National Library of Energy BETA

Sample records for antifungal drug molecules

  1. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Wednesday, 24 February 2010 00:00 Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in

  2. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  3. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  4. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  5. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  6. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  7. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  8. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  9. Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography

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

    Imaging Antifungal Drug Molecules in Action using Soft X-Ray Tomography Print Humankind has benefitted from a long and productive relationship with yeast. For example, fermentation by yeast is an essential step in the production of bread, beer, wine, and even biofuels. However, not all yeast are beneficial. One strain of yeast, Candida albicans, grows unnoticed on most peoples' skin and in the intestines. In response to certain environmental conditions, C. albicans can switch to a pathogenic

  10. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J.; Ellanskaya, Irina; Ellanskaya, legal representative, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2009-09-15

    The invention relates to antifungal compositions and methods for protecting a plant from a fungal pathogen. Compositions including antifungal polypeptides isolated from a fungal fermentation broth are provided.

  11. Imaging Antifungal Drug Molecules in Action using Soft X-Ray...

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

    development. Cell CAT Scans: 3-D Cell Imaging Routine medical x rays, such as chest x rays, can be used to identify a number of diseases. But this technique only produces...

  12. Molecule Nanoweaver Improves Drug Delivery and Treatment Efficacy...

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

    along the synthetic route by using the powerful tool of solid-state NMR analyses. Upon development of a mature protocol, the Molecule Nanoweaver would operate on an assembly...

  13. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J.; Dahlbacka, Glen; Elleskaya, Irina; Ellanskaya, legal representative, Natalia; Herrmann, Rafael; Hunter-Cevera, Jennie; McCutchen, Billy F.; Presnail, James K.; Rice, Janet A.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2011-04-12

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  14. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J.; Dahlbacka, Glen; Ellanskaya, Irina; Ellanskaya, legal representative, Natalia; Herrmann, Rafael; Hunter-Cevera, Jennie; McCutchen, Billy F.; Presnail, James K.; Rice, Janet A.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2012-04-03

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  15. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J.; Dahlbacka, Glen; Ellanskaya, legal representative, Natalia; Herrmann, Rafael; Hunter-Cevera, Jennie; McCutchen, Billy F.; Presnail, James K.; Rice, Janet A.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser; Ellanskaya, deceased, Irina

    2007-12-11

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  16. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J.; Dahlbacka, Glen; Elleskaya, Irina; Ellanskaya, legal representative; Natalia; Herrmann, Rafael; Hunter-Cevera, Jennie; McCutchen, Billy F.; Presnail, James K.; Rice, Janet A.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-08-10

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  17. NERSC Helps Physicists ID New Molecules With Unique Features

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

    applications," they wrote. "These molecules can be used for targeted non-invasive drug delivery. When assembled, the molecules can also form new high strength magnets...

  18. Novel short antibacterial and antifungal peptides with low cytotoxicity:

    Office of Scientific and Technical Information (OSTI)

    Efficacy and action mechanisms (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Novel short antibacterial and antifungal peptides with low cytotoxicity: Efficacy and action mechanisms Citation Details In-Document Search Title: Novel short antibacterial and antifungal peptides with low cytotoxicity: Efficacy and action mechanisms Research highlights: {yields} Short antimicrobial peptides with nine and eleven residues were developed. {yields} These peptides

  19. X-ray characterization of solid small molecule organic materials

    SciTech Connect (OSTI)

    Billinge, Simon; Shankland, Kenneth; Shankland, Norman; Florence, Alastair

    2014-06-10

    The present invention provides, inter alia, methods of characterizing a small molecule organic material, e.g., a drug or a drug product. This method includes subjecting the solid small molecule organic material to x-ray total scattering analysis at a short wavelength, collecting data generated thereby, and mathematically transforming the data to provide a refined set of data.

  20. NERSC Helps Physicists ID New Molecules With Unique Features

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

    NERSC Helps Physicists ID New Molecules With Unique Features NERSC Helps Physicists ID New Molecules With Unique Features Hollow magnetic cage molecules may have applications in technology, healthcare August 10, 2013 NERSC supercomputing resources helped Virginia Commonwealth University (VCU) researchers determine it may be possible to create large, hollow magnetic cage molecules that could be used in medicine as a drug delivery system to noninvasively treat tumors and in other emerging

  1. Cool Magnetic Molecules

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

    and chemistry of small molecules. An international collaboration of researchers from Spain, Scotland, and the U.S. has utilized ALS Beamline 11.3.1 (small-molecule...

  2. Prescription Drugs

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

    Prescription Drugs Prescription Drugs Prescription drug benefits are determined by your medical plan. Contact Prime Therapeutics Prescription drug coverage for retirees Your Blue Cross and Blue Shield of New Mexico (BCBSNM) health plan includes a prescription drug benefit administered by Prime Therapeutics. The cost of the prescription drug plan is included in your medical premiums. Coverage The co-pays for prescription drugs are based on a 3-tier prescription drug benefit. Co-payments are

  3. Cool Magnetic Molecules

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

    Cool Magnetic Molecules Cool Magnetic Molecules Print Wednesday, 25 May 2011 00:00 Certain materials are known to heat up or cool down when they are exposed to a changing magnetic field. This is known as the magnetocaloric effect. All magnetic materials exhibit this effect, but in most cases, it is too small to be technologically useful. Recently, however, the search for special molecules with a surprisingly large capacity to keep cool has heated up, driven by environmental and cost

  4. Cool Magnetic Molecules

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

    of researchers from Spain, Scotland, and the U.S. has utilized ALS Beamline 11.3.1 (small-molecule crystallography) to characterize the design of such "molecular coolers." ...

  5. Cool Magnetic Molecules

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

    Cool Magnetic Molecules Print Certain materials are known to heat up or cool down when they are exposed to a changing magnetic field. This is known as the magnetocaloric effect. All magnetic materials exhibit this effect, but in most cases, it is too small to be technologically useful. Recently, however, the search for special molecules with a surprisingly large capacity to keep cool has heated up, driven by environmental and cost considerations as well as by recent improvements in our ability

  6. Cool Magnetic Molecules

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

    Cool Magnetic Molecules Print Certain materials are known to heat up or cool down when they are exposed to a changing magnetic field. This is known as the magnetocaloric effect. All magnetic materials exhibit this effect, but in most cases, it is too small to be technologically useful. Recently, however, the search for special molecules with a surprisingly large capacity to keep cool has heated up, driven by environmental and cost considerations as well as by recent improvements in our ability

  7. Cool Magnetic Molecules

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

    Cool Magnetic Molecules Print Certain materials are known to heat up or cool down when they are exposed to a changing magnetic field. This is known as the magnetocaloric effect. All magnetic materials exhibit this effect, but in most cases, it is too small to be technologically useful. Recently, however, the search for special molecules with a surprisingly large capacity to keep cool has heated up, driven by environmental and cost considerations as well as by recent improvements in our ability

  8. Roaming Molecule Dynamics

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

    Roaming Molecule Dynamics - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs

  9. Smarter Drugs: How Protein Crystallography Revolutionizes Drug Design

    SciTech Connect (OSTI)

    Smith, Clyde

    2005-04-26

    According to Smith, protein crystallography allows scientists to design drugs in a much more efficient way than the standard methods traditionally used by large drug companies, which can cost close to a billion dollars and take 10 to 15 years. 'A lot of the work can be compressed down,' Smith said. Protein crystallography enables researchers to learn the structure of molecules involved in disease and health. Seeing the loops, folds and placement of atoms in anything from a virus to a healthy cell membrane gives important information about how these things work - and how to encourage, sidestep or stop their functions. Drug design can be much faster when the relationship between structure and function tells you what area of a molecule to target. Smith will use a timeline to illustrate the traditional methods of drug development and the new ways it can be done now. 'It is very exciting work. There have been some failures, but many successes too.' A new drug to combat the flu was developed in a year or so. Smith will tell us how. He will also highlight drugs developed to combat HIV, Tuberculosis, hypertension and Anthrax.

  10. Protein-Based Nanomedicine Platforms for Drug Delivery

    SciTech Connect (OSTI)

    Ma Ham, Aihui; Tang, Zhiwen; Wu, Hong; Wang, Jun; Lin, Yuehe

    2009-08-03

    Drug delivery systems have been developed for many years, however some limitations still hurdle the pace of going to clinical phase, for example, poor biodistribution, drug molecule cytotoxicity, tissue damage, quick clearance from the circulation system, solubility and stability of drug molecules. To overcome the limitations of drug delivery, biomaterials have to be developed and applied to drug delivery to protect the drug molecules and to enhance the drug’s efficacy. Protein-based nanomedicine platforms for drug delivery are platforms comprised of naturally self-assembled protein subunits of the same protein or a combination of proteins making up a complete system. They are ideal for drug delivery platforms due to their biocompatibility and biodegradability coupled with low toxicity. A variety of proteins have been used and characterized for drug delivery systems including the ferritin/apoferritin protein cage, plant derived viral capsids, the small Heat shock protein (sHsp) cage, albumin, soy and whey protein, collagen, and gelatin. There are many different types and shapes that have been prepared to deliver drug molecules using protein-based platforms including the various protein cages, microspheres, nanoparticles, hydrogels, films, minirods and minipellets. There are over 30 therapeutic compounds that have been investigated with protein-based drug delivery platforms for the potential treatment of various cancers, infectious diseases, chronic diseases, autoimmune diseases. In protein-based drug delivery platforms, protein cage is the most newly developed biomaterials for drug delivery and therapeutic applications. Their uniform sizes, multifunctions, and biodegradability push them to the frontier for drug delivery. In this review, the recent strategic development of drug delivery has been discussed with a special emphasis upon the polymer based, especially protein-based nanomedicine platforms for drug delivery. The advantages and disadvantages are also discussed for each type of protein based drug delivery system.

  11. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    DOE Patents [OSTI]

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  12. Single molecule tracking

    DOE Patents [OSTI]

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  13. Single molecule tracking

    DOE Patents [OSTI]

    Shera, E.B.

    1987-10-07

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

  14. Electrochromic Graphene Molecules

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

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  15. Electrochromic Graphene Molecules

    SciTech Connect (OSTI)

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were found to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.

  16. Aromatic molecules as spintronic devices

    SciTech Connect (OSTI)

    Ojeda, J. H.; Orellana, P. A.; Laroze, D.

    2014-03-14

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

  17. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J.; Ellanskaya, I. A.; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  18. Quantum transport through aromatic molecules

    SciTech Connect (OSTI)

    Ojeda, J. H.; Rey-González, R. R.; Laroze, D.

    2013-12-07

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices.

  19. ALSNews Vol. 306

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

    6 Print In This Issue 200th Science Highlight Imaging Antifungal Drug Molecules with Soft X-Ray Tomography Electron Correlation in Iron-based Superconductors A New Route to Nano...

  20. ALSNews Vol. 306

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

    06 Print In This Issue 200th Science Highlight Imaging Antifungal Drug Molecules with Soft X-Ray Tomography Electron Correlation in Iron-based Superconductors A New Route to Nano...

  1. ALSNews Vol. 306

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

    24 February 2010 00:00 In This Issue 200th Science Highlight Imaging Antifungal Drug Molecules with Soft X-Ray Tomography Electron Correlation in Iron-based Superconductors...

  2. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J.; Crane, Virginia C.; Ellanskaya, Irina; Ellanskaya, legal representative, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric J.; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2009-10-06

    The invention relates to compositions including amino acid sequences isolated from fungal fermentation broths and methods for protecting a plant from a pathogen, particularly a fungal pathogen.

  3. Biomimetic Dye Molecules for Solar Cells

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

    cell. The class of dye molecules used in this research is related to the dye that gives blue jeans their color. By choosing organic molecules, an enormous repertoire of possible...

  4. Ultrafast electron diffraction from aligned molecules

    SciTech Connect (OSTI)

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  5. Multifunctional hyper-structured molecules

    SciTech Connect (OSTI)

    Wada, T.; Zhang, Y.; Aoyama, T.; Kubo, Y.; Sasabe, H.

    1998-07-01

    To fill the gap between molecular design and the architecture of three-dimensional functional structures, the authors propose novel hyper-structured molecules (HSMs) based on well-defined and topologically controlled molecular systems. To this end they have developed carbazole dendrimers, trimers, cyclic oligomers and chromogenic calix[4]arenes as HSMs. Photorefractivity was selected as the primary target function of these HSMs. Oligomers developed in their laboratory exhibit intrinsic photocarrier generation, transport, electro-optic, film-forming and poling properties. These multifunctional properties allow us to demonstrate optical image processing using optical phase conjugation. The topological shapes of indoaniline-derived calix[4]arenes were studied by hyper-Rayleigh scattering. The two indoaniline moieties in calix[4]arene derivatives were pre-aligned so as to enhance the net molecular hyperpolarizability. Besides dendric oligomers, cyclic oligomers can be used as a molecular platform which allows molecular level tuning of shape, size and topology for superior opto-electronic functions.

  6. Electrokinetic concentration of charged molecules

    DOE Patents [OSTI]

    Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.; Garguilo, Michael G.

    2002-01-01

    A method for separating and concentrating charged species from uncharged or neutral species regardless of size differential. The method uses reversible electric field induced retention of charged species, that can include molecules and molecular aggregates such as dimers, polymers, multimers, colloids, micelles, and liposomes, in volumes and on surfaces of porous materials. The retained charged species are subsequently quantitatively removed from the porous material by a pressure driven flow that passes through the retention volume and is independent of direction thus, a multi-directional flow field is not required. Uncharged species pass through the system unimpeded thus effecting a complete separation of charged and uncharged species and making possible concentration factors greater than 1000-fold.

  7. Electrorheological crystallization of proteins and other molecules

    DOE Patents [OSTI]

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  8. Electrorheological crystallization of proteins and other molecules

    DOE Patents [OSTI]

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  9. Biomimetic Dye Molecules for Solar Cells

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

    Organic molecules in dye-sensitized solar cells exhibit great potential to increase the efficiency and reduce the cost of photovoltaic power generation by allowing a wide variety ...

  10. Covalent Bonding in Actinide Sandwich Molecules

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

    rows) mix with orbitals of carbon in various configurations has been the subject of debate. Development of more precise models of the electronic structure in molecules with...

  11. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell...

  12. Inverted, semitransparent small molecule photovoltaic cells ...

    Office of Scientific and Technical Information (OSTI)

    small molecule photovoltaic cells Authors: Xiao, Xin 1 ; Lee, Kyusang 1 ; Forrest, Stephen R. 2 + Show Author Affiliations Department of Electrical Engineering and Computer...

  13. Biomimetic Dye Molecules for Solar Cells

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

    Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption....

  14. Covalent Bonding in Actinide Sandwich Molecules

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

    improvements in organometallic catalysts that are employed across industry for the polymerization of organic molecules. In this study, Minasian et al. quantitatively probe...

  15. Pharmacokinetic drivers of toxicity for basic molecules: Strategy to lower pKa results in decreased tissue exposure and toxicity for a small molecule Met inhibitor

    SciTech Connect (OSTI)

    Diaz, Dolores; Ford, Kevin A.; Hartley, Dylan P.; Harstad, Eric B.; Cain, Gary R.; Achilles-Poon, Kirsten; Nguyen, Trung; Peng, Jing; Zheng, Zhong; Merchant, Mark; Sutherlin, Daniel P.; Gaudino, John J.; Kaus, Robert; Lewin-Koh, Sock C.; Choo, Edna F.; Liederer, Bianca M.; Dambach, Donna M.

    2013-01-01

    Several toxicities are clearly driven by free drug concentrations in plasma, such as toxicities related to on-target exaggerated pharmacology or off-target pharmacological activity associated with receptors, enzymes or ion channels. However, there are examples in which organ toxicities appear to correlate better with total drug concentrations in the target tissues, rather than with free drug concentrations in plasma. Here we present a case study in which a small molecule Met inhibitor, GEN-203, with significant liver and bone marrow toxicity in preclinical species was modified with the intention of increasing the safety margin. GEN-203 is a lipophilic weak base as demonstrated by its physicochemical and structural properties: high LogD (distribution coefficient) (4.3) and high measured pKa (7.45) due to the basic amine (N-ethyl-3-fluoro-4-aminopiperidine). The physicochemical properties of GEN-203 were hypothesized to drive the high distribution of this compound to tissues as evidenced by a moderately-high volume of distribution (Vd > 3 l/kg) in mouse and subsequent toxicities of the compound. Specifically, the basicity of GEN-203 was decreased through addition of a second fluorine in the 3-position of the aminopiperidine to yield GEN-890 (N-ethyl-3,3-difluoro-4-aminopiperidine), which decreased the volume of distribution of the compound in mouse (Vd = 1.0 l/kg), decreased its tissue drug concentrations and led to decreased toxicity in mice. This strategy suggests that when toxicity is driven by tissue drug concentrations, optimization of the physicochemical parameters that drive tissue distribution can result in decreased drug concentrations in tissues, resulting in lower toxicity and improved safety margins. -- Highlights: ? Lower pKa for a small molecule: reduced tissue drug levels and toxicity. ? New analysis tools to assess electrostatic effects and ionization are presented. ? Chemical and PK drivers of toxicity can be leveraged to improve safety.

  16. Tumor suppressor molecules and methods of use

    DOE Patents [OSTI]

    Welch, Peter J.; Barber, Jack R.

    2004-09-07

    The invention provides substantially pure tumor suppressor nucleic acid molecules and tumor suppressor polypeptides. The invention also provides hairpin ribozymes and antibodies selective for these tumor suppressor molecules. Also provided are methods of detecting a neoplastic cell in a sample using detectable agents specific for the tumor suppressor nucleic acids and polypeptides.

  17. Attachment of second harmonic-active moiety to molecules for detection of molecules at interfaces

    DOE Patents [OSTI]

    Salafsky, Joshua S.; Eisenthal, Kenneth B.

    2005-10-11

    This invention provides methods of detecting molecules at an interface, which comprise labeling the molecules with a second harmonic-active moiety and detecting the labeled molecules at the interface using a surface selective technique. The invention also provides methods for detecting a molecule in a medium and for determining the orientation of a molecular species within a planar surface using a second harmonic-active moiety and a surface selective technique.

  18. Chiral Isotropic Liquids from Achiral Molecules

    SciTech Connect (OSTI)

    L Hough; M Spannuth; M Nakata; D Coleman; C Jones; G Dantlgraber; C Tschierske; J Watanabe; N Clark; et al.

    2011-12-31

    A variety of simple bent-core molecules exhibit smectic liquid crystal phases of planar fluid layers that are spontaneously both polar and chiral in the absence of crystalline order. We found that because of intralayer structural mismatch, such layers are also only marginally stable against spontaneous saddle splay deformation, which is incompatible with long-range order. This results in macroscopically isotropic fluids that possess only short-range orientational and positional order, in which the only macroscopically broken symmetry is chirality - even though the phases are formed from achiral molecules. Their conglomerate domains exhibit optical rotatory powers comparable to the highest ever found for isotropic fluids of chiral molecules.

  19. Biomimetic Dye Molecules for Solar Cells

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

    electron transfer, for example in hemoglobin and cytochrome c. The active center of these dyes-the heme-is similar to that of porphyrin molecules, but it contains additional atoms...

  20. Biomimetic Dye Molecules for Solar Cells

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

    The most cost-effective solar cells are not high-end, high-efficiency single-crystal devices, but rather low-end cells based on organic molecules or conducting polymers. Vital ...

  1. Do triatomic molecules echo atomic periodicity?

    SciTech Connect (OSTI)

    Hefferlin, R. Barrow, J.

    2015-03-30

    Demonstrations of periodicity among triatomic-molecular spectroscopic constants underscore the role of the periodic law as a foundation of chemistry. The objective of this work is to prepare for another test using vibration frequencies ?{sub 1} of free, ground-state, main-group triatomic molecules. Using data from four data bases and from computation, we have collected ?{sub 1} data for molecules formed from second period atoms.

  2. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Biomimetic Dye Molecules for Solar Cells Print Wednesday, 28 April 2010 00:00 Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most

  3. Recovery of tritium from tritiated molecules

    DOE Patents [OSTI]

    Swansiger, W.A.

    1984-10-17

    This invention relates to the recovery of tritium from various tritiated molecules by reaction with uranium. More particularly, the invention relates to the recovery of tritium from tritiated molecules by reaction with uranium wherein the reaction is conducted in a reactor which permits the reaction to occur as a moving front reaction from the point where the tritium enters the reactor charged with uranium down the reactor until the uranium is exhausted.

  4. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Covalent Bonding in Actinide Sandwich Molecules Print Wednesday, 28 May 2014 00:00 Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic

  5. Sol-gel method for encapsulating molecules

    DOE Patents [OSTI]

    Brinker, C. Jeffrey; Ashley, Carol S.; Bhatia, Rimple; Singh, Anup K.

    2002-01-01

    A method for encapsulating organic molecules, and in particular, biomolecules using sol-gel chemistry. A silica sol is prepared from an aqueous alkali metal silicate solution, such as a mixture of silicon dioxide and sodium or potassium oxide in water. The pH is adjusted to a suitably low value to stabilize the sol by minimizing the rate of siloxane condensation, thereby allowing storage stability of the sol prior to gelation. The organic molecules, generally in solution, is then added with the organic molecules being encapsulated in the sol matrix. After aging, either a thin film can be prepared or a gel can be formed with the encapsulated molecules. Depending upon the acid used, pH, and other processing conditions, the gelation time can be from one minute up to several days. In the method of the present invention, no alcohols are generated as by-products during the sol-gel and encapsulation steps. The organic molecules can be added at any desired pH value, where the pH value is generally chosen to achieve the desired reactivity of the organic molecules. The method of the present invention thereby presents a sufficiently mild encapsulation method to retain a significant portion of the activity of the biomolecules, compared with the activity of the biomolecules in free solution.

  6. A Supramolecular Complex in Small-Molecule Solar Cells based...

    Office of Scientific and Technical Information (OSTI)

    in Small-Molecule Solar Cells based on Contorted Aromatic Molecules Citation Details In-Document Search Title: A Supramolecular Complex in Small-Molecule Solar Cells based on ...

  7. Reliable Energy Level Alignment at Physisorbed Molecule-Metal...

    Office of Scientific and Technical Information (OSTI)

    at Physisorbed Molecule-Metal Interfaces from Density Functional Theory Title: Reliable Energy Level Alignment at Physisorbed Molecule-Metal Interfaces from Density Functional ...

  8. Measurement of the formation rate of muonic hydrogen molecules...

    Office of Scientific and Technical Information (OSTI)

    the formation rate of muonic hydrogen molecules Citation Details In-Document Search Title: Measurement of the formation rate of muonic hydrogen molecules Authors: Andreev, V. A. ; ...

  9. Nanopost Arrays Anchor Molecules, Improve Ion Yields for Laser...

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

    Nanopost Arrays Anchor Molecules, Improve Ion Yields for Laser Mass Spectrometry Oak Ridge ... to detect and analyze molecules by laser mass spectrometry: A matrix of nanoposts ...

  10. Molecule Nanoweaver Creates High-Tech Medical Patches and Multilayered...

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

    Molecule Nanoweaver Creates High-Tech Medical Patches and Multilayered Capsules Technology available for licensing: Molecule Nanoweaver, a unique tool that can be used as both a...

  11. Los Alamos scientists detect and track single molecules with...

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

    molecules with nanoscale carbon cylinders Researchers have now shown that semiconducting carbon nanotubes have the potential to detect and track single molecules in water. January...

  12. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect (OSTI)

    Baker, David

    2014-09-14

    We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.

  13. Cavity sideband cooling of trapped molecules

    SciTech Connect (OSTI)

    Kowalewski, Markus; Vivie-Riedle, Regina de [Department of Chemistry, Ludwig-Maximilian-Universitaet, D-81377 Munich (Germany); Morigi, Giovanna [Departament de Fisica, Universitat Autonoma de Barcelona, E-08193 Bellaterra (Spain); Theoretische Physik, Universitaet des Saarlandes, D-66041 Saarbruecken (Germany); Pinkse, Pepijn W. H. [MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE Enschede (Netherlands)

    2011-09-15

    The efficiency of cavity sideband cooling of trapped molecules is theoretically investigated for the case in which the infrared transition between two rovibrational states is used as a cycling transition. The molecules are assumed to be trapped either by a radiofrequency or optical trapping potential, depending on whether they are charged or neutral, and confined inside a high-finesse optical resonator that enhances radiative emission into the cavity mode. Using realistic experimental parameters and COS as a representative molecular example, we show that in this setup, cooling to the trap ground state is feasible.

  14. Drug Testing Notification | Department of Energy

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

    Drug Testing Notification Drug Testing Notification PDF icon Drug Testing Notification More Documents & Publications Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, ...

  15. Method for sequencing nucleic acid molecules

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-06-06

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  16. Method for sequencing nucleic acid molecules

    DOE Patents [OSTI]

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-05-30

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  17. Seeing Atoms and Molecules in Action with an Electron 'Eye'

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

    Seeing Atoms and Molecules in Action with an Electron 'Eye' ← Previous Next →

  18. Automated imaging system for single molecules

    DOE Patents [OSTI]

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  19. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  20. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  1. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  2. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  3. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  4. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  5. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  6. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  7. Biomimetic Dye Molecules for Solar Cells

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

    Biomimetic Dye Molecules for Solar Cells Print Pressing energy problems provide opportunities for solid-state physicists and chemists to solve a major challenge: solar cell adoption. Though solar cells can use energy directly from the Sun to produce electricity that can be converted efficiently into other kinds of energy, they are currently too costly to compete with traditional (polluting) energy sources. The most cost-effective solar cells are not high-end, high-efficiency single-crystal

  8. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Print Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic actinide "sandwich" complexes that have been lightning rods in

  9. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Print Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic actinide "sandwich" complexes that have been lightning rods in

  10. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Print Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic actinide "sandwich" complexes that have been lightning rods in

  11. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Print Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic actinide "sandwich" complexes that have been lightning rods in

  12. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Print Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic actinide "sandwich" complexes that have been lightning rods in

  13. Covalent Bonding in Actinide Sandwich Molecules

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

    Covalent Bonding in Actinide Sandwich Molecules Print Glenn Seaborg was one of the first scientists to recognize that differences in the degree of covalent bonding in lanthanide and actinide compounds could have profound consequences for their unique chemical reactivity and physical properties. Now, researchers working at ALS Beamline 11.0.2 have found evidence for unexpected bonding interactions in two organometallic actinide "sandwich" complexes that have been lightning rods in

  14. Allosteric Modulation of DNA by Small Molecules

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

    Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell

  15. Drug development and manufacturing

    DOE Patents [OSTI]

    Warner, Benjamin P.; McCleskey, T. Mark; Burrell, Anthony K.

    2015-10-13

    X-ray fluorescence (XRF) spectrometry has been used for detecting binding events and measuring binding selectivities between chemicals and receptors. XRF may also be used for estimating the therapeutic index of a chemical, for estimating the binding selectivity of a chemical versus chemical analogs, for measuring post-translational modifications of proteins, and for drug manufacturing.

  16. Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

    SciTech Connect (OSTI)

    Xiong, Pingping; Li, Jie; Bu, Huaiyu; Wei, Qing; Zhang, Ruolin; Chen, Sanping

    2014-07-01

    Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu{sub 0.5}L]{sub n} (1), [Cu(HL){sub 2}Cl{sub 2}]{sub n} (2), [Cu(HL){sub 2}Cl{sub 2}(H{sub 2}O)] (3), [Cu(L){sub 2}(H{sub 2}O)]{sub n} (4) and [Cu(L)(phen)(HCO{sub 2})]{sub n} (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl{sup -}, and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units –Cu–O–Cu–O– are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated. - Graphical abstract: Copper(II) compounds with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid, were prepared, structurally characterized and investigated for antifungal activity. - Highlights: • The title compounds formed by thermodynamics and thermokinetics. • The five compounds show higher inhibition percentage than reactants. • The structure effect on the antifungal activity.

  17. Identification of cell density signal molecule

    DOE Patents [OSTI]

    Schwarz, R.I.

    1998-04-21

    Disclosed herein is a novel proteinaceous cell density signal molecule (CDS) between 25 and 35 kD, which is secreted by fibroblastic primary avian tendon cells in culture, and causes the cells to self-regulate their proliferation and the expression of differentiated function. It effects an increase of procollagen production in avian tendon cell cultures of ten fold while proliferation rates are decreased. CDS, and the antibodies which recognize them, are important for the development of diagnostics and treatments for injuries and diseases involving connective tissues, particularly tendon. Also disclosed are methods of production and use. 2 figs.

  18. Identification of cell density signal molecule

    DOE Patents [OSTI]

    Schwarz, Richard I.

    1998-01-01

    Disclosed herein is a novel proteinaceous cell density signal molecule (CDS) between 25 and 35 kD, which is secreted by fibroblastic primary avian tendon cells in culture, and causes the cells to self-regulate their proliferation and the expression of differentiated function. It effects an increase of procollagen production in avian tendon cell cultures of ten fold while proliferation rates are decreased. CDS, and the antibodies which recognize them, are important for the development of diagnostics and treatments for injuries and diseases involving connective tissues, particularly tendon. Also disclosed are methods of production and use.

  19. Nanodevices for generating power from molecules and batteryless sensing

    DOE Patents [OSTI]

    Wang, Yinmin; Wang, Xianying; Hamza, Alex V.

    2015-06-09

    A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

  20. Nanodevices for generating power from molecules and batteryless sensing

    DOE Patents [OSTI]

    Wang, Yinmin; Wang, Xianying; Hamza, Alex V.

    2014-07-15

    A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

  1. Models from Big Molecules Captured in a Flash

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

    Models from Big Molecules Captured in a Flash Models from Big Molecules Captured in a Flash Print Sunday, 26 May 2013 00:00 The structures of most of the two million proteins in...

  2. Neutron crystallography aids drug design

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

    Neutron crystallography aids drug design Neutron crystallography aids drug design Researchers have used neutron crystallography for the first time to determine the structure of a clinical drug in complex with its human target enzyme. October 9, 2012 Rich Marquez The Protein Crystallography Station at the Los Alamos Neutron Science Center, where groundbreaking work in new drug-design methods is underway using neutron diffraction techniques. Contact Nancy Ambrosiano Communications Office (505)

  3. DRUG TESING PANEL & CUTOFF CONCENTRATIONS

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

    DRUG TESTING PANEL & CUTOFF CONCENTRATIONS Initial Test Analyte Initial Test Cutoff Concentration Confirmatory Test Analyte Confirmatory Test Cutoff Concentration Marijuana ...

  4. The spontaneous synchronized dance of pairs of water molecules (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect The spontaneous synchronized dance of pairs of water molecules Citation Details In-Document Search Title: The spontaneous synchronized dance of pairs of water molecules Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results

  5. Toroidal nanotraps for cold polar molecules

    SciTech Connect (OSTI)

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-14

    Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, and polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.

  6. Toroidal nanotraps for cold polar molecules

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

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-14

    Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, andmore » polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.« less

  7. Low energy ion-molecule reactions

    SciTech Connect (OSTI)

    Farrar, J.M.

    1993-12-01

    This project is concerned with elucidating the dynamics of elementary ion-molecule reactions at collision energies near and below 1 eV. From measurements of the angular and energy distributions of the reaction products, one can infer intimathe details about the nature of collisions leading to chemical reaction, the geometries and lifetimes of intermediate complexes that govern the reaction dynamics, and the collision energy dependence of these dynamical features. The author employs crossed-beam low energy mass spectrometry technology developed over the last several years, with the focus of current research on proton transfer and hydrogen atom transfer reactions of te O{sup {minus}} ion with species such as HF, H{sub 2}O, and NH{sub 3}.

  8. Time-Resolved SAXS/WAXS Study of the Phase Behavior and Microstructural Evolution of Drug/PEG Solid Dispersions

    SciTech Connect (OSTI)

    Zhu, Qing; Harris, Michael T.; Taylor, Lynne S.

    2013-03-07

    Simultaneous small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) was employed to elucidate the physical state and location of various small molecule drugs blended with polyethylene glycol (PEG), as well as the time dependent microstructural evolution of the systems. Samples were prepared by comelting physical mixtures of the drug and PEG, followed by solidification at 25 C. The model drugs selected encompassed a wide variety of physicochemical properties in terms of crystallization tendency and potential for interaction with PEG. It was observed that compounds which crystallized rapidly and had weak interactions with PEG tended to be excluded from the interlamellar region of the PEG matrix. In contrast, drugs which had favorable interactions with PEG were incorporated into the interlamellar regions of the polymer up until the point at which the drug crystallized whereby phase separation occurred. These factors are likely to impact the effectiveness of drug/PEG systems as drug delivery systems.

  9. Soft-Template-Synthesized Mesoporous Carbon for Oral Drug Delivery

    SciTech Connect (OSTI)

    Saha, Dipendu; Warren, Kaitlyn E; Naskar, Amit K

    2014-01-01

    Template-synthesized mesoporous carbons were successfully used in in vitro investigations of controlled delivery of three model drugs, captopril, furosemide, and ranitidine hydrochloride. Captopril and furosemide exhibited desorption kinetics over 30 40 h, and ranitidine HCl had a complete release time of 5 10 h. As evident from the slow release kinetics, we contend that our mesoporous carbon is an improved drug-delivery medium compared to state-of-the-art porous silica-based substrates. The mesoporous carbons, synthesized from phloroglucinol and lignin, a synthetic and a sustainable precursor, respectively, exhibit BET surface area of 200 400 m2 g-1 and pore volume of 0.2 0.6 cm3 g-1. The phloroglucinol-based carbon has narrower pore widths and higher pore volume than the lignin-derived counterpart and maintains a longer release time. Numerical modeling of the release kinetics data reveals that the diffusivities of all the drugs from lignin-based carbon media are of equivalent magnitude (10-22 to 10-24 m2 s-1). However, a tailored reduction of pore width in the sorbent reduces the diffusivity of smaller drug molecules (captopril) by an order of magnitude. Thus, engineered pore morphology in our synthesized carbon sorbent, along with its potential to tailor the chemistry of its interaction with sorbet, can be exploited for optimal delivery system of a preferred drug within its therapeutic level and below the level of toxicity.

  10. Drug Testing for DOE Positions | Department of Energy

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

    Drug Testing for DOE Positions Drug Testing for DOE Positions Drug Testing for DOE Positions Drug Testing Matrix Secretary Bodman's Memorandum Regarding Drug Testing at DOE Fact ...

  11. Glucose sensing molecules having selected fluorescent properties

    DOE Patents [OSTI]

    Satcher, Jr., Joe H.; Lane, Stephen M.; Darrow, Christopher B.; Cary, Douglas R.; Tran, Joe Anh

    2004-01-27

    An analyte sensing fluorescent molecule that employs intramolecular electron transfer is designed to exhibit selected fluorescent properties in the presence of analytes such as saccharides. The selected fluorescent properties include excitation wavelength, emission wavelength, fluorescence lifetime, quantum yield, photostability, solubility, and temperature or pH sensitivity. The compound comprises an aryl or a substituted phenyl boronic acid that acts as a substrate recognition component, a fluorescence switch component, and a fluorophore. The fluorophore and switch component are selected such that the value of the free energy for electron transfer is less than about 3.0 kcal mol.sup.-1. Fluorescent compounds are described that are excited at wavelengths greater than 400 nm and emit at wavelengths greater than 450 nm, which is advantageous for optical transmission through skin. The fluorophore is typically selected from transition metal-ligand complexes and thiazine, oxazine, oxazone, or oxazine-one as well as anthracene compounds. The fluorescent compound can be immobilized in a glucose permeable biocompatible polymer matrix that is implantable below the skin.

  12. Target molecules detection by waveguiding in a photonic silicon membrane

    DOE Patents [OSTI]

    Letant, Sonia E.; Van Buuren, Anthony; Terminello, Louis; Hart, Bradley R.

    2006-12-26

    Disclosed herein is a porous silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and calculate the concentration of bound target.

  13. Orientational Analysis of Molecules in Thin Films | Stanford Synchrotron

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

    Radiation Lightsource Orientational Analysis of Molecules in Thin Films Monday, September 17, 2012 - 10:00am SSRL Bldg. 137, room 226 Daniel Kaefer The synchrotron-based X-ray absorption spectroscopy is a very powerful tool to unravel the orientation of organic molecules on surfaces or in thin films. This information on the alignment of - most often - highly anisotropic molecules can become crucial if an epitaxial or even crystalline organic growth is desired, if such thin film should serve

  14. Systematic expansion of porous crystals to include large molecules | Center

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

    for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Systematic expansion of porous crystals to include large molecules

  15. Controlling orbital-selective Kondo effects in a single molecule...

    Office of Scientific and Technical Information (OSTI)

    coordination chemistry Citation Details In-Document Search Title: Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry Iron(II) ...

  16. Conference: Frontiers in Laser Cooling, Single-Molecule Biophysics...

    Office of Scientific and Technical Information (OSTI)

    Laser Cooling, Single-Molecule Biophysics, and Energy Science: Remarks from Steve Chu at the Scientific Symposium Held in his Honor Citation Details Title: Frontiers in Laser ...

  17. Entropy-based separation of linear chain molecules by exploiting...

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

    Entropy-based separation of linear chain molecules by exploiting differences in the saturation capacities in cage-type zeolites Previous Next List Rajamani Krishna, Jasper M. van...

  18. Self-contained Kondo effect in single molecules (Journal Article...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Self-contained Kondo effect in single molecules Citation Details ... OSTI Identifier: 877620 Report Number(s): LBNL--57492 Journal ID: ISSN 0031-9007; PRLTAO; ...

  19. Making Maps of the Molecules in Seeds | The Ames Laboratory

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

    Making Maps of the Molecules in Seeds Scientists have advanced methods to make maps of the locations of molecules within plant materials. Resolution of 10 to 50 microns, less than a quarter the size of a human hair, is routinely possible. The trick with plant materials is to extract the molecules delicately from thin slices with a fine laser moving stepwise across the sample.Many molecules are analyzed at once using a very sensitive mass spectrometer in this technique known as matrix-assisted

  20. The photodissociation and reaction dynamics of vibrationally excited molecules

    SciTech Connect (OSTI)

    Crim, F.F.

    1993-12-01

    This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.

  1. Mapping protein collapse with single molecule fluorescence and...

    Office of Scientific and Technical Information (OSTI)

    spectroscopy Citation Details In-Document Search Title: Mapping protein collapse with single molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy ...

  2. Microfabricated injectable drug delivery system

    DOE Patents [OSTI]

    Krulevitch, Peter A.; Wang, Amy W.

    2002-01-01

    A microfabricated, fully integrated drug delivery system capable of secreting controlled dosages of multiple drugs over long periods of time (up to a year). The device includes a long and narrow shaped implant with a sharp leading edge for implantation under the skin of a human in a manner analogous to a sliver. The implant includes: 1) one or more micromachined, integrated, zero power, high and constant pressure generating osmotic engine; 2) low power addressable one-shot shape memory polymer (SMP) valves for switching on the osmotic engine, and for opening drug outlet ports; 3) microfabricated polymer pistons for isolating the pressure source from drug-filled microchannels; 4) multiple drug/multiple dosage capacity, and 5) anisotropically-etched, atomically-sharp silicon leading edge for penetrating the skin during implantation. The device includes an externally mounted controller for controlling on-board electronics which activates the SMP microvalves, etc. of the implant.

  3. Spectroscopic probes of vibrationally excited molecules at chemically significant energies

    SciTech Connect (OSTI)

    Rizzo, T.R.

    1993-12-01

    This project involves the application of multiple-resonance spectroscopic techniques for investigating energy transfer and dissociation dynamics of highly vibrationally excited molecules. Two major goals of this work are: (1) to provide information on potential energy surfaces of combustion related molecules at chemically significant energies, and (2) to test theoretical modes of unimolecular dissociation rates critically via quantum-state resolved measurements.

  4. Electrical, Mechanical and Thermal Properties of Single Molecules

    SciTech Connect (OSTI)

    Tao, Nongjian

    2014-08-20

    The specific aims of the prior DOE grant are to determine the stability of a single molecule bound to two electrodes, study local heating in single molecule junctions due to electron-phonon and electron-electron interactions, measure electron-phonon interactions in single molecule wires; and explore piezoelectric properties of single molecules. We have completed all the major tasks, and also expanded naturally the scope of the project to address several other critical issues in single molecule properties, developed new experimental capabilities, and observed a number of unexpected phenomena. We summarized here some of the findings that are most relevant to the present renewal proposal. More details can be found in the publications resulted from this grant and annual progress reports.

  5. Micro injector sample delivery system for charged molecules

    DOE Patents [OSTI]

    Davidson, James C.; Balch, Joseph W.

    1999-11-09

    A micro injector sample delivery system for charged molecules. The injector is used for collecting and delivering controlled amounts of charged molecule samples for subsequent analysis. The injector delivery system can be scaled to large numbers (>96) for sample delivery to massively parallel high throughput analysis systems. The essence of the injector system is an electric field controllable loading tip including a section of porous material. By applying the appropriate polarity bias potential to the injector tip, charged molecules will migrate into porous material, and by reversing the polarity bias potential the molecules are ejected or forced away from the tip. The invention has application for uptake of charged biological molecules (e.g. proteins, nucleic acids, polymers, etc.) for delivery to analytical systems, and can be used in automated sample delivery systems.

  6. Random Selection for Drug Screening (Technical Report) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Subject: 99 GENERAL AND MISCELLANEOUSMATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; PROBABILITY; SAMPLING; DRUG ABUSE; DRUGS; CRIME DETECTION drug screenings, random selection ...

  7. The statistics of single molecule detection: An overview

    SciTech Connect (OSTI)

    Enderlein, J.; Robbins, D.L.; Ambrose, W.P.

    1995-12-31

    An overview of our recent results in modeling single molecule detection in fluid flow is presented. Our mathematical approach is based on a path integral representation. The model accounts for all experimental details, such as light collection, laser excitation, hydrodynamics and diffusion, and molecular photophysics. Special attention is paid to multiple molecule crossings through the detection volume. Numerical realization of the theory is discussed. Measurements of burst size distributions in single B-phycoerythrin molecule detection experiments are presented and compared with theoretical predictions.

  8. Recent progress in electron scattering from atoms and molecules

    SciTech Connect (OSTI)

    Brunger, M. J.; Buckman, S. J.; Sullivan, J. P.; Palihawadana, P.; Jones, D. B.; Chiari, L.; Pettifer, Z.; Silva, G. B. da; Lopes, M. C. A.; Duque, H. V.; Masin, Z.; Gorfinkiel, J. D.; Garcia, G.; Hoshino, M.; Tanaka, H.; Limão-Vieira, P.

    2014-03-05

    We present and discuss recent results, both experimental and theoretical (where possible), for electron impact excitation of the 3s[3/2 ]{sub 1} and 3s?[1/2 ]{sub 1} electronic states in neon, elastic electron scattering from the structurally similar molecules benzene, pyrazine, and 1,4-dioxane and excitation of the electronic states of the important bio-molecule analogue ?-tetrahydrofurfuryl alcohol. While comparison between theoretical and experimental results suggests that benchmarked cross sections for electron scattering from atoms is feasible in the near-term, significant further theoretical development for electron-molecule collisions, particularly in respect to discrete excitation processes, is still required.

  9. Models from Big Molecules Captured in a Flash

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

    Models from Big Molecules Captured in a Flash Models from Big Molecules Captured in a Flash Print Sunday, 26 May 2013 00:00 The structures of most of the two million proteins in the human body are unknown because they can't be crystallized. Peter Zwart of the Physical Biosciences Division and his colleagues have come up with a new algorithm for efficiently solving the structures of proteins and other big molecules in their more natural fluid states, using the "diffract before destroy"

  10. Understanding Small Molecule Interactions in Metal-Organic Frameworks:

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

    Coupling Experiment with Theory | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Understanding Small Molecule Interactions in Metal-Organic Frameworks: Coupling Experiment with Theory

  11. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy...

    Office of Scientific and Technical Information (OSTI)

    Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Paul Alivisatos titled LBNL in the Chu Era Citation Details In-Document Search Title:...

  12. Efficient Monte Carlo Simulations of Gas Molecules Inside Porous...

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

    Efficient Monte Carlo Simulations of Gas Molecules Inside Porous Materials Previous Next List J. Kim and B. Smit, J. Chem. Theory Comput. 8 (7), 2336 (2012) DOI: 10.1021ct3003699 ...

  13. Isolated menthone reductase and nucleic acid molecules encoding same

    DOE Patents [OSTI]

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  14. Atom-diatom scattering dynamics of spinning molecules

    SciTech Connect (OSTI)

    Eyles, C. J.; Floß, J.; Averbukh, I. Sh.; Leibscher, M.

    2015-01-14

    We present full quantum mechanical scattering calculations using spinning molecules as target states for nuclear spin selective atom-diatom scattering of reactive D+H{sub 2} and F+H{sub 2} collisions. Molecules can be forced to rotate uni-directionally by chiral trains of short, non-resonant laser pulses, with different nuclear spin isomers rotating in opposite directions. The calculations we present are based on rotational wavepackets that can be created in this manner. As our simulations show, target molecules with opposite sense of rotation are predominantly scattered in opposite directions, opening routes for spatially and quantum state selective scattering of close chemical species. Moreover, two-dimensional state resolved differential cross sections reveal detailed information about the scattering mechanisms, which can be explained to a large degree by a classical vector model for scattering with spinning molecules.

  15. Stable Metal-Organic Frameworks Containing Single-Molecule Traps...

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

    Stable Metal-Organic Frameworks Containing Single-Molecule Traps for Enzyme Encapsulation Previous Next List Dawei Feng, Tian-Fu Liu, Jie Su, Mathieu Bosch, Zhangwen Wei, Wei Wan,...

  16. Orientational Analysis of Molecules in Thin Films | Stanford...

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

    Molecules in Thin Films Monday, September 17, 2012 - 10:00am SSRL Bldg. 137, room 226 Daniel Kaefer The synchrotron-based X-ray absorption spectroscopy is a very powerful tool to...

  17. Capture and Release of Guest Molecules by Optical Responsive

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

    Metal-Organic Polyhedra (MOP) | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Capture and Release of Guest Molecules by Optical Responsive Metal-Organic Polyhedra (MOP)

  18. Understanding Enzyme Activity Using Single Molecule Tracking (Poster)

    SciTech Connect (OSTI)

    Liu, Y.-S.; Zeng, Y.; Luo, Y.; Xu, Q.; Himmel, M.; Smith S.; Wei, H.; Ding, S.-Y.

    2009-06-01

    This poster describes single-molecule tracking and total internal reflection fluorescence microscopy. It discusses whether the carbohydrate-binding module (CBM) moves on cellulose, how the CBM binds to cellulose, and the mechanism of cellulosome assembly.

  19. Method of monitoring photoactive organic molecules in-situ during gas-phase deposition of the photoactive organic molecules

    DOE Patents [OSTI]

    Forrest, Stephen R.; Vartanian, Garen; Rolin, Cedric

    2015-06-23

    A method for in-situ monitoring of gas-phase photoactive organic molecules in real time while depositing a film of the photoactive organic molecules on a substrate in a processing chamber for depositing the film includes irradiating the gas-phase photoactive organic molecules in the processing chamber with a radiation from a radiation source in-situ while depositing the film of the one or more organic materials and measuring the intensity of the resulting photoluminescence emission from the organic material. One or more processing parameters associated with the deposition process can be determined from the photoluminescence intensity data in real time providing useful feedback on the deposition process.

  20. Calculations of diatomic molecules with the LCTCO method. Double excited states of the H/sub 2/ molecule

    SciTech Connect (OSTI)

    Kirnos, V.N.; Samsonov, B.F.; Cheglokov, E.I.

    1987-01-01

    Autoionizing states of a molecule are short-lived and decay, as a rule, producing separate particles and ions. In particular, the H/sub 2/ molecule in such states decays into H/sub 2//sup +/ + e/sup -/, H + H/sup +/ + e/sup -/, or dissociates into two neutral H atoms in the ground and excited states. Nonempirical calculations of 20 autoionizing states of the H/sub 2/ molecule are performed in a two-center orbital basis and for two values of the internuclear distance. Results obtained are compared with other results known from the literature.

  1. Extracting vibrational beat signatures in spectrally dense molecules using

    Office of Scientific and Technical Information (OSTI)

    multi-pulse femtosecond coherent anti-Stokes Raman spectroscopy. (Journal Article) | SciTech Connect Extracting vibrational beat signatures in spectrally dense molecules using multi-pulse femtosecond coherent anti-Stokes Raman spectroscopy. Citation Details In-Document Search Title: Extracting vibrational beat signatures in spectrally dense molecules using multi-pulse femtosecond coherent anti-Stokes Raman spectroscopy. No abstract prepared. Authors: Nelson, Thomas Robert ; Urayama, Junji

  2. Inducing and Quantifying Forbidden Reactivity with Single Molecule Polymer

    Office of Scientific and Technical Information (OSTI)

    Mechanochemistry (Journal Article) | SciTech Connect Inducing and Quantifying Forbidden Reactivity with Single Molecule Polymer Mechanochemistry Citation Details In-Document Search Title: Inducing and Quantifying Forbidden Reactivity with Single Molecule Polymer Mechanochemistry Authors: Wang, J ; Kouznetsova, T B ; Niu, Z ; Ong, M T ; Klukovich, H M ; Rheingold, A L ; Martinez, T J ; Craig, S L Publication Date: 2014-11-05 OSTI Identifier: 1184168 Report Number(s): LLNL-JRNL-663754 DOE

  3. Inducing and Quantifying Forbidden Reactivity with Single Molecule Polymer

    Office of Scientific and Technical Information (OSTI)

    Mechanochemistry (Journal Article) | SciTech Connect Inducing and Quantifying Forbidden Reactivity with Single Molecule Polymer Mechanochemistry Citation Details In-Document Search Title: Inducing and Quantifying Forbidden Reactivity with Single Molecule Polymer Mechanochemistry × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information (OSTI) and is provided as a public service. Visit

  4. Mechanistic characterization and crystal structure of a small molecule

    Office of Scientific and Technical Information (OSTI)

    inactivator bound to plasminogen activator inhibitor-1 (Journal Article) | SciTech Connect Mechanistic characterization and crystal structure of a small molecule inactivator bound to plasminogen activator inhibitor-1 Citation Details In-Document Search Title: Mechanistic characterization and crystal structure of a small molecule inactivator bound to plasminogen activator inhibitor-1 Authors: Li, Shih-Hon ; Reinke, Ashley A. ; Sanders, Karen L. ; Emal, Cory D. ; Whisstock, James C. ; Stuckey,

  5. Novel Biosynthetic Pathway for Production of Fatty Acid Derived Molecules -

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

    Energy Innovation Portal Industrial Technologies Industrial Technologies Biomass and Biofuels Biomass and Biofuels Find More Like This Return to Search Novel Biosynthetic Pathway for Production of Fatty Acid Derived Molecules Lawrence Berkeley National Laboratory Contact LBL About This Technology Technology Marketing SummaryJay Keasling and Eric Steen of Berkeley Lab have invented what may be the most efficient metabolic pathway for producing fatty acids, and their derived molecules of

  6. A Suite of Engineered GFP Molecules for Oligomeric Scaffolding (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect A Suite of Engineered GFP Molecules for Oligomeric Scaffolding Citation Details In-Document Search Title: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding Authors: Leibly, David J. ; Arbing, Mark A. ; Pashkov, Inna ; DeVore, Natasha ; Waldo, Geoffrey S. ; Terwilliger, Thomas C. ; Yeates, Todd O. [1] ; LANL) [2] + Show Author Affiliations UCLA ( Publication Date: 2015-11-30 OSTI Identifier: 1227481 Resource Type: Journal Article Resource Relation:

  7. A Suite of Engineered GFP Molecules for Oligomeric Scaffolding (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect A Suite of Engineered GFP Molecules for Oligomeric Scaffolding Citation Details In-Document Search This content will become publicly available on August 31, 2016 Title: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding Authors: Leibly, David J. ; Arbing, Mark A. ; Pashkov, Inna ; DeVore, Natasha ; Waldo, Geoffrey S. ; Terwilliger, Thomas C. ; Yeates, Todd O. Publication Date: 2015-09-01 OSTI Identifier: 1250980 Grant/Contract Number: FC02-02ER63421;

  8. Molecule Nanoweaver Creates High-Tech Medical Patches and Multilayered

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

    Capsules | Argonne National Laboratory Molecule Nanoweaver Creates High-Tech Medical Patches and Multilayered Capsules Technology available for licensing: Molecule Nanoweaver, a unique tool that can be used as both a detector and a fabricator of high-tech patches, multilayered capsules, and other medical products. May increase the market for medical patches Allows creation of medical patches that are more efficient at delivering medication and treatment, speeding up the healing process PDF

  9. Understanding Small-Molecule Interactions in Metal-Organic Frameworks:

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

    Coupling Experiment with Theory | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Understanding Small-Molecule Interactions in Metal-Organic Frameworks: Coupling Experiment with Theory Previous Next List Lee, Jason S.; Vlaisavljevich, Bess; Britt, David K.; Brown, Craig M.; Haranczyk, Maciej; Neaton, Jeffrey B.; Smit, Berend; Long, Jeffrey R.; and Queen, Wendy L.. Understanding Small-Molecule Interactions in Metal-Organic Frameworks: Coupling Experiment with

  10. Nitrogen molecule activation by excited states of copper

    SciTech Connect (OSTI)

    Sanchez-Zamora, M.; Novaro, O.; Ruiz, M.E. )

    1990-04-05

    Ab initio molecular orbital studies that include variational (with a multiconfiguration reference state of 200 states) and perturbational (including over 3 million configurations) configuration interaction calculations were addressed to the interaction of nitrogen molecules with copper. The Cu ground state {sup 2}S and first two excited states {sup 2}P and {sup 2}D were studied as they interact in different geometrical approaches (including side-on and end-on geometries) with ground-state N{sub 2} molecules.

  11. Methods And Devices For Characterizing Duplex Nucleic Acid Molecules

    DOE Patents [OSTI]

    Akeson, Mark; Vercoutere, Wenonah; Haussler, David; Winters-Hilt, Stephen

    2005-08-30

    Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

  12. Isotope separation by photodissociation of Van der Waal's molecules

    DOE Patents [OSTI]

    Lee, Yuan T.

    1977-01-01

    A method of separating isotopes based on the dissociation of a Van der Waal's complex. A beam of molecules of a Van der Waal's complex containing, as one partner of the complex, a molecular species in which an element is present in a plurality of isotopes is subjected to radiation from a source tuned to a frequency which will selectively excite vibrational motion by a vibrational transition or through electronic transition of those complexed molecules of the molecular species which contain a desired isotope. Since the Van der Waal's binding energy is much smaller than the excitational energy of vibrational motion, the thus excited Van der Waal's complex dissociate into molecular components enriched in the desired isotope. The recoil velocity associated with vibrational to translational and rotational relaxation will send the separated molecules away from the beam whereupon the product enriched in the desired isotope can be separated from the constituents of the beam.

  13. Single molecule detection using charge-coupled device array technology

    SciTech Connect (OSTI)

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  14. A general strategy to construct small molecule biosensors in eukaryotes

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

    Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.; Mandell, Daniel J.; Antunes, Mauricio S.; Chari, Raj; Morey, Kevin J.; Rios, Xavier; Medford, June I.; Church, George M.; et al

    2015-12-29

    Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activatesmore » transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.« less

  15. Spectroscopy and reactions of vibrationally excited transient molecules

    SciTech Connect (OSTI)

    Dai, H.L.

    1993-12-01

    Spectroscopy, energy transfer and reactions of vibrationally excited transient molecules are studied through a combination of laser-based excitation techniques and efficient detection of emission from the energized molecules with frequency and time resolution. Specifically, a Time-resolved Fourier Transform Emission Spectroscopy technique has been developed for detecting dispersed laser-induced fluorescence in the IR, visible and UV regions. The structure and spectroscopy of the excited vibrational levels in the electronic ground state, as well as energy relaxation and reactions induced by specific vibronic excitations of a transient molecule can be characterized from time-resolved dispersed fluorescence in the visible and UV region. IR emissions from highly vibrational excited levels, on the other hand, reveal the pathways and rates of collision induced vibrational energy transfer.

  16. Diatomic molecules in optical and microwave dipole traps

    SciTech Connect (OSTI)

    Lysebo, Marius; Veseth, Leif

    2011-03-15

    The dipole forces on rotating diatomic molecules are worked out in detail for optical as well as microwave radiation fields. The objective is in particular to investigate how the dipole forces and potentials depend on the subtle internal structure of the molecule, with special emphasis on hyperfine and Zeeman states. Dipole potentials are obtained from computations of the real part of the complex molecular polarizability, whereas the imaginary part yields the scattering force. Numerical examples are presented for {sup 23}Na{sub 2} and OH for optical (laser) fields related to strong electronic transitions and for microwave fields for the {Lambda} doubling in the OH ground state.

  17. Spectroscopic and dynamical studies of highly energized small polyatomic molecules

    SciTech Connect (OSTI)

    Field, R.W.; Silbey, R.J.

    1990-01-01

    The formyl radical and the acetylene molecule were chosen for these studies. The visible and fluorescence spectra of the formyl radical were recorded, and the spectral results are used as a basis to explain the electronic structure. Optical-optical double resonance studies of acetylene were recorded, and the spectral results are interpreted. The results of Zeeman and Stark anticrossing and quantum beat studies of acetylene are reported, and they provide an unusually detailed view of both Intersystem Crossing and Internal Conversion in small polyatomic molecules. 22 references are cited as resulting from Department of Energy sponsorship of this project.

  18. Meet the world's highest-performance single-molecule diode

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

    Meet the world's highest-performance single-molecule diode Click to share on Facebook (Opens in new window) Click to share on Twitter (Opens in new window) Click to share on Reddit (Opens in new window) Click to share on Pinterest (Opens in new window) This is the world's highest-performance single-molecule diode using a combination of gold electrodes and an ionic solution. (Image: Latha Venkataraman, Columbia University) More » Nanotubes that Assemble Themselves Discover a new way to look at

  19. Structure factors for tunneling ionization rates of diatomic molecules

    SciTech Connect (OSTI)

    Saito, Ryoichi; Tolstikhin, Oleg I.; Madsen, Lars Bojer; Morishita, Toru

    2015-05-15

    Within the leading-order, single-active-electron, and frozen-nuclei approximation of the weak-field asymptotic theory, the rate of tunneling ionization of a molecule in an external static uniform electric field is determined by the structure factor for the highest occupied molecular orbital. We present the results of systematic calculations of structure factors for 40 homonuclear and heteronuclear diatomic molecules by the Hartree–Fock method using a numerical grid-based approach implemented in the program X2DHF.

  20. Analyte sensing mediated by adapter/carrier molecules

    DOE Patents [OSTI]

    Bayley, Hagan; Braha, Orit; Gu, LiQun

    2002-07-30

    This invention relates to an improved method and system for sensing of one or more analytes. A host molecule, which serves as an adapter/carrier, is used to facilitate interaction between the analyte and the sensor element. A detectable signal is produced reflecting the identity and concentration of analyte present.

  1. Translation and integration of numerical atomic orbitals in linear molecules

    SciTech Connect (OSTI)

    Heinäsmäki, Sami

    2014-02-14

    We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively.

  2. Small-Molecule Inhibition of TNF-alpha

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

    Farrington, G., Eldredge, J.K., Day, E.S., Cruz, L.A., Cachero, T.G., Miller, S.K., Friedman, J.E., Choong, I.C., Cunningham, B.C. Small-molecule inhibition of TNF-alpha. Science...

  3. Single Molecule Study of Cellulase Hydrolysis of Crystalline Cellulose

    SciTech Connect (OSTI)

    Liu, Y.-S.; Luo, Y.; Baker, J. O.; Zeng, Y.; Himmel, M. E.; Smith, S.; Ding, S.-Y.

    2009-12-01

    This report seeks to elucidate the role of cellobiohydrolase-I (CBH I) in the hydrolysis of crystalline cellulose. A single-molecule approach uses various imaging techniques to investigate the surface structure of crystalline cellulose and changes made in the structure by CBH I.

  4. Forensic Drug Testing Custody and Control Form

    Broader source: Energy.gov [DOE]

    Forensic Drug Testing Custody and Control Form. A copy of the drug testing custody and control form for DOE contractors to use to comply with the drug testing requirements in 10 CFR part 707, Workplace Substance Abuse Programs at DOE Sites.

  5. Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany...

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

    Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC Intergrated Drug Testing System, PIA, Bechtel ...

  6. Drug Retention Times (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Country of Publication: United States Language: English Subject: 60 APPLIED LIFE SCIENCES; RETENTION; DRUG ABUSE; DRUGS; CRIME DETECTION drugs, retention Word Cloud More Like This ...

  7. Apparatus and method of determining molecular weight of large molecules

    DOE Patents [OSTI]

    Fuerstenau, Stephen; Benner, W. Henry; Madden, Norman; Searles, William

    1998-01-01

    A mass spectrometer determines the mass of multiply charged high molecular weight molecules. This spectrometer utilizes an ion detector which is capable of simultaneously measuring the charge z and transit time of a single ion as it passes through the detector. From this transit time, the velocity of the single ion may then be derived, thus providing the mass-to-charge ratio m/z for a single ion which has been accelerated through a known potential. Given z and m/z, the mass m of the single ion can then be calculated. Electrospray ions with masses in excess of 1 MDa and charge numbers greater than 425 e.sup.- are readily detected. The on-axis single ion detection configuration enables a duty cycle of nearly 100% and extends the practical application of electrospray mass spectrometry to the analysis of very large molecules with relatively inexpensive instrumentation.

  8. Apparatus and method of determining molecular weight of large molecules

    DOE Patents [OSTI]

    Fuerstenau, S.; Benner, W.H.; Madden, N.M.; Searles, W.

    1998-06-23

    A mass spectrometer determines the mass of multiply charged high molecular weight molecules. This spectrometer utilizes an ion detector which is capable of simultaneously measuring the charge z and transit time of a single ion as it passes through the detector. From this transit time, the velocity of the single ion may then be derived, thus providing the mass-to-charge ratio m/z for a single ion which has been accelerated through a known potential. Given z and m/z, the mass m of the single ion can then be calculated. Electrospray ions with masses in excess of 1 MDa and charge numbers greater than 425 e{sup {minus}} are readily detected. The on-axis single ion detection configuration enables a duty cycle of nearly 100% and extends the practical application of electrospray mass spectrometry to the analysis of very large molecules with relatively inexpensive instrumentation. 14 figs.

  9. Subtask 2: Molecules, Materials, and Systems for Solar Electricity | ANSER

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

    Center | Argonne-Northwestern National Laboratory 2: Molecules, Materials, and Systems for Solar Electricity Home > Research > Subtask 2 The above figure depicts the structure of active polymer layers in organic solar cells. The above figure depicts the structure of active polymer layers in organic solar cells. ANSER Center research tests theory-driven ideas to understand at a fundamental level how photovoltaic cell performance is affected by nanoscale/mesoscale

  10. Molecule@MOF: A New Class of Electronic Materials

    Office of Scientific and Technical Information (OSTI)

    22PE Exceptional service in the national interest Sandia National Laboratories Molecule@MOF: A New Class of Electronic Materials A. Alec Talin Sandia National Labs, Livermore, CA aatalin@sandia.gov Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. Remember these? Sandia

  11. Composition for detection of cell density signal molecule

    DOE Patents [OSTI]

    Schwarz, Richard I.

    2001-01-01

    Disclosed herein is a novel proteinaceous cell density signal molecule (CDS), which is secreted by fibroblastic cells in culture, preferably tendon cells, and which provides a means by which the cells self-regulate their proliferation and the expression of differentiated function. CDS, and the antibodies which recognize them, are important for the development of diagnostics and treatments for injuries and diseases involving connective tissues, particularly tendon. Also disclosed are methods of production and use.

  12. Polymer and small molecule based hybrid light source

    DOE Patents [OSTI]

    Choong, Vi-En; Choulis, Stelios; Krummacher, Benjamin Claus; Mathai, Mathew; So, Franky

    2010-03-16

    An organic electroluminescent device, includes: a substrate; a hole-injecting electrode (anode) coated over the substrate; a hole injection layer coated over the anode; a hole transporting layer coated over the hole injection layer; a polymer based light emitting layer, coated over the hole transporting layer; a small molecule based light emitting layer, thermally evaporated over the polymer based light emitting layer; and an electron-injecting electrode (cathode) deposited over the electroluminescent polymer layer.

  13. Probing Valance and Core Excitons in Molecules by Coherent Multidimensional

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

    Spectroscopy with Clasical and Quantum Light | MIT-Harvard Center for Excitonics Valance and Core Excitons in Molecules by Coherent Multidimensional Spectroscopy with Clasical and Quantum Light September 20, 2011 at 3pm/36-428 Shaul Mukamel University of California, Irvine shaul_001 Abstract: Multidimensional spectroscopic techniques which originated with NMR in the 1970's have been extended over the past 18 years to the infrared and visible regimes. Novel extensions of these ideas to study

  14. Ro-vibrational Relaxation Dynamics of PbF Molecules

    SciTech Connect (OSTI)

    Neil Shafer-Ray

    2011-04-08

    In 1950 Purcell and Ramsey suggested that the electron might have a CP-violating electric dipole moment (e-EDM) proportional to its spin angular momentum. This possibility initiated an ongoing hunt for the e-EDM that has been spurred on by the recognition of the importance of CP-violation to the formation of a matter-dominated universe[2] as well as a difference in magnitude of the Supersymmetric and Standard Model[4] prediction for its value. The current limit on the e-EDM is 1.6Eâ??27 e·cm as determined in a Ramsey beam resonance study of the Tl atom. The PbF molecule provides a unique opportunity to measure the e-EDM. The moleculeâ??s odd electron, heavy mass, and large internal field combine to give it an intrinsic sensitivity to an e-EDM that is over three orders of magnitude bigger than that of the Tl atom. In addition to this increased intrinsic sensitivity, the ground state of the PbF molecule allows for a "magic" electric field at which the magnetic moment vanishes[7]. All of these advantages create an opportunity to significantly lower the current limit on the e-EDM. These advantages can only be realized if an intense source of ground-state PbF molecules can be created and detected with high efficiency. The scope of this project is to (1) create a rotationally cold molecular beam source of PbF, (2) achieve a continuous ionization scheme for sensitive state selective detection of the PbF molecule.

  15. Density Functional Theory with Dissipation: Transport through Single Molecules

    SciTech Connect (OSTI)

    Kieron Burke

    2012-04-30

    A huge amount of fundamental research was performed on this grant. Most of it focussed on fundamental issues of electronic structure calculations of transport through single molecules, using density functional theory. Achievements were: (1) First density functional theory with dissipation; (2) Pseudopotential plane wave calculations with master equation; (3) Weak bias limit; (4) Long-chain conductance; and (5) Self-interaction effects in tunneling.

  16. Using Coupled Harmonic Oscillators to Model Some Greenhouse Gas Molecules

    SciTech Connect (OSTI)

    Go, Clark Kendrick C.; Maquiling, Joel T.

    2010-07-28

    Common greenhouse gas molecules SF{sub 6}, NO{sub 2}, CH{sub 4}, and CO{sub 2} are modeled as harmonic oscillators whose potential and kinetic energies are derived. Using the Euler-Lagrange equation, their equations of motion are derived and their phase portraits are plotted. The authors use these data to attempt to explain the lifespan of these gases in the atmosphere.

  17. Anatomic and Functional Imaging of Tagged Molecules in Animals - Energy

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

    Innovation Portal Anatomic and Functional Imaging of Tagged Molecules in Animals Thomas Jefferson National Accelerator Facility Contact TJNAF About This Technology Technology Marketing SummaryA novel functional imaging system for use in the imaging of unrestrained and non-anesthetized small animals or other subjects and a method for acquiring such images and further registering them with anatomical X-ray images previously or subsequently acquired.DescriptionThe apparatus comprises a

  18. Structures of water molecules in carbon nanotubes under electric fields

    SciTech Connect (OSTI)

    Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji

    2015-03-28

    Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.

  19. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    SciTech Connect (OSTI)

    Iancu, Violeta

    2006-08-01

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  20. Neuroimaging for drug addiction and related behaviors

    SciTech Connect (OSTI)

    Parvaz M. A.; Parvaz, M.A.; Alia-Klein, N.; Woicik,P.A.; Volkow, N.D.; Goldstein, R.Z.

    2011-10-01

    In this review, we highlight the role of neuroimaging techniques in studying the emotional and cognitive-behavioral components of the addiction syndrome by focusing on the neural substrates subserving them. The phenomenology of drug addiction can be characterized by a recurrent pattern of subjective experiences that includes drug intoxication, craving, bingeing, and withdrawal with the cycle culminating in a persistent preoccupation with obtaining, consuming, and recovering from the drug. In the past two decades, imaging studies of drug addiction have demonstrated deficits in brain circuits related to reward and impulsivity. The current review focuses on studies employing positron emission tomography (PET), functional magnetic resonance imaging (fMRI), and electroencephalography (EEG) to investigate these behaviors in drug-addicted human populations. We begin with a brief account of drug addiction followed by a technical account of each of these imaging modalities. We then discuss how these techniques have uniquely contributed to a deeper understanding of addictive behaviors.

  1. Automated High Throughput Drug Target Crystallography

    SciTech Connect (OSTI)

    Rupp, B

    2005-02-18

    The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

  2. Novel nuclear magnetic resonance techniques for studying biological molecules

    SciTech Connect (OSTI)

    Laws, David D.

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone ({phi}/{psi}) dihedral angles by comparing experimentally determined {sup 13}C{sub a}, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of {alpha}-helical and {beta}-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly {beta}-sheet.

  3. Molecular Design of Branched and Binary Molecules at Ordered Interfaces

    SciTech Connect (OSTI)

    Kirsten Larson Genson

    2005-12-27

    This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

  4. BEAM TRANSPORT AND STORAGE WITH COLD NEUTRAL ATOMS AND MOLECULES

    SciTech Connect (OSTI)

    Walstrom, Peter L.

    2012-05-15

    A large class of cold neutral atoms and molecules is subject to magnetic field-gradient forces. In the presence of a field, hyperfine atomic states are split into several Zeeman levels. The slopes of these curves vs. field are the effective magnetic moments. By means of optical pumping in a field, Zeeman states of neutral lithium atoms and CaH molecules with effective magnetic moments of nearly {+-} one Bohr magneton can be selected. Particles in Zeeman states for which the energy increases with field are repelled by increasing fields; particles in states for which the energy decreases with field are attracted to increasing fields. For stable magnetic confinement, field-repelled states are required. Neutral-particle velocities in the present study are on the order of tens to hundreds of m/s and the magnetic fields needed for transport and injection are on the order of in the range of 0.01-1T. Many of the general concepts of charged-particle beam transport carry over into neutral particle spin-force optics, but with important differences. In general, the role of bending dipoles in charged particle optics is played by quadrupoles in neutral particle optics; the role of quadrupoles is played by sextupoles. The neutralparticle analog of charge-exchange injection into storage rings is the use of lasers to flip the state of particles from field-seeking to field-repelled. Preliminary tracking results for two neutral atom/molecule storage ring configurations are presented. It was found that orbit instabilities limit the confinment time in a racetrack-shaped ring with discrete magnetic elements with drift spaces between them; stable behavior was observed in a toroidal ring with a continuous sextupole field. An alternative concept using a linear sextupole or octupole channel with solenoids on the ends is presently being considered.

  5. Numerically Solvable Model for Resonant Collisions of Electronswith Diatomic Molecules

    SciTech Connect (OSTI)

    Houfek, Karel; Rescigno, T.N.; McCurdy, C.W.

    2006-01-27

    We describe a simple model for electron-molecule collisions that has one nuclear and one electronic degree of freedom and that can be solved to arbitrarily high precision, without making the Born-Oppenheimer approximation, by employing a combination of the exterior complex scaling method and a finite-element implementation of the discrete variable representation. We compare exact cross sections for vibrational excitation and dissociative attachment with results obtained using the local complex potential approximation as commonly applied in the ''boomerang'' model, and suggest how this two-dimensional model can be used to test the underpinnings of contemporary nonlocal approximations to resonant collisions.

  6. Spectroscopic and dynamical studies of highly energized small polyatomic molecules

    SciTech Connect (OSTI)

    Field, R.W.; Silbey, R.J.

    1993-12-01

    The authors have initiated a program to perform spectroscopic and dynamic studies of small molecules. Large amplitude motions in excited acetylene were discussed along with plans to record the dispersed fluorescence (DF) and the stimulated emission pumping (SEP) spectra. SEP spectra were reported for the formyl radical. A Fourier transform spectrometer was discussed with respect to its ability to probe the structure of radicals. This instrument is capable of performing studies using various techniques such as magnetic rotation spectroscopy and sub-Doppler sideband-OODR Zeman (SOODRZ) spectroscopy.

  7. Vacuum ultraviolet photoionization and photodissociation of polyatomic molecules and radicals

    SciTech Connect (OSTI)

    Ng, C.Y.

    1993-12-01

    In the past decade, tremendous progress has been made in understanding the photodissociation (PD) dynamics of triatomic molecules. However, the PD study of radicals, especially polyatomic radicals, has remained essentially an unexplored research area. Detailed state-to-state PD cross sections for radicals in the UV and VUV provide challenges not only for dynamical calculations, but also for ab initio quantum chemical studies. The authors have developed a laser based pump-probe apparatus for the measurement of absolute PD cross sections for CH{sub 3}S and HS is summarized.

  8. Deterministically Polarized Fluorescence from Single Dye Molecules Aligned in Liquid Crystal Host

    SciTech Connect (OSTI)

    Lukishova, S.G.; Schmid, A.W.; Knox, R.; Freivald, P.; Boyd, R. W.; Stroud, Jr., C. R.; Marshall, K.L.

    2005-09-30

    We demonstrated for the first time to our konwledge deterministically polarized fluorescence from single dye molecules. Planar aligned nematic liquid crystal hosts provide deterministic alignment of single dye molecules in a preferred direction.

  9. DEUTERATED MOLECULES IN ORION KL FROM HERSCHEL/HIFI

    SciTech Connect (OSTI)

    Neill, Justin L.; Crockett, Nathan R.; Bergin, Edwin A.; Pearson, John C.; Xu, Li-Hong

    2013-11-10

    We present a comprehensive study of the deuterated molecules detected in the fullband HIFI survey of the Orion Kleinmann-Low nebula (Orion KL) region. Ammonia, formaldehyde, and methanol and their singly deuterated isotopologues are each detected through numerous transitions in this survey with a wide range in optical depths and excitation conditions. In conjunction with a recent study of the abundance of HDO and H{sub 2}O in Orion KL, this study yields the best constraints on deuterium fractionation in an interstellar molecular cloud to date. As previous studies have found, both the Hot Core and Compact Ridge regions within Orion KL contain significant abundances of deuterated molecules, suggesting an origin in cold grain mantles. In the Hot Core, we find that ammonia is roughly a factor of two more fractionated than water. In the Compact Ridge, meanwhile, we find similar deuterium fractionation in water, formaldehyde, and methanol, with D/H ratios of (2-8) × 10{sup –3}. The [CH{sub 2}DOH]/[CH{sub 3}OD] ratio in the Compact Ridge is found to be 1.2 ± 0.3. The Hot Core generally has lower deuterium fractionation than the Compact Ridge, suggesting a slightly warmer origin, or a greater contribution from warm gas phase chemistry.

  10. In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27

    SciTech Connect (OSTI)

    Acosta-Reyes, Francisco J.; Dardonville, Christophe; Koning, Harry P. de; Natto, Manal; Subirana, Juan A.; Campos, J. Lourdes

    2014-06-01

    New features of an antiprotozoal DNA minor-groove binding drug, which acts as a cross-linking agent, are presented. It also fills the minor groove of DNA completely and prevents the access of proteins. These features are also expected for other minor-groove binding drugs when associated with suitable DNA targets. The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previous studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT){sub 2} with the dicationic drug 4, 4?-bis(imidazolinylamino)diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis, Trichomonas vaginalis, are also reported.

  11. Recent developments with metalloprotease inhibitor class of drug candidates for Botulinum neurotoxins

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

    Kumar, Gyanendra; Swaminathan, Subramanyam

    2015-03-01

    Botulinum Neurotoxins are the most poisonous of all toxins with lethal dose in nanogram quantities. They are also potential biological warfare and bioterrorism agents due to their high toxicity and ease of preparation. On the other hand BoNTs are also being increasingly used for therapeutic and cosmetic purposes, and with that the chances of accidental overdose are increasing. And despite the potential damage they could cause to human health, there are no post-intoxication drugs available so far. But progress is being made in this direction. The crystal structures in native form and bound with substrate peptides have been determined, andmore » these are enabling structure-based drug discovery possible. High throughput assays have also been designed to speed up the screening progress. Substrate-based and small molecule inhibitors have been identified. But turning high affinity inhibitors into clinically viable drug candidates has remained a challenge. We discuss here the latest developments and the future challenges in drug discovery for Botulinum neurotoxins.« less

  12. Recent developments with metalloprotease inhibitor class of drug candidates for Botulinum neurotoxins

    SciTech Connect (OSTI)

    Kumar, Gyanendra; Swaminathan, Subramanyam

    2015-03-01

    Botulinum Neurotoxins are the most poisonous of all toxins with lethal dose in nanogram quantities. They are also potential biological warfare and bioterrorism agents due to their high toxicity and ease of preparation. On the other hand BoNTs are also being increasingly used for therapeutic and cosmetic purposes, and with that the chances of accidental overdose are increasing. And despite the potential damage they could cause to human health, there are no post-intoxication drugs available so far. But progress is being made in this direction. The crystal structures in native form and bound with substrate peptides have been determined, and these are enabling structure-based drug discovery possible. High throughput assays have also been designed to speed up the screening progress. Substrate-based and small molecule inhibitors have been identified. But turning high affinity inhibitors into clinically viable drug candidates has remained a challenge. We discuss here the latest developments and the future challenges in drug discovery for Botulinum neurotoxins.

  13. A Supramolecular Complex in Small-Molecule Solar Cells based on Contorted

    Office of Scientific and Technical Information (OSTI)

    Aromatic Molecules (Journal Article) | SciTech Connect A Supramolecular Complex in Small-Molecule Solar Cells based on Contorted Aromatic Molecules Citation Details In-Document Search Title: A Supramolecular Complex in Small-Molecule Solar Cells based on Contorted Aromatic Molecules Authors: Kang S. ; Kim, J ; Chiu, C ; Ahn, S ; Schiros, T ; Lee, S ; Yager, K ; Toney, M ; Loo, Y ; Nuckolls, C Publication Date: 2012-08-20 OSTI Identifier: 1069683 Report Number(s): BNL--100255-2013-JA Journal

  14. Coherent Anti-Stokes Raman Scattering Spectroscopy of Single Molecules in Solution

    SciTech Connect (OSTI)

    Sunney Xie, Wei Min, Chris Freudiger, Sijia Lu

    2012-01-18

    During this funding period, we have developed two breakthrough techniques. The first is stimulated Raman scattering microscopy, providing label-free chemical contrast for chemical and biomedical imaging based on vibrational spectroscopy. Spontaneous Raman microscopy provides specific vibrational signatures of chemical bonds, but is often hindered by low sensitivity. We developed a three-dimensional multiphoton vibrational imaging technique based on stimulated Raman scattering (SRS). The sensitivity of SRS imaging is significantly greater than that of spontaneous Raman microscopy, which is achieved by implementing high-frequency (megahertz) phase-sensitive detection. SRS microscopy has a major advantage over previous coherent Raman techniques in that it offers background-free and readily interpretable chemical contrast. We demonstrated a variety of biomedical applications, such as differentiating distributions of omega-3 fatty acids and saturated lipids in living cells, imaging of brain and skin tissues based on intrinsic lipid contrast, and monitoring drug delivery through the epidermis. This technology offers exciting prospect for medical imaging. The second technology we developed is stimulated emission microscopy. Many chromophores, such as haemoglobin and cytochromes, absorb but have undetectable fluorescence because the spontaneous emission is dominated by their fast non-radiative decay. Yet the detection of their absorption is difficult under a microscope. We use stimulated emission, which competes effectively with the nonradiative decay, to make the chromophores detectable, as a new contrast mechanism for optical microscopy. We demonstrate a variety of applications of stimulated emission microscopy, such as visualizing chromoproteins, non-fluorescent variants of the green fluorescent protein, monitoring lacZ gene expression with a chromogenic reporter, mapping transdermal drug distribu- tions without histological sectioning, and label-free microvascular imaging based on endogenous contrast of haemoglobin. For all these applications, sensitivity is orders of magnitude higher than for spontaneous emission or absorption contrast, permitting nonfluorescent reporters for molecular imaging. Although we did not accomplish the original goal of detecting single-molecule by CARS, our quest for high sensitivity of nonlinear optical microscopy paid off in providing the two brand new enabling technologies. Both techniques were greatly benefited from the use of high frequency modulation for microscopy, which led to orders of magnitude increase in sensitivity. Extensive efforts have been made on optics and electronics to accomplish these breakthroughs.

  15. Reaction mechanism studies of unsaturated molecules using photofragment translational spectroscopy

    SciTech Connect (OSTI)

    Longfellow, C.A. |

    1996-05-01

    A number of molecules have been studied using the technique of photofragment translational spectroscopy. In Chapter One a brief introduction to the experimental technique is given. In Chapter Two the infrared multiphoton dissociation (IRMPD) of acetic acid is discussed. Carbon dioxide and methane were observed for the first time as products from dissociation under collisionless conditions. Chapter Three relates an IRMPD experiment of hexafluoropropene. The predominant channel produces CFCF{sub 3} or C{sub 2}F{sub 4} and CF{sub 2}, with the heavier species undergoing further dissociation to two CF{sub 2} fragments. In Chapter Four the ultraviolet (UV) dissociation of hexafluoropropene is investigated. Chapter Five explores the IRMPD of octafluoro-1-butene and octafluoro-2-butene.

  16. Transport behavior of water molecules through two-dimensional nanopores

    SciTech Connect (OSTI)

    Zhu, Chongqin; Li, Hui; Meng, Sheng

    2014-11-14

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  17. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print Tuesday, 23 June 2015 13:00 The cancer drug...

  18. Method for loading lipid like vesicles with drugs of other chemicals

    DOE Patents [OSTI]

    Mehlhorn, R.J.

    1998-06-09

    A method for accumulating drugs or other chemicals within synthetic, lipid-like vesicles by means of a pH gradient imposed on the vesicles just prior to use is described. The method is suited for accumulating molecules with basic or acid moieties which are permeable to the vesicles membranes in their uncharged form and for molecules that contain charge moieties that are hydrophobic ions and can therefore cross the vesicle membranes in their charged form. The method is advantageous over prior art methods for encapsulating biologically active materials within vesicles in that is achieves very high degrees of loading with simple procedures that are economical and require little technical expertise, furthermore kits which can be stored for prolonged periods prior to use without impairment of the capacity to achieve drug accumulation are described. A related application of the method consists of using this technology to detoxify animals that have been exposed to poisons with basic, weak acid or hydrophobic charge groups within their molecular structures. 2 figs.

  19. Oligomycin frames a common drug-binding site in the ATP synthase

    SciTech Connect (OSTI)

    Symersky, Jindrich; Osowski, Daniel; Walters, D. Eric; Mueller, David M.

    2015-12-01

    We report the high-resolution (1.9 {angstrom}) crystal structure of oligomycin bound to the subunit c10 ring of the yeast mitochondrial ATP synthase. Oligomycin binds to the surface of the c10 ring making contact with two neighboring molecules at a position that explains the inhibitory effect on ATP synthesis. The carboxyl side chain of Glu59, which is essential for proton translocation, forms an H-bond with oligomycin via a bridging water molecule but is otherwise shielded from the aqueous environment. The remaining contacts between oligomycin and subunit c are primarily hydrophobic. The amino acid residues that form the oligomycin-binding site are 100% conserved between human and yeast but are widely different from those in bacterial homologs, thus explaining the differential sensitivity to oligomycin. Prior genetics studies suggest that the oligomycin-binding site overlaps with the binding site of other antibiotics, including those effective against Mycobacterium tuberculosis, and thereby frames a common 'drug-binding site.' We anticipate that this drug-binding site will serve as an effective target for new antibiotics developed by rational design.

  20. Method for loading lipid like vesicles with drugs of other chemicals

    DOE Patents [OSTI]

    Mehlhorn, Rolf Joachim

    1998-01-01

    A method for accumulating drugs or other chemicals within synthetic, lipid-like vesicles by means of a pH gradient imposed on the vesicles just prior to use is described. The method is suited for accumulating molecules with basic or acid moieties which are permeable to the vesicles membranes in their uncharged form and for molecules that contain charge moieties that are hydrophobic ions and can therefore cross the vesicle membranes in their charged form. The method is advantageous over prior art methods for encapsulating biologically active materials within vesicles in that is achieves very high degrees of loading with simple procedures that are economical and require little technical expertise, furthermore kits which can be stored for prolonged periods prior to use without impairment of the capacity to achieve drug accumulation are described. A related application of the method consists of using this technology to detoxify animals that have been exposed to poisons with basic, weak acid or hydrophobic charge groups within their molecular structures.

  1. Flow cytometry aids basic cell biology research and drug discovery

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

    Flow cytometry aids basic cell biology research and drug discovery Flow cytometry aids basic cell biology research and drug discovery Life Technologies Corporation and LANL have ...

  2. FACT SHEET ON THE CONSEQUENCES OF A FAILED DRUG TEST

    Office of Environmental Management (EM)

    SHEET ON THE CONSEQUENCES OF A POSITIVE DRUG TEST The Secretary has determined that ... The information below summarizes the consequences of a positive test for drugs for each ...

  3. Food and Drug Administration White Oak Campus Environmental Stewardshi...

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

    Food and Drug Administration White Oak Campus Environmental Stewardship and Cost Savings FEMP ESPC Success Story on water conservation and green energy at the Food and Drug ...

  4. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein...

  5. Continuum model for chiral induced spin selectivity in helical molecules

    SciTech Connect (OSTI)

    Medina, Ernesto; González-Arraga, Luis A.; Finkelstein-Shapiro, Daniel; Mujica, Vladimiro; Berche, Bertrand

    2015-05-21

    A minimal model is exactly solved for electron spin transport on a helix. Electron transport is assumed to be supported by well oriented p{sub z} type orbitals on base molecules forming a staircase of definite chirality. In a tight binding interpretation, the spin-orbit coupling (SOC) opens up an effective ?{sub z} ? ?{sub z} coupling via interbase p{sub x,y} ? p{sub z} hopping, introducing spin coupled transport. The resulting continuum model spectrum shows two Kramers doublet transport channels with a gap proportional to the SOC. Each doubly degenerate channel satisfies time reversal symmetry; nevertheless, a bias chooses a transport direction and thus selects for spin orientation. The model predicts (i) which spin orientation is selected depending on chirality and bias, (ii) changes in spin preference as a function of input Fermi level and (iii) back-scattering suppression protected by the SO gap. We compute the spin current with a definite helicity and find it to be proportional to the torsion of the chiral structure and the non-adiabatic Aharonov-Anandan phase. To describe room temperature transport, we assume that the total transmission is the result of a product of coherent steps.

  6. Observing a coherent superposition of an atom and a molecule

    SciTech Connect (OSTI)

    Dowling, Mark R. [School of Physical Sciences, University of Queensland, St. Lucia, Queensland 4072 (Australia); Bartlett, Stephen D. [School of Physics, University of Sydney, Sydney, New South Wales 2006 (Australia); Rudolph, Terry [Optics Section, Blackett Laboratory, Imperial College London, London SW7 2BW (United Kingdom); Institute for Mathematical Sciences, Imperial College London, London SW7 2BW (United Kingdom); Spekkens, Robert W. [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA (United Kingdom)

    2006-11-15

    We demonstrate that it is possible, in principle, to perform a Ramsey-type interference experiment to exhibit a coherent superposition of a single atom and a diatomic molecule. This gedanken experiment, based on the techniques of Aharonov and Susskind [Phys. Rev. 155, 1428 (1967)], explicitly violates the commonly accepted superselection rule that forbids coherent superpositions of eigenstates of differing atom number. A Bose-Einstein condensate plays the role of a reference frame that allows for coherent operations analogous to Ramsey pulses. We also investigate an analogous gedanken experiment to exhibit a coherent superposition of a single boson and a fermion, violating the commonly accepted superselection rule forbidding coherent superpositions of states of differing particle statistics. In this case, the reference frame is realized by a multimode state of many fermions. This latter case reproduces all of the relevant features of Ramsey interferometry, including Ramsey fringes over many repetitions of the experiment. However, the apparent inability of this proposed experiment to produce well-defined relative phases between two distinct systems each described by a coherent superposition of a boson and a fermion demonstrates that there are additional, outstanding requirements to fully 'lift' the univalence superselection rule.

  7. Spin-dependent electron transport in zinc- and manganese-doped adenine molecules

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-01-28

    The spin-dependent electron transport properties of zinc- and manganese-doped adenine molecules connected to zigzag graphene leads are studied in the zero bias regime using the non-equilibrium Green's function method. The conductance of the adenine molecule increased and became spin-dependent when a zinc or manganese atom was doped into the molecules. The effects of a transverse electric field on the spin-polarization of the transmitted electrons were investigated and the spin-polarization was controlled by changing the transverse electric field. Under the presence of a transverse electric field, both the zinc- and manganese-doped adenine molecules acted as spin-filters. The maximum spin-polarization of the manganese-doped adenine molecule was greater than the molecule doped with zinc.

  8. Controlling orbital-selective Kondo effects in a single molecule through

    Office of Scientific and Technical Information (OSTI)

    coordination chemistry (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry Citation Details In-Document Search Title: Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when

  9. Matrix Infrared Spectroscopic and Computational Investigations of Novel Small Uranium Containing Molecules - Final Technical Report

    SciTech Connect (OSTI)

    Andrews, Lester

    2014-10-17

    Direct reactions of f-element uranium, thorium and lanthanide metal atoms were investigated with small molecules. These metal atoms were generated by laser ablation and mixed with the reagent molecules then condensed with noble gases at 4K. The products were analyzed by absorption of infrared light to measure vibrational frequencies which were confirmed by quantum chemical calculations. We have learned more about the reactivity of uranium atoms with common molecules, which will aid in the develolpment of further applications of uranium.

  10. Pre-Designed Single-Molecule Traps for CO2 Capture | Center for Gas

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

    SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Pre-Designed Single-Molecule Traps for CO2 Capture

  11. A Small Molecule That Switches a Ubiquitin Ligase From a Processive...

    Office of Scientific and Technical Information (OSTI)

    Title: A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a Distributive Enzymatic Mechanism Authors: Kathman, Stefan G. ; Span, Ingrid ; Smith, Aaron T. ; Xu, ...

  12. Organic Molecule Functionalized Zn3P2 Nanowire Inorganic-Organic...

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

    Organic Molecule Functionalized Zn3P2 Nanowire Inorganic-Organic Hybrid Thermoelectrics Demonstrates self-catalytic schemes for large-scale synthesis of compound semiconductor ...

  13. THE ORIGIN OF COMPLEX ORGANIC MOLECULES IN PRESTELLAR CORES

    SciTech Connect (OSTI)

    Vastel, C.; Ceccarelli, C.; Lefloch, B.; Bachiller, R.

    2014-11-01

    Complex organic molecules (COMs) have been detected in a variety of environments including cold prestellar cores. Given the low temperatures of these objects, these detections challenge existing models. We report here new observations toward the prestellar core L1544. They are based on an unbiased spectral survey of the 3 mm band at the IRAM 30 m telescope as part of the Large Program ASAI. The observations allow us to provide a full census of the oxygen-bearing COMs in this source. We detected tricarbon monoxide, methanol, acetaldehyde, formic acid, ketene, and propyne with abundances varying from 5 × 10{sup –11} to 6 × 10{sup –9}. The non-LTE analysis of the methanol lines shows that they are likely emitted at the border of the core at a radius of ?8000 AU, where T ? 10 K and n {sub H{sub 2}} ?2 × 10{sup 4} cm{sup –3}. Previous works have shown that water vapor is enhanced in the same region because of the photodesorption of water ices. We propose that a non-thermal desorption mechanism is also responsible for the observed emission of methanol and COMs from the same layer. The desorbed oxygen and a small amount of desorbed methanol and ethene are enough to reproduce the abundances of tricarbon monoxide, methanol, acetaldehyde, and ketene measured in L1544. These new findings open the possibility that COMs in prestellar cores originate in a similar outer layer rather than in the dense inner cores, as previously assumed, and that their formation is driven by the non-thermally desorbed species.

  14. Secretary Bodman's Memorandum Regarding Drug Testing at DOE

    Broader source: Energy.gov [DOE]

    Decisions regarding drug testing for Department of Energy positions that require access authorizations (Security Clearances)

  15. Method and apparatus for passive optical dosimeter comprising caged dye molecules

    DOE Patents [OSTI]

    Sandison, David R.

    2001-07-03

    A new class of ultraviolet dosimeters is made possible by exposing caged dye molecules, which generate a dye molecule on exposure to ultraviolet radiation, to an exterior environment. Applications include sunburn monitors, characterizing the UV exposure history of UV-sensitive materials, especially including structural plastics, and use in disposable `one-use` optical equipment, especially medical devices.

  16. Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

    DOE Patents [OSTI]

    Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia; Hoffbauer, Mark A.; Akhadov, Elshan A.

    2009-12-29

    A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

  17. Organic molecules deposited on graphene: A computational investigation of self-assembly and electronic structure

    SciTech Connect (OSTI)

    Oliveira, I. S. S. de; Miwa, R. H.

    2015-01-28

    We use ab initio simulations to investigate the adsorption and the self-assembly processes of tetracyanoquinodimethane (TCNQ), tetrafluoro-tetracyanoquinodimethane (F4-TCNQ), and tetrasodium 1,3,6,8-pyrenetetrasulfonic acid (TPA) on the graphene surface. We find that there are no chemical bonds at the molecule–graphene interface, even at the presence of grain boundaries on the graphene surface. The molecules bond to graphene through van der Waals interactions. In addition to the molecule–graphene interaction, we performed a detailed study of the role played by the (lateral) molecule–molecule interaction in the formation of the, experimentally verified, self-assembled layers of TCNQ and TPA on graphene. Regarding the electronic properties, we calculate the electronic charge transfer from the graphene sheet to the TCNQ and F4-TCNQ molecules, leading to a p-doping of graphene. Meanwhile, such charge transfer is reduced by an order of magnitude for TPA molecules on graphene. In this case, it is not expected a significant doping process upon the formation of self-assembled layer of TPA molecules on the graphene sheet.

  18. Group specific internal standard technology (GSIST) for simultaneous identification and quantification of small molecules

    DOE Patents [OSTI]

    Adamec, Jiri; Yang, Wen-Chu; Regnier, Fred E

    2014-01-14

    Reagents and methods are provided that permit simultaneous analysis of multiple diverse small molecule analytes present in a complex mixture. Samples are labeled with chemically identical but isotopically distince forms of the labeling reagent, and analyzed using mass spectrometry. A single reagent simultaneously derivatizes multiple small molecule analytes having different reactive functional groups.

  19. Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules

    SciTech Connect (OSTI)

    DePalma, Joseph W.; Wang, Jian; Wexler, Anthony S.; Johnston, Murray V.

    2015-10-21

    Quantum chemical calculations were employed to model the interactions of the [(NH4+)4(HSO4-)4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of the cluster and a carboxylic acid, aldehyde or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient ammonium bisulfate cluster, such as the [(NH4+)4(SO4-)4] cluster, is able to adsorb an oxygenated organic molecule. Although adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is not, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ~1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules.

  20. Resonance reactions and enhancement of weak interactions in collisions of cold molecules

    SciTech Connect (OSTI)

    Flambaum, V. V.; Ginges, J. S. M. [School of Physics, University of New South Wales, Sydney 2052 (Australia)

    2006-08-15

    With the creation of ultracold atoms and molecules, a new type of chemistry - 'resonance' chemistry - emerges: chemical reactions can occur when the energy of colliding atoms and molecules matches a bound state of the combined molecule (Feshbach resonance). This chemistry is rather similar to reactions that take place in nuclei at low energies. In this paper we suggest some problems for future experimental and theoretical work related to the resonance chemistry of ultracold molecules. Molecular Bose-Einstein condensates are particularly interesting because in this system collisions and chemical reactions are extremely sensitive to weak fields; also, a preferred reaction channel may be enhanced due to a finite number of final states. The sensitivity to weak fields arises due to the high density of narrow compound resonances and the macroscopic number of molecules with kinetic energy E=0 (in the ground state of a mean-field potential). The high sensitivity to the magnetic field may be used to measure the distribution of energy intervals, widths, and magnetic moments of compound resonances and study the onset of quantum chaos. A difference in the production rate of right-handed and left-handed chiral molecules may be produced by external electric E and magnetic B fields and the finite width {gamma} of the resonance (correlation {gamma}E{center_dot}B). The same effect may be produced by the parity-violating energy difference in chiral molecules.

  1. Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules

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

    DePalma, Joseph W.; Wang, Jian; Wexler, Anthony S.; Johnston, Murray V.

    2015-10-21

    Quantum chemical calculations were employed to model the interactions of the [(NH4+)4(HSO4-)4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of the cluster and a carboxylic acid, aldehyde or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient ammonium bisulfate cluster, such as the [(NH4+)4(SO4-)4] cluster, is able to adsorb an oxygenated organic molecule.more » Although adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is not, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ~1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules.« less

  2. Controlling the optical dipole force for molecules with field-induced alignment

    SciTech Connect (OSTI)

    Purcell, S. M.; Barker, P. F.

    2010-09-15

    We measure the role of field-induced alignment on the dipole force for molecules using a single focused nonresonant laser beam. We show that through the alignment process we can modify the effective polarizability by field polarization and thus control the center-of-mass motion of the molecule. We observe a maximum change of 20% in the dipole force on CS{sub 2} molecules when changing from linearly to circularly polarized light. Additionally, the effect of the dipole force on different vibrational states is also studied.

  3. Mechanism of Angular Momentum Exchange between Molecules and Laguerre-Gaussian Beams

    SciTech Connect (OSTI)

    Alexandrescu, Adrian; Cojoc, Dan; Fabrizio, Enzo Di

    2006-06-23

    We derive the interaction Hamiltonian between a diatomic molecule and a Laguerre-Gaussian beam under the assumption of a small spread of the center of mass wave function of the molecule in comparison with the beam waist. Considering the dynamical variables of the center of mass, vibrational, rotational, and electronic motion, we show that, within the electronic dipole approximation, the orbital angular momentum of the field couples with the rotational and electronic motion. The changes in the transition probabilities and selection rules induced by the field orbital angular momentum and the applicability of the derived interaction mechanisms for polyatomic molecules are discussed.

  4. Efficient spin filter and spin valve in a single-molecule magnet Fe{sub 4}

    Office of Scientific and Technical Information (OSTI)

    between two graphene electrodes (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Efficient spin filter and spin valve in a single-molecule magnet Fe{sub 4} between two graphene electrodes Citation Details In-Document Search Title: Efficient spin filter and spin valve in a single-molecule magnet Fe{sub 4} between two graphene electrodes We propose a magnetic molecular junction consisting of a single-molecule magnet Fe{sub 4} connected two graphene electrodes

  5. Reconstruction of the Electron Density of Molecules with Single-Axis Alignment

    SciTech Connect (OSTI)

    Starodub, Dmitri

    2011-08-12

    Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. We present two methods of structure solution for this case. One is based on the iterative projection algorithms for phase retrieval applied to the coefficients of the cylindrical harmonic expansion of the molecular electron density. Another is the holographic approach utilizing presence of the strongly scattering reference atom for a specific molecule.

  6. Optically generated ultrasound for enhanced drug delivery

    DOE Patents [OSTI]

    Visuri, Steven R.; Campbell, Heather L.; Da Silva, Luiz

    2002-01-01

    High frequency acoustic waves, analogous to ultrasound, can enhance the delivery of therapeutic compounds into cells. The compounds delivered may be chemotherapeutic drugs, antibiotics, photodynamic drugs or gene therapies. The therapeutic compounds are administered systemically, or preferably locally to the targeted site. Local delivery can be accomplished through a needle, cannula, or through a variety of vascular catheters, depending on the location of routes of access. To enhance the systemic or local delivery of the therapeutic compounds, high frequency acoustic waves are generated locally near the target site, and preferably near the site of compound administration. The acoustic waves are produced via laser radiation interaction with an absorbing media and can be produced via thermoelastic expansion, thermodynamic vaporization, material ablation, or plasma formation. Acoustic waves have the effect of temporarily permeabilizing the membranes of local cells, increasing the diffusion of the therapeutic compound into the cells, allowing for decreased total body dosages, decreased side effects, and enabling new therapies.

  7. FACT SHEET ON THE CONSEQUENCES OF A FAILED DRUG TEST

    Energy Savers [EERE]

    FACT SHEET ON THE CONSEQUENCES OF A POSITIVE DRUG TEST The Secretary has determined that ... The information below summarizes the consequences of a positive test for drugs for each ...

  8. Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC |

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

    Department of Energy Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC PDF icon Intergrated Drug Testing System, PIA, Bechtel Jacobs C ompany, LLC More Documents & Publications Electronic Document Management System PIA, BechtelJacobs Company, LLC Dosimetry Records System PIA, bechtel Jacobs Company, LLC Pension Estimate System PIA, Bechtel

  9. Ionization of oriented carbonyl sulfide molecules by intense circularly polarized laser pulses

    SciTech Connect (OSTI)

    Dimitrovski, Darko; Abu-samha, Mahmoud; Madsen, Lars Bojer; Filsinger, Frank; Meijer, Gerard; Kuepper, Jochen [Lundbeck Foundation Theoretical Center for Quantum System Research, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C (Denmark); Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany); Holmegaard, Lotte; Kalhoej, Line [Department of Chemistry, Aarhus University, DK-8000 Aarhus C (Denmark); Nielsen, Jens H. [Department of Physics, Aarhus University, DK-8000 Aarhus C (Denmark); Stapelfeldt, Henrik [Department of Chemistry, Aarhus University, DK-8000 Aarhus C (Denmark); Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark)

    2011-02-15

    We present combined experimental and theoretical results on strong-field ionization of oriented carbonyl sulfide molecules by circularly polarized laser pulses. The obtained molecular frame photoelectron angular distributions show pronounced asymmetries perpendicular to the direction of the molecular electric dipole moment. These findings are explained by a tunneling model invoking the laser-induced Stark shifts associated with the dipoles and polarizabilities of the molecule and its unrelaxed cation. The focus of the present article is to understand the strong-field ionization of one-dimensionally-oriented polar molecules, in particular asymmetries in the emission direction of the photoelectrons. In the following article [Phys. Rev. A 83, 023406 (2011)] the focus is to understand strong-field ionization from three-dimensionally-oriented asymmetric top molecules, in particular the suppression of electron emission in nodal planes of molecular orbitals.

  10. From Artificial Atoms to Nanocrystal Molecules: Preparation and Properties of More Complex Nanostructures

    SciTech Connect (OSTI)

    Choi, Charina L; Alivisatos, A Paul

    2009-10-20

    Quantum dots, which have found widespread use in fields such as biomedicine, photovoltaics, and electronics, are often called artificial atoms due to their size-dependent physical properties. Here this analogy is extended to consider artificial nanocrystal molecules, formed from well-defined groupings of plasmonically or electronically coupled single nanocrystals. Just as a hydrogen molecule has properties distinct from two uncoupled hydrogen atoms, a key feature of nanocrystal molecules is that they exhibit properties altered from those of the component nanoparticles due to coupling. The nature of the coupling between nanocrystal atoms and its response to vibrations and deformations of the nanocrystal molecule bonds are of particular interest. We discuss synthetic approaches, predicted and observed physical properties, and prospects and challenges toward this new class of materials.

  11. Molecule@MOF: A New Class of Electronic Materials. (Conference) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Molecule@MOF: A New Class of Electronic Materials. Citation Details In-Document Search Title: Molecule@MOF: A New Class of Electronic Materials. Abstract not provided. Authors: Talin, Albert Alec ; Foster, Michael E. ; Stavila, Vitalie ; Leonard, Francois Leonard ; Spataru, Dan Catalin ; Allendorf, Mark D. ; Ford, Alexandra Caroline ; El Gabaly Marquez, Farid Publication Date: 2014-09-01 OSTI Identifier: 1241683 Report Number(s): SAND2014-18122PE 537746 DOE Contract Number:

  12. A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a

    Office of Scientific and Technical Information (OSTI)

    Distributive Enzymatic Mechanism (Journal Article) | SciTech Connect A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a Distributive Enzymatic Mechanism Citation Details In-Document Search Title: A Small Molecule That Switches a Ubiquitin Ligase From a Processive to a Distributive Enzymatic Mechanism Authors: Kathman, Stefan G. ; Span, Ingrid ; Smith, Aaron T. ; Xu, Ziyang ; Zhan, Jennifer ; Rosenzweig, Amy C. ; Statsyuk, Alexander V. [1] + Show Author Affiliations

  13. Laser Induced Nuclear Fusion, LINF, In Muonic Molecules With Ultrashort Super Intense Laser Fields

    SciTech Connect (OSTI)

    Bandrauk, Andre D.; Paramonov, Gennady K.

    2010-02-02

    Muonium molecules where muons replace electrons increase the stability of molecules to ionization at superhigh intensities, I>10{sup 20} W/cm{sup 2}. We show furthermore from numerical simulations that in the nonsymmetric series, pdu, dtu, ptu, the permanent dipole moments can be used to enhance LINF, Laser Induced Nuclear Fusion by laser induced recollision of the light nucleus with the heavier nucleus.

  14. SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

    SciTech Connect (OSTI)

    Professor William Moerner

    2010-07-09

    The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in Tuscany, provides an avenue for scientists from different disciplines to interact and brainstorm and promotes cross-disciplinary collaborations directed toward compelling biological problems.

  15. Inorganic-Organic Molecules and Solids with Nanometer-Sized Pores

    SciTech Connect (OSTI)

    Maverick, Andrew W.

    2011-12-17

    We are constructing porous inorganic-organic hybrid molecules and solids, many of which contain coordinatively unsaturated metal centers. In this work, we use multifunctional ���²-diketone ligands as �¢����building blocks�¢��� to prepare extended-solid and molecular porous materials that are capable of reacting with a variety of guest molecules.

  16. Tracing the structure of asymmetric molecules from high-order harmonic generation

    SciTech Connect (OSTI)

    Chen Yanjun; Zhang, Bing

    2011-11-15

    We investigate high-order harmonic generation (HHG) from asymmetric molecules exposed to intense laser fields. We show that the emissions of odd and even harmonics depend differently on the orientation angle, the internuclear distance, as well as the effective charge. This difference mainly comes from different roles of intramolecular interference in the HHG of odd and even harmonics. These roles map the structure of the asymmetric molecule to the odd vs even HHG spectra.

  17. Viable Single-Molecule Diodes | U.S. DOE Office of Science (SC)

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

    Viable Single-Molecule Diodes Basic Energy Sciences (BES) BES Home About Research Facilities Science Highlights Benefits of BES Funding Opportunities Basic Energy Sciences Advisory Committee (BESAC) Community Resources Contact Information Basic Energy Sciences U.S. Department of Energy SC-22/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-3081 F: (301) 903-6594 E: Email Us More Information » 11.01.15 Viable Single-Molecule Diodes Major milestone in molecular

  18. [alpha]E-catenin is an autoinhibited molecule that coactivates vinculin

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect [alpha]E-catenin is an autoinhibited molecule that coactivates vinculin Citation Details In-Document Search Title: [alpha]E-catenin is an autoinhibited molecule that coactivates vinculin Authors: Choi, Hee-Jung ; Pokutta, Sabine ; Cadwell, Gregory W. ; Bobkov, Andrey A. ; Bankston, Laurie A. ; Liddington, Robert C. ; Weis, William I. [1] ; Sanford-Burnham) [2] + Show Author Affiliations (Stanford-MED) ( Publication Date: 2012-10-02 OSTI Identifier: 1051867

  19. Drug-Free Federal Workplace Testing Implementation Program

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1988-07-29

    The order provides guidance and policy for the administration, application and implementation of the DOE Drug-free Federal Workplace Plan and other regulations that facilitate the maintenance of a drug-free Federal workplace through the establishment of programs to test for the use of illegal drugs. Chg 1, dated 8-21-92

  20. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes

    SciTech Connect (OSTI)

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  1. In situ Formation of Highly Conducting Covalent Au-C Contacts for Single-Molecule Junctions

    SciTech Connect (OSTI)

    Cheng, Z.L.; Hybertsen, M.; Skouta, R.; Vazquez, H.; Widawsky, J.R.; Schneebeli, S.; Chen, W.; Breslow, R.; Venkataraman, L.

    2011-06-01

    Charge transport across metal-molecule interfaces has an important role in organic electronics. Typically, chemical link groups such as thiols or amines are used to bind organic molecules to metal electrodes in single-molecule circuits, with these groups controlling both the physical structure and the electronic coupling at the interface. Direct metal-carbon coupling has been shown through C60, benzene and {pi}-stacked benzene but ideally the carbon backbone of the molecule should be covalently bonded to the electrode without intervening link groups. Here, we demonstrate a method to create junctions with such contacts. Trimethyl tin (SnMe{sub 3})-terminated polymethylene chains are used to form single-molecule junctions with a break-junction technique. Gold atoms at the electrode displace the SnMe{sub 3} linkers, leading to the formation of direct Au-C bonded single-molecule junctions with a conductance that is {approx}100 times larger than analogous alkanes with most other terminations. The conductance of these Au-C bonded alkanes decreases exponentially with molecular length, with a decay constant of 0.97 per methylene, consistent with a non-resonant transport mechanism. Control experiments and ab initio calculations show that high conductances are achieved because a covalent Au-C sigma ({sigma}) bond is formed. This offers a new method for making reproducible and highly conducting metal-organic contacts.

  2. Porous materials with pre-designed single-molecule traps for CO2 selective adsorption

    SciTech Connect (OSTI)

    Li, JR; Yu, JM; Lu, WG; Sun, LB; Sculley, J; Balbuena, PB; Zhou, HC

    2013-02-26

    Despite tremendous efforts, precise control in the synthesis of porous materials with pre-designed pore properties for desired applications remains challenging. Newly emerged porous metal-organic materials, such as metal-organic polyhedra and metal-organic frameworks, are amenable to design and property tuning, enabling precise control of functionality by accurate design of structures at the molecular level. Here we propose and validate, both experimentally and computationally, a precisely designed cavity, termed a 'single-molecule trap', with the desired size and properties suitable for trapping target CO2 molecules. Such a single-molecule trap can strengthen CO2-host interactions without evoking chemical bonding, thus showing potential for CO2 capture. Molecular single-molecule traps in the form of metal-organic polyhedra are designed, synthesised and tested for selective adsorption of CO2 over N-2 and CH4, demonstrating the trapping effect. Building these pre-designed single-molecule traps into extended frameworks yields metal-organic frameworks with efficient mass transfer, whereas the CO2 selective adsorption nature of single-molecule traps is preserved.

  3. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

    SciTech Connect (OSTI)

    Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

    2013-05-01

    New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.

  4. A nonplanar porphyrin-based receptor molecule for chiral amine ligands

    SciTech Connect (OSTI)

    MUZZI,CINZIA M.; MEDFORTH,CRAIG J.; SMITH,KEVIN M.; JIA,SONG-LING; SHELNUTT,JOHN A.

    2000-03-06

    A novel porphyrin-based receptor molecule for chiral amine ligands is described in which nonplanarity of the porphyrin macrocycle is used to orient the ligand and to enhance porphyrin-ligand interactions. The porphyrin macrocycle provides a versatile platform upon which to build elaborate superstructures, and this feature coupled with a rich and well-developed synthetic chemistry has led to the synthesis of many elegant models of heme protein active sites and numerous porphyrin-based receptor molecules. One design feature which is not usually considered in the design of porphyrin-based receptor molecules is nonplanarity of the porphyrin ring, although there are a few systems such as the pyridine sensitive Venus Flytrap and the chirality-memory molecule which illustrate that nonplanar porphyrin-based receptors can display unique and interesting behavior. Given the novel properties of these receptors and the continuing interest in the effects of nonplanarity on the properties of porphyrins the authors decided to investigate in more detail the potential applications of nonplanarity in the design of porphyrin-based receptors. Herein, they describe the design, synthesis, and characterization of a new kind of nonplanar porphyrin-based receptor molecule for chiral amines.

  5. Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry

    SciTech Connect (OSTI)

    Tsukahara, Noriyuki; Kawai, Maki; Takagi, Noriaki; Minamitani, Emi; Kim, Yousoo

    2014-08-07

    Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when attached to Au(111). Two unpaired electrons in the d{sub z}{sup 2} and the degenerate d? orbitals are screened stepwise, resulting in spin and spin+orbital Kondo effects, respectively. We investigated the impact on the Kondo effects of the coordination of CO and NO molecules to the Fe{sup 2+} ion as chemical stimuli by using scanning tunneling microscopy (STM) and density functional theory calculations. The impacts of the two diatomic molecules are different from each other as a result of the different electronic configurations. The coordination of CO converts the spin state from triplet to singlet, and then the Kondo effects completely disappear. In contrast, an unpaired electron survives in the molecular orbital composed of Fe d{sub z}{sup 2} and NO 5? and 2?* orbitals for the coordination of NO, causing a sharp Kondo resonance. The isotropic magnetic response of the peak indicates the origin is the spin Kondo effect. The diatomic molecules attached to the Fe{sup 2+} ion were easily detached by applying a pulsed voltage at the STM junction. These results demonstrate that the single molecule chemistry enables us to switch and control the spin and the many-body quantum states reversibly.

  6. Formation of the diphenyl molecule in the crossed beam reaction of phenyl radicals with benzene

    SciTech Connect (OSTI)

    Zhang Fangtong; Gu Xibin; Kaiser, Ralf I.

    2008-02-28

    The chemical dynamics to form the D5-diphenyl molecule, C{sub 6}H{sub 5}C{sub 6}D{sub 5}, via the neutral-neutral reaction of phenyl radicals (C{sub 6}H{sub 5}) with D6-benzene (C{sub 6}D{sub 6}), was investigated in a crossed molecular beams experiment at a collision energy of 185 kJ mol{sup -1}. The laboratory angular distribution and time-of-flight spectra of the C{sub 6}H{sub 5}C{sub 6}D{sub 5} product were recorded at mass to charge m/z of 159. Forward-convolution fitting of our data reveals that the reaction dynamics are governed by an initial addition of the phenyl radical to the {pi} electron density of the D6-benzene molecule yielding a short-lived C{sub 6}H{sub 5}C{sub 6}D{sub 6} collision complex. The latter undergoes atomic deuterium elimination via a tight exit transition state located about 30 kJ mol{sup -1} above the separated reactants; the overall reaction to form D5-diphenyl from phenyl and D6-benzene was found to be weakly exoergic. The explicit identification of the D5-biphenyl molecules suggests that in high temperature combustion flames, a diphenyl molecule can be formed via a single collision event between a phenyl radical and a benzene molecule.

  7. Theoretical Treatment of the Thermophysical Properties of Fluids Containing Chain-like Molecules

    SciTech Connect (OSTI)

    Carol K. Hall

    2008-11-14

    This research program was designed to enhance our understanding of the behavior of fluids and fluid mixtures containing chain-like molecules. The original objective was to explain and predict the experimentally observed thermophysical properties, including phase equilibria and dynamics, of systems containing long flexible molecules ranging in length from alkanes to polymers. Over the years the objectives were expanded to include the treatment of molecules that were not chain-like. Molecular dynamics and Monte Carlo computer simulations were used to investigate how variations in molecular size, shape and architecture influence the types of phase equilibria, thermodynamic properties, structure and surface interactions that are observed experimentally. The molecular insights and theories resulting from this program could eventually serve as the foundation upon which to build correlations of the properties of fluids that are both directly and indirectly related to the Nation’s energy resources including: petroleum, natural gas, and polymer solutions, melts, blends, and materials.

  8. Elastic Cross Sections for Electron Collisions with Molecules Relevant to Plasma Processing

    SciTech Connect (OSTI)

    Yoon, J.-S.; Song, M.-Y.; Kato, H.; Hoshino, M.; Tanaka, H.; Brunger, M. J.; Buckman, S. J.; Cho, H.

    2010-09-15

    Absolute electron-impact cross sections for molecular targets, including their radicals, are important in developing plasma reactors and testing various plasma processing gases. Low-energy electron collision data for these gases are sparse and only the limited cross section data are available. In this report, elastic cross sections for electron-polyatomic molecule collisions are compiled and reviewed for 17 molecules relevant to plasma processing. Elastic cross sections are essential for the absolute scale conversion of inelastic cross sections, as well as for testing computational methods. Data are collected and reviewed for elastic differential, integral, and momentum transfer cross sections and, for each molecule, the recommended values of the cross section are presented. The literature has been surveyed through early 2010.

  9. Electrochemical assembly of organic molecules by the reduction of iodonium salts

    DOE Patents [OSTI]

    Dirk, Shawn M.; Howell, Stephen W.; Wheeler, David R.

    2009-06-23

    Methods are described for the electrochemical assembly of organic molecules on silicon, or other conducting or semiconducting substrates, using iodonium salt precursors. Iodonium molecules do not assemble on conducting surfaces without a negative bias. Accordingly, the iodonium salts are preferred for patterning applications that rely on direct writing with negative bias. The stability of the iodonium molecule to acidic conditions allows them to be used with standard silicon processing. As a directed assembly process, the use of iodonium salts provides for small features while maintaining the ability to work on a surface and create structures on a wafer level. Therefore, the process is amenable for mass production. Furthermore, the assembled monolayer (or multilayer) is chemically robust, allowing for subsequent chemical manipulations and the introduction of various molecular functionalities for various chemical and biological applications.

  10. Single molecule detection using charge-coupled device array technology. Technical progress report

    SciTech Connect (OSTI)

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  11. Electromagnetic wave propagation in a random distribution of C{sub 60} molecules

    SciTech Connect (OSTI)

    Moradi, Afshin

    2014-10-15

    Propagation of electromagnetic waves in a random distribution of C{sub 60} molecules are investigated, within the framework of the classical electrodynamics. Electronic excitations over the each C{sub 60} molecule surface are modeled by a spherical layer of electron gas represented by two interacting fluids, which takes into account the different nature of the ? and ? electrons. It is found that the present medium supports four modes of electromagnetic waves, where they can be divided into two groups: one group with shorter wavelength than the light waves of the same frequency and the other with longer wavelength than the free-space radiation.

  12. High sensitivity fluorescent single particle and single molecule detection apparatus and method

    DOE Patents [OSTI]

    Mathies, Richard A.; Peck, Konan; Stryer, Lubert

    1990-01-01

    Apparatus is described for ultrasensitive detection of single fluorescent particles down to the single fluorescent molecule limit in a fluid or on a substrate comprising means for illuminating a predetermined volume of the fluid or area of the substrate whereby to emit light including background light from the fluid and burst of photons from particles residing in the area. The photon burst is detected in real time to generate output representative signal. The signal is received and the burst of energy from the fluorescent particles is distinguished from the background energy to provide an indication of the number, location or concentration of the particles or molecules.

  13. Lab Breakthrough: X-ray Laser Captures Atoms and Molecules in Action |

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

    Department of Energy X-ray Laser Captures Atoms and Molecules in Action Lab Breakthrough: X-ray Laser Captures Atoms and Molecules in Action July 18, 2012 - 12:51pm Addthis The Linac Coherent Light Source at SLAC is the world's most powerful X-ray laser, which helps researchers understand the extreme conditions found in the hearts of stars and giant planets guiding research into nuclear fusion, the mechanism that powers the sun. View the entire Lab Breakthrough playlist. Michael Hess Michael

  14. Real-time monitoring and manipulation of single bio-molecules in free solution

    SciTech Connect (OSTI)

    Li, Hung-Wing

    2005-08-01

    The observation and manipulation of single biomolecules allow their dynamic behaviors to be studied to provide insight into molecular genetics, biochip assembly, biosensor design, DNA biophysics. In a PDMS/glass microchannel, a nonuniform electroosmotic flow (EOF) was created. By using a scanning confocal fluorescence microscope and total internal-reflection fluorescence microscope (TIRFM), we demonstrated that negatively charged DNA molecules were focused by the nonuniform EOF into a thin layer at the glass surface. This phenomenon was applied to selectively detect target DNA molecules without requiring the separation of excessive probes and can be applied continuously to achieve high throughput. A variable-angle-TIRFM was constructed for imaging single DNA molecule dynamics at a solid/liquid interface. Implications we have are that the measured intensities cannot be used directly to determine the distances of molecules from the surface and the experimental counting results depict the distance-dependent dynamics of molecules near the surface; Molecules at low ionic strengths experience electrostatic repulsion at distances much further away from the surface than the calculated thickness of the electrical double layer. {delta}-DNA was employed as a nanoprobe for different functionalized surfaces to elucidate adsorption in chromatography. The 12-base unpaired ends of this DNA provide exposed purine and pyrimidine groups for adsorption. Patterns of self-assembled monolayers (SAMs) and patterns of metal oxides are generated. By recording the real-time dynamic motion of DNA molecules at the SAMs/aqueous interface, the various parameters governing the retention of an analyte during chromatographic separation can be studied. Even subtle differences among adsorptive forces can be revealed. Dynamic conformational changes of the prosthetic group, flavin adenine dinucleotide (FAD), in flavoprotein NADH peroxidase, in thioredoxin reductase, and in free solution were monitored with TIWM. FAD bound loosely in the proteins changed from the stacked conformation to the unstacked conformation upon laser excitation. FAD in free solution not only underwent conformational changes but also reacted with each other to form a dimer. Direct measurement of the single-molecule enzymatic cleavage rates of ApaI-DNA complex in the presence of various concentrations of MgCl{sub 2} solution is reported. Results suggest that there exists a distribution of ApaI conformations around the restriction site.

  15. The two polymorphs of N-DNAT, a high nitrogen molecule

    SciTech Connect (OSTI)

    Lee, K.Y.; Chan, M.

    1995-09-01

    A novel azo triazole molecule was prepared. Based on X-ray crystallography data, this molecule, 1,1{prime}-dinitro-3,3{prime}-azo-1,2,4-triazole (N-DNAT) exists in two forms. The yellow color polymorph has a crystal density of 1.701 g/cm{sup 3}, while the density of the orange crystal is 1.831 g/cm{sup 3}. Data from specific impulse (Isp) calculation indicates that N-DNAT is a potential candidate for propellant applications.

  16. Self-contained Kondo effect in single molecules (Journal Article) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Self-contained Kondo effect in single molecules Citation Details In-Document Search Title: Self-contained Kondo effect in single molecules Kondo coupling of f and conduction electrons is a common feature of f-electron intermetallics. Similar effects should occur in carbon ring systems (metallocenes). Evidence for Kondo coupling in Ce(C{sub 8}H{sub 8}){sub 2} (cerocene) and the ytterbocene Cp*{sub 2}Yb(bipy) is reported from magnetic susceptibility and L{sub III}-edge x-ray absorption

  17. Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry

    Office of Scientific and Technical Information (OSTI)

    Inhibition (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition Citation Details In-Document Search Title: Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition Authors: Melillo, Bruno ; Liang, Shuaiyi ; Park, Jongwoo ; Schön, Arne ; Courter, Joel R. ; LaLonde, Judith M. ; Wendler, Daniel J. ; Princiotto, Amy M. ; Seaman, Michael S. ; Freire, Ernesto ;

  18. Measurement of the nuclear polarization of hydrogen and deuterium molecules using a Lamb-shift polarimeter

    SciTech Connect (OSTI)

    Engels, Ralf Gorski, Robert; Grigoryev, Kiril; Mikirtychyants, Maxim; Rathmann, Frank; Seyfarth, Hellmut; Ströher, Hans; Weiss, Philipp; Kochenda, Leonid; Kravtsov, Peter; Trofimov, Viktor; Tschernov, Nikolay; Vasilyev, Alexander; Vznuzdaev, Marat; Schieck, Hans Paetz gen.

    2014-10-15

    Lamb-shift polarimeters are used to measure the nuclear polarization of protons and deuterons at energies of a few keV. In combination with an ionizer, the polarization of hydrogen and deuterium atoms was determined after taking into account the loss of polarization during the ionization process. The present work shows that the nuclear polarization of hydrogen or deuterium molecules can be measured as well, by ionizing the molecules and injecting the H{sub 2}{sup +} (or D{sub 2}{sup +}) ions into the Lamb-shift polarimeter.

  19. Universal basis of two-center functions. Test computations of certain diatomic molecules and ions

    SciTech Connect (OSTI)

    Kirnos, V.F.; Samsonov, B.F.; Cheglokov, E.I.

    1987-05-01

    It is shown that the basis of two-center functions is universal. The dependence of the nuclei of atoms comprising a molecule on charges and on the intranuclear spacing is separated explicitly in the integrals used in analyzing diatomic molecules. The basis integrals constructed once permitted rapid and effective execution of computations for the ground state potential curves for a number of electron systems: H/sub 2/, He/sub 2//sup 2 +/, HeH/sup +/, He/sub 2/, LiH, Li/sub 2/, HeB/sup +/, Be/sub 2/.

  20. Hadronic physics of q anti q light quark mesons, quark molecules and glueballs

    SciTech Connect (OSTI)

    Lindenbaum, S.J.

    1980-10-01

    A brief introduction reviews the development of QCD and defines quark molecules and glueballs. This review is concerned primarily with u, d, and s quarks, which provide practically all of the cross section connected with hadronic interactions. The following topics form the bulk of the paper: status of quark model classification for conventional u, d, s quark meson states; status of multiquark or quark molecule state predictions and experiments; glueballs and how to find them; and the OZI rule in decay and production and how glueballs might affect it. 17 figures, 1 table. (RWR)

  1. Photoinduced nucleation: a novel tool for detecting molecules in air at ultra-low concentrations

    DOE Patents [OSTI]

    Katz, Joseph L.; Lihavainen, Heikki; Rudek, Markus M.; Salter, Brian C.

    2002-01-01

    A method and apparatus for determining the presence of molecules in a gas at concentrations of less than about 100 ppb. Light having wavelengths in the range from about 200 nm to about 350 nm is used to illuminate a flowing sample of the gas causing the molecules if present to form clusters. A mixture of the illuminated gas and a vapor is cooled until the vapor is supersaturated so that there is a small rate of homogeneous nucleation. The supersaturated vapor condenses on the clusters thus causing the clusters to grow to a size sufficient to be counted by light scattering and then the clusters are counted.

  2. Spintronic transport of a non-magnetic molecule between magnetic electrodes

    SciTech Connect (OSTI)

    Kondo, Hisashi; Ohno, Takahisa; Institute of Industrial Science, University of Tokyo, Meguro, Tokyo 153-8505

    2013-12-02

    The spintronic transport properties of a junction system composed of a non-magnetic molecule sandwiched between ferromagnetic metal electrodes are investigated theoretically using a non-equilibrium Green's function method based on density functional theory. It is revealed that in such a system, the molecular magnetic properties induced by hybridization with the magnetic electrodes play a crucial role. Alignment of the induced molecular spin-split levels is strongly related to the spin injection and tunneling magneto-resistance effects. It is found that in the system with weaker molecule-electrode interaction, stronger spintronic effects of the spin injection and tunneling magneto-resistance are observed.

  3. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein kinases found in normal, healthy cells. It has been widely used to fight colon cancers and chronic myeloid leukemia. The protein kinase Abl is involved in regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  4. Takeda Advances Diabetes Drug Development at the ALS

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

    Takeda Advances Diabetes Drug Development at the ALS Takeda Advances Diabetes Drug Development at the ALS Print Tuesday, 19 May 2015 12:25 Type 2 diabetes mellitus (T2DM), characterized by abnormally high blood glucose levels, affects hundreds of millions of people worldwide. In the pursuit to better treat this disease, the human receptor protein GPR40 has been identified by pharmaceutical company Takeda as a potential new drug target. To this end, TAK-875 (fasiglifam), a partial agonist of

  5. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein kinases found in normal, healthy cells. It has been widely used to fight colon cancers and chronic myeloid leukemia. The protein kinase Abl is involved in regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  6. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein kinases found in normal, healthy cells. It has been widely used to fight colon cancers and chronic myeloid leukemia. The protein kinase Abl is involved in regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  7. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein kinases found in normal, healthy cells. It has been widely used to fight colon cancers and chronic myeloid leukemia. The protein kinase Abl is involved in regulating cell growth. Protein kinases have in general been the target of many cancer drug designs, since

  8. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism Print Tuesday, 23 June 2015 13:00 The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein kinases found in normal, healthy cells. It has been widely used to fight colon cancers and chronic myeloid leukemia. The protein kinase Abl is involved in regulating cell

  9. Light Sources Help Discover New Drug Against Melanoma | Department of

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

    Energy Sources Help Discover New Drug Against Melanoma Light Sources Help Discover New Drug Against Melanoma July 18, 2011 - 12:07pm Addthis The new anti-cancer drug, vemurafenib, is the green honeycomb structure at middle left. Four dotted red lines show where it attaches to a target area in the mutated enzyme, disabling it from promoting the growth of tumors. | Image courtesy of Plexxikon Inc. The new anti-cancer drug, vemurafenib, is the green honeycomb structure at middle left. Four

  10. In silico modeling to predict drug-induced phospholipidosis

    SciTech Connect (OSTI)

    Choi, Sydney S.; Kim, Jae S.; Valerio, Luis G. Sadrieh, Nakissa

    2013-06-01

    Drug-induced phospholipidosis (DIPL) is a preclinical finding during pharmaceutical drug development that has implications on the course of drug development and regulatory safety review. A principal characteristic of drugs inducing DIPL is known to be a cationic amphiphilic structure. This provides evidence for a structure-based explanation and opportunity to analyze properties and structures of drugs with the histopathologic findings for DIPL. In previous work from the FDA, in silico quantitative structure–activity relationship (QSAR) modeling using machine learning approaches has shown promise with a large dataset of drugs but included unconfirmed data as well. In this study, we report the construction and validation of a battery of complementary in silico QSAR models using the FDA's updated database on phospholipidosis, new algorithms and predictive technologies, and in particular, we address high performance with a high-confidence dataset. The results of our modeling for DIPL include rigorous external validation tests showing 80–81% concordance. Furthermore, the predictive performance characteristics include models with high sensitivity and specificity, in most cases above ? 80% leading to desired high negative and positive predictivity. These models are intended to be utilized for regulatory toxicology applied science needs in screening new drugs for DIPL. - Highlights: • New in silico models for predicting drug-induced phospholipidosis (DIPL) are described. • The training set data in the models is derived from the FDA's phospholipidosis database. • We find excellent predictivity values of the models based on external validation. • The models can support drug screening and regulatory decision-making on DIPL.

  11. Ancient Proteins Help Unravel a Modern Cancer Drug's Mechanism

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

    Print The cancer drug Gleevec is extremely specific, binding and inhibiting only the cancer-causing tyrosine protein kinase Blc-Abl, while not targeting homologous protein...

  12. Takeda Advances Diabetes Drug Development at the ALS

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

    Takeda Advances Diabetes Drug Development at the ALS Print Type 2 diabetes mellitus (T2DM), characterized by abnormally high blood glucose levels, affects hundreds of millions of...

  13. Non-destructively shattered mesoporous silica for protein drug...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Non-destructively shattered mesoporous silica for protein drug delivery Citation Details In-Document Search Title: Non-destructively shattered mesoporous silica ...

  14. Food and Drug Administration White Oak Campus Environmental Stewardshi...

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

    Oak Campus Environmental Stewardship and Cost Savings FEMP ESPC Success Story on water conservation and green energy at the Food and Drug Administration (FDA) White Oak Campus....

  15. The adsorption properties of CO molecules on single-layer graphene nanoribbons

    SciTech Connect (OSTI)

    Yi, Chenglong; Wang, Weidong, E-mail: wangwd@mail.xidian.edu.cn; Shen, Cuili [School of Electrical and Mechanical Engineering, Xidian University, Xi'an 710071 (China)] [School of Electrical and Mechanical Engineering, Xidian University, Xi'an 710071 (China)

    2014-03-15

    The adsorption properties of CO molecules on graphene nanoribbons (GRNs) are studied through the molecular dynamics (MD) method. The AIREBO and LJ potentials are used to describe the C-C bonds in GNR and the interactions between the carbon atoms in GNR and CO molecules, respectively. The influences of the environmental pressure and charge density on the adsorption properties of CO molecules on GRNs are taken into account in this study. The effects of charges carried by GNRs on the adsorption properties are investigated in two aspects: atom distribution and energy evolution. Its observation from the results shows that the Coulomb force plays a more important role in the adsorption phenomenon than the van der Waals force, and the higher the charge density is, the larger the amount of the adsorbed CO molecules becomes. Low charge densities (<3.291 C/m{sup 2}) do little for the system, that is to say, the GNRs present similar properties to the ones with no charges. However, relatively high charge densities (>4.937 C/m{sup 2}) have an obvious effect on the whole system. The results also indicate that the environmental pressure has great influence on the adsorption properties of COs on GRN, and the higher the pressure is, the greater the adsorption energy becomes.

  16. Practical Calculation of Molecular Acidity with the Aid of a Reference Molecule

    SciTech Connect (OSTI)

    Burger, Steven K; Liu, Shubin; Ayers, Paul W

    2011-02-24

    A set of linear free energy models are presented for determining the pK{sub a} values of amines, alcohols, and carboxylic acids. Models are determined from a series of pK{sub a} predictors, taken both from traditional natural atomic orbital analysis (NAO) and from a novel approach introduced here of using a reference molecule: an ammonium ion for amines and a hydrogen sulfide molecule for alcohols and carboxylic acids. Using these reference molecules, we calculate the barrier to proton transfer and show that a number of properties associated with the transition state are correlated with the pK{sub a}. By considering 38 predictors, we obtain a four-variable model for amines and a three-variable model for oxygen-containing compounds. The model for amines is based on 145 compounds and has a root mean squared error (RMSE) of 0.45 and R{sup 2} = 0.98. The oxygen set has 48 molecules: RMSE = 0.26, and R{sup 2} = 0.993. Similar, linear, and multilinear models are constructed after separating the sets into chemically similar categories: alcohols, carboxylic acids, and primary, secondary, tertiary, and aromatic amines. This separation gives simpler models with relatively low RMSE values, where the most important predictor of the pK{sub a} is the difference in energy between transferring the proton from the reference molecular base to the conjugate acid from the data set.

  17. Tetrakis(1-imidazolyl) borate (BIM4) based zwitterionic and related molecules used as electron injection layers

    DOE Patents [OSTI]

    Li, Huaping; Xu, Yunhua; Bazan, Guillermo C

    2013-02-05

    Tetrakis(1-imidazolyl)borate (BIm4) based zwitterionic and/or related molecules for the fabrication of PLEDs is provided. Device performances with these materials approaches that of devices with Ba/Al cathodes for which the cathode contact is ohmic. Methods of producing such materials, and electron injection layers and devices containing these materials are also provided.

  18. Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses

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

    Yang, Jie; Guehr, Markus; Vecchione, Theodore; Robinson, Matthew S.; Li, Renkai; Hartmann, Nick; Shen, Xiaozhe; Coffee, Ryan; Corbett, Jeff; Fry, Alan; et al

    2016-04-05

    Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angström spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 Å) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule.more » In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Lastly, our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.« less

  19. Ultraviolet light absorbers having two different chromophors in the same molecule

    DOE Patents [OSTI]

    Vogl, Otto (Brooklyn, NY); Li, Shanjun (Brooklyn, NY)

    1988-05-17

    Ultraviolet light absorbing compounds having two different chromophors in the same molecule, particularly the benzotriazole chromophor and either the dihydroxybenzophenone or dihydroxyacetophenone chromophor; specifically, the two compounds 3,5-[di(2H-benzotriazole-2-yl)]-2,4-dihydroxyacetophenone and 3,5-[di(2H-benzotriazole-2-yl)]2,4-dihydroxybenzophenone.

  20. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

    ScienceCinema (OSTI)

    Wieman, Carl

    2011-04-13

    Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  1. Atomic Force Microscopy Studies of Lipophosphoglycan (LPG) Molecules in Lipid Bilayers

    SciTech Connect (OSTI)

    LAST, JULIE A.; HUBER, TINA; SASAKI, DARRYL Y.; SALVATORE, BRIAN; TURCO, SALVATORE J.

    2003-03-01

    Lipophosphoglycan (LPG) is a lypopolysaccharide found on the surface of the parasite Leishmania donovani that is thought to play an essential role in the infection of humans with leishamniasis. LPG acts as an adhesion point for the parasite to the gut of the sand fly, whose bite is responsible for transmitting the disease. In addition, LPG acts to inhibit protein kinase C (PKC) in the human macrophage, possibly by structural changes in the membrane. The Ca{sup 2+} ion is believed to play a role in the infection cycle, acting both as a crosslinker between LPG molecules and by playing a part in modulating PKC activity. To gain insight into the structure of LPG within a supported lipid membrane and into the structural changes that occur due to Ca{sup 2+} ions, we have employed the atomic force microscope (AFM). We have observed that the LPG molecules inhibit bilayer fusion, resulting in bilayer islands on the mica surface. One experiment suggests that the LPG molecules are parallel to the mica surface and that the structure of the LPG changes upon addition of Ca{sup 2+}, with an increase in the height of the LPG molecules from the bilayer surface and an almost complete coverage of LPG on the bilayer island.

  2. Calculation of resonances in a dt{mu} molecule by the R-matrix method

    SciTech Connect (OSTI)

    Mil'nikov, Gennady V.; Nakamura, Hiroki

    2003-03-01

    Using the spectral representation of Green's function, we calculate the density of states and extract parameters of resonances in the scattering system. The method is implemented for the resonances in the dt{mu} molecule below the t{mu} (n=2) threshold.

  3. Regulatory aspects of oncology drug safety evaluation: Past practice, current issues, and the challenge of new drugs

    SciTech Connect (OSTI)

    Rosenfeldt, Hans; Kropp, Timothy; Benson, Kimberly; Ricci, M. Stacey; McGuinn, W. David; Verbois, S. Leigh

    2010-03-01

    The drug development of new anti-cancer agents is streamlined in response to the urgency of bringing effective drugs to market for patients with limited life expectancy. FDA's regulation of oncology drugs has evolved from the practices set forth in Arnold Lehman's seminal work published in the 1950s through the current drafting of a new International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) safety guidance for anti-cancer drug nonclinical evaluations. The ICH combines the efforts of the regulatory authorities of Europe, Japan, and the United States and the pharmaceutical industry from these three regions to streamline the scientific and technical aspects of drug development. The recent development of new oncology drug classes with novel mechanisms of action has improved survival rates for some cancers but also brings new challenges for safety evaluation. Here we present the legacy of Lehman and colleagues in the context of past and present oncology drug development practices and focus on some of the current issues at the center of an evolving harmonization process that will generate a new safety guidance for oncology drugs, ICH S9. The purpose of this new guidance will be to facilitate oncology drug development on a global scale by standardizing regional safety requirements.

  4. Guest Molecule Exchange Kinetics for the 2012 Ignik Sikumi Gas Hydrate Field Trial

    SciTech Connect (OSTI)

    White, Mark D.; Lee, Won Suk

    2014-05-14

    A commercially viable technology for producing methane from natural gas hydrate reservoirs remains elusive. Short-term depressurization field tests have demonstrated the potential for producing natural gas via dissociation of the clathrate structure, but the long-term performance of the depressurization technology ultimately requires a heat source to sustain the dissociation. A decade of laboratory experiments and theoretical studies have demonstrated the exchange of pure CO2 and N2-CO2 mixtures with CH4 in sI gas hydrates, yielding critical information about molecular mechanisms, recoveries, and exchange kinetics. Findings indicated the potential for producing natural gas with little to no production of water and rapid exchange kinetics, generating sufficient interest in the guest-molecule exchange technology for a field test. In 2012 the U.S. DOE/NETL, ConocoPhillips Company, and Japan Oil, Gas and Metals National Corporation jointly sponsored the first field trial of injecting a mixture of N2-CO2 into a CH4-hydrate bearing formation beneath the permafrost on the Alaska North Slope. Known as the Ignik Sikumi #1 Gas Hydrate Field Trial, this experiment involved three stages: 1) the injection of a N2-CO2 mixture into a targeted hydrate-bearing layer, 2) a 4-day pressurized soaking period, and 3) a sustained depressurization and fluid production period. Data collected during the three stages of the field trial were made available after an extensive quality check. These data included continuous temperature and pressure logs, injected and recovered fluid compositions and volumes. The Ignik Sikumi #1 data set is extensive, but contains no direct evidence of the guest-molecule exchange process. This investigation is directed at using numerical simulation to provide an interpretation of the collected data. A numerical simulator, STOMP-HYDT-KE, was recently completed that solves conservation equations for energy, water, mobile fluid guest molecules, and hydrate guest molecules, for up to three gas hydrate guest molecules: CH4, CO2, and N2. The independent tracking of mobile fluid and hydrate guest molecules allows for the kinetic exchange of guest molecules between the mobile fluids and hydrate. The particular interest of this numerical investigation is to determine whether kinetic exchange parameters, determined from laboratory-scale experiments, are directly applicable to interpreting the Ignik Sikumi #1 data.

  5. Shear-stress-induced structural arrangement of water molecules in nanoscale Couette flow with slipping at wall boundary

    SciTech Connect (OSTI)

    Lin, Jau-Wen

    2014-08-07

    This study investigated the structuring of water molecules in a nanoscale Couette flow with the upper plate subjected to lateral forces with various magnitudes and water slipping against a metal wall. It was found that when the upper plate is subjected to a force, the water body deforms into a parallelepiped. Water molecules in the channel are then gradually arranged into lattice positions, creating a layered structure. The structural arrangement of water molecules is caused by the water molecules accommodating themselves to the increase in energy under the application of a lateral force on the moving plate. The ordering arrangement of water molecules increases the rotational degree of freedom, allowing the molecules to increase their Coulomb potential energy through polar rotation that accounts for the energy input through the upper plate. With a force continuously applied to the upper plate, the water molecules in contact with the upper plate move forward until slip between the water and upper plate occurs. The relation between the structural arrangement of water molecules, slip at the wall, and the shear force is studied. The relation between the slip and the locking/unlocking of water molecules to metal atoms is also studied.

  6. A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules

    SciTech Connect (OSTI)

    Stauch, Tim; Dreuw, Andreas

    2014-04-07

    The promising field of mechanochemistry suffers from a general lack of understanding of the distribution and propagation of force in a stretched molecule, which limits its applicability up to the present day. In this article, we introduce the JEDI (Judgement of Energy DIstribution) analysis, which is the first quantum chemical method that provides a quantitative understanding of the distribution of mechanical stress energy among all degrees of freedom in a molecule. The method is carried out on the basis of static or dynamic calculations under the influence of an external force and makes use of a Hessian matrix in redundant internal coordinates (bond lengths, bond angles, and dihedral angles), so that all relevant degrees of freedom of a molecule are included and mechanochemical processes can be interpreted in a chemically intuitive way. The JEDI method is characterized by its modest computational effort, with the calculation of the Hessian being the rate-determining step, and delivers, except for the harmonic approximation, exact ab initio results. We apply the JEDI analysis to several example molecules in both static quantum chemical calculations and Born-Oppenheimer Molecular Dynamics simulations in which molecules are subject to an external force, thus studying not only the distribution and the propagation of strain in mechanically deformed systems, but also gaining valuable insights into the mechanochemically induced isomerization of trans-3,4-dimethylcyclobutene to trans,trans-2,4-hexadiene. The JEDI analysis can potentially be used in the discussion of sonochemical reactions, molecular motors, mechanophores, and photoswitches as well as in the development of molecular force probes.

  7. Drug-Free Federal Workplace Testing Implementation Program

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2012-12-06

    The subject directive provides requirements and responsibilities for the implementation of a workplace program to test for the use of illegal drugs to facilitate the maintenance of a drug-free Federal workplace. In the course of the revision, the document number will change from DOE O 3792.3 to DOE O 343.1.

  8. Drug interactions evaluation: An integrated part of risk assessment of therapeutics

    SciTech Connect (OSTI)

    Zhang, Lei; Reynolds, Kellie S.; Zhao, Ping; Huang, Shiew-Mei

    2010-03-01

    Pharmacokinetic drug interactions can lead to serious adverse events or decreased drug efficacy. The evaluation of a new molecular entity's (NME's) drug-drug interaction potential is an integral part of risk assessment during drug development and regulatory review. Alteration of activities of enzymes or transporters involved in the absorption, distribution, metabolism, or excretion of a new molecular entity by concomitant drugs may alter drug exposure, which can impact response (safety or efficacy). The recent Food and Drug Administration (FDA) draft drug interaction guidance ( (http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm072101.pdf)) highlights the methodologies and criteria that may be used to guide drug interaction evaluation by industry and regulatory agencies and to construct informative labeling for health practitioner and patients. In addition, the Food and Drug Administration established a 'Drug Development and Drug Interactions' website to provide up-to-date information regarding evaluation of drug interactions ( (http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugInteractionsLabeling/ucm080499.htm)). This review summarizes key elements in the FDA drug interaction guidance and new scientific developments that can guide the evaluation of drug-drug interactions during the drug development process.

  9. Alendronate functionalized mesoporous hydroxyapatite nanoparticles for drug delivery

    SciTech Connect (OSTI)

    Li, Dongdong; Zhu, Yuntao; Liang, Zhiqiang

    2013-06-01

    Highlights: ? The synthesized mesoporous hydroxyapatite has nanostructure and bioactivity. ? The materials have high surface area and amino group. ? The materials show higher drug loading and slower release rate than pure HAP. - Abstract: Mesoporous nanosized hydroxyapatite (HAP) functionalized by alendronate (ALN) was synthesized using cationic surfactant CTAB as template. The structural, morphological and textural properties were fully characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR) and N{sub 2} adsorption/desorption. Then the obtained materials were performed as drug delivery carriers using ibuprofen (IBU) as a model drug to investigate their drug storage/release properties in simulated body fluid (SBF). The materials showed relatively slower release rate compared with HAP due to the ionic interaction between -NH{sub 3}{sup +} on the matrix and -COO{sup ?}belongs to IBU. The system provides a new concept for improving the drug loading or slowing down the release rate.

  10. Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis

    DOE Patents [OSTI]

    Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA

    2008-04-29

    The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

  11. Rotational fluctuation of molecules in quantum clusters. I. Path integral hybrid Monte Carlo algorithm

    SciTech Connect (OSTI)

    Miura, Shinichi [Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585 (Japan)

    2007-03-21

    In this paper, we present a path integral hybrid Monte Carlo (PIHMC) method for rotating molecules in quantum fluids. This is an extension of our PIHMC for correlated Bose fluids [S. Miura and J. Tanaka, J. Chem. Phys. 120, 2160 (2004)] to handle the molecular rotation quantum mechanically. A novel technique referred to be an effective potential of quantum rotation is introduced to incorporate the rotational degree of freedom in the path integral molecular dynamics or hybrid Monte Carlo algorithm. For a permutation move to satisfy Bose statistics, we devise a multilevel Metropolis method combined with a configurational-bias technique for efficiently sampling the permutation and the associated atomic coordinates. Then, we have applied the PIHMC to a helium-4 cluster doped with a carbonyl sulfide molecule. The effects of the quantum rotation on the solvation structure and energetics were examined. Translational and rotational fluctuations of the dopant in the superfluid cluster were also analyzed.

  12. High-throughput, dual probe biological assays based on single molecule detection

    DOE Patents [OSTI]

    Hollars, Christopher W.; Huser, Thomas R.; Lane, Stephen M.; Balhorn, Rodney L.; Bakajin, Olgica; Darrow, Christopher; Satcher, Jr., Joe H.

    2006-07-11

    A method and apparatus with the sensitivity to detect and identify single target molecules through the localization of dual, fluorescently labeled probe molecules. This can be accomplished through specific attachment of the taget to a surface or in a two-dimensional (2D) flowing fluid sheet having approximate dimensions of 0.5 .mu.m.times.100 .mu.m.times.100 .mu.m. A device using these methods would have 10.sup.3 10.sup.4 greater throughput than previous one-dimensional (1D) micro-stream devices having 1 .mu.m.sup.3 interrogation volumes and would for the first time allow immuno- and DNA assays at ultra-low (femtomolar) concentrations to be performed in short time periods (.about.10 minutes). The use of novel labels (such as metal or semiconductor nanoparticles) may be incorporated to further extend the sensitivity possibly into the attomolar range.

  13. Communication: Feshbach resonances in the water molecule revealed by state-selective spectroscopy

    SciTech Connect (OSTI)

    Grechko, Maxim; Maksyutenko, Pavlo; Rizzo, Thomas R.; Boyarkin, Oleg V.

    2010-08-28

    We employ triple-resonance vibrational overtone excitation to access quasibound states of water from several fully characterized bound states of the molecule. Comparison of the measured dissociation spectra allows a rigorous assignment of rotational quantum numbers J, nuclear spin and parity, and a tentative vibrational characterization of the observed resonances. Their asymmetrical shapes (Fano profiles) reflect interference of dipole moments for transitions to these resonances with that to the dissociative continuum. The assignments and Fano profile parameters of the resonances stand as a benchmark for the extension of accurate quantum-mechanical calculations to activated complexes of water. The narrow widths of some of these resonances indicate that water molecules may survive for as long as up to 60 ps in states above the dissociation threshold. We consider the possible implication of such long-lived states for the kinetics of water dissociation and the OH+H association reaction.

  14. Interplay of radiative and nonradiative transitions in surface hopping with radiation-molecule interactions

    SciTech Connect (OSTI)

    Bajo, Juan José; Granucci, Giovanni Persico, Maurizio

    2014-01-28

    We implemented a method for the treatment of field induced transitions in trajectory surface hopping simulations, in the framework of the local diabatization scheme, especially suited for on-the-fly dynamics. The method is applied to a simple one-dimensional model with an avoided crossing and compared with quantum wavepacket dynamics. The results show the importance of introducing a proper decoherence correction to surface hopping, in order to obtain meaningful results. Also the energy conservation policy of standard surface hopping must be revised: in fact, the quantum wavepacket energetics is well reproduced if energy absorption/emission is allowed for in the hops determined by radiation-molecule coupling. To our knowledge, this is the first time the issues of decoherence and energy conservation have been analyzed in depth to devise a mixed quantum-classical method for dynamics with molecule-field interactions.

  15. Determination of enthalpies of formation of energetic molecules with composite quantum chemical methods

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

    Manaa, M. Riad; Fried, Laurence E.; Kuo, I-Feng W.

    2016-02-01

    We report gas-phase enthalpies of formation for the set of energetic molecules NTO, DADE, LLM-105, TNT, RDX, TATB, HMX, and PETN using the G2, G3, G4, and ccCA-PS3 quantum composite methods. Calculations for HMX and PETN hitherto represent the largest molecules attempted with these methods. G3 and G4 calculations are typically close to one another, with a larger difference found between these methods and ccCA-PS3. Furthermore there is significant uncertainty in experimental values, the mean absolute deviation between the average experimental value and calculations are 12, 6, 7, and 3 kcal/mol for G2, G3, G4, and ccCA-PS3, respectively.

  16. Theory of femtosecond coherent double-pump single-molecule spectroscopy: Application to light harvesting complexes

    SciTech Connect (OSTI)

    Chen, Lipeng; Zhao, Yang; Gelin, Maxim F.; Domcke, Wolfgang

    2015-04-28

    We develop a first principles theoretical description of femtosecond double-pump single-molecule signals of molecular aggregates. We incorporate all singly excited electronic states and vibrational modes with significant exciton-phonon coupling into a system Hamiltonian and treat the ensuing system dynamics within the Davydov D{sub 1} Ansatz. The remaining intra- and inter-molecular vibrational modes are treated as a heat bath and their effect is accounted for through lineshape functions. We apply our theory to simulate single-molecule signals of the light harvesting complex II. The calculated signals exhibit pronounced oscillations of mixed electron-vibrational (vibronic) origin. Their periods decrease with decreasing exciton-phonon coupling.

  17. The different adsorption mechanism of methane molecule onto a boron nitride and a graphene flakes

    SciTech Connect (OSTI)

    Seyed-Talebi, Seyedeh Mozhgan; Neek-Amal, M.

    2014-10-21

    Graphene and single layer hexagonal boron-nitride are two newly discovered 2D materials with wonderful physical properties. Using density functional theory, we study the adsorption mechanism of a methane molecule over a hexagonal flake of single layer hexagonal boron-nitride (h-BN) and compare the results with those of graphene. We found that independent of the used functional in our ab-initio calculations, the adsorption energy in the h-BN flake is larger than that for graphene. Despite of the adsorption energy profile of methane over a graphene flake, we show that there is a long range behavior beyond minimum energy in the adsorption energy of methane over h-BN flake. This result reveals the higher sensitivity of h-BN sheet to the adsorption of a typical closed shell molecule with respect to graphene. The latter gives insight in the recent experiments of graphene over hexagonal boron nitride.

  18. Small Molecule Adsorption in Open-Site Metal-Organic Frameworks: A

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

    Systematic Density Functional Theory Study for Rational Design | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Small Molecule Adsorption in Open-Site Metal-Organic Frameworks: A Systematic Density Functional Theory Study for Rational Design Previous Next List Kyuho Lee, Joshua D. Howe, Li-Chiang Lin, Berend Smit, and Jeffrey B. Neaton, Chem. Mater. 27, 668-678 (2015) DOI: 10.1021/cm502760q Abstract: Using density functional theory, we systematically

  19. Subtask 1: Molecules, Materials, and Systems for Solar Fuels | ANSER Center

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

    | Argonne-Northwestern National Laboratory 1: Molecules, Materials, and Systems for Solar Fuels Home > Research > Subtask 1 The above figure depicts an iridium catalyst used for water splitting. The above figure depicts an iridium catalyst used for water splitting. The greatest challenge facing the development of solar fuels is efficient fuel production at acceptable rates and driving forces. The ANSER Center is confronting this challenge by taking a hierarchical approach to designing,

  20. Ultraviolet light absorbers having two different chromophors in the same molecule

    DOE Patents [OSTI]

    Vogl, O.; Li, S.

    1983-10-06

    This invention relates to novel ultraviolet light absorbers having two chromophors in the same molecule, and more particularly to benzotriazole substituted dihydroxybenzophenones and acetophenones. More particularly, this invention relates to 3,5-(di(2H-benzotriazole-2-yl))-2,4-dihydroxybenzophenone and 3,5-(di(2H-benzotriazole-2-yl))-2,4-dihydroxyacetophenone which are particularly useful as an ultraviolet light absorbers.

  1. Formation and incorporation of SiF{sub 4} molecules in F-implanted preamorphized Si

    SciTech Connect (OSTI)

    De Salvador, D.; Bisognin, G.; Napolitani, E.; Mastromatteo, M.; Baggio, N.; Carnera, A.; Boscherini, F.; Cristiano, F.

    2009-09-07

    The local structure of fluorine incorporated in crystalline silicon following solid phase epitaxial regrowth was investigated by means of x-ray absorption spectroscopy at the F K-edge. We clearly demonstrate that most F is found in SiF{sub 4} molecules in the crystalline matrix. A kinetic pathway, which explains our observation and which is also able to rationalize previous results in a common and coherent framework, is proposed.

  2. Development of chiral LC-MS methods for small molecules and their applications i

    Office of Scientific and Technical Information (OSTI)

    chiral LC-MS methods for small molecules and their applications i n the analysis of enantiomeric composition and pharmacokinetic studies Meera Jay Desai A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Analytical Chemistry Program of Study Committee: Daniel W. Armstrong, Major Professor Edward S. Yeung Robsrt S. Houk Victor S.-Y. Lin Gregory Phillips Iowa State University Ames, Iowa 2004 .. 11 Graduate

  3. COMPLEX ORGANIC MOLECULES AT HIGH SPATIAL RESOLUTION TOWARD ORION-KL. I. SPATIAL SCALES

    SciTech Connect (OSTI)

    Widicus Weaver, Susanna L.; Friedel, Douglas N. E-mail: friedel@astro.illinois.edu

    2012-08-01

    Here we present high spatial resolution (<1'') observations of molecular emission in Orion-KL conducted using the Combined Array for Research in Millimeter-wave Astronomy. This work was motivated by recent millimeter continuum imaging studies of this region conducted at a similarly high spatial resolution, which revealed that the bulk of the emission arises from numerous compact sources, rather than the larger-scale extended structures typically associated with the Orion Hot Core and Compact Ridge. Given that the spatial extent of molecular emission greatly affects the determination of molecular abundances, it is important to determine the true spatial scale for complex molecules in this region. Additionally, it has recently been suggested that the relative spatial distributions of complex molecules in a source might give insight into the chemical mechanisms that drive complex chemistry in star-forming regions. In order to begin to address these issues, this study seeks to determine the spatial distributions of ethyl cyanide [C{sub 2}H{sub 5}CN], dimethyl ether [(CH{sub 3}){sub 2}O], methyl formate [HCOOCH{sub 3}], formic acid [HCOOH], acetone [(CH{sub 3}){sub 2}CO], SiO, methanol [CH{sub 3}OH], and methyl cyanide [CH{sub 3}CN] in Orion-KL at {lambda} = 3 mm. We find that for all observed molecules, the molecular emission arises from multiple components of the cloud that include a range of spatial scales and physical conditions. Here, we present the results of these observations and discuss the implications for studies of complex molecules in star-forming regions.

  4. Mathematical modeling of the aptamers and its effect on small molecule

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

    transport into the cell | The Ames Laboratory Mathematical modeling of the aptamers and its effect on small molecule transport into the cell In this proposed research, we expect to explore the hypothesis that the levels of accumulation of chemicals by cells can be mediated by mobile intracellular receptors1. As initial evidence of this hypothesis, we have recently determined experimentally that bacterial uptake of a toxin can be increased by aptamer receptors expressed by the cells. We

  5. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol

    DOE Patents [OSTI]

    Brown, Steven; Guss, Adam; Yang, Shihui; Karpinets, Tatiana; Lynd, Lee; Shao, Xiongjun

    2014-01-14

    The present invention provides isolated nucleic acid molecules which encode a mutant acetaldehyde-CoA/alcohol dehydrogenase or mutant alcohol dehydrogenase and confer enhanced tolerance to ethanol. The invention also provides related expression vectors, genetically engineered microorganisms having enhanced tolerance to ethanol, as well as methods of making and using such genetically modified microorganisms for production of biofuels based on fermentation of biomass materials.

  6. SURVIVAL OF INTERSTELLAR MOLECULES TO PRESTELLAR DENSE CORE COLLAPSE AND EARLY PHASES OF DISK FORMATION

    SciTech Connect (OSTI)

    Hincelin, U.; Wakelam, V.; Hersant, F.; Guilloteau, S.; Commerçon, B.

    2013-09-20

    An outstanding question of astrobiology is the link between the chemical composition of planets, comets, and other solar system bodies and the molecules formed in the interstellar medium. Understanding the chemical and physical evolution of the matter leading to the formation of protoplanetary disks is an important step for this. We provide some new clues to this long-standing problem using three-dimensional chemical simulations of the early phases of disk formation: we interfaced the full gas-grain chemical model Nautilus with the radiation-magnetohydrodynamic model RAMSES, for different configurations and intensities of the magnetic field. Our results show that the chemical content (gas and ices) is globally conserved during the collapsing process, from the parent molecular cloud to the young disk surrounding the first Larson core. A qualitative comparison with cometary composition suggests that comets are constituted of different phases, some molecules being direct tracers of interstellar chemistry, while others, including complex molecules, seem to have been formed in disks, where higher densities and temperatures allow for an active grain surface chemistry. The latter phase, and its connection with the formation of the first Larson core, remains to be modeled.

  7. On the calculation of internal forces in mechanically stressed polyatomic molecules

    SciTech Connect (OSTI)

    Avdoshenko, Stanislav M.; Konda, Sai Sriharsha M.; Makarov, Dmitrii E.

    2014-10-07

    We discuss how to define and to compute internal forces in a molecule subjected to mechanical stress. Because of the inherently many-body character of intramolecular interactions, internal forces cannot be uniquely defined without specifying a set of internal coordinates used to describe the molecular structure. When such a set is comprised of 3N − 6 interactomic distances (N being the number of atoms) and includes the bond lengths of interest, we show that the associated forces, while satisfying the equation F = ∂V/∂R (where R is the bond length, F is the internal force in this bond, and V is the potential energy of the molecule), can be determined from the molecular geometry alone. We illustrate these ideas using several toy models ranging from small molecules to a graphene sheet and show that the magnitude of the internal force in a bond is not necessarily a good predictor of its strength in response to mechanical loading. At the same time, analysis of internal forces reveals interesting phenomena such as the force multiplication effect, where weak external forces may, e.g., be used to break strong bonds, and offers insight into the catch-bond phenomenon where chemical reactivity is suppressed through application of a force.

  8. Laser separation of nitrogen isotopes by the IR+UV dissociation of ammonia molecules

    SciTech Connect (OSTI)

    Apatin, V M; Klimin, S A; Laptev, V B; Lokhman, V N; Ogurok, D D; Pigul'skii, S V; Ryabov, E A

    2008-08-31

    The separation of nitrogen isotopes is studied upon successive single-photon IR excitation and UV dissociation of ammonia molecules. The excitation selectivity was provided by tuning a CO{sub 2} laser to resonance with {sup 14}NH{sub 3} molecules [the 9R(30) laser line] or with {sup 15}NH{sub 3} molecules [the 9R(10) laser line]. Isotopic mixtures containing 4.8% and 0.37% (natural content) of the {sup 15}NH isotope were investigated. The dependences of the selectivity and the dissociation yield for each isotopic component on the buffer gas pressure (N{sub 2}, O{sub 2}, Ar) and the ammonia pressure were obtained. In the limit of low NH{sub 3} pressures (0.5-2 Torr), the dissociation selectivity {alpha}(15/14) for {sup 15}N was 17. The selectivity mechanism of the IR+UV dissociation is discussed and the outlook is considered for the development of the nitrogen isotope separation process based on this approach. (laser isotope separation)

  9. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Print Wednesday, 27 February 2008 00:00 The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II

  10. Single Molecule Spectroelectrochemistry of Interfacial Charge Transfer Dynamics In Hybrid Organic Solar Cell

    SciTech Connect (OSTI)

    Pan, Shanlin

    2014-11-16

    Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an electrochemical cell. For example, we are able to use this technique to track electroluminescence of single Au NPs, and the electrodeposition of individual Ag NPs in-situ. These metallic NPs are useful to enhance light harvesting in organic photovoltaic systems. The scattering at the surface of an indium tin oxide (ITO) working electrode was measured during a potential sweep. Utilizing Mie scattering theory and high resolution scanning electron microscopy (SEM), the scattering data were used to calculate current-potential curves depicting the electrodeposition of individual Ag NPs. The oxidation of individual presynthesized and electrodeposited Ag NPs was also investigated using fluorescence and DFS microscopies. Our work has produced 1 US provisional patent, 15 published manuscripts, 1 submitted and two additional in-writing manuscripts. 5 graduate students, 1 postdoctoral student, 1 visiting professor, and two undergraduate students have received research training in the area of electrochemistry and optical spectroscopy under support of this award.

  11. HIV-1 entry inhibition by small-molecule CCR5 antagonists: A combined molecular modeling and mutant study using a high-throughput assay

    SciTech Connect (OSTI)

    Labrecque, Jean; Metz, Markus; Lau, Gloria; Darkes, Marilyn C.; Wong, Rebecca S.Y.; Bogucki, David; Carpenter, Bryon; Chen Gang; Li Tongshuang; Nan, Susan; Schols, Dominique; Bridger, Gary J.; Fricker, Simon P.; Skerlj, Renato T.

    2011-05-10

    Based on the attrition rate of CCR5 small molecule antagonists in the clinic the discovery and development of next generation antagonists with an improved pharmacology and safety profile is necessary. Herein, we describe a combined molecular modeling, CCR5-mediated cell fusion, and receptor site-directed mutagenesis approach to study the molecular interactions of six structurally diverse compounds (aplaviroc, maraviroc, vicriviroc, TAK-779, SCH-C and a benzyloxycarbonyl-aminopiperidin-1-yl-butane derivative) with CCR5, a coreceptor for CCR5-tropic HIV-1 strains. This is the first study using an antifusogenic assay, a model of the interaction of the gp120 envelope protein with CCR5. This assay avoids the use of radioactivity and HIV infection assays, and can be used in a high throughput mode. The assay was validated by comparison with other established CCR5 assays. Given the hydrophobic nature of the binding pocket several binding models are suggested which could prove useful in the rational drug design of new lead compounds.

  12. Takeda Advances Diabetes Drug Development at the ALS

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

    Advances Diabetes Drug Development at the ALS Print Tuesday, 19 May 2015 12:25 Type 2 diabetes mellitus (T2DM), characterized by abnormally high blood glucose levels, affects...

  13. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    a cell's DNA is fatal to the cell, which is why drugs that target topo II serve as agents against bacterial infections and some forms of cancer. This first ever structural...

  14. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Print The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and...

  15. Molecular conformations, interactions, and properties associated with drug

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

    efficiency and clinical performance among VEGFR TK inhibitors Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors Print Monday, 17 September 2012 00:00 Pictured are crystals that contain VEGFR2 tyrosine kinase in complex with an inhibitor from a class of potent anticancer

  16. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Print The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II topoisomerase (topo II) that is responsible for untangling coiled strands of the chromosome during

  17. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Print The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II topoisomerase (topo II) that is responsible for untangling coiled strands of the chromosome during

  18. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Print The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II topoisomerase (topo II) that is responsible for untangling coiled strands of the chromosome during

  19. Topo II: An Enzyme Target for Antibacterial and Cancer Drugs

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

    Topo II: An Enzyme Target for Antibacterial and Cancer Drugs Print The veil has finally been lifted on an enzyme that is critical to the process of DNA transcription and replication and is a prime target of antibacterial and anticancer drugs. Researchers at Berkeley Lab and the University of California, Berkeley, have produced the first three-dimensional structural images of a DNA-bound type II topoisomerase (topo II) that is responsible for untangling coiled strands of the chromosome during

  20. DOE Laboratories Help Develop Promising New Cancer Fighting Drug,

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

    Vemurafenib | Department of Energy Laboratories Help Develop Promising New Cancer Fighting Drug, Vemurafenib DOE Laboratories Help Develop Promising New Cancer Fighting Drug, Vemurafenib August 18, 2011 - 1:03pm Addthis Powerful X-Rays Enable Development of Successful Treatment for Melanoma and Other Life-Threatening Diseases WASHINGTON, DC - Powerful X-ray technology developed at the U.S. Department of Energy's (DOE's) national laboratories is revealing new insights into diseases ranging

  1. Takeda Advances Diabetes Drug Development at the ALS

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

    Takeda Advances Diabetes Drug Development at the ALS Print Type 2 diabetes mellitus (T2DM), characterized by abnormally high blood glucose levels, affects hundreds of millions of people worldwide. In the pursuit to better treat this disease, the human receptor protein GPR40 has been identified by pharmaceutical company Takeda as a potential new drug target. To this end, TAK-875 (fasiglifam), a partial agonist of GPR40, was brought into clinical development by Takeda as a possible new treatment

  2. Flow cytometry aids basic cell biology research and drug discovery

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

    Flow cytometry aids basic cell biology research and drug discovery Flow cytometry aids basic cell biology research and drug discovery Life Technologies Corporation and LANL have released the Attune® Acoustic Focusing Cytometer, featuring a reduced footprint, reduced consumables, and an affordable price. April 3, 2012 Attune® Acoustic Focusing Cytometer The Attune® Acoustic Focusing Cytometer achieves sample throughput at rates over 10 times faster than other cytometers-up to 1,000 μL per

  3. Computer modeling reveals how surprisingly potent hepatitis C drug works

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

    Hepatitis C computer modeling Computer modeling reveals how surprisingly potent hepatitis C drug works A study reveals how daclatasvir targets one of its proteins and causes the fastest viral decline ever seen with anti-HCV drugs - within 12 hours of treatment. February 19, 2013 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

  4. Drug Test Information for HRP-Certified Individuals and HRP Candidates...

    Office of Scientific and Technical Information (OSTI)

    Country of Publication: United States Language: English Subject: 98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL PROTECTION; RELIABILITY; TESTING; DRUGS; PERSONNEL HRP drug ...

  5. Magnetic-field effects in transitions of X Li molecules (X: even isotopes of group II atoms)

    SciTech Connect (OSTI)

    Gopakumar, Geetha; Abe, Minori; Hada, Masahiko; Kajita, Masatoshi

    2011-10-15

    We analyze the Zeeman shift in the (v,N)=(0,0){yields}(1,0) transition frequency of X Li molecules (X: even isotopes of group II atoms), which is of interest in metrology. The Zeeman shift in the transition frequency between stretching states is found to be less than 1 mHz with a magnetic field of 1 G. X {sup 6}Li molecules are more advantageous than X {sup 7}Li molecules for measuring the transition frequency without the Zeeman shift because of the smaller g factor of the Li nuclear spin.

  6. Reconstruction of two-dimensional molecular structure with laser-induced electron diffraction from laser-aligned polyatomic molecules

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

    Yu, Chao; Wei, Hui; Wang, Xu; Le, Anh -Thu; Lu, Ruifeng; Lin, C. D.

    2015-10-27

    Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. Lastly, with picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement.

  7. DFT structural investigation on Fe(1,10-phenanthroline){sub 2} (NCS){sub 2} spin crossover molecule

    SciTech Connect (OSTI)

    Chiş, V.; Isai, R.; Droghetti, A.; Rungger, I.; Sanvito, S.; Morari, C.

    2013-11-13

    Understanding the coupling of spin crossover molecules to metallic surfaces is a key ingredient for harnessing of their remarkable features for future spintronics applications. Here we investigate the structural and electronic properties of deformed Fe(1,10-phenanthroline){sub 2} (NCS){sub 2} molecules, mimicking the possible effects arising from the interaction with a metallic substrate. We find a relatively large structural flexibility for this molecule, accompanied by small changes in their total energy. This suggests that the spin crossover activity can be modulated by the interaction with the substrate.

  8. Statistical Exploration of Electronic Structure of Molecules from Quantum Monte-Carlo Simulations

    SciTech Connect (OSTI)

    Prabhat, Mr; Zubarev, Dmitry; Lester, Jr., William A.

    2010-12-22

    In this report, we present results from analysis of Quantum Monte Carlo (QMC) simulation data with the goal of determining internal structure of a 3N-dimensional phase space of an N-electron molecule. We are interested in mining the simulation data for patterns that might be indicative of the bond rearrangement as molecules change electronic states. We examined simulation output that tracks the positions of two coupled electrons in the singlet and triplet states of an H2 molecule. The electrons trace out a trajectory, which was analyzed with a number of statistical techniques. This project was intended to address the following scientific questions: (1) Do high-dimensional phase spaces characterizing electronic structure of molecules tend to cluster in any natural way? Do we see a change in clustering patterns as we explore different electronic states of the same molecule? (2) Since it is hard to understand the high-dimensional space of trajectories, can we project these trajectories to a lower dimensional subspace to gain a better understanding of patterns? (3) Do trajectories inherently lie in a lower-dimensional manifold? Can we recover that manifold? After extensive statistical analysis, we are now in a better position to respond to these questions. (1) We definitely see clustering patterns, and differences between the H2 and H2tri datasets. These are revealed by the pamk method in a fairly reliable manner and can potentially be used to distinguish bonded and non-bonded systems and get insight into the nature of bonding. (2) Projecting to a lower dimensional subspace ({approx}4-5) using PCA or Kernel PCA reveals interesting patterns in the distribution of scalar values, which can be related to the existing descriptors of electronic structure of molecules. Also, these results can be immediately used to develop robust tools for analysis of noisy data obtained during QMC simulations (3) All dimensionality reduction and estimation techniques that we tried seem to indicate that one needs 4 or 5 components to account for most of the variance in the data, hence this 5D dataset does not necessarily lie on a well-defined, low dimensional manifold. In terms of specific clustering techniques, K-means was generally useful in exploring the dataset. The partition around medoids (pam) technique produced the most definitive results for our data showing distinctive patterns for both a sample of the complete data and time-series. The gap statistic with tibshirani criteria did not provide any distinction across the 2 dataset. The gap statistic w/DandF criteria, Model based clustering and hierarchical modeling simply failed to run on our datasets. Thankfully, the vanilla PCA technique was successful in handling our entire dataset. PCA revealed some interesting patterns for the scalar value distribution. Kernel PCA techniques (vanilladot, RBF, Polynomial) and MDS failed to run on the entire dataset, or even a significant fraction of the dataset, and we resorted to creating an explicit feature map followed by conventional PCA. Clustering using K-means and PAM in the new basis set seems to produce promising results. Understanding the new basis set in the scientific context of the problem is challenging, and we are currently working to further examine and interpret the results.

  9. Generation, Detection and characterization of Gas-Phase Transition Metal containing Molecules

    SciTech Connect (OSTI)

    Steimle, Timothy

    2015-12-15

    The objective of this project was to generate, detect, and characterize small, gas-phase, metal containing molecules. In addition to being relevant to high temperature chemical environments (e.g. plasmas and combustion), gas-phase experiments on metal containing molecules serve as the most direct link to a molecular-level theoretical model for catalysis. Catalysis (i.e. the addition of a small about of recoverable material to control the rate and direction of a chemical reaction) is critical to the petroleum and pharmaceutical industries as well as environmental remediation. Currently, the majority of catalytic materials are based on very expensive metals such as platinum (Pt), palladium (Pd), iridium (Ir,) rhenium (Re), and rhodium (Rh). For example, the catalyst used for converting linear hydrocarbon molecules (e.g. hexane) to cyclic molecules (e.g. cyclohexane) is a mixture of Pt and Re suspended on alumina. It enables straight chain alkanes to be converted into branched-chain alkanes, cyclohexanes and aromatic hydrocarbons which are used, amongst other things, to enhance the octane number of petrol. A second example is the heterogeneous catalysis used in automobile exhaust systems to: a) decrease nitrogen oxide; b) reduce carbon monoxide; and c) oxidize unburned hydrocarbons. The exhaust is vented through a high-surface area chamber lined with Pt, Pd, and Rh. For example, the carbon monoxide is catalytically converted to carbon dioxide by reaction with oxygen. The research results from this work have been published in readily accessible journals1-28. The ground and excited electronic state properties of small metal containing molecules that we determine were: a) electronic state distributions and lifetimes, b) vibrational frequencies, c) bond lengths and angles, d) hyperfine interactions, e) permanent electric dipole moments, mel, and f) magnetic dipoles, μm. In general terms, μel, gives insight into the charge distribution and mm into the number and nature of the unpaired electrons. Analysis of the hyperfine interactions (i.e. Fermi-contact, nuclear electric quadrupole, etc.) is particularly insightful because it results from the interaction of nuclei with non-zero spin and the chemically important valence electrons. The bulk of the spectroscopic techniques used in these studies exploit the sensitivity of laser induced fluorescence (LIF) detection. The spectroscopic schemes employed include: a) cw and pulsed laser field-free(FF) excitation and dispersed LIF (DLIF); b) optical Stark; c) optical Zeeman; d) pump/probe microwave double resonance (PPMODR); e) fluorescence lifetimes, and f) resonant and non-resonant two-photon ionization TOF mass spectrometry. Vibrational spacing, force constants and electronic states distributions are derived from the analysis of pulsed dye laser excitation and DLIF spectra. Geometric structure (bond lengths and angles) and hyperfine parameters are derived from the analysis of cw-laser LIF and PPMODR spectra. Permanent electric dipole moments, mel,, and magnetic dipole moments, mm, are derived from the analysis of optical Stark and Zeeman spectra, respectively. Transition moments are derived from the analysis of radiative lifetimes. A supersonic molecular beam sample of these ephemeral molecules is generated by skimming the products of either a laser ablation/reaction source or a d.c. discharge source.

  10. UNRAVELING THE PHYSICS OF NANOFLUIDIC PHENOMENA AT THE SINGLE-MOLECULE LEVEL

    SciTech Connect (OSTI)

    Fornasiero, Francesco

    2015-10-13

    Despite groundbreaking potential in a broad application space, several nanofluidic phenomena remain poorly understood. Toward advancing the understanding of fluid behavior under nanoscale confinement, we developed a novel, ideal platform for fundamental molecular transport studies, in which the fluidic channel is a single carbon nanotube (CNT). CNTs offer the advantage of simple chemistry and structure, which can be synthetically tuned with nanometer precision and accurately modeled. With combined experimental and computational approaches, we demonstrated that CNT pores with 1-5 nm diameters conduct giant ionic currents that follow an unusual sublinear electrolyte concentration dependence. The large magnitude of the ionic conductance appears to originate from a strong electroosmotic flow in smooth CNT pores. First-principle simulations suggest that electroosmotic flow arises from localized negative polarization charges on carbon atoms near a potassium (K+) ion and from the strong cation-graphitic wall interactions, which drive K+ ions much closer to the wall than chlorides (Cl-). Single-molecule translocation studies reveal that charged molecules may be distinguished from neutral species on the basis of the sign of the transient current change during their passage through the nanopore. Together with shedding light on a few controversial questions in the CNT nanofluidics area, these results may benefit LLNL’s Security Mission by providing the foundation for the development of advanced single-molecule detection system for bio/chem/explosive analytes. In addition, these experimental and computational platforms can be applied to advance fundamental knowledge in other fields, from energy storage and membrane separation to superfluid physics.

  11. The census of complex organic molecules in the solar-type protostar IRAS16293-2422

    SciTech Connect (OSTI)

    Jaber, Ali A.; Ceccarelli, C.; Kahane, C.; Caux, E.

    2014-08-10

    Complex organic molecules (COMs) are considered to be crucial molecules, since they are connected with organic chemistry, at the basis of terrestrial life. More pragmatically, they are molecules which in principle are difficult to synthesize in harsh interstellar environments and, therefore, are a crucial test for astrochemical models. Current models assume that several COMs are synthesized on lukewarm grain surfaces (≳30-40 K) and released in the gas phase at dust temperatures of ≳100 K. However, recent detections of COMs in ≲20 K gas demonstrate that we still need important pieces to complete the puzzle of COMs formation. Here, we present a complete census of the oxygen- and nitrogen-bearing COMs, previously detected in different Interstellar Medium (ISM) regions, toward the solar-type protostar IRAS16293-2422. The census was obtained from the millimeter-submillimeter unbiased spectral survey TIMASSS. Of the 29 COMs searched for, 6 were detected: methyl cyanide, ketene, acetaldehyde, formamide, dimethyl ether, and methyl formate. Multifrequency analysis of the last five COMs provides clear evidence that they are present in the cold (≲30 K) envelope of IRAS16293-2422, with abundances of 0.03-2 × 10{sup –10}. Our data do not allow us to support the hypothesis that the COMs abundance increases with increasing dust temperature in the cold envelope, as expected if COMs were predominately formed on lukewarm grain surfaces. Finally, when also considering other ISM sources, we find a strong correlation over five orders of magnitude between methyl formate and dimethyl ether, and methyl formate and formamide abundances, which may point to a link between these two couples of species in cold and warm gas.

  12. Fragmentation of the adenine and guanine molecules induced by electron collisions

    SciTech Connect (OSTI)

    Minaev, B. F. E-mail: boris@theochem.kth.se; Shafranyosh, M. I.; Svida, Yu. Yu; Sukhoviya, M. I.; Shafranyosh, I. I.; Baryshnikov, G. V.; Minaeva, V. A.

    2014-05-07

    Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10{sup ?15} and 3.2 × 10{sup ?15} cm{sup 2}, respectively. The total cross section for formation of the negative ions is 6.1 × 10{sup ?18} and 7.6 × 10{sup ?18} cm{sup 2} at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.

  13. I CALCULATIONS ON ISOTOPE SEPARATION BY LASER INDUCED PHOTODISSOCIATION OF POLYATOMIC MOLECULES

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

    ; . I CALCULATIONS ON ISOTOPE SEPARATION BY LASER INDUCED PHOTODISSOCIATION OF POLYATOMIC MOLECULES F i n a l Report Willis E . Lamb, JY. U n i v e r s i t y of Arizona Tucson, Arizona 85721 NOTICE report was prepared 86 an account of work sponsored by the United Stater Government. Neither the United S t a m nor the United States Department of Encrwi, nor any of their employees, nor any of thelr contractors, Subcontractors, o r their employer, maker any warranty, exprels or Implied. or apumn my

  14. Porous materials with pre-designed single-molecule traps for CO2 selective

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

    adsorption | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Porous materials with pre-designed single-molecule traps for CO2 selective adsorption Previous Next List Jian-Rong Li, Jiamei Yu, Weigang Lu, Lin-Bing Sun, Julian Sculley, Perla B. Balbuena & Hong-Cai Zhou, Nature Communications 4, Article number: 1538, 2013, DOI: 10.1038/ncomms2552 ncomms2552.html Abstract: Despite tremendous efforts, precise control in the synthesis of porous materials with

  15. Stable Metal-Organic Frameworks Containing Single-Molecule Traps for Enzyme

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

    Encapsulation | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Stable Metal-Organic Frameworks Containing Single-Molecule Traps for Enzyme Encapsulation Previous Next List Dawei Feng, Tian-Fu Liu, Jie Su, Mathieu Bosch, Zhangwen Wei, Wei Wan, Daqiang Yuan, Ying-Pin Chen, Xuan Wang, Kecheng Wang, Xizhen Lian, Zhi-Yuan Gu, Jihye Park, Xiaodong Zou & Hong-Cai Zhou, Nature Communications 6, 5979 (2015) DOI: 10.1038/ncomms6979 179 Abstract: Enzymatic

  16. Phase transition into the metallic state in hypothetical (without molecules) dense atomic hydrogen

    SciTech Connect (OSTI)

    Khomkin, A. L. Shumikhin, A. S.

    2013-10-15

    A simple physical model of the metal-dielectric (vapor-liquid) phase transition in hypothetical (without molecules) atomic hydrogen is proposed. The reason for such a transition is the quantum collective cohesive energy occurring due to quantum electron-electron exchange similar to the cohesive energy in the liquid-metal phase of alkali metals. It is found that the critical parameters of the transition are P{sub c} ? 41000 atm, ?{sub c} ? 0.1 g/cm{sup 3}, and T{sub c} ? 9750 K.

  17. Local spin torque induced by electron electric dipole moment in the YbF molecule

    SciTech Connect (OSTI)

    Fukuda, Masahiro; Senami, Masato; Ogiso, Yoji; Tachibana, Akitomo

    2014-10-06

    In this study, we show the modification of the equation of motion of the electronic spin, which is derived by the quantum electron spin vorticity principle, by the effect of the electron electric dipole moment (EDM). To investigate the new contribution to spin torque by EDM, using first principle calculations, we visualize distributions of the local spin angular momentum density and local spin torque density of the YbF molecule on which the static electric field and magnetic field are applied at t = 0.

  18. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen

    2000-01-01

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  19. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2006-10-17

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  20. Electron tunnelling through single azurin molecules can be on/off switched by voltage pulses

    SciTech Connect (OSTI)

    Baldacchini, Chiara; Kumar, Vivek; Bizzarri, Anna Rita; Cannistraro, Salvatore

    2015-05-04

    Redox metalloproteins are emerging as promising candidates for future bio-optoelectronic and nano-biomemory devices, and the control of their electron transfer properties through external signals is still a crucial task. Here, we show that a reversible on/off switching of the electron current tunnelling through a single protein can be achieved in azurin protein molecules adsorbed on gold surfaces, by applying appropriate voltage pulses through a scanning tunnelling microscope tip. The observed changes in the hybrid system tunnelling properties are discussed in terms of long-sustained charging of the protein milieu.

  1. Many-body electronic structure and Kondo properties of cobalt-porphyrin molecules.

    SciTech Connect (OSTI)

    Reboredo, Fernando A; Tiago, Murilo L; Dagotto, Elbio R; Dias Da Silva, Luis G; Ulloa, Sergio E

    2009-01-01

    We use a unique combination of first principles many-body methods and the numerical renormalization-group technique to study the Kondo regime of cobalt-porphyrin compounds adsorbed on a Cu(111) surface. We find the Kondo temperature to be highly sensitive to both molecule charging and distance to the surface, which can explain the variations observed in recent scanning tunneling spectroscopy measurements. We discuss the importance of manybody effects in the molecular electronic structure controlling this phenomenon and suggest scenarios where enhanced temperatures can be achieved in experiments.

  2. Observation of spectral evolution during the formation of a Ni2 kondo molecule

    SciTech Connect (OSTI)

    Madhavan, V.; Jamneala, T.; Nagaoka, K.; Chen, W.; Li, Je-Luen; Louie, Steven G.; Crommie, M.F.

    2002-04-15

    We have used atomic manipulation and scanning tunneling spectroscopy to study the evolution in electronic properties that occurs as two Ni atoms are merged into a single magnetic molecule on Au(111). We observe energetic shifting of molecular d-orbitals and a strong decrease in the molecular Kondo temperature as Ni-Ni separation is reduced to 3.4+ or -0.3Angstroms. These results are qualitatively explained by a combination of spin-1/2-s-d model and density-functional calculations.

  3. Quantum Tunneling of Water in Beryl. A New State of the Water Molecule

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

    Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani; Prisk, Timothy R.; Mamontov, Eugene; Podlesnyak, Andrey; Ehlers, George; Seel, Andrew G.; Wesolowski, David J.; Anovitz, Lawrence M.

    2016-04-22

    When using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. Additionally, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

  4. Direct imaging of rotational wave-packet dynamics of diatomic molecules

    SciTech Connect (OSTI)

    Dooley, P. W.; Lee, Kevin F.; Corkum, P. B.; Litvinyuk, I. V.; Rayner, D. M.; Villeneuve, D. M.; Spanner, M.

    2003-08-01

    We use linearly polarized 45 fs pulses to create rotational wave packets in N{sub 2} and O{sub 2}. We Coulomb explode molecules with a high-intensity circularly polarized pulse and use an ion imaging detector to measure a series of two-dimensional projections of the wave packet's angular distribution in 27 fs increments. We highlight the evolving wave packet near the first, second, sixth, and tenth full revival times and also near the one-eighth, one-quarter, one-half, and three-quarter fractional revivals.

  5. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Gallivan, Justin [Emory University] [Emory University

    2012-03-21

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  6. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Gallivan, Justin [Emory University

    2013-01-22

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  7. Collision lifetimes of polyatomic molecules at low temperatures: Benzene–benzene vs benzene–rare gas atom collisions

    SciTech Connect (OSTI)

    Cui, Jie; Krems, Roman V.; Li, Zhiying

    2014-10-28

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom–molecule interaction. We then compare the results of the atom–benzene calculations with those for benzene–benzene collisions. The comparison illustrates that the mean lifetimes of the benzene–benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene–benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  8. A modular molecular framework for utility in small-molecule solution-processed organic photovoltaic devices

    SciTech Connect (OSTI)

    Welch, Gregory C; Perez, Louis A.; Hoven, Corey V.; Zhang, Yuan; Dang, Xuan-Dung; Sharenko, Alexander; Toney, Michael F.; Kramer, Edward J.; Nguyen, Thuc-Quyen; Bazan, Guillermo C.

    2011-01-01

    We report on the design, synthesis and characterization of light harvesting small molecules for use in solution-processed small molecule bulk heterojunction (SM-BHJ) solar cell devices. These molecular materials are based upon an acceptor/donor/acceptor (A/D/A) core with donor endcapping units. Utilization of a dithieno(3,2-b;2',3'-d)silole (DTS) donor and pyridal[2,1,3]thiadiazole (PT) acceptor leads to strong charge transfer characteristics, resulting in broad optical absorption spectra extending well beyond 700 nm. SM-BHJ solar cell devices fabricated with the specific example 5,5'-bis{7-(4-(5-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-c]pyridine}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (6) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor component showed short circuit currents above -10 mA cm-2 and power conversion efficiencies (PCEs) over 3%. Thermal processing is a critical factor in obtaining favorable active layer morphologies and high PCE values. A combination of UV-visible spectroscopy, conductive and photo-conductive atomic force microscopies, dynamic secondary mass ion spectrometry (DSIMS), and grazing incident wide angle X-ray scattering (GIWAXS) experiments were carried out to characterize how thermal treatment influences the active layer structure and organization.

  9. A study of competitive adsorption of organic molecules onto mineral oxides using DRIFTS

    SciTech Connect (OSTI)

    Joan E. Thomas, Michael J. Kelley

    2010-02-01

    Analysis of DRIFTS spectra was used for a quantitative study of competitive adsorption of myristic and salicylic acids onto kaolinite or {gamma}-alumina. Peaks unique to the ring or the chain were selected and single molecule studies used as calibration. Samples were exposed to hexane solution containing equal molecular quantities of each acid. The surface loading of salicylic acid was not influenced by the presence of myristic acid on either mineral but the maximum loading of myristic acid was decreased (46-50%) by salicylic acid. Displacement of myristic acid from {gamma}-alumina, but not kaolinite, was observed when excess salicylic acid remained in solution. A 25% increase in the maximum loading was observed for kaolinite, but not for{gamma}-alumina. On {gamma}-alumina, after a loading of 1 molecule per nm{sup 2}, increased exposure resulted in salicylic acid adsorption only, this value is approximately the same for salicylic acid adsorption from aqueous solution or for water washed hexane treated samples. Thus a set of sites for adsorption of either acid is indicated together with other energetically less favorable sites, which can be occupied by salicylic, but not by myristic, acid.

  10. Nanostructures of Liquid Crystal Phases in Mixtures of Bent-core and Rod-shaped Molecules

    SciTech Connect (OSTI)

    S Hong; R Verduzco; J Gleeson; S Sprunt; A Jakli

    2011-12-31

    We report small angle x-ray scattering (SAXS) studies of isotropic, nematic, and smectic mesophases formed by binary mixtures of bent-core (BC) and rod-shaped (RS) molecules. While optical studies indicate that the components are fully miscible, SAXS reveals fascinating structures that are consistent with segregation on a nanoscopic scale. We find that tilted smectic clusters, which have been previously reported in both the nematic and isotropic states of the pure BC materials, are also present in mixtures with up to 50 wt% of the RS compound; this is consistent with previous dielectric and flexoelectric studies on such mixtures. Unexpectedly in this concentration range the clusters are present in the isotropic and in the induced smectic phase range, as well as throughout the nematic phase. The results in the smectic phase also reveal complex layering phenomena, providing important insight into the interaction between bent and rod-shaped molecules. These studies will be crucial in the design of promising new functional nanomaterials.

  11. Nanostructures of liquid crystal phases in mixtures of bent-core and rod-shaped molecules

    SciTech Connect (OSTI)

    Hong, S. H.; Gleeson, J. T.; Sprunt, S.; Verduzco, R.; Jakli, A.

    2011-06-15

    We report small angle x-ray scattering (SAXS) studies of isotropic, nematic, and smectic mesophases formed by binary mixtures of bent-core (BC) and rod-shaped (RS) molecules. While optical studies indicate that the components are fully miscible, SAXS reveals fascinating structures that are consistent with segregation on a nanoscopic scale. We find that tilted smectic clusters, which have been previously reported in both the nematic and isotropic states of the pure BC materials, are also present in mixtures with up to 50 wt% of the RS compound; this is consistent with previous dielectric and flexoelectric studies on such mixtures. Unexpectedly in this concentration range the clusters are present in the isotropic and in the induced smectic phase range, as well as throughout the nematic phase. The results in the smectic phase also reveal complex layering phenomena, providing important insight into the interaction between bent and rod-shaped molecules. These studies will be crucial in the design of promising new functional nanomaterials.

  12. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    SciTech Connect (OSTI)

    Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

    2014-10-14

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW₁₂O₄₀³⁻, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  13. Rovibrational effects on nuclear shielding of apex nuclei in bent molecules

    SciTech Connect (OSTI)

    Osten, H.; Jameson, C.J.

    1985-05-15

    The isotope shifts of non-end nuclei with lone pairs are generally larger than those of nuclei without lone pairs. Using the bent triatomic molecule as a prototype, we examine the mass and temperature dependence of the mean bond angle deformation and the mean displacement along a bond due to centrifugal stretching and anharmonic vibration. We find that the temperature dependence of <..delta cap alpha..> determines whether the temperature dependence of the shielding of the apex nucleus will be normal ((dsigma/sub 0//dT)<0) or abnormal. The dominant contribution of the rotation to the temperature dependence of <..delta cap alpha..> in the hydrides can lead to opposing temperature effects on shielding while the mass effects lead to normal isotope shifts. We performed similar calculations for the trigonal pyramidal molecules in order to explain the observed abnormal temperature dependence of the /sup 15/N and /sup 31/P nuclear shielding in NH/sub 3/ and PH/sub 3/.

  14. Single-molecule imaging at high fluorophore concentrations by local activation of dye

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

    Geertsema, Hylkje J.; Mangel, Walter F.; Schulte, Aartje C.; Spenkelink, Lisanne M.; McGrath, William J.; Morrone, Seamus R.; Sohn, Jungsan; Robinson, Andrew; van Oijen, Antoine M.

    2015-02-17

    Single-molecule fluorescence microscopy is a powerful approach to observe biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual, labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Then, making use ofmore » short-distance energy-transfer mechanisms, the fluorescence from only those proteins bound to their substrate are selectively activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 (IFI16) with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease (pVIc-AVP) on DNA in the presence of a background of hundreds of nM Cy5 fluorophore.« less

  15. A study of competitive adsorption of organic molecules onto mineral oxides using DRIFTS

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

    Joan E. Thomas; Kelley, Michael J.

    2009-10-20

    In this study, analysis of DRIFTS spectra was used for a quantitative study of competitive adsorption of myristic and salicylic acids onto kaolinite or γ-alumina. Peaks unique to the ring or the chain were selected and single molecule studies used as calibration. Samples were exposed to hexane solution containing equal molecular quantities of each acid. The surface loading of salicylic acid was not influenced by the presence of myristic acid on either mineral but the maximum loading of myristic acid was decreased (46-50%) by salicylic acid. Displacement of myristic acid from {gamma}-alumina, but not kaolinite, was observed when excess salicylicmore » acid remained in solution. A 25% increase in the maximum loading was observed for kaolinite, but not for{gamma}-alumina. On {gamma}-alumina, after a loading of 1 molecule per nm2, increased exposure resulted in salicylic acid adsorption only, this value is approximately the same for salicylic acid adsorption from aqueous solution or for water washed hexane treated samples. Thus a set of sites for adsorption of either acid is indicated together with other energetically less favorable sites, which can be occupied by salicylic, but not by myristic, acid.« less

  16. 2012 SINGLE MOLECULE APPROACHES TO BIOLOGY GORDON RESEARCH CONFERENCE (JULY 15-20, 2012 - MOUNT SNOW RESORT, WEST DOVER VT)

    SciTech Connect (OSTI)

    Fernandez, Julio [Columbia University

    2012-04-20

    Single molecule techniques are rapidly occupying a central role in biological research at all levels. This transition was made possible by the availability and dissemination of robust techniques that use fluorescence and force probes to track the conformation of molecules one at a time, in vitro as well as in live cells. Single-molecule approaches have changed the way many biological problems are studied. These novel techniques provide previously unobtainable data on fundamental biochemical processes that are essential for all forms of life. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of the molecular systems that underpin the functioning of living cells. Hence, our conference seeks to disseminate the implementation and use of single molecule techniques in the pursuit of new biological knowledge. Topics covered include: Molecular Motors on the Move; Origin And Fate Of Proteins; Physical Principles Of Life; Molecules and Super-resolution Microscopy; Nanoswitches In Action; Active Motion Or Random Diffusion?; Building Blocks Of Living Cells; From Molecular Mechanics To Physiology; Tug-of-war: Force Spectroscopy Of Single Proteins.

  17. The use of carbon stable isotope ratios in drugs characterization

    SciTech Connect (OSTI)

    Magdas, D. A. Cristea, G. Bot, A. Mirel, V.

    2013-11-13

    Isotopic Ratio Mass Spectrometry (IRMS) is an effective toll to be used for drug product authentication. The isotopic composition could be used to assist in the differentiation between batches of drugs and assist in the identification of counterfeit materials on the market. Only two factors affect the isotopic ratios in pharmaceutical components: the isotopic composition of the raw materials and the synthetic processes performed upon them. Counterfeiting of pharmaceutical drugs threatens consumer confidence in drug products companies' economical well-being. In this preliminary study, the analyzed samples consist in two types of commercially available analgesics, which were purchases from Romanian pharmacies. Differences in δ{sup 13}C between batches from −29.7 to −31.6% were observed, demonstrating that this method can be used to differentiate among individual drug batches and subsequently identify counterfeits on the market. On the other hand, carbon isotopic ratios differences among producers were recorded, the variations being between −31.3 to −34.9% for the same type of analgesic, but from different manufactures.

  18. Electromagnetic field triggered drug and chemical delivery via liposomes

    DOE Patents [OSTI]

    Liburdy, R.P.

    1993-03-02

    The present invention relates to a system and to a method of delivering a drug to a preselected target body site of a patient, comprising the steps of encapsulating the chemical agent within liposomes, essentially temperature insensitive, i.e. not having a specific predetermined phase transition temperature within the specific temperature range of drug administration; administering the liposomes to the target body site; and subjecting the target body site to nonionizing electromagnetic fields in an area of the preselected target body in order to release the chemical agent from the liposomes at a temperature of between about +10 and 65 C. The invention further relates to the use of the liposomes to bind to the surface of or to enter target tissue or an organ in a living system, and, when subjected to a nonionizing field, to release a drug from the liposomes into the target site.

  19. Electromagnetic field triggered drug and chemical delivery via liposomes

    DOE Patents [OSTI]

    Liburdy, Robert P.

    1993-01-01

    The present invention relates to a system and to a method of delivering a drug to a preselected target body site of a patient, comprising the steps of encapsulating the chemical agent within liposomes, essentially temperature insensitive, i.e. not having a specific predetermined phase transition temperature within the specific temperature range of drug administration; administering the liposomes to the target body site; and subjecting the target body site to nonionizing electromagnetic fields in an area of the preselected target body in order to release said chemical agent from the liposomes at a temperature of between about +10 and 65.degree. C. The invention further relates to the use of said liposomes to bind to the surface of or to enter target tissue or an organ in a living system, and, when subjected to a nonionizing field, to release a drug from the liposomes into the target site.

  20. X-ray Spectroscopy for Quality Control of Chemotherapy Drugs

    SciTech Connect (OSTI)

    Greaves, E. D.; Barros, H.; Bermudez, J.; Sajo-Bohus, L.; Angeli-Greaves, M.

    2007-10-26

    We develop a method, employing Compton peak standardization and the use of matrix-matched spiked samples with Total Reflection X-ray Fluorescence (TXRF), for the determination of platinum plasma concentrations of patients undergoing chemotherapy with Pt-bearing drugs. Direct blood plasma analysis attains Pt detection limits of 70 ng/ml. Measurement results of prescribed drug doses are compared to achieved blood Pt concentrations indicating a lack of expected correlations. Direct analysis of Pt-containing infused drugs from a variety of suppliers indicates cases of abnormal concentrations which raises quality control issues. We demonstrate the potential usefulness of the method for pharmacokinetic studies or for routine optimization and quality control of Pt chemotherapy treatments.

  1. Intercalation of organic molecules into SnS{sub 2} single crystals

    SciTech Connect (OSTI)

    Toh, M.L.; Tan, K.J.; Wei, F.X.; Zhang, K.K.; Jiang, H.; Kloc, C.

    2013-02-15

    SnS{sub 2} is a layered semiconductor with a van der Waals gap separating the covalently bonded layers. In this study, post-synthesis intercalation of donor organic amine molecules, such as ethylenediamine (en), into tin disulfide and secondary intercalation of p-phenylenediamine (PPD) and 1, 5-naphthalenediamine (NDA) into SnS{sub 2e}n have been verified with X-ray diffraction. PPD and NDA did not intercalate directly even during prolonged annealing but replaced en readily if en was already present in the van der Waals gap. The c-lattice dilation is proportional to the intercalant size. Unit cell lattices of intercalated products were determined from the positions of the X-ray diffraction peaks. Optical images taken during the intercalation showed that intercalation progressed from the periphery towards the interior of the crystal. TEM diffraction patterns in the [0 0 1] direction of SnS{sub 2} after intercalation revealed defects and stacking mismatches among the SnS{sub 2} layers caused by the intercalation. UV-Vis absorption studies showed a red shift in the band edge of the SnS{sub 2} material after intercalation. The band edge was 2.2 eV for pristine SnS{sub 2}; after intercalation with en or PPD, the absorbance spectra band edges shifted to approximately 0.7 eV or 0.5 eV, respectively. - Graphical Abstract: SnS{sub 2} single crystals were intercalated with organic amine molecules such as ethylenediamine, phenylenediamine and naphthalenediamine. Absorption studies showed red shift of band edge after intercalation, which was consistent with optical observations. X-ray diffraction indicated lattice dilation in the c-lattice of SnS{sub 2} after intercalation. Highlights: Black-Right-Pointing-Pointer Organic molecules intercalated inhomogenously between covalently bonded SnS{sub 2} layers. Black-Right-Pointing-Pointer Ethylenediamine (en) intercalate directly into SnS{sub 2}. Black-Right-Pointing-Pointer Phenylenediamine (PPD) and naphthalenediamine (NDA) can be intercalated into SnS{sub 2} secondary. Black-Right-Pointing-Pointer In a secondary intercalation the bonds between layers are weakened by direct intercalation of (en). Black-Right-Pointing-Pointer The optical band gap of SnS{sub 2} is reduced due to intercalation.

  2. Theoretical study of the rhodium dimer interaction with the hydrogen molecule

    SciTech Connect (OSTI)

    Castillo, S.; Cruz, A.; Cuan, A.

    1995-12-31

    The C{sub 2v} potential energy surfaces for the end-on and side-on approaches of H{sub 2} to the rhodium dimer were studied through self-consistent-field (SCF) and multiconfigurational SCF calculations, followed by extensive variational plus second-order multireference Moller-Plesset perturbational configuration interaction (CIPSI) calculations. Relativistic effective core potentials were used to replace the core electrons of the rhodium atoms. Together with the Rh{sub 2}-H{sub 2} interaction, the spectroscopic constants for the {sup 5}{summation}{sub g}{sup +}, {sup 1}{summation}{sub g}{sup +}, {sup 3}II{sub {mu}}, and {sup 1}II{sub {mu}} states of Rh{sub 2} are reported. It was found that the potential energy curves of the parallel and the perpendicular Rh{sub 2}({sup 5}{summation}{sub g}) interaction with H{sub 2} show that the rhodium dimer has the ability to capture and break the H{sub 2} molecule. The parallel interaction presents a soft potential barrier of 7.8 kcal/mol, energy necessary to surmount before the capture and breaking of the H-H bond. In the perpendicular interaction, Rh{sub 2} captures and breaks spontaneously H{sub 2}. The potential energy curve of the parallel Rh{sub 2}({sup 1}{summation}{sub g}) + H{sub 2} interaction shows that Rh{sub 2} also captures and breaks spontaneously the H{sub 2}, with a very deep well of 92.7 kcal/mol, while in the perpendicular approach, Rh{sub 2} has to surmount again a soft barrier of 5.2 kcal/mol to capture and break the H{sub 2} molecule. Finally, the energy curves of the parallel Rh{sub 2}({sup 1,3}II{sub {mu}}) + H{sub 2} interactions present capture and breaking with very small barriers. The perpendicular interactions capture and scisse the hydrogen molecule spontaneously. 35 refs., 6 tabs.

  3. Multiple scattering of electrons in solids and molecules: A cluster-model approach

    SciTech Connect (OSTI)

    Garcia de Abajo, F. J.; Van Hove, M. A.; Fadley, C. S.

    2001-02-15

    A method for the simulation of electron scattering and diffraction in solids and molecules within the cluster approach is presented with explicit applications to photoelectron diffraction, electron scattering in molecules, and low-energy electron diffraction. No approximations are made beyond the muffin-tin model, and, in particular, an exact representation of the free-electron Green function is used. All multiple-scattering paths are accounted for up to an order of scattering that ensures convergence. The method relies upon a convenient separation of the free-electron Green function in rotation matrices and translations along the z axis, which greatly reduces the computation time and storage demand. The evaluation of the multiple-scattering expansion is implemented using the fully convergent recursion method, which permits one to perform an iterative refinement of the final-state wave function, as expressed in the basis set of spherical harmonics attached to each atom of the cluster. Examples are offered in which the direct multiple-scattering expansion and the more elaborated simultaneous relaxation method fail to converge, whereas the recursion method leads to convergence. The computation time needed by the resulting computer program of electron diffraction in atomic clusters to determine the self-consistently scattered wave function is proportional to N{sup 2}(l{sub max}+1){sup 3}, where N is the number of atoms in the cluster and l{sub max} is the maximum angular momentum for which the scattering phase shifts take non-negligible values. Within this method it is possible to establish that in practical cases N>1000 might be needed for a convergence of the cluster size, although the angular averaging inherent in many experiments may reduce this. The recursion method was also modified to reduce the effort in computing angular distributions of photoelectrons and low-energy diffracted electrons, which now require negligible time for each angle of emission once the wave function has been determined for a given electron energy. Angle and energy distributions of core-level photoemission, elastic scattering of electrons from a free molecule, and low-energy electron diffraction in large-unit-cell surfaces are calculated.

  4. Solution-Procesed Small-Molecule OLED Luminaire for Interior Illumination

    SciTech Connect (OSTI)

    Parker, Ian

    2012-02-29

    Prototype lighting panels and luminaires were fabricated using DuPont Displays solution-processed small-molecule OLED technology. These lighting panels were based on a spatially-patterned, 3-color design, similar in concept to an OLED display panel, with materials chosen to maximize device efficacy. The majority of the processing steps take place in air (rather than high vacuum). Optimization of device architecture, processing and construction was undertaken, with a final prototype design of 50 cm{sup 2} being fabricated and tested. Performance of these panels reached 35 lm/W at illuminant-A. A unique feature of this technology is the ability to color tune the emission, and color temperatures ranging from 2700 to > 6,500K were attained in the final build. Significant attention was paid to low-cost fabrication techniques.

  5. Crystallography Without Crystals: Determining the Structure of Individual Biological Molecules and Nanoparticles

    ScienceCinema (OSTI)

    Ourmazd, Abbas [University of Wisconsin, Milwaukee, Wisconsin, USA

    2010-01-08

    Ever shattered a valuable vase into 10 to the 6th power pieces and tried to reassemble it under a light providing a mean photon count of 10 minus 2 per detector pixel with shot noise? If you can do that, you can do single-molecule crystallography. This talk will outline how this can be done in principle. In more technical terms, the talk will describe how the combination of scattering physics and Bayesian algorithms can be used to reconstruct the 3-D diffracted intensity distribution from a collection of individual 2-D diffiraction patterns down to a mean photon count of 10 minus 2 per pixel, the signal level anticipated from the Linac Coherent Light Source, and hence determine the structure of individual macromolecules and nanoparticles.

  6. Interaction of mineral surfaces with simple organci molecules by diffuse reflectance IR spectroscopy (DRIFT)

    SciTech Connect (OSTI)

    Joan Thomas; Michael Kelley

    2007-06-18

    Diffuse reflectance Fourier-transform infrared spectroscopy (DRIFTS) was used to characterize multi-layers of lysine, glutamic acid and salicylic acid on ?-alumina and kaolinite surfaces. The results agreed well with those previously obtained by ATR-IR in aqueous media where available, indicating that DRIFT may be regarded as effectively an in-situ spectroscopy for these materials. In the case of salicylic acid adsorption onto ?-alumina, DRIFTS was used to identify monolayer coverage and to detect molecules down to coverage of 3% of a monolayer. The spectroscopic results as to coverage were confirmed by analysis of the solutions used for treatment. The spectra obtained allowed identification of changes in the bonding environment with increasing surface coverage. DRIFTS, offers several advantages in terms of materials, experimental technique and data treatment, motivating further investigations.

  7. High resolution mass spectrometry method and system for analysis of whole proteins and other large molecules

    DOE Patents [OSTI]

    Reilly, Peter T. A. [Knoxville, TN; Harris, William A. [Naperville, IL

    2010-03-02

    A matrix assisted laser desorption/ionization (MALDI) method and related system for analyzing high molecular weight analytes includes the steps of providing at least one matrix-containing particle inside an ion trap, wherein at least one high molecular weight analyte molecule is provided within the matrix-containing particle, and MALDI on the high molecular weight particle while within the ion trap. A laser power used for ionization is sufficient to completely vaporize the particle and form at least one high molecular weight analyte ion, but is low enough to avoid fragmenting the high molecular weight analyte ion. The high molecular weight analyte ion is extracted out from the ion trap, and is then analyzed using a detector. The detector is preferably a pyrolyzing and ionizing detector.

  8. Mixtures of ions and amphiphilic molecules in slit-like pores: A density functional approach

    SciTech Connect (OSTI)

    Pizio, O.; Rżysko, W. Sokołowski, S.; Sokołowska, Z.

    2015-04-28

    We investigate microscopic structure and thermodynamic properties of a mixture that contains amphiphilic molecules and charged hard spheres confined in slit-like pores with uncharged hard walls. The model and the density functional approach are the same as described in details in our previous work [Pizio et al., J. Chem. Phys. 140, 174706 (2014)]. Our principal focus is in exploring the effects brought by the presence of ions on the structure of confined amphiphilic particles. We have found that for some cases of anisotropic interactions, the change of the structure of confined fluids occurs via the first-order transitions. Moreover, if anions and cations are attracted by different hemispheres of amphiphiles, a charge at the walls appears at the zero value of the wall electrostatic potential. For a given thermodynamic state, this charge is an oscillating function of the pore width.

  9. Enhancement of ultracold molecule formation by local control in the nanosecond regime

    SciTech Connect (OSTI)

    Carini, J. L.; Kallush, S.; Kosloff, R.; Gould, P. L.

    2015-02-01

    We describe quantum simulations of ultracold 87Rb2 molecule formation using photoassociation (PA) with nanosecond-time-scale pulses of frequency chirped light. In particular, we compare the case of a linear chirp to one where the frequency evolution is optimized by local control (LC) of the phase, and find that LC can provide a significant enhancement. The resulting optimal frequency evolution corresponds to a rapid jump from the PA absorption resonance to a downward transition to a bound level of the lowest triplet state. We also consider the case of two frequencies and investigate interference effects. The assumed chirp parameters should be achievable with nanosecond pulse shaping techniques and are predicted to provide a significant enhancement over recent experiments with linear chirps.

  10. The crystal structure of methane B at 8 GPa—An ?-Mn arrangement of molecules

    SciTech Connect (OSTI)

    Maynard-Casely, H. E. Lundegaard, L. F.; Loa, I.; McMahon, M. I.; Gregoryanz, E.; Nelmes, R. J.; Loveday, J. S.

    2014-12-21

    From a combination of powder and single-crystal synchrotron x-ray diffraction data we have determined the carbon substructure of phase B of methane at a pressure of ?8 GPa. We find this substructure to be cubic with space group I4{sup ¯}3m and 58 molecules in the unit cell. The unit cell has a lattice parameter a = 11.911(1) Å at 8.3(2) GPa, which is a factor of ?2 larger than had previously been proposed by Umemoto et al. [J. Phys.: Condens. Matter 14, 10675 (2002)]. The substructure as now solved is not related to any close-packed arrangement, contrary to previous proposals. Surprisingly, the arrangement of the carbon atoms is isostructural with that of ?-manganese at ambient conditions.

  11. Exciton dissociation and interdot transport in CdSe quantum-dot molecules

    SciTech Connect (OSTI)

    Franceschetti, Alberto; Zunger, Alex

    2001-04-15

    One of the most important parameters that determine the transport properties of a quantum dot array is the exciton dissociation energy, i.e., the energy {Delta}E required to dissociate an exciton into an electron and a hole localized in different dots. We show that a pseudopotential calculation for a dot molecule, coupled with a basic configuration interaction calculation of the exciton energy levels, provides directly the exciton dissociation energy, including the effects of wave function overlap, screened Coulomb attraction between the electron and the hole in different dots, and polarization effects. We find that {Delta}E decreases as the interdot distance decreases and as the dielectric constant of the medium increases.

  12. Collision dynamics of polyatomic molecules containing carbon rings at low temperatures

    SciTech Connect (OSTI)

    Li, Zhiying; Heller, Eric J.; Krems, Roman V.

    2014-09-14

    We explore the collision dynamics of complex hydrocarbon molecules (benzene, coronene, adamantane, and anthracene) containing carbon rings in a cold buffer gas of {sup 3}He. For benzene, we present a comparative analysis of the fully classical and fully quantum calculations of elastic and inelastic scattering cross sections at collision energies between 1 and 10 cm{sup ?1}. The quantum calculations are performed using the time-independent coupled channel approach and the coupled-states approximation. We show that the coupled-states approximation is accurate at collision energies between 1 and 20 cm{sup ?1}. For the classical dynamics calculations, we develop an approach exploiting the rigidity of the carbon rings and including low-energy vibrational modes without holonomic constraints. Our results illustrate the effect of the molecular shape and the vibrational degrees of freedom on the formation of long-lived resonance states that lead to low-temperature clustering.

  13. Observation of quantum interferences via light-induced conical intersections in diatomic molecules

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

    Natan, Adi; Ware, Matthew R.; Prabhudesai, Vaibhav S.; Lev, Uri; Bruner, Barry D.; Heber, Oded; Bucksbaum, Philip H.

    2016-04-07

    We observe energy-dependent angle-resolved diffraction patterns in protons from strong-field dissociation of the molecular hydrogen ion H+2. The interference is a characteristic of dissociation around a laser-induced conical intersection (LICI), which is a point of contact between two surfaces in the dressed 2-dimensional Born-Oppenheimer potential energy landscape of a diatomic molecule in a strong laser field. The interference magnitude and angular period depend strongly on the energy difference between the initial state and the LICI, consistent with coherent diffraction around a cone-shaped potential barrier whose width and thickness depend on the relative energy of the initial state and the conemore » apex. As a result, these findings are supported by numerical solutions of the time-dependent Schrodinger equation for similar experimental conditions.« less

  14. Enhancement of ultracold molecule formation by local control in the nanosecond regime

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

    Carini, J. L.; Kallush, S.; Kosloff, R.; Gould, P. L.

    2015-02-01

    We describe quantum simulations of ultracold 87Rb2 molecule formation using photoassociation (PA) with nanosecond-time-scale pulses of frequency chirped light. In particular, we compare the case of a linear chirp to one where the frequency evolution is optimized by local control (LC) of the phase, and find that LC can provide a significant enhancement. The resulting optimal frequency evolution corresponds to a rapid jump from the PA absorption resonance to a downward transition to a bound level of the lowest triplet state. We also consider the case of two frequencies and investigate interference effects. The assumed chirp parameters should be achievablemore » with nanosecond pulse shaping techniques and are predicted to provide a significant enhancement over recent experiments with linear chirps.« less

  15. Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition

    SciTech Connect (OSTI)

    Wang, Jin; Lu, Qiang N.; Lu, H PETER.

    2006-07-01

    The study of associations between two biomolecules is the key to understand molecular recognition and function. Molecular function is often thought to be determined by the underlying structures. Here, combining single molecule study of protein binding with an energy landscape inspired microscopic model, we found strong evidences that bio-molecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse grained molecular dynamics performed on the residue level with the energy function biased towards the native binding structure (Go model). With our model, the underlying free energy landscape of the binding can be explored. Two distinct conformational states as free energy minimum, one with partially folding of CBD and significant binding of CBD to CDC42, and another with native folding of CBD and native binding of CBD to CDC42, are clearly seen. This shows the binding process proceeds with significant interface binding of CBD with CDC42 first without complete folding of CBD. Finally binding and folding are coupled with each other cooperatively to reach the native binding state. The single molecule experimental finding of the dynamic fluctuations between the loosely bound and closely bound conformational states can be identified with theoretically calculated free energy minimum and quantitatively explained in our model as a result of binding associated with large conformational changes. Theoretical predictions have identified certain key residues for binding which are consistent with mutational experiments. The combined study provides a test ground for fundamental mechanisms as well as insights into design and further explorations on biomolecular recognition with large conformational changes.

  16. Sensitivity of transitions in internal rotor molecules to a possible variation of the proton-to-electron mass ratio

    SciTech Connect (OSTI)

    Jansen, Paul; Ubachs, Wim; Bethlem, Hendrick L.; Kleiner, Isabelle; Xu, Li-Hong

    2011-12-15

    Recently, methanol was identified as a sensitive target system to probe variations of the proton-to-electron mass ratio {mu}[Jansen et al., Phys. Rev. Lett. 106, 100801 (2011)]. The high sensitivity of methanol originates from the interplay between overall rotation and hindered internal rotation of the molecule; that is, transitions that convert internal rotation energy into overall rotation energy, or vice versa, have an enhanced sensitivity coefficient, K{sub {mu}}. As internal rotation is a common phenomenon in polyatomic molecules, it is likely that other molecules display similar or even larger effects. In this paper we generalize the concepts that form the foundation of the high sensitivity in methanol and use this to construct an approximate model which makes it possible to estimate the sensitivities of transitions in internal rotor molecules with C{sub 3v} symmetry, without performing a full calculation of energy levels. We find that a reliable estimate of transition sensitivities can be obtained from the three rotational constants (A, B, and C) and three torsional constants (F, V{sub 3}, and {rho}). This model is verified by comparing obtained sensitivities for methanol, acetaldehyde, acetamide, methyl formate, and acetic acid with a full analysis of the molecular Hamiltonian. Of the molecules considered, methanol is by far the most suitable candidate for laboratory and cosmological tests searching for a possible variation of {mu}.

  17. Drug release from hydrazone-containing peptide amphiphiles

    SciTech Connect (OSTI)

    Matson, John B.; Stupp, Samuel I.

    2012-03-15

    Hydrolytically-labile hydrazones in peptide amphiphiles were studied as degradable tethers for release of the drug nabumetone from nanofiber gels. On-resin addition of the novel compound tri-Boc-hydrazido adipic acid to a lysine E-amine allowed for precise placement of a hydrazide in a peptide sequence.

  18. Memorandum, Drug Testing at DOE- September 14, 2007

    Broader source: Energy.gov [DOE]

    Department of Energy (DOE) Q or L access authorization (security clearance) will be in Testing Designated Positions (TDP) as specified in DOE Order 3792.3, Drug-Free Federal Workplace Testing Implementation Program, for Federal employees, and Title 10, Code of Federal Regulations, Part 707, Workplace Substance Abuse Programs at DOE Sites, for contractor employees.

  19. A numerical study of the phase behaviors of drug particle/star triblock copolymer mixtures in dilute solutions for drug carrier application

    SciTech Connect (OSTI)

    Wang, Shanhui; Tong, Chaohui; Zhu, Yuejin

    2014-04-14

    The complex microstructures of drug particle/ABA star triblock copolymer in dilute solutions have been investigated by a theoretical approach which combines the self-consistent field theory and the hybrid particle-field theory. Simulation results reveal that, when the volume fraction of drug particles is smaller than the saturation concentration, the drug particle encapsulation efficiency is 100%, and micelle loading capacity increases with increasing particle volume fraction. When the volume fraction of drug particles is equal to the saturation concentration, the micelles attain the biggest size, and micelle loading capacity reaches a maximum value which is independent of the copolymer volume fraction. When the volume fraction of drug particles is more than the saturation concentration, drug particle encapsulation efficiency decreases with increasing volume fraction of drug particles. Furthermore, it is found that the saturation concentration scales linearly with the copolymer volume fraction. The above simulation results are in good agreement with experimental results.

  20. On the importance of nuclear quantum motions in near edge x-ray absorption fine structure (NEXAFS) spectroscopy of molecules

    SciTech Connect (OSTI)

    Schwartz, Craig P.; Uejio, Janel S.; Saykally, Richard J.; Prendergast, David

    2009-02-26

    We report the effects of sampling nuclear quantum motion with path integral molecular dynamics (PIMD) on calculations of the nitrogen K-edge spectra of two isolated organic molecules. S-triazine, a prototypical aromatic molecule occupying primarily its vibrational ground state at room temperature, exhibits substantially improved spectral agreement when nuclear quantum effects are included via PIMD, as compared to the spectra obtained from either a single fixed-nuclei based calculation or from a series of configurations extracted from a classical molecular dynamics trajectory. Nuclear quantum dynamics can accurately explain the intrinsic broadening of certain features. Glycine, the simplest amino acid, is problematic due to large spectral variations associated with multiple energetically accessible conformations at the experimental temperature. This work highlights the sensitivity of NEXAFS to quantum nuclear motions in molecules, and the necessity of accurately sampling such quantum motion when simulating their NEXAFS spectra.

  1. Separation and counting of single molecules through nanofluidics, programmable electrophoresis, and nanoelectrode-gated tunneling and dielectric detection

    DOE Patents [OSTI]

    Lee, James W.; Thundat, Thomas G.

    2006-04-25

    An apparatus for carrying out the separation, detection, and/or counting of single molecules at nanometer scale. Molecular separation is achieved by driving single molecules through a microfluidic or nanofluidic medium using programmable and coordinated electric fields. In various embodiments, the fluidic medium is a strip of hydrophilic material on nonconductive hydrophobic surface, a trough produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base, or a covered passageway produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base together with a nonconductive cover on the parallel strips of hydrophobic nonconductive material. The molecules are detected and counted using nanoelectrode-gated electron tunneling methods, dielectric monitoring, and other methods.

  2. VirtualToxLab — A platform for estimating the toxic potential of drugs, chemicals and natural products

    SciTech Connect (OSTI)

    Vedani, Angelo; Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel ; Dobler, Max; Smieško, Martin

    2012-06-01

    The VirtualToxLab is an in silico technology for estimating the toxic potential (endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity) of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of proteins, known or suspected to trigger adverse effects. The toxic potential, a non-linear function ranging from 0.0 (none) to 1.0 (extreme), is derived from the individual binding affinities of a compound towards currently 16 target proteins: 10 nuclear receptors (androgen, estrogen ?, estrogen ?, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor ?, progesterone, thyroid ?, and thyroid ?), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, and 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). The interface to the technology allows building and uploading molecular structures, viewing and downloading results and, most importantly, rationalizing any prediction at the atomic level by interactively analyzing the binding mode of a compound with its target protein(s) in real-time 3D. The VirtualToxLab has been used to predict the toxic potential for over 2500 compounds: the results are posted on (http://www.virtualtoxlab.org). The free platform — the OpenVirtualToxLab — is accessible (in client–server mode) over the Internet. It is free of charge for universities, governmental agencies, regulatory bodies and non-profit organizations. -- Highlights: ? In silico technology for estimating the toxic potential of drugs and chemicals. ? Simulation of binding towards 16 proteins suspected to trigger adverse effects. ? Mechanistic interpretation and real-time 3D visualization. ? Accessible over the Internet. ? Free of charge for universities, governmental agencies, regulatory bodies and NPOs.

  3. A single-molecule approach to ZnO defect studies: Single photons and single defects

    SciTech Connect (OSTI)

    Jungwirth, N. R.; Pai, Y. Y.; Chang, H. S.; MacQuarrie, E. R.; Nguyen, K. X.; Fuchs, G. D.

    2014-07-28

    Investigations that probe defects one at a time offer a unique opportunity to observe properties and dynamics that are washed out of ensemble measurements. Here, we present confocal fluorescence measurements of individual defects in ZnO nanoparticles and sputtered films that are excited with sub-bandgap energy light. Photon correlation measurements yield both antibunching and bunching, indicative of single-photon emission from isolated defects that possess a metastable shelving state. The single-photon emission is in the range of ?560–720?nm and typically exhibits two broad spectral peaks separated by ?150?meV. The excited state lifetimes range from 1 to 13?ns, consistent with the finite-size and surface effects of nanoparticles and small grains. We also observe discrete jumps in the fluorescence intensity between a bright state and a dark state. The dwell times in each state are exponentially distributed and the average dwell time in the bright (dark) state does (may) depend on the power of the exciting laser. Taken together, our measurements demonstrate the utility of a single-molecule approach to semiconductor defect studies and highlight ZnO as a potential host material for single-defect based applications.

  4. Sequential data assimilation for single-molecule FRET photon-counting data

    SciTech Connect (OSTI)

    Matsunaga, Yasuhiro; Kidera, Akinori; Sugita, Yuji

    2015-06-07

    Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from “replicated” molecular dynamics (MD) simulations. A particle filter using a large number of “replicated” MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.

  5. Molecule-based approach for computing chemical-reaction rates in upper atmosphere hypersonic flows.

    SciTech Connect (OSTI)

    Gallis, Michail A.; Bond, Ryan Bomar; Torczynski, John Robert

    2009-08-01

    This report summarizes the work completed during FY2009 for the LDRD project 09-1332 'Molecule-Based Approach for Computing Chemical-Reaction Rates in Upper-Atmosphere Hypersonic Flows'. The goal of this project was to apply a recently proposed approach for the Direct Simulation Monte Carlo (DSMC) method to calculate chemical-reaction rates for high-temperature atmospheric species. The new DSMC model reproduces measured equilibrium reaction rates without using any macroscopic reaction-rate information. Since it uses only molecular properties, the new model is inherently able to predict reaction rates for arbitrary nonequilibrium conditions. DSMC non-equilibrium reaction rates are compared to Park's phenomenological non-equilibrium reaction-rate model, the predominant model for hypersonic-flow-field calculations. For near-equilibrium conditions, Park's model is in good agreement with the DSMC-calculated reaction rates. For far-from-equilibrium conditions, corresponding to a typical shock layer, the difference between the two models can exceed 10 orders of magnitude. The DSMC predictions are also found to be in very good agreement with measured and calculated non-equilibrium reaction rates. Extensions of the model to reactions typically found in combustion flows and ionizing reactions are also found to be in very good agreement with available measurements, offering strong evidence that this is a viable and reliable technique to predict chemical reaction rates.

  6. Universal and nonuniversal statistical properties of levels and intensities for chaotic Rydberg molecules

    SciTech Connect (OSTI)

    Lombardi, M.; Seligman, T.H. (Laboratoire de Spectrometrie Physique-Universite Joseph Fourier de Grenoble, Boite Postale No. 87, 38402 Saint Martin d'Heres, CEDEX (France))

    1993-05-01

    We study Rydberg molecules taking into account the interaction between the rotational motion of the nuclei and the radial motion of the electron. This situation can be treated to a good approximation in quantum mechanics by the multichannel quantum-defect method which in turn has a well-defined classical limit. We are able to calculate very long sequences of levels and the corresponding amplitudes of wave packets. This allows us to study the statistical properties of both in detail. Our interest focuses on aspects of quantum chaos'' that can be particularly well understood in this case. Our main result is that, in a completely chaotic classical situation, where statistics of quantum-level spacings follow the expected universal Gaussian-orthogonal-ensemble behavior, and statistics of line intensities display the expected universal Porter-Thomas behavior, nonuniversal properties are explicitly contained in correlations between intensities and spacings, determined by the time needed for the classical system to mix on a length scale given by the quantum wavelength.

  7. Shapiro-like resonance in ultracold molecule production via an oscillating magnetic field

    SciTech Connect (OSTI)

    Liu Bin; Fu Libin; Liu Jie

    2010-01-15

    We study the process of the production of ultracold molecules from ultracold atoms using a sinusoidally oscillating magnetic-field modulation. Our study is based on a two-mode mean-field treatment of the problem. When the magnetic field is resonant roughly with the molecular binding energy, Shapiro-like resonances are observed. Their resonance profiles are well fitted by the Lorentzian functions. The linewidths depend on both the amplitude and the duration of the applied modulations and are found to be dramatically broadened by the thermal dephasing effect. The resonance centers shift due to both the many-body effect and the finite temperature effect. Our theory is consistent with a recent experiment [S. T. Thompson, E. Hodby, and C. E. Wieman, Phys. Rev. Lett. 95, 190404 (2005)]. Our model predicts a 1/3 ceiling for the molecular production yield in uncondensed ultracold atomic clouds for a long coupling time, while for condensed atoms the optimal conversion yield could be beyond the limit.

  8. Efficient solution-processed small molecule: Cadmium selenide quantum dot bulk heterojunction solar cells

    SciTech Connect (OSTI)

    Gupta, Vinay; Department of Physics, University of California, Santa Barbara, California 93106 ; Upreti, Tanvi; Chand, Suresh

    2013-12-16

    We report bulk heterojunction solar cells based on blends of solution-processed small molecule [7,7?-(4,4-bis(2-ethylhexyl)-4H-silolo[3,2-b:4,5-b?]dithiophene-2,6-diyl) bis(6-fluoro-4-(5?-hexyl-[2,2?-bithiophen]-5yl)benzo[c] [1,2,5] thiadiazole)] p-DTS(FBTTh{sub 2}){sub 2}: Cadmium Selenide (CdSe) (70:30, 60:40, 50:50, and 40:60) in the device configuration: Indium Tin Oxide /poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)/p-DTS(FBTTh{sub 2}){sub 2}: CdSe/Ca/Al. The optimized ratio of p-DTS(FBTTh{sub 2}){sub 2}:CdSe::60:40 leads to a short circuit current density (J{sub sc})?=?5.45?mA/cm{sup 2}, open circuit voltage (V{sub oc})?=?0.727?V, and fill factor (FF)?=?51%, and a power conversion efficiency?=?2.02% at 100 mW/cm{sup 2} under AM1.5G illumination. The J{sub sc} and FF are sensitive to the ratio of p-DTS(FBTTh{sub 2}){sub 2}:CdSe, which is a crucial factor for the device performance.

  9. Signatures of the molecular potential in the ellipticity of high-order harmonics from aligned molecules

    SciTech Connect (OSTI)

    Sherratt, Paul A. J.; Ramakrishna, S.; Seideman, Tamar

    2011-05-15

    We explore the information content of the polarization of high-order harmonics emitted from aligned molecules driven by a linearly polarized field. The study builds upon our previous work [Ramakrishna et al., Phys. Rev. A 81, 021802(R) (2010)], which illustrated that the phase of the continuum electronic wave function, and hence the underlying molecular potential, is responsible, at least in part, for the ellipticity observed in harmonic spectra. We use a simple model potential and systematically vary the potential parameters to investigate the sense in which, and the degree to which, the shape of the molecular potential is imprinted onto the polarization of the emitted harmonics. Strong ellipticity is observed over a wide range of potential parameters, suggesting that the emission of elliptically polarized harmonics is a general phenomenon, yet qualitatively determined by the molecular properties. The sensitivity of the ellipticity to the model parameters invites the use of ellipticity measurements as a probe of the continuum wave function and the underlying molecular potential.

  10. XAFS investigation of polyamidoxime-bound uranyl contests the paradigm from small molecule studies

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

    Mayes, Richard T.; Piechowicz, Marek; Lin, Zekai; Veith, Gabriel M.; Dai, Sheng; Lin, Wenbin; Abney, C. W.; Bryantsev, V. S.

    2015-11-12

    In this study, limited resource availability and population growth have motivated interest in harvesting valuable metals from unconventional reserves, but developing selective adsorbents for this task requires structural knowledge of metal binding environments. Amidoxime polymers have been identified as the most promising platform for large-scale extraction of uranium from seawater. However, despite more than 30 years of research, the uranyl coordination environment on these adsorbents has not been positively identified. We report the first XAFS investigation of polyamidoxime-bound uranyl, with EXAFS fits suggesting a cooperative chelating model, rather than the tridentate or η2 motifs proposed by small molecule and computationalmore » studies. Samples exposed to environmental seawater also display a feature consistent with a μ2-oxo-bridged transition metal in the uranyl coordination sphere, suggesting in situ formation of a specific binding site or mineralization of uranium on the polymer surface. These unexpected findings challenge several long-held assumptions and have significant implications for development of polymer adsorbents with high selectivity.« less

  11. Computational screening of large molecule adsorption by metal-organic frameworks.

    SciTech Connect (OSTI)

    Allendorf, Mark D.; Greathouse, Jeffery A.

    2010-04-01

    Grand canonical Monte Carlo simulations were performed to investigate trends in low-pressure adsorption of a broad range of organic molecules by a set of metal-organic frameworks (MOFs). The organic analytes considered here are relevant to applications in chemical detection: small aromatics (o-, m-, and p-xylene), polycyclic aromatic hydrocarbons (naphthalene, anthracene, phenanthrene), explosives (TNT and RDX), and chemical warfare agents (GA and VM). The framework materials included several Zn-MOFs (IRMOFs 1-3, 7, 8), a Cr-MOF (CrMIL-53lp), and a Cu-MOF (HKUST-1). Many of the larger organics were significantly adsorbed by the target MOFs at low pressure, which is consistent with the exceptionally high isosteric heats of adsorption (25 kcal/mol - 60 kcal/mol) for this range of analyte. At a higher loading pressure of 101 kPa, the Zn-MOFs show a much higher volumetric uptake than either CrMIL-53-lp or HKUST-1 for all types of analyte. Within the Zn-MOF series, analyte loading is proportional to free volume, and loading decreases with increasing analyte size due to molecular packing effects. CrMIL-53lp showed the highest adsorption energy for all analytes, suggesting that this material may be suitable for low-level detection of organics.

  12. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

    SciTech Connect (OSTI)

    Nikiforov, Alexander; Gamez, Jose A.; Thiel, Walter; Huix-Rotllant, Miquel; Filatov, Michael

    2014-09-28

    Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.

  13. FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein...

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

    FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein Structure Data Taken at ALS FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein Structure Data...

  14. Resisting Resistance: Developing New Drugs to Combat Antibiotic Resistant

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

    Bacteria - Grover Waldrop, Department of Biological Sciences Resisting Resistance: Developing New Drugs to Combat Antibiotic Resistant Bacteria Grover Waldrop, Department of Biological Sciences As the problem of antibiotic resistant pathogenic bacteria steadily worsens there remains an urgent need to develop new antibiotics and new targets for antibiotics. Dr. Grover Waldrop, LSU Department of Biological Sciences, is working with a new target for antibiotics the enzyme acetyl-CoA

  15. Artificial Cells for Advanced Drug Delivery - Energy Innovation Portal

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

    Biomass and Biofuels Biomass and Biofuels Find More Like This Return to Search Artificial Cells for Advanced Drug Delivery Colorado School of Mines Contact CSM About This Technology Technology Marketing SummaryThis invention takes advantage of the unique surface chemistry of a ZnO crystalline nanostructure to catalyze a variety of chemical reactions. DescriptionOne such reaction is the hydrogenation of carbon dioxide to methanol. Alcohols interacts both molecularly and dissociatively with the

  16. Harnessing Molecule-solid Duality of Nanoclusters/nanoparticles for Nanoscale Control of Size Shape and Alloying

    SciTech Connect (OSTI)

    J Yin; P Hu; B Wanjala; O Malis; C Zhong

    2011-12-31

    This report demonstrates a molecule-solid duality concept for nanoscale control of size, shape and alloying by showing novel evolution of binary copper and gold nanoclusters or nanoparticles towards alloy nanocubes, as evidenced by in situ real time synchrotron X-ray diffraction characterization.

  17. Photo-assisted intersystem crossing: The predominant triplet formation mechanism in some isolated polycyclic aromatic molecules excited with pulsed lasers

    SciTech Connect (OSTI)

    Johnson, Philip M.; Sears, Trevor J.

    2015-07-28

    Naphthalene, anthracene, and phenanthrene are shown to have very long-lived triplet lifetimes when the isolated molecules are excited with nanosecond pulsed lasers resonant with the lowest singlet state. For naphthalene, triplet state populations are created only during the laser pulse, excluding the possibility of normal intersystem crossing at the one photon level, and all molecules have triplet lifetimes greater than hundreds of microseconds, similar to the behavior previously reported for phenylacetylene. Although containing 7–12 thousand cm⁻¹ of vibrational energy, the triplet molecules have ionization thresholds appropriate to vibrationless T₁ states. The laser power dependences (slopes of log-log power plots) of the excited singlet and triplet populations are about 0.7 for naphthalene and about 0.5 for anthracene. Kinetic modeling of the power dependences successfully reproduces the experimental results and suggests that the triplet formation mechanism involves an enhanced spin orbit coupling caused by sigma character in states at the 2-photon level. Symmetry Adapted Cluster-Configuration Interaction calculations produced excited state absorption spectra to provide guidance for estimating kinetic rates and the sigma character present in higher electronic states. It is concluded that higher excited state populations are significant when larger molecules are excited with pulsed lasers and need to be taken into account whenever discussing the molecular photodynamics.

  18. Photoluminescence Enhancement in CdSe/ZnS–DNA linked–Au Nanoparticle Heterodimers Probed by Single Molecule Spectroscopy

    SciTech Connect (OSTI)

    Cotlet, M.; Maye, M.M.; Gang, O.

    2010-07-26

    Photoluminescence enhancement of up to 20 fold is demonstrated at the single molecule level for heterodimers composed of a core/shell CdSe/ZnS semiconductive quantum dot and a gold nanoparticle of 60 nm size separated by a 32 nm-long dsDNA linker when employing optical excitation at wavelengths near the surface plasmon resonance of the gold nanoparticle.

  19. Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Leo Holberg and Allen Mills

    ScienceCinema (OSTI)

    Holberg, Leo; Mills, Allen [NIST

    2011-04-28

    Leo Holberg and Allen Mills present a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

  20. Integration of biological ion channels onto optically addressable micro-fluidic electrode arrays for single molecule characterization.

    SciTech Connect (OSTI)

    Brozik, Susan Marie; Frink, Laura J. Douglas; Bachand, George David; Keller, David J.; Patrick, Elizabeth L.; Marshall, Jason A.; Ortiz, Theodore P.; Meyer, Lauren A.; Davis, Ryan W.; Brozik, James A.; Flemming, Jeb Hunter

    2004-12-01

    The challenge of modeling the organization and function of biological membranes on a solid support has received considerable attention in recent years, primarily driven by potential applications in biosensor design. Affinity-based biosensors show great promise for extremely sensitive detection of BW agents and toxins. Receptor molecules have been successfully incorporated into phospholipid bilayers supported on sensing platforms. However, a collective body of data detailing a mechanistic understanding of membrane processes involved in receptor-substrate interactions and the competition between localized perturbations and delocalized responses resulting in reorganization of transmembrane protein structure, has yet to be produced. This report describes a systematic procedure to develop detailed correlation between (recognition-induced) protein restructuring and function of a ligand gated ion channel by combining single molecule fluorescence spectroscopy and single channel current recordings. This document is divided into three sections: (1) reported are the thermodynamics and diffusion properties of gramicidin using single molecule fluorescence imaging and (2) preliminary work on the 5HT{sub 3} serotonin receptor. Thirdly, we describe the design and fabrication of a miniaturized platform using the concepts of these two technologies (spectroscopic and single channel electrochemical techniques) for single molecule analysis, with a longer term goal of using the physical and electronic changes caused by a specific molecular recognition event as a transduction pathway in affinity based biosensors for biotoxin detection.

  1. Theoretical and experimental quantification of doubly and singly differential cross sections for electron-induced ionization of isolated tetrahydrofuran molecules

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

    Champion, Christophe; Quinto, Michele A.; Bug, Marion U.; Baek, Woon Y.; Weck, Philippe F.

    2014-07-29

    Electron-induced ionization of the commonly used surrogate of the DNA sugar-phosphate backbone, namely, the tetrahydrofuran molecule, is here theoretically described within the 1st Born approximation by means of quantum-mechanical approach. Comparisons between theory and recent experiments are reported in terms of doubly and singly differential cross sections.

  2. Photo-assisted intersystem crossing: The predominant triplet formation mechanism in some isolated polycyclic aromatic molecules excited with pulsed lasers

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

    Johnson, Philip M.; Sears, Trevor J.

    2015-07-28

    Naphthalene, anthracene, and phenanthrene are shown to have very long-lived triplet lifetimes when the isolated molecules are excited with nanosecond pulsed lasers resonant with the lowest singlet state. For naphthalene, triplet state populations are created only during the laser pulse, excluding the possibility of normal intersystem crossing at the one photon level, and all molecules have triplet lifetimes greater than hundreds of microseconds, similar to the behavior previously reported for phenylacetylene. Although containing 7–12 thousand cm⁻¹ of vibrational energy, the triplet molecules have ionization thresholds appropriate to vibrationless T₁ states. The laser power dependences (slopes of log-log power plots) ofmore » the excited singlet and triplet populations are about 0.7 for naphthalene and about 0.5 for anthracene. Kinetic modeling of the power dependences successfully reproduces the experimental results and suggests that the triplet formation mechanism involves an enhanced spin orbit coupling caused by sigma character in states at the 2-photon level. Symmetry Adapted Cluster-Configuration Interaction calculations produced excited state absorption spectra to provide guidance for estimating kinetic rates and the sigma character present in higher electronic states. It is concluded that higher excited state populations are significant when larger molecules are excited with pulsed lasers and need to be taken into account whenever discussing the molecular photodynamics.« less

  3. Food and Drug Administration White Oak Campus Environmental Stewardship and Cost Savings

    Broader source: Energy.gov [DOE]

    FEMP ESPC Success Story on water conservation and green energy at the Food and Drug Administration (FDA) White Oak Campus.

  4. Observation of cold Rb{sub 2} molecules trapped in an optical dipole trap using a laser-pulse-train technique

    SciTech Connect (OSTI)

    Menegatti, Carlos R.; Marangoni, Bruno S.; Marcassa, Luis G.

    2011-11-15

    In this work, we have developed and characterized a laser-pulse-train technique to observe cold Rb{sub 2} molecules trapped in an optical dipole trap. The molecules are produced in a magneto-optical trap, and then loaded into a crossed optical dipole trap. The time evolution of the molecular population is obtained by applying a laser pulse train, which photoionizes the ground-state molecules through intermediate molecular bands. Our results show that this technique allows us to obtain a faster data acquisition rate of the time evolution of the molecule population than other techniques.

  5. Size-dependent fluorescence of bioaerosols: Mathematical model using fluorescing and absorbing molecules in bacteria

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

    Hill, Steven C.; Williamson, Chatt C.; Doughty, David C.; Pan, Yong-Le; Santarpia, Joshua L.; Hill, Hanna H.

    2015-02-02

    This paper uses a mathematical model of fluorescent biological particles composed of bacteria and/or proteins (mostly as in Hill et al., 2013 [23]) to investigate the size-dependence of the total fluorescence emitted in all directions. The model applies to particles which have negligible reabsorption of fluorescence within the particle. The specific particles modeled here are composed of ovalbumin and of a generic Bacillus. The particles need not be spherical, and in some cases need not be homogeneous. However, the results calculated in this paper are for spherical homogeneous particles. Light absorbing and fluorescing molecules included in the model are aminomore » acids, nucleic acids, and several coenzymes. Here the excitation wavelength is 266 nm. The emission range, 300 to 370 nm, encompasses the fluorescence of tryptophan. The fluorescence cross section (CF) is calculated and compared with one set of published measured values. We investigate power law (Ady) approximations to CF, where d is diameter, and A and y are parameters adjusted to fit the data, and examine how y varies with d and composition, including the fraction as water. The particle's fluorescence efficiency (QF=CF/geometric-cross-section) can be written for homogeneous particles as QabsRF, where Qabs is the absorption efficiency, and RF, the fraction of the absorbed light emitted as fluorescence, is independent of size and shape. When QF is plotted vs. mid or mi(mr-1)d, where m=mr+imi is the complex refractive index, the plots for different fractions of water in the particle tend to overlap.« less

  6. Solvation of molecules in superfluid helium enhances the “interaction induced localization” effect

    SciTech Connect (OSTI)

    Walewski, ?ukasz Forbert, Harald; Marx, Dominik

    2014-04-14

    Atomic nuclei become delocalized at low temperatures as a result of quantum effects, whereas they are point-like in the high temperature (classical) limit. For non-interacting nuclei, the delocalization upon lowering the temperature is quantitatively described in terms of the thermal de Broglie wavelength of free particles. Clearly, light non-interacting nuclei – the proton being a prominent one – are much more delocalized at low temperatures compared to heavy nuclei, such as non-interacting oxygen having water in mind. However, strong interactions due to chemical bonding in conjunction with ultra-low temperatures characteristic to superfluid helium nanodroplets change this common picture substantially for nuclei in molecules or clusters. It turns out that protons shared in hydrogen bonds undergo an extreme “interaction induced localization” at temperatures on the order of 1 K, which compresses the protonic spatial distributions to the size of the much heavier donor or acceptor atoms, such as O or Cl nuclei, corresponding to about 0.1% of the volume occupied by a non-interacting proton at the same temperature. Moreover, applying our recently developed hybrid ab initio path integral molecular dynamics/bosonic path integral Monte Carlo quantum simulation technique to a HCl/water cluster, HCl(H{sub 2}O){sub 4}, we find that helium solvation has a significant additional localizing effect of up to about 30% in volume. In particular, the solvent-induced excess localization is the stronger the lesser the given nucleus is already localized in the gas phase reference situation.

  7. Chromosomal Rainbows detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors

    SciTech Connect (OSTI)

    O'Brien, Benjamin; Jossart, Gregg H.; Ito, Yuko; Greulich-Bode, Karin M.; Weier, Jingly F.; Munne, Santiago; Clark, Orlo H.; Weier, Heinz-Ulrich G.

    2010-08-19

    Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene could be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'-end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners. We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabase-pair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine mapping of breakpoints in papillary thyroid cancer (PTC).

  8. Size-dependent fluorescence of bioaerosols: Mathematical model using fluorescing and absorbing molecules in bacteria

    SciTech Connect (OSTI)

    Hill, Steven C.; Williamson, Chatt C.; Doughty, David C.; Pan, Yong-Le; Santarpia, Joshua L.; Hill, Hanna H.

    2015-02-02

    This paper uses a mathematical model of fluorescent biological particles composed of bacteria and/or proteins (mostly as in Hill et al., 2013 [23]) to investigate the size-dependence of the total fluorescence emitted in all directions. The model applies to particles which have negligible reabsorption of fluorescence within the particle. The specific particles modeled here are composed of ovalbumin and of a generic Bacillus. The particles need not be spherical, and in some cases need not be homogeneous. However, the results calculated in this paper are for spherical homogeneous particles. Light absorbing and fluorescing molecules included in the model are amino acids, nucleic acids, and several coenzymes. Here the excitation wavelength is 266 nm. The emission range, 300 to 370 nm, encompasses the fluorescence of tryptophan. The fluorescence cross section (CF) is calculated and compared with one set of published measured values. We investigate power law (Ady) approximations to CF, where d is diameter, and A and y are parameters adjusted to fit the data, and examine how y varies with d and composition, including the fraction as water. The particle's fluorescence efficiency (QF=CF/geometric-cross-section) can be written for homogeneous particles as QabsRF, where Qabs is the absorption efficiency, and RF, the fraction of the absorbed light emitted as fluorescence, is independent of size and shape. When QF is plotted vs. mid or mi(mr-1)d, where m=mr+imi is the complex refractive index, the plots for different fractions of water in the particle tend to overlap.

  9. Two-photon Photoemission of Organic Semiconductor Molecules on Ag(111)

    SciTech Connect (OSTI)

    Yang, Aram; Yang, Aram

    2008-05-15

    Angle- and time-resolved two-photon photoemission (2PPE) was used to study systems of organic semiconductors on Ag(111). The 2PPE studies focused on electronic behavior specific to interfaces and ultrathin films. Electron time dynamics and band dispersions were characterized for ultrathin films of a prototypical n-type planar aromatic hydrocarbon, PTCDA, and representatives from a family of p-type oligothiophenes.In PTCDA, electronic behavior was correlated with film morphology and growth modes. Within a fewmonolayers of the interface, image potential states and a LUMO+1 state were detected. The degree to which the LUMO+1 state exhibited a band mass less than a free electron mass depended on the crystallinity of the layer. Similarly, image potential states were measured to have free electron-like effective masses on ordered surfaces, and the effective masses increased with disorder within the thin film. Electron lifetimes were correlated with film growth modes, such that the lifetimes of electrons excited into systems created by layer-by-layer, amorphous film growth increased by orders of magnitude by only a few monolayers from the surface. Conversely, the decay dynamics of electrons in Stranski-Krastanov systems were limited by interaction with the exposed wetting layer, which limited the barrier to decay back into the metal.Oligothiophenes including monothiophene, quaterthiophene, and sexithiophene were deposited on Ag(111), and their electronic energy levels and effective masses were studied as a function of oligothiophene length. The energy gap between HOMO and LUMO decreased with increasing chain length, but effective mass was found to depend on domains from high- or low-temperature growth conditions rather than chain length. In addition, the geometry of the molecule on the surface, e.g., tilted or planar, substantially affected the electronic structure.

  10. Water-soluble carbon nanotube compositions for drug delivery and medicinal applications

    DOE Patents [OSTI]

    Tour, James M.; Lucente-Schultz, Rebecca; Leonard, Ashley; Kosynkin, Dmitry V.; Price, Brandi Katherine; Hudson, Jared L.; Conyers, Jr., Jodie L.; Moore, Valerie C.; Casscells, S. Ward; Myers, Jeffrey N.; Milas, Zvonimir L.; Mason, Kathy A.; Milas, Luka

    2014-07-22

    Compositions comprising a plurality of functionalized carbon nanotubes and at least one type of payload molecule are provided herein. The compositions are soluble in water and PBS in some embodiments. In certain embodiments, the payload molecules are insoluble in water. Methods are described for making the compositions and administering the compositions. An extended release formulation for paclitaxel utilizing functionalized carbon nanotubes is also described.

  11. The influence of field-free orientation on the predissociation dynamics of the NaI molecule

    SciTech Connect (OSTI)

    Zhao, Ze-Yu; Han, Yong-Chang, E-mail: ychan@dlut.edu.cn; Yu, Jie; Cong, Shu-Lin [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China)] [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China)

    2014-01-28

    The orientation and predissociation dynamics of the NaI molecule are studied by using a time-dependent wavepacket method. The NaI molecule is first pre-oriented by a single-cycle pulse (SCP) in terahertz (THz) region and then predissociated by a femtosecond pump pulse. The influence of the molecular field-free orientation on the predissociation dynamics is studied in detail. We calculate the radial and angular distributions, the molecular orientation degrees, and the time-dependent populations for both the ground and excited electronic states. It is found that the pre-orientation affects the angular distributions significantly, and that it has weak influence on the radial distributions. By varying the delay time between the THz SCP and the pump pulse, the angular distribution of the fragments from the predissociation can be manipulated.

  12. Features of the spectral dependences of transmittance of organic semiconductors based on tert-butyl substituted lutetium phthalocyanine molecules

    SciTech Connect (OSTI)

    Belogorokhov, I. A.; Tikhonov, E. V.; Dronov, M. A.; Belogorokhova, L. I.; Ryabchikov, Yu. V.; Tomilova, L. G.; Khokhlov, D. R.

    2011-11-15

    Vibronic properties of organic semiconductors based on tert-butyl substituted phthalocyanine lutetium diphthalocyanine molecules are studied by IR and Raman spectroscopy. It is shown that substitution of several carbon atoms in initial phthalocyanine (Pc) ligands with {sup 13}C isotope atoms causes a spectral shift in the main absorption lines attributed to benzene, isoindol, and peripheral C-H groups. A comparison of spectral characteristics showed that the shift can vary from 3 to 1 cm{sup -1}.

  13. Fuel Synthesis Catalysis Laboratory: Catalytic Testing for Thermochemical Transformations of Molecules (Fact Sheet), NREL (National Renewable Energy Laboratory)

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

    Synthesis Catalysis Laboratory Catalytic testing for thermochemical transformations of molecules NREL is a national laboratory of the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, operated by the Alliance for Sustainable Energy, LLC. NREL's Fuel Synthesis Catalysis Laboratory (FSCL) provides a wide range of capabilities in heterogeneous catalyst testing. Current research areas of emphasis include the transformation of biomass pyrolysis and gasification products to

  14. Gas Phase Reactions between Fuel Molecules and Halogens: A Review of the Reaction between Atomic Chlorine and Ammonia

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

    Steven Ewa Xuefei Tao Jingjing Alecu Mielke Papajak Xu Yu Zheng Annual Report Combustion Energy Frontier Research Center Princeton, NJ Sept. 23, 2010 Truhlar group University of Minnesota Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules * We proposed a new approximation called the multi-structural method with torsional anharmonicity (MS-T) to calculate conformational-vibrational-rotational partition functions. * It is applicable for

  15. Rotational fluctuation of molecules in quantum clusters. II. Molecular rotation and superfluidity in OCS-doped helium-4 clusters

    SciTech Connect (OSTI)

    Miura, Shinichi [Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585 (Japan)

    2007-03-21

    In this paper, quantum fluctuations of a carbonyl sulfide molecule in helium-4 clusters are studied as a function of cluster size N in a small-to-large size regime (2{<=}N{<=}64). The molecular rotation of the dopant shows nonmonotonic size dependence in the range of 10{<=}N{<=}20, reflecting the density distribution of the helium atoms around the molecule. The size dependence on the rotational constant shows a plateau for N{>=}20, which is larger than the experimental nanodroplet value. Superfluid response of the doped cluster is found to show remarkable anisotropy especially for N{<=}20. The superfluid fraction regarding the axis perpendicular to the molecular axis shows a steep increase at N=10, giving the significant enhancement of the rotational fluctuation of the molecule. On the other hand, the superfluid fraction regarding the axis parallel to the molecular axis reaches 0.9 at N=5, arising from the bosonic exchange cycles of the helium atoms around the molecular axis. The anisotropy in the superfluid response is found to be the direct consequence of the configurations of the bosonic exchange cycles.

  16. ELECTRON IRRADIATION OF CARBON DISULFIDE-OXYGEN ICES: TOWARD THE FORMATION OF SULFUR-BEARING MOLECULES IN INTERSTELLAR ICES

    SciTech Connect (OSTI)

    Maity, Surajit; Kaiser, Ralf I. [Department of Chemistry, University of Hawai'i at Manoa, Honolulu, HI 96822 (United States)

    2013-08-20

    The formation of sulfur-bearing molecules in interstellar ices was investigated during the irradiation of carbon disulfide (CS{sub 2})-oxygen (O{sub 2}) ices with energetic electrons at 12 K. The irradiation-induced chemical processing of these ices was monitored online and in situ via Fourier transform infrared spectroscopy to probe the newly formed products quantitatively. The sulfur-bearing molecules produced during the irradiation were sulfur dioxide (SO{sub 2}), sulfur trioxide (SO{sub 3}), and carbonyl sulfide (OCS). Formations of carbon dioxide (CO{sub 2}), carbon monoxide (CO), and ozone (O{sub 3}) were observed as well. To fit the temporal evolution of the newly formed products and to elucidate the underlying reaction pathways, kinetic reaction schemes were developed and numerical sets of rate constants were derived. Our studies suggest that carbon disulfide (CS{sub 2}) can be easily transformed to carbonyl sulfide (OCS) via reactions with suprathermal atomic oxygen (O), which can be released from oxygen-containing precursors such as water (H{sub 2}O), carbon dioxide (CO{sub 2}), and/or methanol (CH{sub 3}OH) upon interaction with ionizing radiation. This investigation corroborates that carbonyl sulfide (OCS) and sulfur dioxide (SO{sub 2}) are the dominant sulfur-bearing molecules in interstellar ices.

  17. On the influence of singlet oxygen molecules on the speed of flame propagation in methane-air mixture

    SciTech Connect (OSTI)

    Starik, A.M.; Kozlov, V.E.; Titova, N.S.

    2010-02-15

    The effect of the presence of singlet oxygen molecules O{sub 2}(a{sup 1}{delta}{sub g}) in a CH{sub 4}-air mixture on the speed of laminar flame propagation is considered. The known experimental data on the laminar flame speed and ignition delay are used to validate the developed kinetic model involving electronically excited oxygen molecules O{sub 2}(a{sup 1}{delta}{sub g}) and O{sub 2}(b{sup 1}{sigma}{sub g}{sup +}). Numerical simulation shows that the presence of 10% O{sub 2}(a{sup 1}{delta}{sub g}) in molecular oxygen enables to increase significantly (by a factor of 1.7) the speed of flame propagation in a fuel-lean ({phi}=0.45) methane-air mixture. The main reason for such an acceleration of flame propagation is the intensification of chain reactions due to addition of singlet delta oxygen molecules. For a fuel-rich mixture ({phi}=1.9), the growth in the flame speed is significantly smaller and attains a factor of 1.4. (author)

  18. Developing new optical imaging techniques for single particle and molecule tracking in live cells

    SciTech Connect (OSTI)

    Sun, Wei

    2010-12-15

    Differential interference contrast (DIC) microscopy is a far-field as well as wide-field optical imaging technique. Since it is non-invasive and requires no sample staining, DIC microscopy is suitable for tracking the motion of target molecules in live cells without interfering their functions. In addition, high numerical aperture objectives and condensers can be used in DIC microscopy. The depth of focus of DIC is shallow, which gives DIC much better optical sectioning ability than those of phase contrast and dark field microscopies. In this work, DIC was utilized to study dynamic biological processes including endocytosis and intracellular transport in live cells. The suitability of DIC microscopy for single particle tracking in live cells was first demonstrated by using DIC to monitor the entire endocytosis process of one mesoporous silica nanoparticle (MSN) into a live mammalian cell. By taking advantage of the optical sectioning ability of DIC, we recorded the depth profile of the MSN during the endocytosis process. The shape change around the nanoparticle due to the formation of a vesicle was also captured. DIC microscopy was further modified that the sample can be illuminated and imaged at two wavelengths simultaneously. By using the new technique, noble metal nanoparticles with different shapes and sizes were selectively imaged. Among all the examined metal nanoparticles, gold nanoparticles in rod shapes were found to be especially useful. Due to their anisotropic optical properties, gold nanorods showed as diffraction-limited spots with disproportionate bright and dark parts that are strongly dependent on their orientation in the 3D space. Gold nanorods were developed as orientation nanoprobes and were successfully used to report the self-rotation of gliding microtubules on kinesin coated substrates. Gold nanorods were further used to study the rotational motions of cargoes during the endocytosis and intracellular transport processes in live mammalian cells. New rotational information was obtained: (1) during endocytosis, cargoes lost their rotation freedom at the late stage of internalization; (2) cargoes performed train-like motion when they were transported along the microtubule network by motor proteins inside live cells; (3) During the pause stage of fast axonal transport, cargoes were still bound to the microtubule tracks by motor proteins. Total internal reflection fluorescence microscopy (TIRFM) is another non-invasive and far-field optical imaging technique. Because of its near-field illumination mechanism, TIRFM has better axial resolution than epi-fluorescence microscopy and confocal microscopy. In this work, an auto-calibrated, prism type, angle-scanning TIRFM instrument was built. The incident angle can range from subcritical angles to nearly 90{sup o}, with an angle interval less than 0.2{sup o}. The angle precision of the new instrument was demonstrated through the finding of the surface plasmon resonance (SPR) angle of metal film coated glass slide. The new instrument improved significantly the precision in determining the axial position. As a result, the best obtained axial resolution was {approx} 8 nm, which is better than current existing instruments similar in function. The instrument was further modified to function as a pseudo TIRF microscope. The illumination depth can be controlled by changing the incident angle of the excitation laser beam or adjusting the horizontal position of the illumination laser spot on the prism top surface. With the new technique, i.e., variable-illumination-depth pseudo TIRF microscopy, the whole cell body from bottom to top was scanned.

  19. Determining the exact number of dye molecules attached to colloidal CdSe/ZnS quantum dots in Förster resonant energy transfer assemblies

    SciTech Connect (OSTI)

    Kaiser, Uwe; Jimenez de Aberasturi, Dorleta; Vázquez-González, Margarita; Carrillo-Carrion, Carolina; Niebling, Tobias; Parak, Wofgang J.; Heimbrodt, Wolfram

    2015-01-14

    Semiconductor quantum dots functionalized with organic dye molecules are important tools for biological sensor applications. Energy transfer between the quantum dot and the attached dyes can be utilized for sensing. Though important, the determination of the real number of dye molecules attached per quantum dot is rather difficult. In this work, a method will be presented to determine the number of ATTO-590 dye molecules attached to CdSe/ZnS quantum dots based on time resolved spectral analysis. The energy transfer from the excited quantum dot to the attached ATTO-590 dye leads to a reduced lifetime of the quantum dot's excitons. The higher the concentration of dye molecules, the shorter the excitonic lifetime becomes. However, the number of dye molecules attached per quantum dot will vary. Therefore, for correctly explaining the decay of the luminescence upon photoexcitation of the quantum dot, it is necessary to take into account the distribution of the number of dyes attached per quantum dot. A Poisson distribution of the ATTO-590 dye molecules not only leads to excellent agreement between experimental and theoretical decay curves but also additionally yields the average number of dye molecules attached per quantum dot. In this way, the number of dyes per quantum dot can be conveniently determined.

  20. Luminescent systems based on the isolation of conjugated PI systems and edge charge compensation with polar molecules on a charged nanostructured surface

    DOE Patents [OSTI]

    Ivanov, Ilia N.; Puretzky, Alexander A.; Zhao, Bin; Geohegan, David B.; Styers-Barnett, David J.; Hu, Hui

    2014-07-15

    A photoluminescent or electroluminescent system and method of making a non-luminescent nanostructured material into such a luminescent system is presented. The method of preparing the luminescent system, generally, comprises the steps of modifying the surface of a nanostructured material to create isolated regions to act as luminescent centers and to create a charge imbalance on the surface; applying more than one polar molecule to the charged surface of the nanostructured material; and orienting the polar molecules to compensate for the charge imbalance on the surface of the nanostructured material. The compensation of the surface charge imbalance by the polar molecules allows the isolated regions to exhibit luminescence.

  1. Fact Sheet on the Consequences of a Positive Drug Test | Department of

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

    Energy Fact Sheet on the Consequences of a Positive Drug Test Fact Sheet on the Consequences of a Positive Drug Test FACT SHEET ON THE CONSEQUENCES OF A POSITIVE DRUG TEST The Secretary has determined that applicants for, and holders of, a DOE "Q" or "L" access authorization (security clearance) will be in Testing Designated Positions (TDP) as specified in DOE Order 3792.3, Drug-Free Federal Workplace Testing Implementation Program, for federal employees, and Title 10

  2. Reporting Prescription Drugs, Over-the-Counter Medications, and Dietary Supplements

    SciTech Connect (OSTI)

    Center for Human Reliability Studies

    2008-02-01

    Overview of types of prescription drugs and over-the-counter medications that must be reported in DOE's Human Reliability Program.

  3. Re-Defining Photovoltaic Efficiency Through Molecule Scale Control. Final Report

    SciTech Connect (OSTI)

    Yardley, James T.

    2015-04-30

    The direct conversion of sunlight into electricity represents one of the most important general means for sustainable energy production. Most modern photovoltaic cells are based on some form of semiconductor material such as silicon that is described by a characteristic energy or ''bandgap''. For solar rays with photon energy lower than the bandgap no absorption occurs and thus no energy is generated. For solar rays with photon energy greater than the bandgap, light may be absorbed to create a pair of electrical charges but only one bandgap of energy is created, leaving any additional energy lost as heat. Thus low bandgap materials can use a great part of the spectrum but can lose much of that energy; high bandgap materials fail to capture much of the spectrum. Thus there is a limit to the efficiency of such a solar cell that turns out to be about 32%. This limit is known as the Shockely-Queisser Limit. The Columbia EFRC program is dedicated to exploration of concepts that in principle can provide for efficiencies beyond this limit. One concept that this EFRC has explored for enhancing the efficiency of solar photovoltaic cells is called “Singlet Fission.” In this concept the absorption of light rays with photon energy at least twice the value of the basic bandgap for the system can produce two pairs of electrical charge carriers. If properly implemented this in principle can significantly reduce the energy lost as heat and give rise to solar cell efficiencies greater than the Shockley-Queisser limit. The problem is that there are virtually no materials that can undergo this process effectively. We have developed new materials that have demonstrated singlet fission efficiencies of almost 100%. We understand how these materials work and we have learned how to design many more systems in the future. So far we have only demonstrated the basic capability for efficient singlet fission. Much more work will be required to design and engineer specific materials that can be used practically in a solar cell system. In addition much work will be required to envision and demonstrate effective device structures that can utilize this concept. However these discoveries do provide the basis for an entirely new set of opportunities for more efficient solar energy generation moving beyond the Shockley-Queisser limit. A second part of the EFRC research program has been to investigate the material and device properties of an entirely new set of materials based on two-dimensional sheets (“ultra-thin”) with thicknesses of only one atom, or a single molecule or just a few atoms. These materials can exhibit conducting, insulating, and semiconducting character and thus they can form the basis for entirely new types of electrical devices. Recent fundamental investigations of these materials, at Columbia and elsewhere, demonstrate clearly that the flow of electrical charges in these systems is fundamentally different from the nature of electrical current flow in conventional materials. This fact presents many possibilities for new photovoltaic device concepts. The EFRC research team has achieved world leadership in the creation and understanding of these materials and in developing the fabrication techniques necessary to create useful devices from them. We have developed the basic fabrication methodology to build structures of these materials into complex device structures, layer by layer. Our EFRC research team has pioneered the synthesis and understanding for graphene, perhaps the simplest of these materials. Graphene can function as a highly transparent conducting material, capable of funneling an electrical charge over reasonable distances without significant energy loss. The EFRC program has also pioneered the development of ultra-thin sheets that function in a way analogous to semiconductor materials as well as sheets that act as electrical insulators. These developments therefore enable the construction of solar cells based on totally different physics from conventional cells. Because the electrons in these ultra-thin sheets interact strongly they will exhibit behaviors quite different from conventional materials with potential to operate at efficiencies beyond the Shockley-Queisser limit. In our EFRC program we have laid out many of the fundamental properties of these materials including the development of unique fabrication techniques. We discovered several new effects that demonstrate strong electron coupling. We have demonstrated the first solar cell that can actually generate electrical power at a high basic efficiency from these fundamentally new materials. There is much more science and technology required before these devices can become practical, but there is also very strong activity worldwide to build electronic devices from these materials, thus providing infrastructure and technical capability to develop these concepts.

  4. Discovery of Small Molecule Isozyme Non-specific Inhibitors of Mammalian Acetyl-CoA Carboxylase 1 and 2

    SciTech Connect (OSTI)

    Corbett, J.; Freeman-Cook, K; Elliott, R; Vajdos, F; Rajamohan, F; Kohls, D; Marr, E; Harwood Jr., H; Esler, W; et al.

    2010-01-01

    Screening Pfizer's compound library resulted in the identification of weak acetyl-CoA carboxylase inhibitors, from which were obtained rACC1 CT-domain co-crystal structures. Utilizing HTS hits and structure-based drug discovery, a more rigid inhibitor was designed and led to the discovery of sub-micromolar, spirochromanone non-specific ACC inhibitors. Low nanomolar, non-specific ACC-isozyme inhibitors that exhibited good rat pharmacokinetics were obtained from this chemotype.

  5. DETECTION OF FeCN (X {sup 4}{Delta}{sub i} ) IN IRC+10216: A NEW INTERSTELLAR MOLECULE

    SciTech Connect (OSTI)

    Zack, L. N.; Halfen, D. T.; Ziurys, L. M.

    2011-06-01

    A new interstellar molecule, FeCN (X {sup 4}{Delta}{sub i} ), has been detected in the envelope of the carbon-rich asymptotic giant branch star, IRC+10216. This work is the first definitive detection of an iron-bearing molecule in the interstellar medium and is based on newly measured rest frequencies. Eight successive rotational transitions of this linear free radical in the lowest spin ladder, {Omega} = 7/2, were observed at 2 and 3 mm using the Arizona Radio Observatory (ARO) 12 m telescope. Three transitions appear as single, unblended features at the 1-2 mK level and exhibit characteristic IRC+10216 line profiles; one had previously been observed with the IRAM 30 m telescope. Two other transitions are partially blended, but exhibit distinct emission at the FeCN frequencies. The remaining transitions are either completely contaminated, or are too high in energy. Comparison of the ARO and IRAM data suggests a source size for FeCN of {approx}30'' in IRC+10216, indicating an outer shell distribution, as expected for a free radical. The column density derived for FeCN is N{sub tot} = 8.6 x 10{sup 11} cm{sup -2} with a rotational temperature of T{sub rot} = 21 K. The fractional abundance of this molecule is [FeCN]/[H{sub 2}] {approx} 2-7 x 10{sup -10}-comparable to that of MgCN and KCN in IRC+10216. FeCN is likely formed by gas-phase reactions of Fe{sup +} or neutral iron; the latter has a significant gas-phase abundance in the outer shell. The detection of FeCN is further evidence that metal cyanides/isocyanides dominate the chemistry of refractory elements in IRC+10216.

  6. Resonance enhanced multiphoton and single-photon ionization of molecules and molecular fragments. Final report, May 1993--April 1997

    SciTech Connect (OSTI)

    McKoy, V.

    1998-09-01

    Resonance enhanced multiphoton ionization (REMPI) utilizes pulsed laser radiation to prepare a molecule in an excited state via absorption of one or more photons and to subsequently ionize that level before it decays. A remarkable feature of REMPI is that the very narrow bandwidth of laser radiation makes it possible to select a specific rotational level in the initial (ground) state and to prepare the excited state of interest in a single rotational level. Thus, by suitable choice of the excitation step, it is possible to selectively ionize a species that may be present. The key objective of the effort is to carry out quantitative studies of REMPI of molecules and molecular fragments, as well as of single-photon ionization of these species by coherent VUV radiation, in order to provide a robust description of significant spectral features of interest in related experiments and needed insight into the underlying dynamics of these spectra. A major focus of the effort is joint theoretical and experimental studies of these ion rotational distributions which are being widely studied by the zero-kinetic-energy (ZEKE) technique. This technique, which is based on the detection of photoelectrons resulting from pulsed-field ionization of very high Rydberg states lying just below an ion threshold, makes it possible to obtain cation distributions with subwavenumber resolution. The unprecedented resolution of this ZEKE technique is opening up entirely new vistas in studies of photoionization dynamics, ion spectroscopy, and state-selected ion-molecule reactions. Emerging applications built on the ultra-high resolution of this technique include its use for accurate determination of thermochemically important ionization energies, for characterization of ion rovibrational level structure of large organic molecules, of elemental clusters, and of weakly bound molecular complexes, for probing reactive fragments, and for pump-probe photoelectron studies of wavepacket dynamics. This surge of experimental activity in ultra-high resolution studies of molecular photoelectron spectra continues to raise new theoretical challenges and has provided the stimulus for several of the collaborations with experimental groups in North America and Europe.

  7. Reaction Kinetics of Water Molecules with Oxygen Vacancies on Rutile TiO2(110)

    SciTech Connect (OSTI)

    Petrik, Nikolay G.; Kimmel, Gregory A.

    2015-09-16

    The formation of bridging hydroxyls (OHb) via reactions of water molecules with oxygen vacancies (VO) on reduced TiO2(110) surfaces is studied using infrared reflection-absorption spectroscopy (IRAS), electron-stimulated desorption (ESD), and photon-stimulated desorption (PSD). Narrow IRAS peaks at 2737 cm-1 and 3711 cm-1 are observed for stretching vibrations of ODb and OHb on TiO2(110), respectively. IRAS measurements with s- and p-polarized light demonstrate that the bridging hydroxyls are oriented normal to the (110) surface. The IR peaks disappear after the sample is exposed to O2 or annealed in the temperature range of 400 – 600 K (correlating with the temperature at which pairs of OHb’s reform water and then desorb), which is consistent with their identification as bridging hydroxyls. We have studied the kinetics of water reacting with the vacancies by monitoring the formation of bridging hydroxyls (using IRAS) as a function of the annealing temperature for a small amount of water initially dosed on the TiO2(110) at low temperature. Separate experiments have also monitored the loss of water molecules (using water ESD) and vacancies (using the CO photooxidation reaction) due to the reactions of water molecules with the vacancies. All three techniques show that the reaction rate becomes appreciable for T > 150 K and that the reactions largely complete for T > 250 K. The temperature-dependent water-VO reaction kinetics are consistent with a Gaussian distribution of activation energies with Ea = 0.545 eV, ΔEa(FWHM) = 0.125 eV, and a “normal” prefactor, v = 1012 s-1. In contrast, a single activation energy with a physically reasonable prefactor does not fit the data well. Our experimental activation energy is close to theoretical estimates for the diffusion of water molecules along the Ti5c rows on the reduced TiO2(110) surface, which suggests that the diffusion of water controls the water – VO reaction rate.

  8. Final Report on ``Theories of Strong Electron Correlations in Molecules and Solids’’ - DE-FG02-97ER45640

    SciTech Connect (OSTI)

    Cox, Daniel L

    2013-04-15

    The PI led theoretical studies of correlated hybridization in transition metal complexes, compounds, and molecules, and of electron transport in DNA associated with nanoelectronic conformations attached to gold electrodes and in the presence of DNA repair proteins.

  9. Shape resonances in ground-state diatomic molecules: General trends and the example of RbCs

    SciTech Connect (OSTI)

    Londono, B. E.; Mahecha, J. E.; Luc-Koenig, E.; Crubellier, A.

    2010-07-15

    The presence of shape resonances due to tunneling through the centrifugal barrier modifies strongly the dynamics of cold atom scattering. As shown on the example of the ground and lowest triplet electronic states of the {sup 85}Rb{sup 133}Cs molecule, the crucial parameter is, as usual for cold collisions, the scattering length. A general description of shape resonances of diatomic molecules is given from three simple single channel asymptotic models, whose respective performances are discussed. The first model, which consists of a R{sup -6} potential limited at short range by a repulsive wall, positioned to reproduce the s-wave scattering length, accounts satisfactorily for the main system-independent properties of shape resonances. Introduction in the model of energy- and angular-momentum-dependent nodal lines specific to the inner part of the potential greatly improves its efficiency. When the energy and angular momentum dependence of the nodal lines cannot be deduced from full potential calculations or from experiment, a rough, but universal, estimate of these properties is obtained by extending the R{sup -6} behavior of the potential up to the origin.

  10. REACTIVE DESORPTION AND RADIATIVE ASSOCIATION AS POSSIBLE DRIVERS OF COMPLEX MOLECULE FORMATION IN THE COLD INTERSTELLAR MEDIUM

    SciTech Connect (OSTI)

    Vasyunin, A. I.; Herbst, Eric E-mail: eh2ef@virginia.edu

    2013-05-20

    The recent discovery of terrestrial-type organic species such as methyl formate and dimethyl ether in the cold interstellar gas has proved that the formation of organic matter in the Galaxy begins at a much earlier stage of star formation than was previously thought. This discovery represents a challenge for astrochemical modelers. The abundances of these molecules cannot be explained by the previously developed ''warm-up'' scenario, in which organic molecules are formed via diffusive chemistry on surfaces of interstellar grains starting at 30 K, and then released to the gas at higher temperatures during later stages of star formation. In this article, we investigate an alternative scenario in which complex organic species are formed via a sequence of gas-phase reactions between precursor species formed on grain surfaces and then ejected into the gas via efficient reactive desorption, a process in which non-thermal desorption occurs as a result of conversion of the exothermicity of chemical reactions into the ejection of products from the surface. The proposed scenario leads to reasonable if somewhat mixed results at temperatures as low as 10 K and may be considered as a step toward the explanation of abundances of terrestrial-like organic species observed during the earliest stages of star formation.

  11. Long-lived charge carrier generation in ordered films of a covalent perylenediimide–diketopyrrolopyrrole–perylenediimide molecule

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

    Hartnett, Patrick E.; Dyar, Scott M.; Margulies, Eric A.; Shoer, Leah E.; Cook, Andrew W.; Eaton, Samuel W.; Marks, Tobin J.; Wasielewski, Michael R.

    2015-07-31

    The photophysics of a covalently linked perylenediimide–diketopyrrolopyrrole–perylenediimide acceptor–donor–acceptor molecule (PDI–DPP–PDI, 1) were investigated and found to be markedly different in solution versus in unannealed and solvent annealed films. Photoexcitation of 1 in toluene results in quantitative charge separation in τ = 3.1 ± 0.2 ps, with charge recombination in τ = 340 ± 10 ps, while in unannealed/disordered films of 1, charge separation occurs in τ < 250 fs, while charge recombination displays a multiexponential decay in ~6 ns. The absence of long-lived, charge separation in the disordered film suggests that few free charge carriers are generated. In contrast, uponmore » CH₂Cl₂ vapor annealing films of 1, grazing-incidence X-ray scattering shows that the molecules form a more ordered structure. Photoexcitation of the ordered films results in initial formation of a spin-correlated radical ion pair (electron–hole pair) as indicated by magnetic field effects on the formation of free charge carriers which live for ~4 μs. This result has significant implications for the design of organic solar cells based on covalent donor–acceptor systems and shows that long-lived, charge-separated states can be achieved by controlling intramolecular charge separation dynamics in well-ordered systems.« less

  12. Long-lived charge carrier generation in ordered films of a covalent perylenediimide–diketopyrrolopyrrole–perylenediimide molecule

    SciTech Connect (OSTI)

    Hartnett, Patrick E.; Dyar, Scott M.; Margulies, Eric A.; Shoer, Leah E.; Cook, Andrew W.; Eaton, Samuel W.; Marks, Tobin J.; Wasielewski, Michael R.

    2015-07-31

    The photophysics of a covalently linked perylenediimide–diketopyrrolopyrrole–perylenediimide acceptor–donor–acceptor molecule (PDI–DPP–PDI, 1) were investigated and found to be markedly different in solution versus in unannealed and solvent annealed films. Photoexcitation of 1 in toluene results in quantitative charge separation in τ = 3.1 ± 0.2 ps, with charge recombination in τ = 340 ± 10 ps, while in unannealed/disordered films of 1, charge separation occurs in τ < 250 fs, while charge recombination displays a multiexponential decay in ~6 ns. The absence of long-lived, charge separation in the disordered film suggests that few free charge carriers are generated. In contrast, upon CH₂Cl₂ vapor annealing films of 1, grazing-incidence X-ray scattering shows that the molecules form a more ordered structure. Photoexcitation of the ordered films results in initial formation of a spin-correlated radical ion pair (electron–hole pair) as indicated by magnetic field effects on the formation of free charge carriers which live for ~4 μs. This result has significant implications for the design of organic solar cells based on covalent donor–acceptor systems and shows that long-lived, charge-separated states can be achieved by controlling intramolecular charge separation dynamics in well-ordered systems.

  13. Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain

    SciTech Connect (OSTI)

    Mortenson, David E.; Kreitler, Dale F.; Yun, Hyun Gi; Gellman, Samuel H., E-mail: gellman@chem.wisc.edu; Forest, Katrina T., E-mail: gellman@chem.wisc.edu [University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-12-01

    Two structures of a small protein with a defined tertiary fold, the isolated Pin1 WW domain, have been determined via racemic crystallization with small-molecule additives. These additives, which are either racemic or achiral, appear to stabilize a dynamic loop region of the structure. The human Pin1 WW domain is a small autonomously folding protein that has been useful as a model system for biophysical studies of ?-sheet folding. This domain has resisted previous attempts at crystallization for X-ray diffraction studies, perhaps because of intrinsic conformational flexibility that interferes with the formation of a crystal lattice. Here, the crystal structure of the human Pin1 WW domain has been obtained via racemic crystallization in the presence of small-molecule additives. Both enantiomers of a 36-residue variant of the Pin1 WW domain were synthesized chemically, and the l- and d-polypeptides were combined to afford diffracting crystals. The structural data revealed packing interactions of small carboxylic acids, either achiral citrate or a d,l mixture of malic acid, with a mobile loop region of the WW-domain fold. These interactions with solution additives may explain our success in crystallization of this protein racemate. Molecular-dynamics simulations starting from the structure of the Pin1 WW domain suggest that the crystal structure closely resembles the conformation of this domain in solution. The structural data presented here should provide a basis for further studies of this important model system.

  14. Breast cancer drugs dampen vascular functions by interfering with nitric oxide signaling in endothelium

    SciTech Connect (OSTI)

    Gajalakshmi, Palanivel; Priya, Mani Krishna; Pradeep, Thangaraj; Behera, Jyotirmaya; Muthumani, Kandasamy; Madhuwanti, Srinivasan; Saran, Uttara; Chatterjee, Suvro

    2013-06-01

    Widely used chemotherapeutic breast cancer drugs such as Tamoxifen citrate (TC), Capecitabine (CP) and Epirubicin (EP) are known to cause various cardiovascular side-effects among long term cancer survivors. Vascular modulation warrants nitric oxide (NO) signal transduction, which targets the vascular endothelium. We hypothesize that TC, CP and EP interference with the nitric oxide downstream signaling specifically, could lead to cardiovascular dysfunctions. The results demonstrate that while all three drugs attenuate NO and cyclic guanosine mono-phosphate (cGMP) production in endothelial cells, they caused elevated levels of NO in the plasma and RBC. However, PBMC and platelets did not show any significant changes under treatment. This implies that the drug effects are specific to the endothelium. Altered eNOS and phosphorylated eNOS (Ser-1177) localization patterns in endothelial cells were observed following drug treatments. Similarly, the expression of phosphorylated eNOS (Ser-1177) protein was decreased under the treatment of drugs. Altered actin polymerization was also observed following drug treatment, while addition of SpNO and 8Br-cGMP reversed this effect. Incubation with the drugs decreased endothelial cell migration whereas addition of YC-1, SC and 8Br-cGMP recovered the effect. Additionally molecular docking studies showed that all three drugs exhibited a strong binding affinity with the catalytic domain of human sGC. In conclusion, results indicate that TC, CP and EP cause endothelial dysfunctions via the NO–sGC–cGMP pathway and these effects could be recovered using pharmaceutical agonists of NO signaling pathway. Further, the study proposes a combination therapy of chemotherapeutic drugs and cGMP analogs, which would confer protection against chemotherapy mediated vascular dysfunctions in cancer patients. - Highlights: • NO production is reduced in endothelial cells under breast cancer drug treatment. • Cellular cGMP level is decreased under the treatments of breast cancer drugs. • Breast cancer drugs induce vasoconstriction by interfering with NO pathway. • NO donors, cGMP analogs rescue breast cancer drug induced endothelial dysfunctions.

  15. Comparison of light out-coupling enhancements in single-layer blue-phosphorescent organic light emitting diodes using small-molecule or polymer hosts

    SciTech Connect (OSTI)

    Chang, Yung-Ting; Liu, Shun-Wei; Yuan, Chih-Hsien; Lee, Chih-Chien; Ho, Yu-Hsuan; Wei, Pei-Kuen; Chen, Kuan-Yu; Lee, Yi-Ting; Wu, Min-Fei; Chen, Chin-Ti E-mail: chihiwu@cc.ee.ntu.edu.tw; Wu, Chih-I E-mail: chihiwu@cc.ee.ntu.edu.tw

    2013-11-07

    Single-layer blue phosphorescence organic light emitting diodes (OLEDs) with either small-molecule or polymer hosts are fabricated using solution process and the performances of devices with different hosts are investigated. The small-molecule device exhibits luminous efficiency of 14.7?cd/A and maximum power efficiency of 8.39?lm/W, which is the highest among blue phosphorescence OLEDs with single-layer solution process and small molecular hosts. Using the same solution process for all devices, comparison of light out-coupling enhancement, with brightness enhancement film (BEF), between small-molecule and polymer based OLEDs is realized. Due to different dipole orientation and anisotropic refractive index, polymer-based OLEDs would trap less light than small molecule-based OLEDs internally, about 37% better based simulation results. In spite of better electrical and spectroscopic characteristics, including ambipolar characteristics, higher carrier mobility, higher photoluminescence quantum yield, and larger triplet state energy, the overall light out-coupling efficiency of small molecule-based devices is worse than that of polymer-based devices without BEF. However, with BEF for light out-coupling enhancement, the improved ratio in luminous flux and luminous efficiency for small molecule based device is 1.64 and 1.57, respectively, which are significantly better than those of PVK (poly-9-vinylcarbazole) devices. In addition to the theoretical optical simulation, the experimental data also confirm the origins of differential light-outcoupling enhancement. The maximum luminous efficiency and power efficiency are enhanced from 14.7?cd/A and 8.39?lm/W to 23?cd/A and 13.2?lm/W, respectively, with laminated BEF, which are both the highest so far for single-layer solution-process blue phosphorescence OLEDs with small molecule hosts.

  16. Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality

    SciTech Connect (OSTI)

    Brito Silva, C. A. Jr.; Granhen, E. R. [Pos-Graduacao em Engenharia Eletrica, Universidade Federal do Para, 66075-900 Belem, PA (Brazil); Silva, S. J. S. da; Leal, J. F. P. [Pos-Graduacao em Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Del Nero, J. [Departamento de Fisica, Universidade Federal do Para, 66075-110 Belem, PA (Brazil); Divisao de Metrologia de Materiais, Instituto Nacional de Metrologia, Normalizacao e Qualidade Industrial, 25250-020 Duque de Caxias, RJ (Brazil); Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil); Pinheiro, F. A. [Instituto de Fisica, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

    2010-08-15

    We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

  17. EXPERIMENTAL STUDY OF CO{sub 2} FORMATION BY SURFACE REACTIONS OF NON-ENERGETIC OH RADICALS WITH CO MOLECULES

    SciTech Connect (OSTI)

    Oba, Yasuhiro; Watanabe, Naoki; Kouchi, Akira; Hama, Tetsuya; Pirronello, Valerio

    2010-04-01

    Surface reactions between carbon monoxide and non-energetic hydroxyl radicals were carried out at 10 K and 20 K in order to investigate possible reaction pathways to yield carbon dioxide in dense molecular clouds. Hydroxyl radicals, produced by dissociating water molecules in microwave-induced plasma, were cooled down to 100 K prior to the introduction of CO. The abundances of species were monitored in situ using a Fourier transform infrared spectrometer. Formation of CO{sub 2} was clearly observed, even at 10 K, suggesting that reactions of CO with OH proceed with little or no activation barrier. The present results indicate that CO{sub 2} formation, due to reactions between CO and OH, occurs in tandem with H{sub 2}O formation, and this may lead to the formation of CO{sub 2} ice in polar environments, as typically observed in molecular clouds.

  18. Surface-supported Ag islands stabilized by a quantum size effect: Their interaction with small molecules relevant to ethylene epoxidation

    SciTech Connect (OSTI)

    Shao, Dahai

    2013-05-15

    This dissertation focuses on how QSE-stabilized, surface-supported Ag nanoclusters will interact with ethylene or oxygen. Experiments are performed to determine whether the QSE-mediated Ag islands react differently toward adsorption of ethylene or oxygen, or whether the adsorption of these small molecules will affect the QSE-mediated stability of Ag islands. Studies of the interaction of oxygen with Ag/Si(111)-7×7 were previously reported, but these studies were performed at a low Ag coverage where 3D Ag islands were not formed. So the study of such a system at a higher Ag coverage will be a subject of this work. The interaction of ethylene with Ag/Si(111)-7×7, as well as the interaction of oxygen with Ag/NiAl(110) are also important parts of this study.

  19. Effects of polymethylmethacrylate-transfer residues on the growth of organic semiconductor molecules on chemical vapor deposited graphene

    SciTech Connect (OSTI)

    Kratzer, Markus Teichert, Christian; Bayer, Bernhard C.; Kidambi, Piran R.; Matkovi?, Aleksandar; Gaji?, Radoš; Cabrero-Vilatela, Andrea; Weatherup, Robert S.; Hofmann, Stephan

    2015-03-09

    Scalably grown and transferred graphene is a highly promising material for organic electronic applications, but controlled interfacing of graphene thereby remains a key challenge. Here, we study the growth characteristics of the important organic semiconductor molecule para-hexaphenyl (6P) on chemical vapor deposited graphene that has been transferred with polymethylmethacrylate (PMMA) onto oxidized Si wafer supports. A particular focus is on the influence of PMMA residual contamination, which we systematically reduce by H{sub 2} annealing prior to 6P deposition. We find that 6P grows in a flat-lying needle-type morphology, surprisingly independent of the level of PMMA residue and of graphene defects. Wrinkles in the graphene typically act as preferential nucleation centers. Residual PMMA does however limit the length of the resulting 6P needles by restricting molecular diffusion/attachment. We discuss the implications for organic device fabrication, with particular regard to contamination and defect tolerance.

  20. The HD molecule in small and medium cages of clathrate hydrates: Quantum dynamics studied by neutron scattering measurements and computation

    SciTech Connect (OSTI)

    Colognesi, Daniele; Celli, Milva; Ulivi, Lorenzo; Powers, Anna; Xu, Minzhong; Bačić, Zlatko

    2014-10-07

    We report inelastic neutron scattering (INS) measurements on molecular hydrogen deuteride (HD) trapped in binary cubic (sII) and hexagonal (sH) clathrate hydrates, performed at low temperature using two different neutron spectrometers in order to probe both energy and momentum transfer. The INS spectra of binary clathrate samples exhibit a rich structure containing sharp bands arising from both the rotational transitions and the rattling modes of the guest molecule. For the clathrates with sII structure, there is a very good agreement with the rigorous fully quantum simulations which account for the subtle effects of the anisotropy, angular and radial, of the host cage on the HD microscopic dynamics. The sH clathrate sample presents a much greater challenge, due to the uncertainties regarding the crystal structure, which is known only for similar crystals with different promoter, but nor for HD (or H{sub 2}) plus methyl tert-butyl ether (MTBE-d12)

  1. Synthesis and characterization of polylactide/doxorubicin/magnetic nanoparticles composites for drug delivery

    SciTech Connect (OSTI)

    Mhlanga, Nikiwe; Ray, Suprakas Sinha

    2015-05-22

    Magnetic iron oxide nanoparticles have potential to transform conventional therapeutics, through targeted delivery by external magnetic field modulation. Conventional drug delivery lacks specificity; both normal and infected cells are exposed to toxic drugs. Consequently, the toxicity towards healthy cells leads to detrimental side effects which are formidable. However, iron oxide research in biomedicine has been hindered by their lack of stability. This study reports on the stabilization of iron oxide by polylactide (PLA). Besides affording stable iron oxide, PLA is also good for sustained delivery of the drug. PLA/doxorubicin/magnetic nanoparticles (PLA/DOX/MNPs) spheres were synthesized by solvent evaporation method and DOX anticancer drug was encapsulated. The spheres were characterized using scanning electron microscope, Fourier transform infrared microscope, thermogravimetric analyzer and UV-visible spectroscopy, which ascertained formation of the anticipated spheres and incorporation of DOX. In vitro drug release studies were carried out in both phosphate buffer (pH 7.4) and acetate buffer (pH 4.6) and they showed the same trend in both mediums. Drug release kinetics followed Higuchi model, which proved drug release by diffusion via a diffusion gradient.

  2. Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-[alpha

    SciTech Connect (OSTI)

    Carter, Percy H.; Scherle, Peggy A.; Muckelbauer, Jodi K.; Voss, Matthew E.; Liu, Rui-qin; Thompson III, Lorin A.; Xu, Meizhong; Lo, Yvonne C.; Li, Zhong; Strzemienski, Paul; Yang, Gengjie; Falahatpishen, Nikoo; Farrow, Neil A.; Tebben, Andrew J.; Underwood, Denis; Trzaskos, James M.; Friedman, Steven M.; Newton, Robert C.; Decicco, Carl P.

    2010-03-05

    The binding of tumor necrosis factor alpha (TNF-{alpha}) to the type-1 TNF receptor (TNFRc1) plays an important role in inflammation. Despite the clinical success of biologics (antibodies, soluble receptors) for treating TNF-based autoimmune conditions, no potent small molecule antagonists have been developed. Our screening of chemical libraries revealed that N-alkyl 5-arylidene-2-thioxo-1,3-thiazolidin-4-ones were antagonists of this protein-protein interaction. After chemical optimization, we discovered IW927, which potently disrupted the binding of TNF-{alpha} to TNFRc1 (IC{sub 50} = 50 nM) and also blocked TNF-stimulated phosphorylation of I{kappa}-B in Ramos cells (IC{sub 50} = 600 nM). This compound did not bind detectably to the related cytokine receptors TNFRc2 or CD40, and did not display any cytotoxicity at concentrations as high as 100 {micro}M. Detailed evaluation of this and related molecules revealed that compounds in this class are 'photochemically enhanced' inhibitors, in that they bind reversibly to the TNFRc1 with weak affinity (ca. 40-100 mM) and then covalently modify the receptor via a photochemical reaction. We obtained a crystal structure of IV703 (a close analog of IW927) bound to the TNFRc1. This structure clearly revealed that one of the aromatic rings of the inhibitor was covalently linked to the receptor through the main-chain nitrogen of Ala-62, a residue that has already been implicated in the binding of TNF-{alpha} to the TNFRc1. When combined with the fact that our inhibitors are reversible binders in light-excluded conditions, the results of the crystallography provide the basis for the rational design of nonphotoreactive inhibitors of the TNF-{alpha}-TNFRc1 interaction.

  3. Vascular endothelial growth factor-D is a key molecule that enhances lymphatic metastasis of soft tissue sarcomas

    SciTech Connect (OSTI)

    Yanagawa, Takashi; Shinozaki, Tetsuya; Watanabe, Hideomi; Saito, Kenichi; Raz, Avraham; Takagishi, Kenji

    2012-04-15

    Studies on lymph node metastasis of soft tissue sarcomas are insufficient because of its rarity. In this study, we examined the expressions of vascular endothelial growth factor (VEGF)-C and VEGF-D in soft tissue sarcomas metastasized to lymph nodes. In addition, the effects of the two molecules on the barrier function of a lymphatic endothelial cell monolayer against sarcoma cells were analyzed. We examined 7 patients who had soft tissue sarcomas with lymph node metastases and who had undergone neither chemotherapy nor radiotherapy before lymphadenectomy. Immunohistochemistry revealed that 2 of 7 sarcomas that metastasized to lymph nodes expressed VEGF-C both in primary and metastatic lesions. On the other hand, VEGF-D expression was detected in 4 of 7 primary and 7 of 7 metastatic lesions, respectively. Interestingly, 3 cases that showed no VEGF-D expression at primary sites expressed VEGF-D in metastatic lesions. Recombinant VEGF-C at 10{sup -8} and VEGF-D at 10{sup -7}and 10{sup -8} g/ml significantly increased the random motility of lymphatic endothelial cells compared with controls. VEGF-D significantly increased the migration of sarcoma cells through lymphatic endothelial monolayers. The fact that VEGF-D induced the migration of fibrosarcomas through the lymphatic endothelial monolayer is the probable reason for the strong relationship between VEGF-D expression and lymph node metastasis in soft tissue sarcomas. The important propensities of this molecule for the increase of lymph node metastases are not only lymphangiogenesis but also down-regulation of the barrier function of lymphatic endothelial monolayers, which facilitates sarcoma cells entering the lymphatic circulation.

  4. Hepatocyte-based in vitro model for assessment of drug-induced cholestasis

    SciTech Connect (OSTI)

    Chatterjee, Sagnik; Richert, Lysiane; Augustijns, Patrick; Annaert, Pieter

    2014-01-01

    Early detection of drug-induced cholestasis remains a challenge during drug development. We have developed and validated a biorelevant sandwich-cultured hepatocytes- (SCH) based model that can identify compounds causing cholestasis by altering bile acid disposition. Human and rat SCH were exposed (24–48 h) to known cholestatic and/or hepatotoxic compounds, in the presence or in the absence of a concentrated mixture of bile acids (BAs). Urea assay was used to assess (compromised) hepatocyte functionality at the end of the incubations. The cholestatic potential of the compounds was expressed by calculating a drug-induced cholestasis index (DICI), reflecting the relative residual urea formation by hepatocytes co-incubated with BAs and test compound as compared to hepatocytes treated with test compound alone. Compounds with clinical reports of cholestasis, including cyclosporin A, troglitazone, chlorpromazine, bosentan, ticlopidine, ritonavir, and midecamycin showed enhanced toxicity in the presence of BAs (DICI ? 0.8) for at least one of the tested concentrations. In contrast, the in vitro toxicity of compounds causing hepatotoxicity by other mechanisms (including diclofenac, valproic acid, amiodarone and acetaminophen), remained unchanged in the presence of BAs. A safety margin (SM) for drug-induced cholestasis was calculated as the ratio of lowest in vitro concentration for which was DICI ? 0.8, to the reported mean peak therapeutic plasma concentration. SM values obtained in human SCH correlated well with reported % incidence of clinical drug-induced cholestasis, while no correlation was observed in rat SCH. This in vitro model enables early identification of drug candidates causing cholestasis by disturbed BA handling. - Highlights: • Novel in vitro assay to detect drug-induced cholestasis • Rat and human sandwich-cultured hepatocytes (SCH) as in vitro models • Cholestatic compounds sensitize SCH to toxic effects of accumulating bile acids • Drug-induced cholestasis index (DICI) as measure of a drug's cholestatic signature • In vitro findings correlate well with clinical reports on cholestasis.

  5. FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein

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

    Structure Data Taken at ALS FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein Structure Data Taken at ALS FDA Approves Drug for Type 2 Diabetes Invented with Aid of Protein Structure Data Taken at ALS Print Friday, 24 May 2013 13:44 In January 2013, the U.S. Food and Drug Administration approved NESINA for the treatment of type 2 diabetes in adults as an adjunct to diet and exercise. NESINA uses a novel mechanism of action to lower blood glucose levels. A dipeptidyl

  6. Structural and optoelectronic properties of hybrid bulk-heterojunction materials based on conjugated small molecules and mesostructured TiO{sub 2}

    SciTech Connect (OSTI)

    Phan, Hung [Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 (United States); Jahnke, Justin P.; Chmelka, Bradley F. [Department of Chemical Engineering, University of California, Santa Barbara, California 93106 (United States); Nguyen, Thuc-Quyen, E-mail: quyen@chem.ucsb.edu [Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 (United States); Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah (Saudi Arabia)

    2014-06-09

    Improved hybrid bulk-heterojunction materials was fabricated by spin-casting a benchmark conjugated small molecule, namely, 3,6-bis(5-(benzofuran-2-yl)thiophen-2-yl)-2,5-bis(2-ethylhexyl) pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione (DPP(TBFu){sub 2}), into mesostructured TiO{sub 2}. Due to both a reduced molecular size and less hydrophobic nature of the conjugated molecules (relative to conjugated polymers), homogeneous and improved infiltration into the mesoporous TiO{sub 2} are achieved without the need for pre-treatment of the TiO{sub 2}. Remarkably, this small molecule can realize loadings of up to 25% of the total pore volume—2.5× the typical loadings achieved for conjugated polymers. The small molecule loading was determined using dynamic secondary ion mass spectroscopy and absorption spectroscopy. Further characterization such as charge transfer and nanoscale conducting atomic force microscopy helps to demonstrate the promise and viability of small molecule donors for hybrid optoelectronic devices.

  7. Anti-addiction drug ibogaine inhibits voltage-gated ionic currents: A study to assess the drug's cardiac ion channel profile

    SciTech Connect (OSTI)

    Koenig, Xaver; Kovar, Michael; Rubi, Lena; Mike, Agnes K.; Lukacs, Peter; Gawali, Vaibhavkumar S.; Todt, Hannes; Hilber, Karlheinz; Sandtner, Walter

    2013-12-01

    The plant alkaloid ibogaine has promising anti-addictive properties. Albeit not licenced as a therapeutic drug, and despite hints that ibogaine may perturb the heart rhythm, this alkaloid is used to treat drug addicts. We have recently reported that ibogaine inhibits human ERG (hERG) potassium channels at concentrations similar to the drugs affinity for several of its known brain targets. Thereby the drug may disturb the heart's electrophysiology. Here, to assess the drug's cardiac ion channel profile in more detail, we studied the effects of ibogaine and its congener 18-Methoxycoronaridine (18-MC) on various cardiac voltage-gated ion channels. We confirmed that heterologously expressed hERG currents are reduced by ibogaine in low micromolar concentrations. Moreover, at higher concentrations, the drug also reduced human Na{sub v}1.5 sodium and Ca{sub v}1.2 calcium currents. Ion currents were as well reduced by 18-MC, yet with diminished potency. Unexpectedly, although blocking hERG channels, ibogaine did not prolong the action potential (AP) in guinea pig cardiomyocytes at low micromolar concentrations. Higher concentrations (? 10 ?M) even shortened the AP. These findings can be explained by the drug's calcium channel inhibition, which counteracts the AP-prolonging effect generated by hERG blockade. Implementation of ibogaine's inhibitory effects on human ion channels in a computer model of a ventricular cardiomyocyte, on the other hand, suggested that ibogaine does prolong the AP in the human heart. We conclude that therapeutic concentrations of ibogaine have the propensity to prolong the QT interval of the electrocardiogram in humans. In some cases this may lead to cardiac arrhythmias. - Highlights: • We study effects of anti-addiction drug ibogaine on ionic currents in cardiomyocytes. • We assess the cardiac ion channel profile of ibogaine. • Ibogaine inhibits hERG potassium, sodium and calcium channels. • Ibogaine’s effects on ion channels are a potential source of cardiac arrhythmias. • 18-Methoxycoronaridine has a lower affinity for cardiac ion channels than ibogaine.

  8. Laser-activated nano-biomaterials for tissue repair and controlled drug release

    SciTech Connect (OSTI)

    Matteini, P; Ratto, F; Rossi, F; Pini, R

    2014-07-31

    We present recent achievements of minimally invasive welding of biological tissue and controlled drug release based on laser-activated nano-biomaterials. In particular, we consider new advancements in the biomedical application of near-IR absorbing gold nano-chromophores as an original solution for the photothermal repair of surgical incisions and as nanotriggers of controlled drug release from hybrid biopolymer scaffolds. (laser biophotonics)

  9. ORISE Research Participation Programs at the U.S. Food and Drug

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

    Administration Research Participation Programs at the U.S. Food and Drug Administration (FDA) Home About FDA About ORISE Current Research Opportunities Site Map Contact ORISE Facebook Twitter Applicants Current Research Participants Sponsors/Mentors How to Do Business with ORISE search Search Welcome to the ORISE Research Participation Programs at the U.S. Food and Drug Administration (FDA). On this site you will find information about these educational and training programs, designed to

  10. Spontaneous Liver Rupture After Treatment With Drug-Eluting Beads (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Spontaneous Liver Rupture After Treatment With Drug-Eluting Beads Citation Details In-Document Search Title: Spontaneous Liver Rupture After Treatment With Drug-Eluting Beads Spontaneous rupture of hepatocellular carcinoma (HCC) after transcatheter arterial chemoembolization (TACE) is a rare and life-threatening complication. Pathophysiologic mechanisms are not yet fully known; it is suggested that rupture is preceded by reactive tissue edema and intratumerous

  11. ATHENA desktop human "body" could reduce need for animal drug tests

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

    ATHENA could reduce need for animal drug tests ATHENA desktop human "body" could reduce need for animal drug tests ATHENA project team is developing four human organ constructs that are based on a significantly miniaturized platform. March 26, 2014 Los Alamos National Laboratory scientist Rashi Iyer leads the ATHENA organ project. Los Alamos National Laboratory scientist Rashi Iyer leads the ATHENA organ project. Contact Nancy Ambrosiano Communications Office (505) 667-0471 Email

  12. ATHENA desktop human "body" reduces need for animal drug tests

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

    ATHENA desktop human "body" ATHENA desktop human "body" reduces need for animal drug tests ATHENA project team is developing four human organ constructs that are based on a significantly miniaturized platform. December 22, 2014 ATHENA desktop human "body" reduces need for animal drug tests ATHENA project team is developing four human organ constructs that are based on a significantly miniaturized platform. Contact Nancy Ambrosiano Communications Office (505)

  13. Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice

    SciTech Connect (OSTI)

    Deprez-Poulain, Rebecca; Hennuyer, Nathalie; Bosc, Damien; Liang, Wenguang G.; Enée, Emmanuelle; Marechal, Xavier; Charton, Julie; Totobenazara, Jane; Berte, Gonzague; Jahklal, Jouda; Verdelet, Tristan; Dumont, Julie; Dassonneville, Sandrine; Woitrain, Eloise; Gauriot, Marion; Paquet, Charlotte; Duplan, Isabelle; Hermant, Paul; Cantrelle, François- Xavier; Sevin, Emmanuel; Culot, Maxime; Landry, Valerie; Herledan, Adrien; Piveteau, Catherine; Lippens, Guy; Leroux, Florence; Tang, Wei-Jen; van Endert, Peter; Staels, Bart; Deprez, Benoit

    2015-09-23

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer’s disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisingly impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes.

  14. Subunits of highly Fluorescent Protein R-Phycoerythrin as Probes for Cell Imaging and Single-Molecule Detection

    SciTech Connect (OSTI)

    Dragan Isailovic

    2005-12-17

    The purposes of our research were: (1) To characterize subunits of highly fluorescent protein R-Phycoerythrin (R-PE) and check their suitability for single-molecule detection (SMD) and cell imaging, (2) To extend the use of R-PE subunits through design of similar proteins that will be used as probes for microscopy and spectral imaging in a single cell, and (3) To demonstrate a high-throughput spectral imaging method that will rival spectral flow cytometry in the analysis of individual cells. We first demonstrated that R-PE subunits have spectroscopic and structural characteristics that make them suitable for SMD. Subunits were isolated from R-PE by high-performance liquid chromatography (HPLC) and detected as single molecules by total internal reflection fluorescence microscopy (TIRFM). In addition, R-PE subunits and their enzymatic digests were characterized by several separation and detection methods including HPLC, capillary electrophoresis, sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE) and HPLC-electrospray ionization mass spectrometry (ESI-MS). Favorable absorption and fluorescence of the R-PE subunits and digest peptides originate from phycoerythrobilin (PEB) and phycourobilin (PUB) chromophores that are covalently attached to cysteine residues. High absorption coefficients and strong fluorescence (even under denaturing conditions), broad excitation and emission fluorescence spectra in the visible region of electromagnetic spectrum, and relatively low molecular weights make these molecules suitable for use as fluorescence labels of biomolecules and cells. We further designed fluorescent proteins both in vitro and in vivo (in Escherichia coli) based on the highly specific attachment of PEB chromophore to genetically expressed apo-subunits of R-PE. In one example, apo-alpha and apo-beta R-PE subunits were cloned from red algae Polisiphonia boldii (P. boldii), and expressed in E. coli. Although expressed apo-subunits formed inclusion bodies, fluorescent holo-subunits were formed after incubation of E. coli cells with PEB. Spectroscopic characterization of holo-subunits confirmed that the attachment of PEB chromophore to apo-subunits yielded holo-subunits containing both PEB and urobilin (UB). Fluorescence and differential interference contrast (DIC) microscopy showed polar location of holo-subunit inclusion bodies in E. coli cells. In another example, R-PE apo-subunits were genetically fused to cytoplasmic and periplasmic versions of E. coli maltose binding protein (MBP). Fluorescent proteins formed after attachment of PEB to MBP-subunit fusions in vitro and in vivo contained PEB as the sole chromophore, were soluble, and displayed high orange fluorescence. Fluorescence microscopy showed that fusions are located either throughout cells or at cell poles. In addition, cells containing fluorescent holo-subunits or MBP-subunit fusions were up to ten times brighter than control cells as measured by flow cytometry. Results show that the fluorescent proteins formed after non-enzymatic attachment of PEB to R-PE subunit fusions could be used as reporters of gene expression and protein localization in cells as well as fluorescence labels in flow cytometry. Finally, we demonstrated a high-throughput method able to record emission fluorescence spectra of individual cells containing fluorescent proteins. Upon excitation with a 488 mn argon-ion laser many bacterial cells were imaged by a 20X microscope objective while they moved through a capillary tube. Fluorescence was dispersed by a transmission diffraction grating, and an intensified charge-coupled device (ICCD) camera simultaneously recorded the zero and the first orders of the fluorescence from each cell. Single-cell fluorescence spectra were reconstructed from the distance between zero-order and first-order maxima as well as the length and the pixel intensity distribution of the first-order images. By using this approach, the emission spectrum of E. coli cells expressing green fluorescent protein (GFP) was reconstructed. Also, fluorescence spectra of E

  15. Dose critical in-vivo detection of anti-cancer drug levels in blood

    DOE Patents [OSTI]

    Miller, Holly H.; Hirschfeld, deceased, Tomas B.

    1991-01-01

    A method and apparatus are disclosed for the in vivo and in vitro detection and measurement of dose critical levels of DNA-binding anti-cancer drug levels in biological fluids. The apparatus comprises a laser based fiber optic sensor (optrode) which utilizes the secondary interactions between the drug and an intercalating fluorochrome bound to a probe DNA, which in turn is attached to the fiber tip at one end thereof. The other end of the optical fiber is attached to an illumination source, detector and recorder. The fluorescence intensity is measured as a function of the drug concentration and its binding constant to the probe DNA. Anticancer drugs which lend themselves to analysis by the use of the method and the optrode of the present invention include doxorubicin, daunorubicin, carminomycin, aclacinomycin, chlorambucil, cyclophosphamide, methotrexate, 5-uracil, arabinosyl cytosine, mitomycin, cis-platinum 11 diamine dichloride procarbazine, vinblastine vincristine and the like. The present method and device are suitable for the continuous monitoring of the levels of these and other anticancer drugs in biological fluids such as blood, serum, urine and the like. The optrode of the instant invention also enables the measurement of the levels of these drugs from a remote location and from multiple samples.

  16. Cool Magnetic Molecules

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

    ... Underlying the magnetocaloric effect is the idea that magnetism is the result of the ... with the magnetic field, the magnetic entropy (disorder) of the system decreases; if ...

  17. Cool Magnetic Molecules

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

    Conversely, introducing a magnetic field to certain materials will cause the material to heat up. This happens because, as the spins in such (paramagnetic) materials align with...

  18. Roaming Molecule Dynamics

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

    ... Software Computations Uncertainty Quantification Stochastic About CRF Transportation Energy Consortiums Engine Combustion Heavy Duty Heavy Duty Low-Temperature & Diesel Combustion ...

  19. Cool Magnetic Molecules

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

    enhanced magnetic refrigeration at very low temperatures. Not Your Mother's Refrigerator Magnets Some day soon, magnets could do more than clutter up the front of your...

  20. Cool Magnetic Molecules

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

    for applications involving enhanced magnetic refrigeration at very low temperatures. ... In molecular form, "nanomagnets" might just be the key to refrigeration that uses less ...

  1. Cool Magnetic Molecules

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

    (Gd). While some of this research is focused on materials that would operate near room temperature, Karotsis et al. here investigate the magnetic cooling properties of...

  2. Application of quantitative time-lapse imaging (QTLI) for evaluation of Mrp2-based drug–drug interaction induced by liver metabolites

    SciTech Connect (OSTI)

    Nakanishi, Takeo; Ikenaga, Miho; Fukuda, Hajime; Matsunaga, Norikazu; Tamai, Ikumi

    2012-09-01

    We previously reported a quantitative time-lapse imaging (QTLI)-based analysis method to assess drug–drug interactions (DDI) at multidrug resistance-associated protein 2 (Mrp2) in rat sandwich-cultured hepatocyte (SCH) system, utilizing the fluorescent Mrp2 substrate, 5-(and 6)-carboxy-2?,7?-dichlorofluorescein (CDF). Here, we aimed to examine the feasibility of using QTLI to evaluate DDI involving drug metabolite(s) generated in hepatocytes. We used estradiol (E2) and bilirubin as model compounds; both are not substrates of MRP2, whereas their hepatic metabolites, estradiol-17?-glucuronide (E17G) or bilirubin glucuronides, are known to be its substrates as well as inhibitors. When rat SCHs were pre-exposed with E2, fluorescence of CDF accumulated in bile canaliculi decreased depending upon both the duration of pre-exposure and the concentration of extracellular E2. The decrease corresponded with the increase in intracellular concentration of E17G in hepatocytes. Furthermore, cytotoxicity of vinblastine, a substrate of MRP2, was enhanced in SCHs treated with E2. Similarly, CDF accumulated in bile canaliculi was significantly reduced in rat SCHs pre-exposed with bilirubin. In conclusion, these results suggest that phase II biotransformation of a competitor is reflected in alteration of MRP2-mediated CDF transport detected in QTLI. The QTLI might provide a convenient platform to evaluate transporter-based DDIs involving hepatic metabolites of drug candidates without the need to identify the metabolites. -- Highlights: ? Mrp2-mediated CDF transport is inhibited by E2, but not E17G in vesicle study. ? Both E2 and E17G do not compromise CDF formation from CDFDA in hepatocytes. ? CDF accumulation in bile canaliculi is inhibited by E2 or E17G in QTLI. ? Increasing exposure to E2 decreases CDF accumulation in bile canaliculi in QTLI. ? QTLI is feasible to assess Mrp2-based DDI involving drug metabolite in hepatocytes.

  3. Improved production of Br atoms near zero speed by photodissociating laser aligned Br{sub 2} molecules

    SciTech Connect (OSTI)

    Deng, L. Z., E-mail: lzdeng@phy.ecnu.edu.cn; Yin, J. P., E-mail: jpyin@phy.ecnu.edu.cn [State Key Laboratory of Precision Spectroscopy, Department of Physics, East China Normal University, Shanghai 200062 (China)

    2014-10-28

    We theoretically investigated the improvement on the production rate of the decelerated bromine (Br) atoms near zero speed by photodissociating laser aligned Br{sub 2} precursors. Adiabatic alignment of Br{sub 2} precursors exposed to long laser pulses with duration on the order of nanoseconds was investigated by solving the time-dependent Schrödinger equation. The dynamical fragmentation of adiabatically aligned Br{sub 2} precursors was simulated and velocity distribution of the Br atoms produced was analyzed. Our study shows that the larger the degree of the precursor alignment, ?cos{sup 2}???, the higher the production rate of the decelerated Br atoms near zero speed. For Br{sub 2} molecules with an initial rotational temperature of ?1 K, a ?cos{sup 2}??? value of ?0.88 can result in an improvement factor of over ?20 on the production rate of the decelerated Br atoms near zero speed, requiring a laser intensity of only ?1 × 10{sup 12} W/cm{sup 2} for alignment.

  4. Studies of minute quantities of natural abundance molecules using 2D heteronuclear correlation spectroscopy under 100kHz MAS

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

    Nishiyama, Y.; Kobayashi, T.; Malon, M.; Singappuli-Arachchige, D.; Slowing, I. I.; Pruski, M.

    2015-02-16

    Two-dimensional 1H{13C} heteronuclear correlation solid-state NMR spectra of naturally abundant solid materials are presented, acquired using the 0.75-mm magic angle spinning (MAS) probe at spinning rates up to 100 kHz. In spite of the miniscule sample volume (290 nL), high-quality HSQC-type spectra of bulk samples as well as surface-bound molecules can be obtained within hours of experimental time. The experiments are compared with those carried out at 40 kHz MAS using a 1.6-mm probe, which offered higher overall sensitivity due to a larger rotor volume. The benefits of ultrafast MAS in such experiments include superior resolution in 1H dimensionmore » without resorting to 1H–1H homonuclear RF decoupling, easy optimization, and applicability to mass-limited samples. As a result, the HMQC spectra of surface-bound species can be also acquired under 100 kHz MAS, although the dephasing of transverse magnetization has significant effect on the efficiency transfer under MAS alone.« less

  5. Multi-layer Lanczos iteration approach to calculations of vibrational energies and dipole transition intensities for polyatomic molecules

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

    Yu, Hua-Gen

    2015-01-28

    We report a rigorous full dimensional quantum dynamics algorithm, the multi-layer Lanczos method, for computing vibrational energies and dipole transition intensities of polyatomic molecules without any dynamics approximation. The multi-layer Lanczos method is developed by using a few advanced techniques including the guided spectral transform Lanczos method, multi-layer Lanczos iteration approach, recursive residue generation method, and dipole-wavefunction contraction. The quantum molecular Hamiltonian at the total angular momentum J = 0 is represented in a set of orthogonal polyspherical coordinates so that the large amplitude motions of vibrations are naturally described. In particular, the algorithm is general and problem-independent. An applicationmore » is illustrated by calculating the infrared vibrational dipole transition spectrum of CH₄ based on the ab initio T8 potential energy surface of Schwenke and Partridge and the low-order truncated ab initio dipole moment surfaces of Yurchenko and co-workers. A comparison with experiments is made. The algorithm is also applicable for Raman polarizability active spectra.« less

  6. Cell recognition molecule L1 promotes embryonic stem cell differentiation through the regulation of cell surface glycosylation

    SciTech Connect (OSTI)

    Li, Ying; Department of Clinical Laboratory, Second Affiliated Hospital of Dalian Medical University, Dalian 116023 ; Huang, Xiaohua; Department of Clinical Biochemistry, College of Laboratory Medicine, Dalian Medical University, Dalian 116044 ; An, Yue; Ren, Feng; Yang, Zara Zhuyun; Zhu, Hongmei; Zhou, Lei; Department of Anatomy and Developmental Biology, Monash University, Clayton 3800 ; He, Xiaowen; Schachner, Melitta; Xiao, Zhicheng; Department of Anatomy and Developmental Biology, Monash University, Clayton 3800 ; Ma, Keli; Li, Yali; Department of Anatomy, National University of Singapore, Singapore 119078

    2013-10-25

    Highlights: •Down-regulating FUT9 and ST3Gal4 expression blocks L1-induced neuronal differentiation of ESCs. •Up-regulating FUT9 and ST3Gal4 expression in L1-ESCs depends on the activation of PLC?. •L1 promotes ESCs to differentiate into neuron through regulating cell surface glycosylation. -- Abstract: Cell recognition molecule L1 (CD171) plays an important role in neuronal survival, migration, differentiation, neurite outgrowth, myelination, synaptic plasticity and regeneration after injury. Our previous study has demonstrated that overexpressing L1 enhances cell survival and proliferation of mouse embryonic stem cells (ESCs) through promoting the expression of FUT9 and ST3Gal4, which upregulates cell surface sialylation and fucosylation. In the present study, we examined whether sialylation and fucosylation are involved in ESC differentiation through L1 signaling. RNA interference analysis showed that L1 enhanced differentiation of ESCs into neurons through the upregulation of FUT9 and ST3Gal4. Furthermore, blocking the phospholipase C? (PLC?) signaling pathway with either a specific PLC? inhibitor or knockdown PLC? reduced the expression levels of both FUT9 and ST3Gal4 mRNAs and inhibited L1-mediated neuronal differentiation. These results demonstrate that L1 promotes neuronal differentiation from ESCs through the L1-mediated enhancement of FUT9 and ST3Gal4 expression.

  7. A spectroscopic view of internal conversion in a small polyatomic molecule: Sub-Doppler intracavity dye laser spectroscopy of thioformaldehyde

    SciTech Connect (OSTI)

    Clouthier, D.J. (Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055 (United States)); Huang, G.; Merer, A.J. (Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B. C. V6T 1Z1 (Canada))

    1992-08-01

    Intracavity dye laser spectroscopy has been used to obtain sub-Doppler spectra of selected rotational lines in the {ital {tilde A}} {sup 1}{ital A}{sub 2}--{ital {tilde X}} {sup 1}{ital A}{sub 1} 4{sup 1}{sub 0} band of thioformaldehyde with very high resolution and sensitivity. Many of the spectra show extra lines due to perturbations involving high vibrational levels of the ground state. Most of the perturbations observed for {ital K}{sup {prime}}{sub {ital a}} = 0 and 4 are found to correlate well with previous observations of anomalously long single rotational level fluorescence lifetimes and reduced quantum yields (J. Dunlop and D. J. Clouthier, J. Chem. Phys. {bold 93}, 6371 (1990)). {ital S}{sub 1}--{ital S}{sub 0} interaction matrix elements of 0.001--0.006 cm{sup {minus}1} are found for levels involved in simple two level perturbations. The large number of small random perturbations by levels of the ground state is indicative of the first stages of the onset of quantum chaos in a small molecule. Some larger perturbations in the rotational structure are also observed; these are caused by additional local interactions with levels of the nearby triplet state.

  8. Electron correlations and two-photon states in polycyclic aromatic hydrocarbon molecules: A peculiar role of geometry

    SciTech Connect (OSTI)

    Aryanpour, Karan; Shukla, Alok; Mazumdar, Sumit; College of Optical Sciences, University of Arizona, Tucson, Arizona 85721

    2014-03-14

    We present numerical studies of one- and two-photon excited states ordering in a number of polycyclic aromatic hydrocarbon molecules: coronene, hexa-peri-hexabenzocoronene, and circumcoronene, all possessing D{sub 6h} point group symmetry versus ovalene with D{sub 2h} symmetry, within the Pariser-Parr-Pople model of interacting ?-electrons. The calculated energies of the two-photon states as well as their relative two-photon absorption cross-sections within the interacting model are qualitatively different from single-particle descriptions. More remarkably, a peculiar role of molecular geometry is found. The consequence of electron correlations is far stronger for ovalene, where the lowest spin-singlet two-photon state is a quantum superposition of pairs of lowest spin triplet states, as in the linear polyenes. The same is not true for D{sub 6h} group hydrocarbons. Our work indicates significant covalent character, in valence bond language, of the ground state, the lowest spin triplet state and a few of the lowest two-photon states in D{sub 2h} ovalene but not in those with D{sub 6h} symmetry.

  9. Interaction energy and itinerant ferromagnetism in a strongly interacting Fermi gas in the absence of molecule formation

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

    He, Lianyi

    2014-11-26

    In this study, we investigate the interaction energy and the possibility of itinerant ferromagnetism in a strongly interacting Fermi gas at zero temperature in the absence of molecule formation. The interaction energy is obtained by summing the perturbative contributions of Galitskii-Feynman type to all orders in the gas parameter. It can be expressed by a simple phase-space integral of an in-medium scattering phase shift. In both three and two dimensions (3D and 2D), the interaction energy shows a maximum before reaching the resonance from the Bose-Einstein condensate side, which provides a possible explanation of the experimental measurements of the interactionmore » energy. This phenomenon can be theoretically explained by the qualitative change of the nature of the binary interaction in the medium. The appearance of an energy maximum has significant effects on the itinerant ferromagnetism. In 3D, the ferromagnetic transition is reentrant and itinerant ferromagnetism exists in a narrow window around the energy maximum. In 2D, the present theoretical approach suggests that itinerant ferromagnetism does not exist, which reflects the fact that the energy maximum becomes much lower than the energy of the fully polarized state.« less

  10. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    SciTech Connect (OSTI)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France)] [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)] [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  11. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    SciTech Connect (OSTI)

    Dardi, P.S.

    1984-11-01

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

  12. Surface-induced anisotropic orientations of interfacial ethanol molecules at air/sapphire (1-102) and ethanol/sapphire (1-102) interfaces

    SciTech Connect (OSTI)

    Sung, J.; Waychunas, G. A.; Shen, Y. R.

    2011-06-01

    Sum frequency vibrational spectroscopy was used to study the interfacial arrangement of ethanol molecules at the vapor/α-Al{sub 2}O{sub 3} (1{bar 1}02 ) and α-Al{sub 2}O{sub 3} (1{bar 1}02 )/ethanol liquid interfaces. The spectra in the C-H range show that ethanol molecules adsorbed from vapor onto α-Al{sub 2}O{sub 3} (1{bar 1}02 ) surface have a welldefined anisotropic arrangement following the structure of the α-Al{sub 2}O{sub 3} (1{bar 1}02 ) surface. The arrangement can be explained by the formation of two specific hydrogen bonds between the adsorbed ethanol molecule and hydroxyls on the sapphire surface. At the α-Al{sub 2}O{sub 3} (1{bar 1}02 )/ethanol liquid interface, the first ethanol monolayer assumes a similar anisotropic arrangement as in the case of an ethanol monolayer on the dry sapphire surface. The second monolayer has a rather broad orientation distribution that is azimuthally nearly isotropic, but with molecules flipped 180 degrees with respect to those in the first monolayer.

  13. Benchmark atomization energy of ethane : importance of accurate zero-point vibrational energies and diagonal Born-Oppenheimer corrections for a 'simple' organic molecule.

    SciTech Connect (OSTI)

    Karton, A.; Martin, J. M. L.; Ruscic, B.; Chemistry; Weizmann Institute of Science

    2007-06-01

    A benchmark calculation of the atomization energy of the 'simple' organic molecule C2H6 (ethane) has been carried out by means of W4 theory. While the molecule is straightforward in terms of one-particle and n-particle basis set convergence, its large zero-point vibrational energy (and anharmonic correction thereto) and nontrivial diagonal Born-Oppenheimer correction (DBOC) represent interesting challenges. For the W4 set of molecules and C2H6, we show that DBOCs to the total atomization energy are systematically overestimated at the SCF level, and that the correlation correction converges very rapidly with the basis set. Thus, even at the CISD/cc-pVDZ level, useful correlation corrections to the DBOC are obtained. When applying such a correction, overall agreement with experiment was only marginally improved, but a more significant improvement is seen when hydrogen-containing systems are considered in isolation. We conclude that for closed-shell organic molecules, the greatest obstacles to highly accurate computational thermochemistry may not lie in the solution of the clamped-nuclei Schroedinger equation, but rather in the zero-point vibrational energy and the diagonal Born-Oppenheimer correction.

  14. Food and drug reward: overlapping circuits in human obesity and addiction

    SciTech Connect (OSTI)

    Volkow N. D.; Wang G.; Volkow, N.D.; Wang, G.-J.; Fowler, J.S.; Tomasi, D.; Baler, R.

    2012-12-01

    Both drug addiction and obesity can be defined as disorders in which the saliency value of one type of reward (drugs and food, respectively) becomes abnormally enhanced relative to, and at the expense of others. This model is consistent with the fact that both drugs and food have powerful reinforcing effects - partly mediated by dopamine increases in the limbic system - that, under certain circumstances or in vulnerable individuals, could overwhelm the brain's homeostatic control mechanisms. Such parallels have generated significant interest in understanding the shared vulnerabilities and trajectories between addiction and obesity. Now, brain imaging discoveries have started to uncover common features between these two conditions and to delineate some of the overlapping brain circuits whose dysfunctions may explain stereotypic and related behavioral deficits in human subjects. These results suggest that both obese and drug addicted individuals suffer from impairments in dopaminergic pathways that regulate neuronal systems associated not only with reward sensitivity and incentive motivation, but also with conditioning (memory/learning), impulse control (behavioral inhibition), stress reactivity and interoceptive awareness. Here, we integrate findings predominantly derived from positron emission tomography that investigate the role of dopamine in drug addiction and in obesity and propose an updated working model to help identify treatment strategies that may benefit both of these conditions.

  15. Mesoporous Fe{sub 3}O{sub 4}/hydroxyapatite composite for targeted drug delivery

    SciTech Connect (OSTI)

    Gu, Lina; He, Xiaomei; Wu, Zhenyu

    2014-11-15

    Highlights: • Mesoporous Fe{sub 3}O{sub 4}/hydroxyapatite composite was synthesized by a simple, efficient and environmental friendly method. • The prepared material had a large surface area, high pore volume, and good magnetic separability. • DOX-loaded Fe{sub 3}O{sub 4}/hydroxyapatite composite exhibited surprising slow drug release behavior and pH-dependent behavior. - Abstract: In this contribution, we introduced a simple, efficient, and green method of preparing a mesoporous Fe{sub 3}O{sub 4}/hydroxyapatite (HA) composite. The as-prepared material had a large surface area, high pore volume, and good magnetic separability, which made it suitable for targeted drug delivery systems. The chemotherapeutic agent doxorubicin (DOX) was used to investigate the drug release behavior of Fe{sub 3}O{sub 4}/HA composite. The drug release profiles displayed a little burst effect and pH-dependent behavior. The release rate of DOX at pH 5.8 was larger than that at pH 7.4, which could be attributed to DOX protonation in acid medium. In addition, the released DOX concentrations remained at 0.83 and 1.39 ?g/ml at pH 7.4 and 5.8, respectively, which indicated slow, steady, and safe release rates. Therefore, the as-prepared Fe{sub 3}O{sub 4}/hydroxyapatite composite could be an efficient platform for targeted anticancer drug delivery.

  16. ROVIBRATIONAL LINE LISTS FOR NINE ISOTOPOLOGUES OF THE CO MOLECULE IN THE X {sup 1}?{sup +} GROUND ELECTRONIC STATE

    SciTech Connect (OSTI)

    Li, Gang; Gordon, Iouli E.; Rothman, Laurence S. [Harvard-Smithsonian Center for Astrophysics, Atomic and Molecular Physics Division, Cambridge, MA 02138 (United States); Tan, Yan; Hu, Shui-Ming [Hefei National Laboratory for Sciences at Microscale, University of Science and Technology of China, 230026 Hefei (China); Kassi, Samir; Campargue, Alain [Laboratoire Interdisciplinaire de Physique, CNRS UMR 5588, Université Joseph Fourier de Grenoble, B.P. 87, F-38402 Saint-Martin-d'Hères Cedex (France); Medvedev, Emile S., E-mail: igordon@cfa.harvard.edu [The Institute of Problems of Chemical Physics, Russian Academy of Science, Prospect Akademika Semenova 1, 142432 Chernogolovka (Russian Federation)

    2015-01-01

    Extensive rovibrational line lists were computed for nine isotopologues of the CO molecule, namely, {sup 12}C{sup 16}O, {sup 12}C{sup 17}O, {sup 12}C{sup 18}O, {sup 13}C{sup 16}O, {sup 13}C{sup 17}O, {sup 13}C{sup 18}O, {sup 14}C{sup 16}O, {sup 14}C{sup 17}O, and {sup 14}C{sup 18}O in the ground electronic state with v ? 41, ?v ? 11, and J ? 150. The line intensity and position calculations were carried out using a newly determined piece-wise dipole moment function (DMF) in conjunction with the wavefunctions calculated from an experimentally determined potential energy function from Coxon and Hajigeorgiou. A direct-fit method that simultaneously fits all the reliable experimental rovibrational matrix elements has been used to construct the dipole moment function near equilibrium internuclear distance. In order to extend the amount and quality of input experimental parameters, new Cavity Ring Down Spectroscopy experiments were carried out to enable measurements of the lines in the 4-0 band with low uncertainty as well as the first measurements of lines in the 6-0 band. A new high-level ab initio DMF, derived from a finite field approach has been calculated to cover internuclear distances far from equilibrium. Accurate partition sums have been derived for temperatures up to 9000 K. In addition to air- and self-induced broadening and shift parameters, those induced by CO{sub 2} and H{sub 2} are now provided for planetary applications. A complete set of broadening and shift parameters was calculated based on sophisticated extrapolation of high-quality measured data. The line lists, which follow HITRAN formalism, are provided as supplementary material.

  17. Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice

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

    Deprez-Poulain, Rebecca; Hennuyer, Nathalie; Bosc, Damien; Liang, Wenguang G.; Enée, Emmanuelle; Marechal, Xavier; Charton, Julie; Totobenazara, Jane; Berte, Gonzague; Jahklal, Jouda; et al

    2015-09-23

    Insulin-degrading enzyme (IDE) is a protease that cleaves insulin and other bioactive peptides such as amyloid-β. Knockout and genetic studies have linked IDE to Alzheimer’s disease and type-2 diabetes. As the major insulin-degrading protease, IDE is a candidate drug target in diabetes. Here we have used kinetic target-guided synthesis to design the first catalytic site inhibitor of IDE suitable for in vivo studies (BDM44768). Crystallographic and small angle X-ray scattering analyses show that it locks IDE in a closed conformation. Among a panel of metalloproteases, BDM44768 selectively inhibits IDE. Acute treatment of mice with BDM44768 increases insulin signalling and surprisinglymore » impairs glucose tolerance in an IDE-dependent manner. These results confirm that IDE is involved in pathways that modulate short-term glucose homeostasis, but casts doubt on the general usefulness of the inhibition of IDE catalytic activity to treat diabetes.« less

  18. Oral administration of drugs with hypersensitivity potential induces germinal center hyperplasia in secondary lymphoid organ/tissue in Brown Norway rats, and this histological lesion is a promising candidate as a predictive biomarker for drug hypersensitivity occurrence in humans

    SciTech Connect (OSTI)

    Tamura, Akitoshi Miyawaki, Izuru; Yamada, Toru; Kimura, Juki; Funabashi, Hitoshi

    2013-08-15

    It is important to evaluate the potential of drug hypersensitivity as well as other adverse effects during the preclinical stage of the drug development process, but validated methods are not available yet. In the present study we examined whether it would be possible to develop a new predictive model of drug hypersensitivity using Brown Norway (BN) rats. As representative drugs with hypersensitivity potential in humans, phenytoin (PHT), carbamazepine (CBZ), amoxicillin (AMX), and sulfamethoxazole (SMX) were orally administered to BN rats for 28 days to investigate their effects on these animals by examinations including observation of clinical signs, hematology, determination of serum IgE levels, histology, and flow cytometric analysis. Skin rashes were not observed in any animals treated with these drugs. Increases in the number of circulating inflammatory cells and serum IgE level did not necessarily occur in the animals treated with these drugs. However, histological examination revealed that germinal center hyperplasia was commonly induced in secondary lymphoid organs/tissues in the animals treated with these drugs. In cytometric analysis, changes in proportions of lymphocyte subsets were noted in the spleen of the animals treated with PHT or CBZ during the early period of administration. The results indicated that the potential of drug hypersensitivity was identified in BN rat by performing histological examination of secondary lymphoid organs/tissues. Data obtained herein suggested that drugs with hypersensitivity potential in humans gained immune reactivity in BN rat, and the germinal center hyperplasia induced by administration of these drugs may serve as a predictive biomarker for drug hypersensitivity occurrence. - Highlights: • We tested Brown Norway rats as a candidate model for predicting drug hypersensitivity. • The allergic drugs did not induce skin rash, whereas D-penicillamine did so in the rats. • Some of allergic drugs increased inflammatory cells and IgE, but the others did not. • The allergic drugs commonly induced germinal center hyperplasia in lymphoid tissues. • Some of these allergic drugs transiently increased CD4{sup +}CD25{sup +} T cells in the spleen.

  19. Use of supercritical fluid solution expansion processes for drug delivery, particle synthesis, and thin film deposition

    SciTech Connect (OSTI)

    Hybertson, B.M.

    1992-01-01

    Properties of the gases and aerosols resulting from the expansion of supercritical fluid solutions were studied. Film deposition, particle formation, and drug delivery processes using supercritical fluids were developed. Thin films of palladium, copper, aluminum, silver, and silicon dioxide were deposited by a method called supercritical fluid transport-chemical deposition (SFT-CD). In each case, a precursor compound was dissolved in a supercritical fluid and the solution was allowed to expand through a restrictor nozzle into a reaction chamber at subcritical pressure, resulting in the formation of aerosol particles of the precursor. A chemical reaction was induced to occur at the surface of a substrate, resulting in deposition of a thin film. Micron-sized particles of aluminum fluoride and copper oxide were synthesized by a method called supercritical fluid transport-chemical formation of particles (SFT-CFP). The process was similar to that in SFT-CD, but the chemical reactions were induced to occur in the gas phase instead of at a substrate surface, resulting in the formation of fine particles. A new method of pulmonary drug delivery called supercritical fluid drug delivery (SFDD) was conceived and demonstrated. In SFDD a drug compound is dissolved in a supercritical fluid, and the solution is allowed to expand through a restrictor nozzle. The resultant aerosol is directly inhaled by a human or animal subject and the fine drug particles are deposited in the lungs. Menthol, vanillin, camphor, cholesterol, Sudan III, and Oil Blue N were used as model drug compounds for SFDD. Delivery of [alpha]-tocopherol to rat lung tissue was demonstrated, with observed increases of 80-290% above background levels.

  20. SU-F-19A-08: Optimal Time Release Schedule of In-Situ Drug Release During Permanent Prostate Brachytherapy

    SciTech Connect (OSTI)

    Cormack, R; Ngwa, W; Makrigiorgos, G; Tangutoori, S; Rajiv, K; Sridhar, S

    2014-06-15

    Purpose: Permanent prostate brachytherapy spacers can be used to deliver sustained doses of radiosentitizing drug directly to the target, in order to enhance the radiation effect. Implantable nanoplatforms for chemo-radiation therapy (INCeRTs) have a maximum drug capacity and can be engineered to control the drug release schedule. The optimal schedule for sensitization during continuous low dose rate irradiation is unknown. This work studies the optimal release schedule of drug for both traditional sensitizers, and those that work by suppressing DNA repair processes. Methods: Six brachytherapy treatment plans were used to model the anatomy, implant geometry and calculate the spatial distribution of radiation dose and drug concentrations for a range of drug diffusion parameters. Three state partial differential equations (cells healthy, damaged or dead) modeled the effect of continuous radiation (radiosensitivities ?,?) and cellular repair (time tr) on a cell population. Radiosensitization was modeled as concentration dependent change in ?,? or tr which with variable duration under the constraint of fixed total drug release. Average cell kill was used to measure effectiveness. Sensitization by means of both enhanced damage and reduced repair were studied. Results: Optimal release duration is dependent on the concentration of radiosensitizer compared to the saturation concentration (csat) above which additional sensitization does not occur. Long duration drug release when enhancing ? or ? maximizes cell death when drug concentrations are generally over csat. Short term release is optimal for concentrations below saturation. Sensitization by suppressing repair has a similar though less distinct trend that is more affected by the radiation dose distribution. Conclusion: Models of sustained local radiosensitization show potential to increase the effectiveness of radiation in permanent prostate brachytherapy. INCeRTs with high drug capacity produce the greatest benefit with drug release over weeks. If in-vivo drug concentrations are not able to approach saturation concentration, durations of days is optimal. DOD 1R21CA16977501; A. David Mazzone Awards Program 2012PD164.

  1. Arranging Prescription Drug Coverage for Extended Stays (Travel or Long-Term Work Assignments) When Outside the United States

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

    Arranging Prescription Drug Coverage for Extended Stays (Travel or Long-Term Work Assignments) When Outside the United States Planning an extended vacation or working abroad? rx_lanl_override_0311 Maintaining prescription coverage and accessing care for long-term stays abroad What you need to know about override requests and obtaining Rx drugs. Your BCBSNM prescription drug coverage limits override requests to a 90-day supply. Override requests cannot be approved - and are not available -

  2. Novel short antibacterial and antifungal peptides with low cytotoxicit...

    Office of Scientific and Technical Information (OSTI)

    Ning Chen, Wei ; Ming Li, Chang ; Xu, Rong 1 ; Lamrani, Mouad 3 ; Mu, Yuguang, E-mail: ygmu@ntu.edu.sg 2 ; Leong, Susanna Su Jan 1 ; Wook Chang, Matthew, E-mail: ...

  3. A two transition state model for radical-molecule reactions : applications to isomeric branching in the OH-isoprene reaction.

    SciTech Connect (OSTI)

    Greenwald, E. E.; North, S. W.; Georgievskii, Y.; Klippenstein, S. J.; Chemistry; Texas A&M Univ.; SNL

    2007-06-28

    A two transition state model is applied to the prediction of the isomeric branching in the addition of hydroxyl radical to isoprene. The outer transition state is treated with phase space theory fitted to long-range transition state theory calculations on an electrostatic potential energy surface. High-level quantum chemical estimates are applied to the treatment of the inner transition state. A one-dimensional master equation based on an analytic reduction from two-dimensions for a particular statistical assumption about the rotational part of the energy transfer kernel is employed in the calculation of the pressure dependence of the addition process. We find that an accurate treatment of the two separate transition state regions, at the energy and angular momentum resolved level, is essential to the prediction of the temperature dependence of the addition rate. The transition from a dominant outer transition state to a dominant inner transition state is shown to occur at about 275 K, with significant effects from both transition states over the 30-500 K temperature range. Modest adjustments in the ab initio predicted inner saddle point energies yield predictions that are in quantitative agreement with the available high-pressure limit experimental observations and qualitative agreement with those in the falloff regime. The theoretically predicted capture rate is reproduced to within 10% by the expression [1.71 x 10-10(T/298)-2.58 exp(-608.6/RT) + 5.47 x 10-11(T/298)-1.78 exp(-97.3/RT); with R = 1.987 and T in K] cm3 molecule-1 s-1 over the 30-500 K range. A 300 K branching ratio of 0.67:0.02:0.02:0.29 was determined for formation of the four possible OH-isoprene adduct isomers 1, 2, 3, and 4, respectively, and was found to be relatively insensitive to temperature. An Arrhenius activation energy of -0.77 kcal/mol was determined for the high-pressure addition rate constants around 300 K.

  4. Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site

    SciTech Connect (OSTI)

    Yang, Jingsong; Campobasso, Nino; Biju, Mangatt P.; Fisher, Kelly; Pan, Xiao-Qing; Cottom, Josh; Galbraith, Sarah; Ho, Thau; Zhang, Hong; Hong, Xuan; Ward, Paris; Hofmann, Glenn; Siegfried, Brett; Zappacosta, Francesca; Washio, Yoshiaki; Cao, Ping; Qu, Junya; Bertrand, Sophie; Wang, Da-Yuan; Head, Martha S.; Li, Hu; Moores, Sheri; Lai, Zhihong; Johanson, Kyung; Burton, George; Erickson-Miller, Connie; Simpson, Graham; Tummino, Peter; Copeland, Robert A.; Oliff, Allen

    2014-10-02

    c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the {alpha}I helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the {alpha}I helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

  5. Plasmon Mapping in Metallic Nanostructures and its Application to Single Molecule Surface Enhanced Raman Scattering: Imaging Electromagnetic Hot-Spots and Analyte Location

    SciTech Connect (OSTI)

    Camden, Jon P

    2013-07-16

    A major component of this proposal is to elucidate the connection between optical and electron excitation of plasmon modes in metallic nanostructures. These accomplishments are reported: developed a routine protocol for obtaining spatially resolved, low energy EELS spectra, and resonance Rayleigh scattering spectra from the same nanostructures.; correlated optical scattering spectra and plasmon maps obtained using STEM/EELS.; and imaged electromagnetic hot spots responsible for single-molecule surface-enhanced Raman scattering (SMSERS).

  6. Resilience of all-carbon molecules C sub 60 , C sub 70 , and C sub 84 : A surface-scattering time-of-flight investigation

    SciTech Connect (OSTI)

    Beck, R.D.; St. John, P.; Alvarez, M.M.; Diederich, F.; Whetten, R.L. )

    1991-10-17

    Ion beam scattering experiments on the larger carbon molecules (C{sub 60}{sup {plus minus}}, C{sub 70}{sup +} C{sub 80}{sup +}) demonstrate their exceptionally high stability with respect to impact-induced fragmentation processes. The charged molecules are formed by ultraviolet laser desorption of high purity molecular samples into a pulsed helium jet. Extracted ions impact Si(100) or graphite (0001) in a high-resolution ion beam/surface collider with mass time-of-flight and angular analysis. Collisions are highly inelastic processes: a large fraction of the entire perpendicular momentum component is lost, and 60 {plus minus} 20% of the component is either lost or exchanged. No more than 10% of the incident ions are returned, which is attributed to neutralization during the collision event. In contrast to all molecular ions (benzene and naphthalene cations) and cluster (alkali-metal halides), these molecules exhibit no evidence for impact-induced fragmentation, even at impact energies exceeding 200 eV. In the case of C{sub 60}{sup {minus}}, both the intact parent ion and ejected electrons are detected, with the latter becoming dominant above 120 eV impact energy. C{sub 60}{sup +} is found to have an exceptionally low energy threshold for inducing sputtering processes of adsorbed overlayers on graphite. Some of these results may be interpretable in terms of the unique structural-energetic characteristics of the fullerene family. The results are compared to recent computer simulations of the impact event, which predict high resilience for these molecules.

  7. NADPH oxidase and lipid raft-associated redox signaling are required for PCB153-induced upregulation of cell adhesion molecules in human brain endothelial cells

    SciTech Connect (OSTI)

    Eum, Sung Yong Andras, Ibolya; Hennig, Bernhard; Toborek, Michal

    2009-10-15

    Exposure to persistent organic pollutants, such as polychlorinated biphenyls (PCBs), can lead to chronic inflammation and the development of vascular diseases. Because cell adhesion molecules (CAMs) of the cerebrovascular endothelium regulate infiltration of inflammatory cells into the brain, we have explored the molecular mechanisms by which ortho-substituted polychlorinated biphenyls (PCBs), such as PCB153, can upregulate CAMs in brain endothelial cells. Exposure to PCB153 increased expression of intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1), as well as elevated adhesion of leukocytes to brain endothelial cells. These effects were impeded by inhibitors of EGFR, JAKs, or Src activity. In addition, pharmacological inhibition of NADPH oxidase or disruption of lipid rafts by cholesterol depleting agents blocked PCB153-induced phosphorylation of JAK and Src kinases and upregulation of CAMs. In contrast, silencing of caveolin-1 by siRNA interference did not affect upregulation of ICAM-1 and VCAM-1 in brain endothelial cells stimulated by PCB153. Results of the present study indicate that lipid raft-dependent NADPH oxidase/JAK/EGFR signaling mechanisms regulate the expression of CAMs in brain endothelial cells and adhesion of leukocytes to endothelial monolayers. Due to its role in leukocyte infiltration, induction of CAMs may contribute to PCB-induced cerebrovascular disorders and neurotoxic effects in the CNS.

  8. A Mathematical Tumor Model with Immune Resistance and Drug Therapy: An Optimal Control Approach

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

    De Pillis, L. G.; Radunskaya, A.

    2001-01-01

    We present a competition model of cancer tumor growth that includes both the immune system response and drug therapy. This is a four-population model that includes tumor cells, host cells, immune cells, and drug interaction. We analyze the stability of the drug-free equilibria with respect to the immune response in order to look for target basins of attraction. One of our goals was to simulate qualitatively the asynchronous tumor-drug interaction known as “Jeffs phenomenon.” The model we develop is successful in generating this asynchronous response behavior. Our other goal was to identify treatment protocols that could improve standard pulsed chemotherapymore » regimens. Using optimal control theory with constraints and numerical simulations, we obtain new therapy protocols that we then compare with traditional pulsed periodic treatment. The optimal control generated therapies produce larger oscillations in the tumor population over time. However, by the end of the treatment period, total tumor size is smaller than that achieved through traditional pulsed therapy, and the normal cell population suffers nearly no oscillations.« less

  9. Development of monoclonal antibodies to human microsomal epoxide hydrolase and analysis of “preneoplastic antigen”-like molecules

    SciTech Connect (OSTI)

    Duan, Hongying; Yoshimura, Kazunori; Kobayashi, Nobuharu; Sugiyama, Kazuo; Sawada, Jun-ichi; Saito, Yoshiro; Morisseau, Christophe; Hammock, Bruce D.; Akatsuka, Toshitaka

    2012-04-01

    Microsomal epoxide hydrolase (mEH) is a drug metabolizing enzyme which resides on the endoplasmic reticulum (ER) membrane and catalyzes the hydration of reactive epoxide intermediates that are formed by cytochrome P450s. mEH is also thought to have a role in bile acid transport on the plasma membrane of hepatocytes. It is speculated that efficient execution of such multiple functions is secured by its orientation and association with cytochrome P450 enzymes on the ER membrane and formation of a multiple transport system on the plasma membrane. In certain disease status, mEH loses its association with the membrane and can be detected as distinct antigens in the cytosol of preneoplastic foci of liver (preneoplastic antigen), in the serum in association with hepatitis C virus infection (AN antigen), or in some brain tumors. To analyze the antigenic structures of mEH in physiological and pathological conditions, we developed monoclonal antibodies against different portions of mEH. Five different kinds of antibodies were obtained: three, anti-N-terminal portions; one anti-C-terminal; and one, anti-conformational epitope. By combining these antibodies, we developed antigen detection methods which are specific to either the membrane-bound form or the linearized form of mEH. These methods detected mEH in the culture medium released from a hepatocellular carcinoma cell line and a glioblastoma cell line, which was found to be a multimolecular complex with a unique antigenic structure different from that of the membrane-bound form of mEH. These antibodies and antigen detection methods may be useful to study pathological changes of mEH in various human diseases. -- Highlights: ? Monoclonal antibodies against different portions of mEH were developed. ? They discriminate between the membrane-bound and the linearized forms of mEH. ? We analyze the antigenic structure of the altered form of mEH in tumor cells. ? Preneoplastic antigen is a multimolecular complex of mEH with a unique structure.

  10. Structures of Pseudomonas aeruginosa ?-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form

    SciTech Connect (OSTI)

    Baum, Bernhard; Lecker, Laura S. M.; Zoltner, Martin; Jaenicke, Elmar; Schnell, Robert; Hunter, William N.; Brenk, Ruth

    2015-07-28

    Three crystal structures of recombinant P. aeruginosa FabF are reported: the apoenzyme, an active-site mutant and a complex with a fragment of a natural product inhibitor. The characterization provides reagents and new information to support antibacterial drug discovery. Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are urgently sought. In this endeavour, accurate structures of molecular targets can support early-stage drug discovery. Here, crystal structures, in three distinct forms, of recombinant Pseudomonas aeruginosa ?-ketoacyl-(acyl-carrier-protein) synthase II (FabF) are presented. This enzyme, which is involved in fatty-acid biosynthesis, has been validated by genetic and chemical means as an antibiotic target in Gram-positive bacteria and represents a potential target in Gram-negative bacteria. The structures of apo FabF, of a C164Q mutant in which the binding site is altered to resemble the substrate-bound state and of a complex with 3-(benzoylamino)-2-hydroxybenzoic acid are reported. This compound mimics aspects of a known natural product inhibitor, platensimycin, and surprisingly was observed binding outside the active site, interacting with a symmetry-related molecule. An unusual feature is a completely buried potassium-binding site that was identified in all three structures. Comparisons suggest that this may represent a conserved structural feature of FabF relevant to fold stability. The new structures provide templates for structure-based ligand design and, together with the protocols and reagents, may underpin a target-based drug-discovery project for urgently needed antibacterials.

  11. Memorandum, AU-1 Clarification on the Drug Testing Custody and Control Form for Department of Energy Contractors

    Broader source: Energy.gov [DOE]

    Memorandum from Matthew Moury, AU-1 clarifying the drug testing custody and control form for DOE contractors. This memo clarifies the correct form for DOE contractors to use when submitting their samples to a drug testing facility in accordance with 10 CFR part 707, Workplace Substance Programs at DOE Sites

  12. Drug Discovery

    SciTech Connect (OSTI)

    Ellingson; Sally

    2014-05-02

    Sally Ellingson harnesses the massive power of supercomputing to seek the next generation of pharmaceuticals

  13. Drug Discovery

    ScienceCinema (OSTI)

    Ellingson; Sally

    2014-05-23

    Sally Ellingson harnesses the massive power of supercomputing to seek the next generation of pharmaceuticals

  14. Targeted Delivery of Drugs to Brain Tumors (LBNL Summer Lecture Series)

    ScienceCinema (OSTI)

    Forte, Trudy

    2011-04-28

    Summer Lecture Series 2007: Trudy Forte of Berkeley Lab's Life Sciences Division will discuss her work developing nano-sized low-density lipoprotein (LDL) particles that can be used as a safe and effective means of delivering anticancer drugs to brain tumors, particularly glioblastoma multiforme. This is the most common malignant brain tumor in adults and one of the deadliest forms of cancer. Her research team found that the synthetic LDL particles can target and kill such tumors cells in vitro. The nanoparticles are composed of a lipid core surrounded by a peptide. The peptide contains an amino acid sequence that recognizes the LDL receptor, and the lipid core has the ability to accumulate anti-cancer drugs.

  15. Experimental search for the radiative capture reaction d + d {yields} {sup 4}He + {gamma} from the dd{mu} muonic molecule state J = 1

    SciTech Connect (OSTI)

    Baluev, V. V.; Bogdanova, L. N.; Bom, V. R.; Demin, D. L.; Eijk, C. W. E. van; Filchenkov, V. V.; Grafov, N. N.; Grishechkin, S. K.; Gritsaj, K. I.; Konin, A. D.; Mikhailyukov, K. L.; Rudenko, A. I.; Vinogradov, Yu. I.; Volnykh, V. P.; Yukhimchuk, A. A.; Yukhimchuk, S. A.

    2011-07-15

    A search for the muon-catalyzed fusion reaction d + d {yields} {sup 4}He + {gamma} in the dd{mu} muonic molecule was performed using the experimental installation TRITON with BGO detectors for {gamma}-quanta. A high-pressure target filled with deuterium was exposed to the negative muon beam of the JINR Phasotron to detect {gamma}-quanta with the energy 23.8 MeV. An experimental estimation for the yield of radiative deuteron capture from the dd{mu} state J = 1 was obtained at the level of {eta}{sub {gamma}} {<=} 8 Multiplication-Sign 10{sup -7} per fusion.

  16. Characterization and validation of an in silico toxicology model to predict the mutagenic potential of drug impurities*

    SciTech Connect (OSTI)

    Valerio, Luis G.; Cross, Kevin P.

    2012-05-01

    Control and minimization of human exposure to potential genotoxic impurities found in drug substances and products is an important part of preclinical safety assessments of new drug products. The FDA's 2008 draft guidance on genotoxic and carcinogenic impurities in drug substances and products allows use of computational quantitative structure–activity relationships (QSAR) to identify structural alerts for known and expected impurities present at levels below qualified thresholds. This study provides the information necessary to establish the practical use of a new in silico toxicology model for predicting Salmonella t. mutagenicity (Ames assay outcome) of drug impurities and other chemicals. We describe the model's chemical content and toxicity fingerprint in terms of compound space, molecular and structural toxicophores, and have rigorously tested its predictive power using both cross-validation and external validation experiments, as well as case studies. Consistent with desired regulatory use, the model performs with high sensitivity (81%) and high negative predictivity (81%) based on external validation with 2368 compounds foreign to the model and having known mutagenicity. A database of drug impurities was created from proprietary FDA submissions and the public literature which found significant overlap between the structural features of drug impurities and training set chemicals in the QSAR model. Overall, the model's predictive performance was found to be acceptable for screening drug impurities for Salmonella mutagenicity. -- Highlights: ? We characterize a new in silico model to predict mutagenicity of drug impurities. ? The model predicts Salmonella mutagenicity and will be useful for safety assessment. ? We examine toxicity fingerprints and toxicophores of this Ames assay model. ? We compare these attributes to those found in drug impurities known to FDA/CDER. ? We validate the model and find it has a desired predictive performance.

  17. Different origin of adipogenic stem cells influences the response to antiretroviral drugs

    SciTech Connect (OSTI)

    Gibellini, Lara; De Biasi, Sara; Nasi, Milena; Carnevale, Gianluca; Pisciotta, Alessandra; Bianchini, Elena; Bartolomeo, Regina; Polo, Miriam; De Pol, Anto; Pinti, Marcello; Cossarizza, Andrea

    2015-10-01

    Lipodystrophy (LD) is a main side effect of antiretroviral therapy for HIV infection, and can be provoked by nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs). LD exists in different forms, characterized by fat loss, accumulation, or both, but its pathogenesis is still unclear. In particular, few data exist concerning the effects of antiretroviral drugs on adipocyte differentiation. Adipose tissue can arise either from mesenchymal stem cells (MSCs), that include bone marrow-derived MSCs (hBM-MSCs), or from ectodermal stem cells, that include dental pulp stem cells (hDPSCs). To analyze whether the embryonal origin of adipocytes might impact the occurrence of different phenotypes in LD, we quantified the effects of several antiretroviral drugs on the adipogenic differentiation of hBM-MSCs and hDPSCs. hBM-MSCs and hDPSCs were isolated from healthy donors. Cells were treated with 10 and 50 μM stavudine (d4T), efavirenz (EFV), atazanavir (ATV), ritonavir (RTV), and ATV-boosted RTV. Viability and adipogenesis were evaluated by staining with propidium iodide, oil red, and adipoRed; mRNA levels of genes involved in adipocyte differentiation, i.e. CCAAT/enhancer-binding protein alpha (CEBPα) and peroxisome proliferator-activated receptor gamma (PPARγ), and in adipocyte functions, i.e. fatty acid synthase (FASN), fatty acid binding protein-4 (FABP4), perilipin-1 (PLIN1) and 1-acylglycerol-3-phosphate O-acyltransferase-2 (AGPAT2), were quantified by real time PCR. We found that ATV, RTV, EFV, and ATV-boosted RTV, but not d4T, caused massive cell death in both cell types. EFV and d4T affected the accumulation of lipid droplets and induced changes in mRNA levels of genes involved in adipocyte functions in hBM-MSCs, while RTV and ATV had little effects. All drugs stimulated the accumulation of lipid droplets in hDPSCs. Thus, the adipogenic differentiation of human stem cells can be influenced by antiretroviral drugs, and depends, at least in part, on their embryonal origin. - Highlights: • ATV, RTV, EFV and ATV-boosted RTV induce massive cell death in hBM-MSCs and hDPSCs. • EFV and d4T strongly affect the accumulation of lipid droplets in hBM-MSCs. • All drugs stimulate the accumulation of lipid droplets in hDPSCs.

  18. Free-complement local-Schrödinger-equation method for solving the Schrödinger equation of atoms and molecules: Basic theories and features

    SciTech Connect (OSTI)

    Nakatsuji, Hiroshi Nakashima, Hiroyuki

    2015-02-28

    The free-complement (FC) method is a general method for solving the Schrödinger equation (SE): The produced wave function has the potentially exact structure as the solution of the Schrödinger equation. The variables included are determined either by using the variational principle (FC-VP) or by imposing the local Schrödinger equations (FC-LSE) at the chosen set of the sampling points. The latter method, referred to as the local Schrödinger equation (LSE) method, is integral-free and therefore applicable to any atom and molecule. The purpose of this paper is to formulate the basic theories of the LSE method and explain their basic features. First, we formulate three variants of the LSE method, the AB, HS, and H{sup T}Q methods, and explain their properties. Then, the natures of the LSE methods are clarified in some detail using the simple examples of the hydrogen atom and the Hooke’s atom. Finally, the ideas obtained in this study are applied to solving the SE of the helium atom highly accurately with the FC-LSE method. The results are very encouraging: we could get the world’s most accurate energy of the helium atom within the sampling-type methodologies, which is comparable to those obtained with the FC-VP method. Thus, the FC-LSE method is an easy and yet a powerful integral-free method for solving the Schrödinger equation of general atoms and molecules.

  19. Ultra-low-temperature reactions of C({sup 3}P{sub 0}) atoms with benzene molecules in helium droplets

    SciTech Connect (OSTI)

    Krasnokutski, Serge A. Huisken, Friedrich

    2014-12-07

    The reaction of carbon atoms with benzene has been investigated in liquid helium droplets at T = 0.37 K. We found an addition of the carbon atom to form an initial intermediate complex followed by a ring opening and the formation of a seven-membered ring. In contrast to a previous gas phase study, the reaction is frozen after these steps and the loss of hydrogen does not occur. A calorimetric technique was applied to monitor the energy balance of the reaction. It was found that more than 267 kJ mol{sup ?1} were released in this reaction. This estimation is in line with quantum chemical calculations of the formation energy of a seven-membered carbon ring. It is suggested that reactions of this kind could be responsible for the low abundance of small polycyclic aromatic hydrocarbon molecules in the interstellar medium. We also found the formation of weakly bonded water-carbon adducts, in which the carbon atom is linked to the oxygen atom of the water molecule with a binding energy of about 33.4 kJ mol{sup ?1}.

  20. Theoretical study on the ground state of the polar alkali-metal-barium molecules: Potential energy curve and permanent dipole moment

    SciTech Connect (OSTI)

    Gou, Dezhi; Kuang, Xiaoyu Gao, Yufeng; Huo, Dongming

    2015-01-21

    In this paper, we systematically investigate the electronic structure for the {sup 2}Σ{sup +} ground state of the polar alkali-metal-alkaline-earth-metal molecules BaAlk (Alk = Li, Na, K, Rb, and Cs). Potential energy curves and permanent dipole moments (PDMs) are determined using power quantum chemistry complete active space self-consistent field and multi-reference configuration interaction methods. Basic spectroscopic constants are derived from ro-vibrational bound state calculation. From the calculations, it is shown that BaK, BaRb, and BaCs molecules have moderate values of PDM at the equilibrium bond distance (BaK:1.62 D, BaRb:3.32 D, and BaCs:4.02 D). Besides, the equilibrium bond length (4.93 Å and 5.19 Å) and dissociation energy (0.1825 eV and 0.1817 eV) for the BaRb and BaCs are also obtained.