in operating conditions, precise engine tuning on a prescribed range of fuel properties is commonly performed to avoid dynamic instabilities. This has raised concerns regarding the use of imported liquefied natural gas (LNG) and natural gas liquids (NGL’s) to offset a reduction in the domestic natural gas supply, which when introduced into the pipeline could alter the fuel BTU content and subsequently exacerbate problems such as combustion instabilities. The intent of this study is to investigate the sensitivity of dynamically unstable test rigs to changes in fuel composition and heat content. Fuel Wobbe number was controlled by blending methane and natural gas with various amounts of ethane, propane and nitrogen. Changes in combustion instabilities were observed, in both atmospheric and pressurized test rigs, for fuels containing high concentrations of propane (> 62% by vol). However, pressure oscillations measured while operating on typical “LNG like” fuels did not appear to deviate significantly from natural gas and methane flame responses. Mechanisms thought to produce changes in the dynamic response are discussed.

  15. Hydrodynamic instability growth and mix experiments at the National Ignition Facility

    SciTech Connect (OSTI)

    Smalyuk, V. A.; Barrios, M.; Caggiano, J. A.; Casey, D. T.; Cerjan, C. J.; Clark, D. S.; Edwards, M. J.; Haan, S. W.; Hammel, B. A.; Hamza, A.; Hsing, W. W.; Hurricane, O.; Kroll, J.; Landen, O. L.; Lindl, J. D.; Ma, T.; McNaney, J. M.; Mintz, M.; Parham, T.; Peterson, J. L.; and others

    2014-05-15

    Hydrodynamic instability growth and its effects on implosion performance were studied at the National Ignition Facility [G. H. Miller, E. I. Moses, and C. R. Wuest, Opt. Eng. 443, 2841 (2004)]. Implosion performance and mix have been measured at peak compression using plastic shells filled with tritium gas and containing embedded localized carbon-deuterium diagnostic layers in various locations in the ablator. Neutron yield and ion temperature of the deuterium-tritium fusion reactions were used as a measure of shell-gas mix, while neutron yield of the tritium-tritium fusion reaction was used as a measure of implosion performance. The results have indicated that the low-mode hydrodynamic instabilities due to surface roughness were the primary culprits for yield degradation, with atomic ablator-gas mix playing a secondary role. In addition, spherical shells with pre-imposed 2D modulations were used to measure instability growth in the acceleration phase of the implosions. The capsules were imploded using ignition-relevant laser pulses, and ablation-front modulation growth was measured using x-ray radiography for a shell convergence ratio of ?2. The measured growth was in good agreement with that predicted, thus validating simulations for the fastest growing modulations with mode numbers up to 90 in the acceleration phase. Future experiments will be focused on measurements at higher convergence, higher-mode number modulations, and growth occurring during the deceleration phase.

  16. Robustness of the filamentation instability in arbitrarily oriented magnetic field: Full three dimensional calculation

    SciTech Connect (OSTI)

    Bret, A., E-mail: antoineclaude.bret@uclm.es [ETSI Industriales, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain and Instituto de Investigaciones Energticas y Aplicaciones Industriales, Campus Universitario de Ciudad Real, 13071 Ciudad Real (Spain)

    2014-02-15

    The filamentation (Weibel) instability plays a key role in the formation of collisionless shocks which are thought to produce Gamma-Ray-Bursts and High-Energy-Cosmic-Rays in astrophysical environments. While it has been known for long that a flow-aligned magnetic field can completely quench the instability, it was recently proved in 2D that in the cold regime, such cancelation is possible if and only if the field is perfectly aligned. Here, this result is finally extended to a 3D geometry. Calculations are conducted for symmetric and asymmetric counter-streaming relativistic plasma shells. 2D results are retrieved in 3D: the instability can never be completely canceled for an oblique magnetic field. In addition, the maximum growth-rate is always larger for wave vectors lying in the plan defined by the flow and the oblique field. On the one hand, this bears consequences on the orientation of the generated filaments. On the other hand, it certifies 2D simulations of the problem can be performed without missing the most unstable filamentation modes.

  17. A GSC Global Genome Census (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  18. Ion-temperature-gradient sensitivity of the hydrodynamic instability caused by shear in the magnetic-field-aligned plasma flow

    SciTech Connect (OSTI)

    Mikhailenko, V. V.; Mikhailenko, V. S.; Lee, Hae June; Koepke, M. E.

    2014-07-15

    The cross-magnetic-field (i.e., perpendicular) profile of ion temperature and the perpendicular profile of the magnetic-field-aligned (parallel) plasma flow are sometimes inhomogeneous for space and laboratory plasma. Instability caused either by a gradient in the ion-temperature profile or by shear in the parallel flow has been discussed extensively in the literature. In this paper, (1) hydrodynamic plasma stability is investigated, (2) real and imaginary frequency are quantified over a range of the shear parameter, the normalized wavenumber, and the ratio of density-gradient and ion-temperature-gradient scale lengths, and (3) the role of inverse Landau damping is illustrated for the case of combined ion-temperature gradient and parallel-flow shear. We find that increasing the ion-temperature gradient reduces the instability threshold for the hydrodynamic parallel-flow shear instability, also known as the parallel Kelvin-Helmholtz instability or the D'Angelo instability. We also find that a kinetic instability arises from the coupled, reinforcing action of both free-energy sources. For the case of comparable electron and ion temperature, we illustrate analytically the transition of the D'Angelo instability to the kinetic instability as (a) the shear parameter, (b) the normalized wavenumber, and (c) the ratio of density-gradient and ion-temperature-gradient scale lengths are varied and we attribute the changes in stability to changes in the amount of inverse ion Landau damping. We show that near a normalized wavenumber k{sub ?}?{sub i} of order unity (i) the real and imaginary values of frequency become comparable and (ii) the imaginary frequency, i.e., the growth rate, peaks.

  19. PARTICLE-IN-CELL SIMULATIONS OF CONTINUOUSLY DRIVEN MIRROR AND ION CYCLOTRON INSTABILITIES IN HIGH BETA ASTROPHYSICAL AND HELIOSPHERIC PLASMAS

    SciTech Connect (OSTI)

    Riquelme, Mario A.; Quataert, Eliot; Verscharen, Daniel E-mail: eliot@berkeley.edu

    2015-02-10

    We use particle-in-cell simulations to study the nonlinear evolution of ion velocity space instabilities in an idealized problem in which a background velocity shear continuously amplifies the magnetic field. We simulate the astrophysically relevant regime where the shear timescale is long compared to the ion cyclotron period, and the plasma beta is ? ? 1-100. The background field amplification in our calculation is meant to mimic processes such as turbulent fluctuations or MHD-scale instabilities. The field amplification continuously drives a pressure anisotropy with p > p {sub ?} and the plasma becomes unstable to the mirror and ion cyclotron instabilities. In all cases, the nonlinear state is dominated by the mirror instability, not the ion cyclotron instability, and the plasma pressure anisotropy saturates near the threshold for the linear mirror instability. The magnetic field fluctuations initially undergo exponential growth but saturate in a secular phase in which the fluctuations grow on the same timescale as the background magnetic field (with ?B ? 0.3 (B) in the secular phase). At early times, the ion magnetic moment is well-conserved but once the fluctuation amplitudes exceed ?B ? 0.1 (B), the magnetic moment is no longer conserved but instead changes on a timescale comparable to that of the mean magnetic field. We discuss the implications of our results for low-collisionality astrophysical plasmas, including the near-Earth solar wind and low-luminosity accretion disks around black holes.

  20. Comparative genomics of the lactic acid bacteria

    SciTech Connect (OSTI)

    Makarova, K.; Slesarev, A.; Wolf, Y.; Sorokin, A.; Mirkin, B.; Koonin, E.; Pavlov, A.; Pavlova, N.; Karamychev, V.; Polouchine, N.; Shakhova, V.; Grigoriev, I.; Lou, Y.; Rokhsar, D.; Lucas, S.; Huang, K.; Goodstein, D. M.; Hawkins, T.; Plengvidhya, V.; Welker, D.; Hughes, J.; Goh, Y.; Benson, A.; Baldwin, K.; Lee, J.-H.; Diaz-Muniz, I.; Dosti, B.; Smeianov, V,; Wechter, W.; Barabote, R.; Lorca, G.; Altermann, E.; Barrangou, R.; Ganesan, B.; Xie, Y.; Rawsthorne, H.; Tamir, D.; Parker, C.; Breidt, F.; Broadbent, J.; Hutkins, R.; O'Sullivan, D.; Steele, J.; Unlu, G.; Saier, M.; Klaenhammer, T.; Richardson, P.; Kozyavkin, S.; Weimer, B.; Mills, D.

    2006-06-01

    Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

  1. Fueling the Future with Fungal Genomics

    SciTech Connect (OSTI)

    Grigoriev, Igor V.; Cullen, Daniel; Hibbett, David; Goodwin, Stephen B.; Jeffries, Thomas W.; Kubicek, Christian P.; Kuske, Cheryl; Magnuson, Jon K.; Martin, Francis; Spatafora, Joey; Tsang, Adrian; Baker, Scott E.

    2011-04-29

    Fungi play important roles across the range of current and future biofuel production processes. From crop/feedstock health to plant biomass saccharification, enzyme production to bioprocesses for producing ethanol, higher alcohols or future hydrocarbon biofuels, fungi are involved. Research and development are underway to understand the underlying biological processes and improve them to make bioenergy production efficient on an industrial scale. Genomics is the foundation of the systems biology approach that is being used to accelerate the research and development efforts across the spectrum of topic areas that impact biofuels production. In this review, we discuss past, current and future advances made possible by genomic analyses of the fungi that impact plant/feedstock health, degradation of lignocellulosic biomass and fermentation of sugars to ethanol, hydrocarbon biofuels and renewable chemicals.

  2. Implications of the Human Genome Project

    SciTech Connect (OSTI)

    Kitcher, P.

    1998-11-01

    The Human Genome Project (HGP), launched in 1991, aims to map and sequence the human genome by 2006. During the fifteen-year life of the project, it is projected that $3 billion in federal funds will be allocated to it. The ultimate aims of spending this money are to analyze the structure of human DNA, to identify all human genes, to recognize the functions of those genes, and to prepare for the biology and medicine of the twenty-first century. The following summary examines some of the implications of the program, concentrating on its scientific import and on the ethical and social problems that it raises. Its aim is to expose principles that might be used in applying the information which the HGP will generate. There is no attempt here to translate the principles into detailed proposals for legislation. Arguments and discussion can be found in the full report, but, like this summary, that report does not contain any legislative proposals.

  3. Genome Science and Personalized Cancer Treatment

    SciTech Connect (OSTI)

    Gray, Joe

    2009-08-07

    August 4, 2009 Berkeley Lab lecture: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks particularly with regard to breast cancer.

  4. Genome Science and Personalized Cancer Treatment

    SciTech Connect (OSTI)

    Gray, Joe

    2009-08-04

    Summer Lecture Series 2009: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks particularly with regard to breast cancer.

  5. Integrative Genomics and Computational Systems Medicine

    SciTech Connect (OSTI)

    McDermott, Jason E.; Huang, Yufei; Zhang, Bing; Xu, Hua; Zhao, Zhongming

    2014-01-01

    The exponential growth in generation of large amounts of genomic data from biological samples has driven the emerging field of systems medicine. This field is promising because it improves our understanding of disease processes at the systems level. However, the field is still in its young stage. There exists a great need for novel computational methods and approaches to effectively utilize and integrate various omics data.

  6. Genome Science and Personalized Cancer Treatment

    ScienceCinema (OSTI)

    Gray, Joe

    2010-01-08

    August 4, 2009 Berkeley Lab lecture: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks ? particularly with regard to breast cancer.

  7. On some operations suggested by genome evolution

    SciTech Connect (OSTI)

    Dassow, J.; Mitrana, V.

    1996-12-31

    Three operations involved in the genome evolution namely, inversion, transposition and duplication, are considered as operations on strings and languages. We show that, for any pair of these operations, there is a language family which is closed under one of the operations and not closed under the second one; however, under some mild conditions the closure of a language family under one of the operations implies that it also closed with respect to another one. 15 refs.

  8. Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; Hauser, Loren John; Wanchai, Visanu; Land, Miriam L; Timm, Collin M; Lu, Tse-Yuan S; Schadt, Christopher Warren; Doktycz, Mitchel John; et al

    2016-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The speciesmore » P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but this needs to be experimentally characterized with ecologically relevant phenotype properties. This study justifies the need to sequence multiple isolates, especially from P. fluorescens group in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.« less

  9. Origins of the Human Genome Project

    DOE R&D Accomplishments [OSTI]

    Cook-Deegan, Robert (Affiliation: Institute of Medicine, National Academy of Sciences)

    1993-07-01

    The human genome project was borne of technology, grew into a science bureaucracy in the United States and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

  10. Comparative genome analysis of Bacillus cereus group genomes withBacillus subtilis

    SciTech Connect (OSTI)

    Anderson, Iain; Sorokin, Alexei; Kapatral, Vinayak; Reznik, Gary; Bhattacharya, Anamitra; Mikhailova, Natalia; Burd, Henry; Joukov, Victor; Kaznadzey, Denis; Walunas, Theresa; D'Souza, Mark; Larsen, Niels; Pusch,Gordon; Liolios, Konstantinos; Grechkin, Yuri; Lapidus, Alla; Goltsman,Eugene; Chu, Lien; Fonstein, Michael; Ehrlich, S. Dusko; Overbeek, Ross; Kyrpides, Nikos; Ivanova, Natalia

    2005-09-14

    Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1,381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

  11. Insights from twenty years of bacterial genome sequencing

    SciTech Connect (OSTI)

    Land, Miriam L; Hauser, Loren John; Jun, Se Ran; Nookaew, Intawat; Leuze, Michael Rex; Ahn, Tae-Hyuk; Karpinets, Tatiana V; Lund, Ole; Kora, Guruprasad H; Wassenaar, Trudy; Poudel, Suresh; Ussery, David W

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

  12. Insights into bilaterian evolution from three spiralian genomes

    SciTech Connect (OSTI)

    Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin; Edsinger-Gonzales, Eric; Havlak, Paul; Hellsten, Uffe; Kuo, Dian-Han; Larsson, Tomas; Lv, Jie; Arendt, Detlev; Savage, Robert; Osoegawa, Kazutoyo; de Jong, Pieter; Grimwood, Jane; Chapman, Jarrod A.; Shapiro, Harris; Otillar, Robert P.; Terry, Astrid Y.; Boore, Jeffrey L.; Grigoriev, Igor V.; Lindberg, David R.; Seaver, Elaine C.; Weisblat, David A.; Putnam, Nicholas H.; Rokhsar, Daniel S.; Aerts, Andrea

    2012-01-07

    Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

  13. The amphioxus genome and the evolution of the chordate karyotype

    SciTech Connect (OSTI)

    Putnam, Nicholas H.; Butts, Thomas; Ferrier, David E.K.; Furlong, Rebecca F.; Hellsten, Uffe; Kawashima, Takeshi; Robinson-Rechavi, Marc; Shoguchi, Eiichi; Terry, Astrid; Yu, Jr-Kai; Benito-Gutierrez, Elia; Dubchak, Inna; Garcia-Fernandez, Jordi; Gibson-Brown, Jeremy J.; Grigoriev, Igor V.; Horton, Amy C.; de Jong, Pieter J.; Jurka, Jerzy; Kapitonov, Vladimir; Kohara, Yuji; Kuroki, Yoko; Lindquist, Erika; Lucas, Susan; Osoegawa, Kazutoyo; Pennacchio, Len A.; Salamov, Asaf A.; Satou, Yutaka; Sauka-Spengler, Tatjana; Schmutz [, Jeremy; Shin-I, Tadasu; Toyoda, Atsushi; Bronner-Fraser, Marianne; Fujiyama, Asao; Holland, Linda Z.; Holland, Peter W. H.; Satoh, Nori; Rokhsar, Daniel S.

    2008-04-01

    Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage with a fossil record dating back to the Cambrian. We describe the structure and gene content of the highly polymorphic {approx}520 million base pair genome of the Florida lancelet Branchiostoma floridae, and analyze it in the context of chordate evolution. Whole genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets, and vertebrates), and allow reconstruction of not only the gene complement of the last common chordate ancestor, but also a partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

  14. Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Hodges, Scott [University of California, Santa Barbara

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  15. Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Hodges, Scott [University of California, Santa Barbara] [University of California, Santa Barbara

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  16. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Shuster, Stephen [Penn State University] [Penn State University

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  17. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Shuster, Stephen [Penn State University

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  18. The genome of black cottonwood, Populus trichocarpa (Torr.&Gray)

    SciTech Connect (OSTI)

    Tuskan, G.A.; DiFazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev,I.; Hellsten, U.; Putnam, N.; Ralph, S.; Rombauts, S.; Salamov, A.; Schein, J.; Sterck, L.; Aerts, A.; Bhalerao, R.R.; Bhalerao, R.P.; Blaudez, D.; Boerjan, W.; Brun, A.; Brunner, A.; Busov, V.; Campbell, M.; Carlson, J.; Chalot, M.; Chapman, J.; Chen, G.-L.; Cooper, D.; Coutinho,P.M.; Couturier, J.; Covert, S.; Cronk, Q.; Cunningham, R.; Davis, J.; Degroeve, S.; Dejardin, A.; dePamphillis, C.; Detter, J.; Dirks, B.; Dubchak, I.; Duplessis, S.; Ehiting, J.; Ellis, B.; Gendler, K.; Goodstein, D.; Gribskov, M.; Grimwood, J.; Groover, A.; Gunter, L.; Hamberger, B.; Heinze, B.; Helariutta, Y.; Henrissat, B.; Holligan, D.; Holt, R.; Huang, W.; Islam-Faridi, N.; Jones, S.; Jones-Rhoades, M.; Jorgensen, R.; Joshi, C.; Kangasjarvi, J.; Karlsson, J.; Kelleher, C.; Kirkpatrick, R.; Kirst, M.; Kohler, A.; Kalluri, U.; Larimer, F.; Leebens-Mack, J.; Leple, J.-C.; Locascio, P.; Lou, Y.; Lucas, S.; Martin,F.; Montanini, B.; Napoli, C.; Nelson, D.R.; Nelson, D.; Nieminen, K.; Nilsson, O.; Peter, G.; Philippe, R.; Pilate, G.; Poliakov, A.; Razumovskaya, J.; Richardson, P.; Rinaldi, C.; Ritland, K.; Rouze, P.; Ryaboy, D.; Schmutz, J.; Schrader, J.; Segerman, B.; Shin, H.; Siddiqui,A.; Sterky, F.; Terry, A.; Tsai, C.; Uberbacher, E.; Unneberg, P.; Vahala, J.; Wall, K.; Wessler, S.; Yang, G.; Yin, T.; Douglas, C.; Marra,M.; Sandberg, G.; Van der Peer, Y.; Rokhsar, D.

    2006-09-01

    We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication and gross chromosomal rearrangement appear to proceed substantially slower in Populus relative to Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average between 1.4-1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.

  19. Rayleigh-Taylor instability at spherical interfaces between viscous fluids: Fluid/vacuum interface

    SciTech Connect (OSTI)

    Terrones, Guillermo; Carrara, Mark D.

    2015-05-01

    For a spherical interface of radius R separating two different homogeneous regions of incompressible viscous fluids under the action of a radially directed acceleration, we perform a linear stability analysis in terms of spherical surface harmonics Y n to derive the dispersion relation. The instability behavior is investigated by computing the growth rates and the most-unstable modes as a function of the spherical harmonic degree n. This general methodology is applicable to the entire parameter space spanned by the Atwood number, the viscosity ratio, and the dimensionless number B = (αRΡ²2/μ²²/³ R (where αR, Ρ2 and μ2 are the local radial acceleration at the interface, and the density and viscosity of the denser overlying fluid, respectively). While the mathematical formulation here is general, this paper focuses on instability that arises at a spherical viscous fluid/vacuum interface as there is a great deal to be learned from the effects of one-fluid viscosity and sphericity alone. To quantify and understand the effect that curvature and radial accelerationhave on the Rayleigh-Taylor instability, a comparison of the growth rates, under homologous driving conditions, between the planar and spherical interfaces is performed. The derived dispersion relation for the planar interface accounts for an underlying finite fluid region of thickness L and normal acceleration αR. Under certain conditions, the development of the most-unstable modes at a spherical interface can take place via the superposition of two adjacent spherical harmonics Yn and Yn+1. This bimodality in the evolution of disturbances in the linear regime does not have a counterpart in the planar configuration where the most-unstable modes are associated with a unique wave number.

  20. Nonlinear instability of an Oldroyd elasticoviscous magnetic nanofluid saturated in a porous medium

    SciTech Connect (OSTI)

    Moatimid, Galal M.; Alali, Elham M. M. Ali, Hoda S. M.

    2014-09-15

    Through viscoelastic potential theory, a Kelvin-Helmholtz instability of two semi-infinite fluid layers, of Oldroydian viscoelastic magnetic nanofluids (MNF), is investigated. The system is saturated by porous medium through two semi-infinite fluid layers. The Oldroyd B model is utilized to describe the rheological behavior of viscoelastic MNF. The system is influenced by uniform oblique magnetic field that acts at the surface of separation. The model is used for the MNF incorporated the effects of uniform basic streaming and viscoelasticity. Therefore, a mathematical simplification must be considered. A linear stability analysis, based upon the normal modes analysis, is utilized to find out the solutions of the equations of motion. The onset criterion of stability is derived; analytically and graphs have been plotted by giving numerical values to the various parameters. These graphs depict the stability characteristics. Regions of stability and instability are identified and discussed in some depth. Some previous studies are recovered upon appropriate data choices. The stability criterion in case of ignoring the relaxation stress times is also derived. To relax the mathematical manipulation of the nonlinear approach, the linearity of the equations of motion is taken into account in correspondence with the nonlinear boundary conditions. Taylor's theory is adopted to expand the governing nonlinear characteristic equation according to of the multiple time scales technique. This analysis leads to the well-known GinzburgLandau equation, which governs the stability criteria. The stability criteria are achieved theoretically. To simplify the mathematical manipulation, a special case is considered to achieve the numerical estimations. The influence of orientation of the magnetic fields on the stability configuration, in linear as well as nonlinear approaches, makes a dual role for the magnetic field strength in the stability graphs. Stability diagram is plotted for different sets of physical parameters. A new stability as well as instability region, in the parameter space, appears due to the nonlinear effects.

  1. FORMATION OF GIANT PLANETS BY DISK INSTABILITY ON WIDE ORBITS AROUND PROTOSTARS WITH VARIED MASSES

    SciTech Connect (OSTI)

    Boss, Alan P.

    2011-04-10

    Doppler surveys have shown that more massive stars have significantly higher frequencies of giant planets inside {approx}3 AU than lower mass stars, consistent with giant planet formation by core accretion. Direct imaging searches have begun to discover significant numbers of giant planet candidates around stars with masses of {approx}1 M{sub sun} to {approx}2 M{sub sun} at orbital distances of {approx}20 AU to {approx}120 AU. Given the inability of core accretion to form giant planets at such large distances, gravitational instabilities of the gas disk leading to clump formation have been suggested as the more likely formation mechanism. Here, we present five new models of the evolution of disks with inner radii of 20 AU and outer radii of 60 AU, for central protostars with masses of 0.1, 0.5, 1.0, 1.5, and 2.0 M{sub sun}, in order to assess the likelihood of planet formation on wide orbits around stars with varied masses. The disk masses range from 0.028 M{sub sun} to 0.21 M{sub sun}, with initial Toomre Q stability values ranging from 1.1 in the inner disks to {approx}1.6 in the outer disks. These five models show that disk instability is capable of forming clumps on timescales of {approx}10{sup 3} yr that, if they survive for longer times, could form giant planets initially on orbits with semimajor axes of {approx}30 AU to {approx}70 AU and eccentricities of {approx}0 to {approx}0.35, with initial masses of {approx}1 M{sub Jup} to {approx}5 M{sub Jup}, around solar-type stars, with more protoplanets forming as the mass of the protostar (and protoplanetary disk) is increased. In particular, disk instability appears to be a likely formation mechanism for the HR 8799 gas giant planetary system.

  2. Computational and experimental studies of hydrodynamic instabilities and turbulent mixing: Review of VNIIEF efforts. Summary report

    SciTech Connect (OSTI)

    Andronov, V.A.; Zhidov, I.G.; Meskov, E.E.; Nevmerzhitskii, N.V.; Nikiforov, V.V.; Razin, A.N.; Rogatchev, V.G.; Tolshmyakov, A.I.; Yanilkin, Y.V.

    1994-12-31

    The report presents the basic results of some calculations, theoretical and experimental efforts in the study of Rayleigh-Taylor, Kelvin-Helmholtz, Richtmyer-Meshkov instabilities and the turbulent mixing which is caused by their evolution. Since the late forties the VNIIEF has been conducting these investigations. This report is based on the data which were published in different times in Russian and foreign journals. The first part of the report deals with calculations an theoretical techniques for the description of hydrodynamic instabilities applied currently, as well as with the results of several individual problems and their comparison with the experiment. These methods can be divided into two types: direct numerical simulation methods and phenomenological methods. The first type includes the regular 2D and 3D gasdynamical techniques as well as the techniques based on small perturbation approximation and on incompressible liquid approximation. The second type comprises the techniques based on various phenomenological turbulence models. The second part of the report describes the experimental methods and cites the experimental results of Rayleigh-Taylor and Richtmyer-Meskov instability studies as well as of turbulent mixing. The applied methods were based on thin-film gaseous models, on jelly models and liquid layer models. The research was done for plane and cylindrical geometries. As drivers, the shock tubes of different designs were used as well as gaseous explosive mixtures, compressed air and electric wire explosions. The experimental results were applied in calculational-theoretical technique calibrations. The authors did not aim at covering all VNIIEF research done in this field of science. To a great extent the choice of the material depended on the personal contribution of the author in these studies.

  3. Rayleigh-Taylor instability at spherical interfaces between viscous fluids: Fluid/vacuum interface

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Terrones, Guillermo; Carrara, Mark D.

    2015-05-01

    For a spherical interface of radius R separating two different homogeneous regions of incompressible viscous fluids under the action of a radially directed acceleration, we perform a linear stability analysis in terms of spherical surface harmonics Y n to derive the dispersion relation. The instability behavior is investigated by computing the growth rates and the most-unstable modes as a function of the spherical harmonic degree n. This general methodology is applicable to the entire parameter space spanned by the Atwood number, the viscosity ratio, and the dimensionless number B = (αRΡ²2/μ²²)¹/³ R (where αR, Ρ2 and μ2 are the localmore » radial acceleration at the interface, and the density and viscosity of the denser overlying fluid, respectively). While the mathematical formulation here is general, this paper focuses on instability that arises at a spherical viscous fluid/vacuum interface as there is a great deal to be learned from the effects of one-fluid viscosity and sphericity alone. To quantify and understand the effect that curvature and radial accelerationhave on the Rayleigh-Taylor instability, a comparison of the growth rates, under homologous driving conditions, between the planar and spherical interfaces is performed. The derived dispersion relation for the planar interface accounts for an underlying finite fluid region of thickness L and normal acceleration αR. Under certain conditions, the development of the most-unstable modes at a spherical interface can take place via the superposition of two adjacent spherical harmonics Yn and Yn+1. This bimodality in the evolution of disturbances in the linear regime does not have a counterpart in the planar configuration where the most-unstable modes are associated with a unique wave number.« less

  4. Is a Higgs vacuum instability fatal for high-scale inflation?

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kearney, John; Yoo, Hojin; Zurek, Kathryn M.

    2015-06-25

    We study the inflationary evolution of a scalar field h with an unstable potential for the case where the Hubble parameter H during inflation is larger than the instability scale ΛI of the potential. Quantum fluctuations in the field of size δh ~ H/2π imply that the unstable part of the potential is sampled during inflation. We investigate the evolution of these fluctuations to the unstable regime and in particular whether they generate cosmological defects or even terminate inflation. We apply the results of a toy scalar model to the case of the Standard Model (SM) Higgs boson, the quarticmore » of which evolves to negative values at high scales, and extend previous analyses of Higgs dynamics during inflation utilizing statistical methods to a perturbative and fully gauge-invariant formulation. We show that the dynamics are controlled by the renormalization group-improved quartic coupling λ(μ) evaluated at a scale μ = H, such that Higgs fluctuations are enhanced by the instability if H > ΛI. Even if H > ΛI, the instability in the Standard Model Higgs potential does not end inflation; instead the universe slowly sloughs off crunching patches of space that never come to dominate the evolution. As inflation proceeds past 50 e-folds, a significant proportion of patches exits inflation in the unstable vacuum, and as much as 1% of the spacetime can rapidly evolve to a defect. Depending on the nature of these defects, however, the resulting universe could still be compatible with ours.« less

  5. Non-modal analysis of the diocotron instability for cylindrical geometry with conducting boundary

    SciTech Connect (OSTI)

    Mikhailenko, V. V.; Seok Kim, Jin; Jo, Younghyun; June Lee, Hae; Mikhailenko, V. S.; Kharkiv National Automobile and Highway University, 61002 Kharkiv

    2014-05-15

    The temporal evolution of the linear diocotron instability of a cylindrical annular plasma column surrounded by a conducting boundary has been investigated by using the methodology of the cylindrical shearing modes. The linear solution of the initial and boundary-value problems is obtained which is valid for any time at which linear effects dominate. The solution reveals that the initial perturbations of the electron density pass through the stage of the non-modal evolution when the perturbation experiences spatio-temporal distortion pertinent to the considered geometry of the electron column. The result is confirmed by a two-dimensional cylindrical particle-in-cell simulation.

  6. Perturbative analysis of sheared flow Kelvin-Helmholtz instability in a weakly relativistic magnetized electron fluid

    SciTech Connect (OSTI)

    Sundar, Sita; Das, Amita; Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar-382428 (India)

    2012-05-15

    In the interaction of intense lasers with matter/plasma, energetic electrons having relativistic energies get created. These energetic electrons can often have sheared flow profiles as they propagate through the plasma medium. In an earlier study [Phys. Plasmas 17, 022101 (2010)], it was shown that a relativistic sheared electron flow modifies the growth rate and threshold condition of the conventional Kelvin-Helmholtz instability. A perturbative analytic treatment for the case of weakly relativistic regime has been provided here. It provides good agreement with the numerical results obtained earlier.

  7. Light induced instability mechanism in amorphous InGaZn oxide semiconductors

    SciTech Connect (OSTI)

    Robertson, John; Guo, Yuzheng

    2014-04-21

    A model of the negative bias illumination stress instability in InGaZn oxide is presented, based on the photo-excitation of electrons from oxygen interstitials. The O interstitials are present to compensate hydrogen donors. The O interstitials are found to spontaneously form in O-rich conditions for Fermi energies at the conduction band edge, much more easily that in related oxides. The excited electrons give rise to a persistent photoconductivity due to an energy barrier to recombination. The formation energy of the O interstitials varies with their separation from the H donors, which leads to a voltage stress dependence on the compensation.

  8. Simulating Rayleigh-Taylor (RT) instability using PPM hydrodynamics @scale on Roadrunner (u)

    SciTech Connect (OSTI)

    Woodward, Paul R; Dimonte, Guy; Rockefeller, Gabriel M; Fryer, Christopher L; Dimonte, Guy; Dai, W; Kares, R. J.

    2011-01-05

    The effect of initial conditions on the self-similar growth of the RT instability is investigated using a hydrodynamics code based on the piecewise-parabolic-method (PPM). The PPM code was converted to the hybrid architecture of Roadrunner in order to perform the simulations at extremely high speed and spatial resolution. This paper describes the code conversion to the Cell processor, the scaling studies to 12 CU's on Roadrunner and results on the dependence of the RT growth rate on initial conditions. The relevance of the Roadrunner implementation of this PPM code to other existing and anticipated computer architectures is also discussed.

  9. Experimental characterization of pressure drops and channel instabilities in helical coil SG tubes

    SciTech Connect (OSTI)

    Colombo, M.; Cammi, A.; De Amicis, J.; Ricotti, M. E. [Politecnico di Milano, Dept. of Energy, Nuclear Engineering Div. - CeSNEF, Via La Masa 34, 20156, Milano (Italy)

    2012-07-01

    Helical tube heat exchangers provide better heat transfer characteristics, an improved capability to accommodate stresses due to thermal expansions and a more compact design with respect to straight tube heat exchangers. For these advantages they are considered as an option for the Steam Generator (SG) of many new reactor projects of Generation III+ and Generation IV. In particular, their compactness fits well with the requirements of Small-medium Modular Reactors (SMRs) of integral design, where all the primary system components are located inside the reactor vessel. In this framework, thermal hydraulics of helical pipes has been studied in recent years by Politecnico di Milano in different experimental campaigns. Experiments have been carried out in a full-scale open loop test facility installed at SIET labs in Piacenza (Italy)), to simulate the SG of a typical SMR. The facility includes two helical pipes (1 m coil diameter, 32 m length, 8 m height), connected via lower and upper headers. Following recently completed experimental campaigns dedicated to pressure drops and density wave instabilities, this paper deals with a new experimental campaign focused on both pressure drops (single-phase flow and two-phase flow, laminar and turbulent regimes) and flow instabilities. The availability of a large number of experimental data, in particular on two-phase flow, is of fundamental interest for correlation development, model validation and code assessment. Two-phase pressure drops have been measured in adiabatic conditions, ranging from 200 to 600 kg/m{sup 2}s for the mass flux, from 30 to 60 bar for the pressure and from 0.1 to 1.0 for the flow quality. The channel characteristics mass flow rate - pressure drop has been determined experimentally in the range 10-40 bar, varying the mass flow rate at a fixed value of the thermal flux. In addition, single-phase pressure drops have been measured in both laminar and turbulent conditions. Density wave instabilities have been studied at mass flux from 100 to 400 kg/m{sup 2}s and pressure from 10 to 20 bar, to confirm the particular behavior of the stability boundary in helical geometry at low pressure and low mass flow rate. Finally, starting from the unstable regions identified from the experimental channel characteristics, Ledinegg type instabilities have been investigated to drawn stability maps with complete stable and unstable regions in the dimensionless plane N sub-N pch. (authors)

  10. 1 Hz FLARING IN SAX J1808.4-3658: FLOW INSTABILITIES NEAR THE PROPELLER STAGE

    SciTech Connect (OSTI)

    Patruno, Alessandro; Watts, Anna; Klein Wolt, Marc; Wijnands, Rudy; Van der Klis, Michiel

    2009-12-20

    We present a simultaneous periodic and aperiodic timing study of the accreting millisecond X-ray pulsar SAX J1808.4-3658. We analyze five outbursts of the source and for the first time provide a full and systematic investigation of the enigmatic phenomenon of the 1 Hz flares observed during the final stages of some of the outbursts. We show that links between pulsations and 1 Hz flares might exist, and suggest that they are related with hydrodynamic disk instabilities that are triggered close to the disk-magnetosphere boundary layer when the system is entering the propeller regime.

  11. Genome-wide experimental determination of barriers to horizontal gene

    Office of Scientific and Technical Information (OSTI)

    transfer (Journal Article) | SciTech Connect Genome-wide experimental determination of barriers to horizontal gene transfer Citation Details In-Document Search Title: Genome-wide experimental determination of barriers to horizontal gene transfer Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we

  12. INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY (Technical

    Office of Scientific and Technical Information (OSTI)

    Report) | SciTech Connect Technical Report: INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY Citation Details In-Document Search Title: INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY The aim of the work reported is to study Shewanella population genomics, and to understand the evolution, ecophysiology, and speciation of Shewanella. The tasks supporting this aim are: to study genetic and ecophysiological bases defining the core and diversification of Shewanella

  13. GLAMM: Genome-Linked Application for Metabolic Maps

    SciTech Connect (OSTI)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  14. Integrated Genome-Based Studies of Shewanella Ecophysiology (Technical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Report) | SciTech Connect Integrated Genome-Based Studies of Shewanella Ecophysiology Citation Details In-Document Search Title: Integrated Genome-Based Studies of Shewanella Ecophysiology As a part of the Shewanella Federation project, we have used integrated genomic, proteomic and computational technologies to study various aspects of energy metabolism of two Shewanella strains from a systems-level perspective. Authors: Zhou, Jizhong ; He, Zhili Publication Date: 2014-04-08 OSTI

  15. INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY (Technical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Report) | SciTech Connect INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY Citation Details In-Document Search Title: INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY The aim of the work reported is to study Shewanella population genomics, and to understand the evolution, ecophysiology, and speciation of Shewanella. The tasks supporting this aim are: to study genetic and ecophysiological bases defining the core and diversification of Shewanella species; to determine

  16. The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospiracrunogena

    Office of Scientific and Technical Information (OSTI)

    XCL-2 (Journal Article) | SciTech Connect Journal Article: The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospiracrunogena XCL-2 Citation Details In-Document Search Title: The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospiracrunogena XCL-2 Presented here is the complete genome sequence ofThiomicrospira crunogena XCL-2, representative of ubiquitouschemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-seahydrothermal vents. This gammaproteobacterium has a single

  17. The Impact of Structural Genomics: Expectations and Outcomes (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect The Impact of Structural Genomics: Expectations and Outcomes Citation Details In-Document Search Title: The Impact of Structural Genomics: Expectations and Outcomes Structural Genomics (SG) projects aim to expand our structural knowledge of biological macromolecules, while lowering the average costs of structure determination. We quantitatively analyzed the novelty, cost, and impact of structures solved by SG centers, and contrast these results with traditional

  18. Towards a Library of Standard Operating Procedures (SOPs) for (meta)genomic annotation

    SciTech Connect (OSTI)

    Kyrpides, Nikos; Angiuoli, Samuel V.; Cochrane, Guy; Field, Dawn; Garrity, George; Gussman, Aaron; Kodira, Chinnappa D.; Klimke, William; Kyrpides, Nikos; Madupu, Ramana; Markowitz, Victor; Tatusova, Tatiana; Thomson, Nick; White, Owen

    2008-04-01

    Genome annotations describe the features of genomes and accompany sequences in genome databases. The methodologies used to generate genome annotation are diverse and typically vary amongst groups. Descriptions of the annotation procedure are helpful in interpreting genome annotation data. Standard Operating Procedures (SOPs) for genome annotation describe the processes that generate genome annotations. Some groups are currently documenting procedures but standards are lacking for structure and content of annotation SOPs. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse a central online repository of SOPs.

  19. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    SciTech Connect (OSTI)

    Ivanova, N; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla L.; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Han, Cliff; Detter, J C; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Genome Project Standards in a New Era of Sequencing

    SciTech Connect (OSTI)

    GSC Consortia; HMP Jumpstart Consortia; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G.; Hostetler, J.; Muzny, D.; Detter, J. C.; Ali, J.; Birren, B.; Bruce, D. C.; Buhay, C.; Cole, J. R.; Ding, Y.; Dugan, S.; Field, D.; Garrity, G. M.; Gibbs, R.; Graves, T.; Han, C. S.; Harrison, S. H.; Highlander, S.; Hugenholtz, P.; Khouri, H. M.; Kodira, C. D.; Kolker, E.; Kyrpides, N. C.; Lang, D.; Lapidus, A.; Malfatti, S. A.; Markowitz, V.; Metha, T.; Nelson, K. E.; Parkhill, J.; Pitluck, S.; Qin, X.; Read, T. D.; Schmutz, J.; Sozhamannan, S.; Strausberg, R.; Sutton, G.; Thomson, N. R.; Tiedje, J. M.; Weinstock, G.; Wollam, A.

    2009-06-01

    For over a decade, genome 43 sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole genome sequencing that requires a careful reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker 'draft', however these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better reflect the quality of the genome sequence, based on our collective understanding of the different technologies, available assemblers, and the varied efforts to improve upon drafted genomes. Due to the increasingly rapid pace of genomics we avoided the use of rigid numerical thresholds in our definitions to take into account the types of products achieved by any combination of technology, chemistry, assembler, or improvement/finishing process.

  1. Finishing The Euchromatic Sequence Of The Human Genome

    SciTech Connect (OSTI)

    Rubin, Edward M.; Lucas, Susan; Richardson, Paul; Rokhsar, Daniel; Pennacchio, Len

    2004-09-07

    The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process.The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers {approx}99% of the euchromatic genome and is accurate to an error rate of {approx}1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number,birth and death. Notably, the human genome seems to encode only20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.

  2. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis....

  3. Genomic Encyclopedia of Fungi (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis....

  4. The Methanosarcina barkeri genome: comparative analysis withMethanosar...

    Office of Scientific and Technical Information (OSTI)

    All three genomes share a conserved double origin of replication and many gene clusters. ... proximal to the origin of replication with interspecies gene similarities as high as 95%. ...

  5. Genome sequencing of the Trichoderma reesei QM9136 mutant identifies...

    Office of Scientific and Technical Information (OSTI)

    Vienna Univ. of Technology, Vienna (Austria) IFP Energies Nouvelles, Rueil-Malmaison (France) Sorbonne Univ., Paris (France) Joint Genome Inst., Walnut Creek, CA (United States). ...

  6. Joint Genome Institute Progress Report 2002-2005

    SciTech Connect (OSTI)

    Gilbert, David

    2005-10-03

    Progress report covering activities at the DOE-Joint Genome Institute in Walnut Creek, California for the period 2002-2005.

  7. Fueling Future with Algal Genomics Grigoriev, Igor 59 BASIC BIOLOGICAL

    Office of Scientific and Technical Information (OSTI)

    play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world...

  8. Exploring the Genome and Proteome of Desulfitobacterium hafniense...

    Office of Scientific and Technical Information (OSTI)

    Exploring the Genome and Proteome of Desulfitobacterium hafniense DCB2 for its Protein ... hafniense DCB2 for its Protein Complexes Involved in Metal Reduction and ...

  9. Multiplex automated genome engineering Church, George M; Wang...

    Office of Scientific and Technical Information (OSTI)

    Multiplex automated genome engineering Church, George M; Wang, Harris H; Isaacs, Farren J The present invention relates to automated methods of introducing multiple nucleic acid...

  10. Rich Genomics Resources Facilitate Progress in Understanding Wood Formation

    SciTech Connect (OSTI)

    Tuskan, Gerald [Oak Ridge National Laboratory

    2014-03-20

    Gerald Tuskan, Oak Ridge National Laboratory, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif

  11. INTEGRATED GENOME-BASED STUDIES OF SHEWANELLA ECOPHYSIOLOGY TIEDJE...

    Office of Scientific and Technical Information (OSTI)

    BIOLOGICAL SCIENCES The aim of the work reported is to study Shewanella population genomics, and to understand the evolution, ecophysiology, and speciation of Shewanella. The...

  12. Rapid genome resequencing of an atoxigenic strain of Aspergillus...

    Office of Scientific and Technical Information (OSTI)

    United States Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks Word Cloud More Like This Free Publicly Accessible Full...

  13. Fungal Genomics Program Grigoriev, Igor 59 BASIC BIOLOGICAL SCIENCES...

    Office of Scientific and Technical Information (OSTI)

    and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world...

  14. Uses of antimicrobial genes from microbial genome Sorek, Rotem...

    Office of Scientific and Technical Information (OSTI)

    We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their...

  15. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    SciTech Connect (OSTI)

    Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Goker, Markus; Spring, Stefan; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2009-05-20

    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. DOE human genome program contractor-grantee workshop VI

    SciTech Connect (OSTI)

    1997-10-01

    Research is presented from the workshop on the Human Genome Project. Topics include sequencing, genetic mapping, informatics, ethical and legal issues, and infrastructure.

  17. Genomic Sequence Comparisons, 1987-2003 Final Report

    SciTech Connect (OSTI)

    George M. Church

    2004-07-29

    This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed to one of the first complete DOE genome sequences, in 1997, that of Methanobacterium thermoautotropicum, a species of great relevance to energy-rich gas production.

  18. Genomic library construction (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Details In-Document Search Title: Genomic library construction Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions...

  19. Integrated Genome-Based Studies of Shewanella Ecophysiology ...

    Office of Scientific and Technical Information (OSTI)

    genomic, proteomic and computational technologies to study various aspects of energy metabolism of two Shewanella strains from a systems-level perspective. Authors: Zhou, Jizhong ;...

  20. Next Generation Sequencing at the University of Chicago Genomics...

    Office of Scientific and Technical Information (OSTI)

    University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation sequencing, Sanger sequencing genotyping and...

  1. Genomics and Systems Biology of Tuberculosis (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Galagan, James

    2011-04-25

    James Galagan from the Broad Institute spoke about the "Genomics and Systems Biology of TB" on March 26, 2009 during the 4th Annual User Meeting

  2. JGI Fungal Genomics Program Grigoriev, Igor V. 99; BIOFUELS;...

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  3. Genomic Encyclopedia of Fungi Grigoriev, Igor 59 BASIC BIOLOGICAL...

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  4. Building international genomics collaboration for global health security

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; Vuyisich, Momchilo

    2015-12-07

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installationmore » of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.« less

  5. Energy Department Awards $92 Million for Genomics Research |...

    Office of Science (SC) Website

    Energy Department Awards 92 Million for Genomics Research News News Home Featured ... Contact Information Office of Science U.S. Department of Energy 1000 Independence Ave., SW ...

  6. Genomic Encyclopedia of Fungi (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  7. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  8. Fungal Genomics Program (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  9. New culturing tool reveals a full genome from single cells

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    New culturing tool reveals New culturing tool reveals a full genome from single cells A new technique for genetic analysis, "gel microdroplets," helps scientists generate complete...

  10. Target Selection and Deselection at the Berkeley Structural Genomics...

    Office of Scientific and Technical Information (OSTI)

    structural complement of proteins in the minimal organisms Mycoplasma genitalium and M. ... genome sizes; the latter characteristic has earned them the name "minimal organisms" 1,2 . ...

  11. A Celebration of The Genome, 1953-2003

    Office of Scientific and Technical Information (OSTI)

    in history, the sequencing of the human genome, and the 50th anniversary of James Watson and Francis Crick's Nobel Prize winning description of the DNA double helix. ...

  12. Trichoderma: the genomics of opportunistic success

    SciTech Connect (OSTI)

    Druzhinina, Irina S.; Seiboth, Verena Seidl; Estrella, Alfredo Herrera; Horwitz, Benjamin A.; Kenerley, Charles M.; Monte, Enrique; Mukherjee, Prasun K.; Zeilinger, Susanne; Grigoriev, Igor V.; Kubicek, Christian P.

    2011-01-01

    Trichoderma is a genus of common filamentous fungi that display a remarkable range of lifestyles and interactions with other fungi, animals and plants. Because of their ability to antagonize plant-pathogenic fungi and to stimulate plant growth and defence responses, some Trichoderma strains are used for biological control of plant diseases. In this Review, we discuss recent advances in molecular ecology and genomics which indicate that the interactions of Trichoderma spp. with animals and plants may have evolved as a result of saprotrophy on fungal biomass (mycotrophy) and various forms of parasitism on other fungi (mycoparasitism), combined with broad environmental opportunism.

  13. DOE Joint Genome Institute 2008 Progress Report

    SciTech Connect (OSTI)

    Gilbert, David

    2009-03-12

    While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing process that dominated how sequencing was done in the last decade is being replaced by a variety of new processes and sequencing instruments. The JGI, with an increasing number of next-generation sequencers, whose throughput is 100- to 1,000-fold greater than the Sanger capillary-based sequencers, is increasingly focused in new directions on projects of scale and complexity not previously attempted. These new directions for the JGI come, in part, from the 2008 National Research Council report on the goals of the National Plant Genome Initiative as well as the 2007 National Research Council report on the New Science of Metagenomics. Both reports outline a crucial need for systematic large-scale surveys of the plant and microbial components of the biosphere as well as an increasing need for large-scale analysis capabilities to meet the challenge of converting sequence data into knowledge. The JGI is extensively discussed in both reports as vital to progress in these fields of major national interest. JGI's future plan for plants and microbes includes a systematic approach for investigation of these organisms at a scale requiring the special capabilities of the JGI to generate, manage, and analyze the datasets. JGI will generate and provide not only community access to these plant and microbial datasets, but also the tools for analyzing them. These activities will produce essential knowledge that will be needed if we are to be able to respond to the world's energy and environmental challenges. As the JGI Plant and Microbial programs advance, the JGI as a user facility is also evolving. The Institute has been highly successful in bending its technical and analytical skills to help users solve large complex problems of major importance, and that effort will continue unabated. The JGI will increasingly move from a central focus on 'one-off' user projects coming from small user communities to much larger scale projects driven by systematic and problem-focused approaches to selection of sequencing targets. Entire communities of scientists working in a particular field, such as feedstock improvement or biomass degradation, will be users of this information. Despite this new emphasis, an investigator-initiated user program will remain. This program in the future will replace small projects that increasingly can be accomplished without the involvement of JGI, with imaginative large-scale 'Grand Challenge' projects of foundational relevance to energy and the environment that require a new scale of sequencing and analysis capabilities. Close interactions with the DOE Bioenergy Research Centers, and with other DOE institutions that may follow, will also play a major role in shaping aspects of how the JGI operates as a user facility. Based on increased availability of high-throughput sequencing, the JGI will increasingly provide to users, in addition to DNA sequencing, an array of both pre- and post-sequencing value-added capabilities to accelerate their science.

  14. Webinar: Materials Genome Initative | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    Below is the text version of the webinar titled "Materials Genome Initiative," originally presented on December 2, 2014. In addition to this text version of the audio, you can access the presentation slides. Alli Aman: -today's webinar. I am going to go through a few housekeeping items before I turn it over to today's presenters. First of all, thank you so much for joining today. Today's webinar is being recorded, so a recording along with slides will be posted to our website in about

  15. N-BODY SIMULATION OF PLANETESIMAL FORMATION THROUGH GRAVITATIONAL INSTABILITY OF A DUST LAYER IN LAMINAR GAS DISK

    SciTech Connect (OSTI)

    Michikoshi, Shugo; Kokubo, Eiichiro [Center for Computational Astrophysics, National Astronomical Observatory of Japan, Osawa, Mitaka, Tokyo 181-8588 (Japan); Inutsuka, Shu-ichiro, E-mail: michikoshi@cfca.j, E-mail: kokubo@th.nao.ac.j, E-mail: inutsuka@nagoya-u.j [Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602 (Japan)

    2010-08-20

    We investigate the formation process of planetesimals from the dust layer by the gravitational instability in the gas disk using local N-body simulations. The gas is modeled as a background laminar flow. We study the formation process of planetesimals and its dependence on the strength of the gas drag. Our simulation results show that the formation process is divided into three stages qualitatively: the formation of wake-like density structures, the creation of planetesimal seeds, and their collisional growth. The linear analysis of the dissipative gravitational instability shows that the dust layer is secularly unstable although Toomre's Q value is larger than unity. However, in the initial stage, the growth time of the gravitational instability is longer than that of the dust sedimentation and the decrease in the velocity dispersion. Thus, the velocity dispersion decreases and the disk shrinks vertically. As the velocity dispersion becomes sufficiently small, the gravitational instability finally becomes dominant. Then wake-like density structures are formed by the gravitational instability. These structures fragment into planetesimal seeds. The seeds grow rapidly owing to mutual collisions.

  16. The effects of early time laser drive on hydrodynamic instability growth in National Ignition Facility implosions

    SciTech Connect (OSTI)

    Peterson, J. L.; Clark, D. S.; Suter, L. J.; Masse, L. P.

    2014-09-15

    Defects on inertial confinement fusion capsule surfaces can seed hydrodynamic instability growth and adversely affect capsule performance. The dynamics of shocks launched during the early period of x-ray driven National Ignition Facility (NIF) implosions determine whether perturbations will grow inward or outward at peak implosion velocity and final compression. In particular, the strength of the first shock, launched at the beginning of the laser pulse, plays an important role in determining Richtmyer-Meshkov (RM) oscillations on the ablation front. These surface oscillations can couple to the capsule interior through subsequent shocks before experiencing Rayleigh-Taylor (RT) growth. We compare radiation hydrodynamic simulations of NIF implosions to analytic theories of the ablative RM and RT instabilities to illustrate how early time laser strength can alter peak velocity growth. We develop a model that couples the RM and RT implosion phases and captures key features of full simulations. We also show how three key parameters can control the modal demarcation between outward and inward growth.

  17. NON-BAROTROPIC LINEAR ROSSBY WAVE INSTABILITY IN THREE-DIMENSIONAL DISKS

    SciTech Connect (OSTI)

    Lin, Min-Kai

    2013-03-10

    Astrophysical disks with localized radial structure, such as protoplanetary disks containing dead zones or gaps due to disk-planet interaction, may be subject to the non-axisymmetric Rossby wave instability (RWI) that leads to vortex formation. The linear instability has recently been demonstrated in three-dimensional (3D) barotropic disks. It is the purpose of this study to generalize the 3D linear problem to include an energy equation, thereby accounting for baroclinity in three dimensions. Linear stability calculations are presented for radially structured, vertically stratified, geometrically thin disks with non-uniform entropy distribution in both directions. Polytropic equilibria are considered but adiabatic perturbations assumed. The unperturbed disk has a localized radial density bump, making it susceptible to the RWI. The linearized fluid equations are solved numerically as a partial differential equation eigenvalue problem. Emphasis on the ease of method implementation is given. It is found that when the polytropic index is fixed and adiabatic index increased, non-uniform entropy has negligible effect on the RWI growth rate, but pressure and density perturbation magnitudes near a pressure enhancement increase away from the midplane. The associated meridional flow is also qualitatively changed from homentropic calculations. Meridional vortical motion is identified in the nonhomentropic linear solution, as well as in a nonlinear global hydrodynamic simulation of the RWI in an initially isothermal disk evolved adiabatically. Numerical results suggest that buoyancy forces play an important role in the internal flow of Rossby vortices.

  18. Fractional frequency instability in the 10{sup -14} range with a thermal beam optical frequency reference

    SciTech Connect (OSTI)

    McFerran, John J.; Luiten, Andre N. [School of Physics, University of Western Australia, 35 Stirling Highway, Crawley 6009, W.A. (Australia)

    2010-02-15

    We demonstrate a means of increasing the signal-to-noise ratio in a Ramsey-Borde interferometer with spatially separated oscillatory fields on a thermal atomic beam. The {sup 1}S{sub 0}{r_reversible}{sup 3}P{sub 1} intercombination line in neutral {sup 40}Ca is used as a frequency discriminator, with an extended cavity diode laser at 423 nm probing the ground state population after a Ramsey-Borde sequence of 657 nm light-field interactions with the atoms. Evaluation of the instability of the Ca frequency reference is carried out by comparison with (i) a hydrogen-maser and (ii) a cryogenic sapphire oscillator. In the latter case the Ca reference exhibits a square-root {Lambda} variance of 9.2x10{sup -14} at 1 s and 2.0x10{sup -14} at 64 s. This is an order-of-magnitude improvement for optical beam frequency references, to our knowledge. The shot noise of the readout fluorescence produces a limiting square-root {Lambda} variance of 7x10{sup -14}/{radical}({tau}), highlighting the potential for improvement. This work demonstrates the feasibility of a portable frequency reference in the optical domain with 10{sup -14} range frequency instability.

  19. Heat loads to divertor nearby components from secondary radiation evolved during plasma instabilities

    SciTech Connect (OSTI)

    Sizyuk, V. Hassanein, A.

    2015-01-15

    A fundamental issue in tokamak operation related to power exhaust during plasma instabilities is the understanding of heat and particle transport from the core plasma into the scrape-off layer and to plasma-facing materials. During abnormal and disruptive operation in tokamaks, radiation transport processes play a critical role in divertor/edge-generated plasma dynamics and are very important in determining overall lifetimes of the divertor and nearby components. This is equivalent to or greater than the effect of the direct impact of escaped core plasma on the divertor plate. We have developed and implemented comprehensive enhanced physical and numerical models in the upgraded HEIGHTS package for simulating detailed photon and particle transport in the evolved edge plasma during various instabilities. The paper describes details of a newly developed 3D Monte Carlo radiation transport model, including optimization methods of generated plasma opacities in the full range of expected photon spectra. Response of the ITER divertor's nearby surfaces due to radiation from the divertor-developed plasma was simulated by using actual full 3D reactor design and magnetic configurations. We analyzed in detail the radiation emission spectra and compared the emission of both carbon and tungsten as divertor plate materials. The integrated 3D simulation predicted unexpectedly high damage risk to the open stainless steel legs of the dome structure in the current ITER design from the intense radiation during a disruption on the tungsten divertor plate.

  20. Visible-light-induced instability in amorphous metal-oxide based TFTs for transparent electronics

    SciTech Connect (OSTI)

    Ha, Tae-Jun

    2014-10-15

    We investigate the origin of visible-light-induced instability in amorphous metal-oxide based thin film transistors (oxide-TFTs) for transparent electronics by exploring the shift in threshold voltage (V{sub th}). A large hysteresis window in amorphous indium-gallium-zinc-oxide (a-IGZO) TFTs possessing large optical band-gap (?3 eV) was observed in a visible-light illuminated condition whereas no hysteresis window was shown in a dark measuring condition. We also report the instability caused by photo irradiation and prolonged gate bias stress in oxide-TFTs. Larger V{sub th} shift was observed after photo-induced stress combined with a negative gate bias than the sum of that after only illumination stress and only negative gate bias stress. Such results can be explained by trapped charges at the interface of semiconductor/dielectric and/or in the gate dielectric which play a role in a screen effect on the electric field applied by gate voltage, for which we propose that the localized-states-assisted transitions by visible-light absorption can be responsible.

  1. Magnetorotational Instability: Nonmodal Growth and the Relationship of Global Modes to the Shearing Box

    SciTech Connect (OSTI)

    J Squire, A Bhattacharjee

    2014-07-01

    We study the magnetorotational instability (MRI) (Balbus & Hawley 1998) using non-modal stability techniques.Despite the spectral instability of many forms of the MRI, this proves to be a natural method of analysis that is well-suited to deal with the non-self-adjoint nature of the linear MRI equations. We find that the fastest growing linear MRI structures on both local and global domains can look very diff#11;erent to the eigenmodes, invariably resembling waves shearing with the background flow (shear waves). In addition, such structures can grow many times faster than the least stable eigenmode over long time periods, and be localized in a completely di#11;fferent region of space. These ideas lead for both axisymmetric and non-axisymmetric modes to a natural connection between the global MRI and the local shearing box approximation. By illustrating that the fastest growing global structure is well described by the ordinary diff#11;erential equations (ODEs) governing a single shear wave, we find that the shearing box is a very sensible approximation for the linear MRI, contrary to many previous claims. Since the shear wave ODEs are most naturally understood using non-modal analysis techniques, we conclude by analyzing local MRI growth over finite time-scales using these methods. The strong growth over a wide range of wave-numbers suggests that non-modal linear physics could be of fundamental importance in MRI turbulence (Squire & Bhattacharjee 2014).

  2. Particle Energization via Tearing Instability with Global Self-Organization Constraints

    SciTech Connect (OSTI)

    Sarff, John; Guo, Fan

    2015-07-21

    The presentation reviews how tearing magnetic reconnection leads to powerful ion energization in reversed field pinch (RFP) plasmas. A mature MHD model for tearing instability has been developed that captures key nonlinear dynamics from the global to intermediate spatial scales. A turbulent cascade is also present that extends to at least the ion gyroradius scale, within which important particle energization mechanisms are anticipated. In summary, Ion heating and acceleration associated with magnetic reconnection from tearing instability is a powerful process in the RFP laboratory plasma (gyro-resonant and stochastic processes are likely candidates to support the observed rapid heating and other features, reconnection-driven electron heating appears weaker or even absent, energetic tail formation for ions and electrons). Global self-organization strongly impacts particle energization (tearing interactions that span to core to edge, global magnetic flux change produces a larger electric field and runaway, correlations in electric and magnetic field fluctuations needed for dynamo feedback, impact of transport processes (which can be quite different for ions and electrons), inhomogeneity on the system scale, e.g., strong edge gradients).

  3. ON THE INSTABILITY OF TROPICAL WESTERN PACIFIC WARM POOL DURING THE BOREAL WINTER AND SPRING

    SciTech Connect (OSTI)

    BARR-KUMARAKULASINGHE,S.A.

    1998-03-23

    A source of instability in the western Pacific warm pool is shown to be due to sea surface elevation variations caused by changes in the zonal sea-surface temperature (SST) gradient and the changes in the Pacific Ocean basin length in relation to the warm pool latitudinal location. The variation of the sea-surface elevation is measured by using the thermocline depth response calculated from a two-layer ocean. The warm pool is shown to be barely at equilibrium during the boreal late winter and early spring by comparing the measured thermocline at 110{degree}W, 0{degree}E with the calculated thermocline depth. Based on this analysis, a failure or reversal of the climatological zonal winds are apparently not a necessary precursor for the instability of the warm pool and initiation of a warm event. A warm event can be initiated by an increase in the size of the warm pool and/or an increase in zonal SST differences during the boreal/winter spring. This mechanism could be an alternate mechanism for El-Nino Southern Oscillation (ENSO) dynamics to that postulated by Bjeknes (1969).

  4. Pressure fluctuations beneath instability wavepackets and turbulent spots in a hypersonic boundary layer

    SciTech Connect (OSTI)

    Casper, Katya M.; Beresh, Steven J.; Schneider, Steven P.

    2014-09-09

    To investigate the pressure-fluctuation field beneath turbulent spots in a hypersonic boundary layer, a study was conducted on the nozzle wall of the Boeing/AFOSR Mach-6 Quiet Tunnel. Controlled disturbances were created by pulsed-glow perturbations based on the electrical breakdown of air. Under quiet-flow conditions, the nozzle-wall boundary layer remains laminar and grows very thick over the long nozzle length. This allows the development of large disturbances that can be well-resolved with high-frequency pressure transducers. A disturbance first grows into a second-mode instability wavepacket that is concentrated near its own centreline. Weaker disturbances are seen spreading from the centre. The waves grow and become nonlinear before breaking down to turbulence. The breakdown begins in the core of the packets where the wave amplitudes are largest. Second-mode waves are still evident in front of and behind the breakdown point and can be seen propagating in the spanwise direction. The turbulent core grows downstream, resulting in a spot with a classical arrowhead shape. Behind the spot, a low-pressure calmed region develops. However, the spot is not merely a localized patch of turbulence; instability waves remain an integral part. Limited measurements of naturally occurring disturbances show many similar characteristics. From the controlled disturbance measurements, the convection velocity, spanwise spreading angle, and typical pressure-fluctuation field were obtained.

  5. Magnetization anomaly of Nb3Al strands and instability of Nb3Al Rutherford cables

    SciTech Connect (OSTI)

    Yamada, Ryuji; /Fermilab; Kikuchi, Akihiro; /Tsukuba Magnet Lab; Wake, Masayoshi; /KEK, Tsukuba

    2006-08-01

    Using a Cu stabilized Nb{sub 3}Al strand with Nb matrix, a 30 meter long Nb{sub 3}Al Rutherford cable was made by a collaboration of Fermilab and NIMS. Recently the strand and cable were tested. In both cases instability was observed at around 1.5 Tesla. The magnetization of this Nb{sub 3}Al strand was measured first using a balanced coil magnetometer at 4.2 K. Strands showed an anomalously large magnetization behavior around at 1.6 T, which is much higher than the usual B{sub c2} {approx} 0.5 Tesla (4.2 K) of Nb matrix. This result is compared with the magnetization data of short strand samples using a SQUID magnetometer, in which a flux-jump signal was observed at 0.5 Tesla, but not at higher field. As a possible explanation for this magnetization anomaly, the interfilament coupling through the thin Nb films in the strands is suggested. The instability problem observed in low field tests of the Nb{sub 3}Al Rutherford cables is attributed to this effect.

  6. Pressure fluctuations beneath instability wavepackets and turbulent spots in a hypersonic boundary layer

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Casper, Katya M.; Beresh, Steven J.; Schneider, Steven P.

    2014-09-09

    To investigate the pressure-fluctuation field beneath turbulent spots in a hypersonic boundary layer, a study was conducted on the nozzle wall of the Boeing/AFOSR Mach-6 Quiet Tunnel. Controlled disturbances were created by pulsed-glow perturbations based on the electrical breakdown of air. Under quiet-flow conditions, the nozzle-wall boundary layer remains laminar and grows very thick over the long nozzle length. This allows the development of large disturbances that can be well-resolved with high-frequency pressure transducers. A disturbance first grows into a second-mode instability wavepacket that is concentrated near its own centreline. Weaker disturbances are seen spreading from the centre. The wavesmore » grow and become nonlinear before breaking down to turbulence. The breakdown begins in the core of the packets where the wave amplitudes are largest. Second-mode waves are still evident in front of and behind the breakdown point and can be seen propagating in the spanwise direction. The turbulent core grows downstream, resulting in a spot with a classical arrowhead shape. Behind the spot, a low-pressure calmed region develops. However, the spot is not merely a localized patch of turbulence; instability waves remain an integral part. Limited measurements of naturally occurring disturbances show many similar characteristics. From the controlled disturbance measurements, the convection velocity, spanwise spreading angle, and typical pressure-fluctuation field were obtained.« less

  7. An instability of hyperbolic space under the Yang-Mills flow

    SciTech Connect (OSTI)

    Gegenberg, Jack; Day, Andrew C.; Liu, Haitao; Seahra, Sanjeev S.

    2014-04-15

    We consider the Yang-Mills flow on hyperbolic 3-space. The gauge connection is constructed from the frame-field and (not necessarily compatible) spin connection components. The fixed points of this flow include zero Yang-Mills curvature configurations, for which the spin connection has zero torsion and the associated Riemannian geometry is one of constant curvature. We analytically solve the linearized flow equations for a large class of perturbations to the fixed point corresponding to hyperbolic 3-space. These can be expressed as a linear superposition of distinct modes, some of which are exponentially growing along the flow. The growing modes imply the divergence of the (gauge invariant) perturbative torsion for a wide class of initial data, indicating an instability of the background geometry that we confirm with numeric simulations in the partially compactified case. There are stable modes with zero torsion, but all the unstable modes are torsion-full. This leads us to speculate that the instability is induced by the torsion degrees of freedom present in the Yang-Mills flow.

  8. Spatial growth of the current-driven instability in relativistic jets

    SciTech Connect (OSTI)

    Mizuno, Yosuke; Hardee, Philip E.; Nishikawa, Ken-Ichi

    2014-04-01

    We investigated the influence of velocity shear and a radial density profile on the spatial development of the current-driven (CD) kink instability along helically magnetized relativistic jets via three-dimensional relativistic magnetohydrodynamic simulations. In this study, we use a nonperiodic computational box, the jet flow is initially established across the computational grid, and a precessional perturbation at the inlet triggers growth of the kink instability. If the velocity shear radius is located inside the characteristic radius of the helical magnetic field, a static nonpropagating CD kink is excited as the perturbation propagates down the jet. Temporal growth disrupts the initial flow across the computational grid not too far from the inlet. On the other hand, if the velocity shear radius is outside the characteristic radius of the helical magnetic field, the kink is advected with the flow and grows spatially down the jet. In this case, flow is maintained to much larger distances from the inlet. The effect of different radial density profiles is more subtle. When the density increases with radius, the kink appears to saturate by the end of the simulation without apparent disruption of the helical twist. This behavior suggests that relativistic jets consisting of a tenuous spine surrounded by a denser medium with a velocity shear radius outside the radius of the maximum toroidal magnetic field have a relatively stable configuration.

  9. Observations of supra-arcade fans: instabilities at the head of reconnection jets

    SciTech Connect (OSTI)

    Innes, D. E.; Guo, L.-J.; Schmit, D.; Bhattacharjee, A.; Huang, Y.-M.

    2014-11-20

    Supra-arcade fans are bright, irregular regions of emission that develop during eruptive flares above flare arcades. The underlying flare arcades are thought to be a consequence of magnetic reconnection along a current sheet in the corona. At the same time, theory predicts plasma jets from the reconnection sites which are extremely difficult to observe directly because of their low densities. It has been suggested that the dark supra-arcade downflows (SADs) seen falling through supra-arcade fans may be low-density jet plasma. The head of a low-density jet directed toward higher-density plasma would be Rayleigh-Taylor unstable, and lead to the development of rapidly growing low- and high-density fingers along the interface. Using Solar Dynamics Observatory/Atmospheric Imaging Assembly 131 images, we show details of SADs seen from three different orientations with respect to the flare arcade and current sheet, and highlight features that have been previously unexplained, such as the splitting of SADs at their heads, but are a natural consequence of instabilities above the arcade. Comparison with three-dimensional magnetohydrodynamic simulations suggests that SADs are the result of secondary instabilities of the Rayleigh-Taylor type in the exhaust of reconnection jets.

  10. Single bunch transverse instability in a circular accelerator with chromaticity and space charge

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Balbekov, V.

    2015-10-21

    The transverse instability of a bunch in a circular accelerator is elaborated in this paper. A new tree-modes model is proposed and developed to describe the most unstable modes of the bunch. This simple and flexible model includes chromaticity and space charge, and can be used with any bunch and wake forms. The dispersion equation for the bunch eigentunes is obtained in form of a third-order algebraic equation. The known head-tail and TMCI modes appear as the limiting cases which are distinctly bounded at zero chromaticity only. It is shown that the instability parameters depend only slightly on the bunchmore » model but they are rather sensitive to the wake shape. In particular, space charge effects are investigated in the paper and it is shown that their influence depends on sign of wake field enhancing the bunch stability if the wake is negative. In addition, the resistive wall wake is considered in detail including a comparison of single and collective effects. A comparison of the results with earlier publications is carried out.« less

  11. Recombinant transfer in the basic genome of E. coli

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dixit, Purushottam; Studier, F. William; Pang, Tin Yau; Maslov, Sergei

    2015-07-07

    An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly betweenmoregenomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.41% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kbp. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. As a result, most recombinant transfers seem likely to be due to generalized transduction by co-evolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.less

  12. Simulation of e-cloud driven instability and its attenuation using a simulated feedback system in the CERN SPS

    SciTech Connect (OSTI)

    Vay, J.-L.; Furman, M. A.

    2010-12-13

    Electron clouds have been shown to trigger fast growing instabilities on proton beams circulating in the SPS, and a feedback system to control the single-bunch instabilities is under active development. We present the latest improvements to the WARP-POSINST simulation framework and feedback model, and its application to the self-consistent simulations of two consecutive bunches interacting with an electron cloud in the SPS. Simulations using an idealized feedback system exhibit adequate mitigation of the instability providing that the cutoff of the feedback bandwidth is at or above 450 MHz. Artifacts from numerical noise of the injected distribution of electrons in the modeling of portions of bunch trains are discussed, and benchmarking of WARP against POSINST and HEADTAIL are presented.

  13. MetaGenomic Assembly by Merging (MeGAMerge)

    Energy Science and Technology Software Center (OSTI)

    2015-08-03

    "MetaGenomic Assembly by Merging" (MeGAMerge)Is a novel method of merging of multiple genomic assembly or long read data sources for assembly by use of internal trimming/filtering of data, followed by use of two 3rd party tools to merge data by overlap based assembly.

  14. Draft Genome Sequence of Neurospora crassa Strain FGSC 73

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Baker, Scott E.; Schackwitz, Wendy; Lipzen, Anna; Martin, Joel; Haridas, Sajeet; LaButti, Kurt; Grigoriev, Igor V.; Simmons, Blake A.; McCluskey, Kevin

    2015-04-02

    We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a, trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models.

  15. Development of Mechanistic Modeling Capabilities for Local Neutronically-Coupled Flow-Induced Instabilities in Advanced Water-Cooled Reactors

    SciTech Connect (OSTI)

    Michael Podowski

    2009-11-30

    The major research objectives of this project included the formulation of flow and heat transfer modeling framework for the analysis of flow-induced instabilities in advanced light water nuclear reactors such as boiling water reactors. General multifield model of two-phase flow, including the necessary closure laws. Development of neurton kinetics models compatible with the proposed models of heated channel dynamics. Formulation and encoding of complete coupled neutronics/thermal-hydraulics models for the analysis of spatially-dependent local core instabilities. Computer simulations aimed at testing and validating the new models of reactor dynamics.

  16. Complete genome sequence of Cellulomonas flavigena type strain (134T)

    SciTech Connect (OSTI)

    Abt, Birte; Foster, Brian; Lapidus, Alla L.; Clum, Alicia; Sun, Hui; Pukall, Rudiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. The Genome of the Western Clawed Frog Xenopus tropicalis

    SciTech Connect (OSTI)

    Hellsten, Uffe; Harland, Richard M.; Gilchrist, Michael J.; Hendrix, David; Jurka, Jerzy; Kapitonov, Vladimir; Ovcharenko, Ivan; Putnam, Nicholas H.; Shu, Shengqiang; Taher, Leila; Blitz, Ira L.; Blumberg, Bruce; Dichmann, Darwin S.; Dubchak, Inna; Amaya, Enrique; Detter, John C.; Fletcher, Russell; Gerhard, Daniela S.; Goodstein, David; Graves, Tina; Grigoriev, Igor V.; Grimwood, Jane; Kawashima, Takeshi; Lindquist, Erika; Lucas, Susan M.; Mead, Paul E.; Mitros, Therese; Ogino, Hajime; Ohta, Yuko; Poliakov, Alexander V.; Pollet, Nicolas; Robert, Jacques; Salamov, Asaf; Sater, Amy K.; Schmutz, Jeremy; Terry, Astrid; Vize, Peter D.; Warren, Wesley C.; Wells, Dan; Wills, Andrea; Wilson, Richard K.; Zimmerman, Lyle B.; Zorn, Aaron M.; Grainger, Robert; Grammer, Timothy; Khokha, Mustafa K.; Richardson, Paul M.; Rokhsar, Daniel S.

    2009-10-01

    The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes over 20,000 protein-coding genes, including orthologs of at least 1,700 human disease genes. Over a million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like other tetrapods, the genome contains gene deserts enriched for conserved non-coding elements. The genome exhibits remarkable shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.

  18. The Trichoplax Genome and the Nature of Placozoans

    SciTech Connect (OSTI)

    Srivastava, Mansi; Begovic, Emina; Chapman, Jarrod; Putnam, Nicholas H.; Hellsten, Uffe; Kawashima, Takeshi; Kuo, Alan; Mitros, Therese; Salamov, Asaf; Carpenter, Meredith L.; Signorovitch, Ana Y.; Moreno, Maria A.; Kamm, Kai; Grimwood, Jane; Schmutz, Jeremy; Shapiro, Harris; Grigoriev, Igor V.; Buss, Leo W.; Schierwater, Bernd; Dellaporta, Stephen L.; Rokhsar, Daniel S.

    2008-08-01

    Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits conserved gene content, gene structure, and synteny relative to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signaling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.

  19. Genomic Island Identification Software v 1.0

    Energy Science and Technology Software Center (OSTI)

    2014-08-25

    Genomic islands are key mobile DNA elements in bacterial evolution, that can distinguish pathogenic strains from each other, or distinguish pathogenic strains from non-pathogenic strains. Their detection in genomes is a challenging problem. We present 3 main software components that attack the island detection problem on two different bases: 1) the preference of islands to insert in chromosomal tRNA or tmRNA genes (islander.pl), and 2) islands’ sporadic occurrence among closely related strains. The latter principlemore » is employed in both an algorithm (learnedPhyloblocks.pl) and a visualization method (panGenome.pl). Component islander.pl finds islands based on their preference for a particular target gene type. We annotate each tRNA and tmRNA gene, find fragments of each such gene as candidates for the distal ends of islands, and filter candidates to remove false positives. Component learnedPhyloblocks.pl uses islands found by islander.pl and other methods as a training set to find new islands. Reference genomes are aligned using mugsy, then the “phylotypes” or patterns of occurrence in the reference set are determined for each position in the target genome, and those phylotypes most enriched in the training set of islands are followed to detect yet more islands. Component panGenome.pl produces a big-data visualization of the chromosomally-ordered “pan-genome”, that includes every gene of every reference genome (x-axis, pan-genome order; y-axis, reference genomes; color-coding, gene presence/absence etc.), islands appearing as dark patches.« less

  20. Genomic Island Identification Software v 1.0

    SciTech Connect (OSTI)

    2014-08-25

    Genomic islands are key mobile DNA elements in bacterial evolution, that can distinguish pathogenic strains from each other, or distinguish pathogenic strains from non-pathogenic strains. Their detection in genomes is a challenging problem. We present 3 main software components that attack the island detection problem on two different bases: 1) the preference of islands to insert in chromosomal tRNA or tmRNA genes (islander.pl), and 2) islands? sporadic occurrence among closely related strains. The latter principle is employed in both an algorithm (learnedPhyloblocks.pl) and a visualization method (panGenome.pl). Component islander.pl finds islands based on their preference for a particular target gene type. We annotate each tRNA and tmRNA gene, find fragments of each such gene as candidates for the distal ends of islands, and filter candidates to remove false positives. Component learnedPhyloblocks.pl uses islands found by islander.pl and other methods as a training set to find new islands. Reference genomes are aligned using mugsy, then the ?phylotypes? or patterns of occurrence in the reference set are determined for each position in the target genome, and those phylotypes most enriched in the training set of islands are followed to detect yet more islands. Component panGenome.pl produces a big-data visualization of the chromosomally-ordered ?pan-genome?, that includes every gene of every reference genome (x-axis, pan-genome order; y-axis, reference genomes; color-coding, gene presence/absence etc.), islands appearing as dark patches.