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Sample search results for: ab initio fragment

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1 Present and Future Prospects of Protein Structure Prediction Sung-Joon Park Department of Chemistry, Faculty of Science, Kobe University
 

Summary:  ://theory.chem.sci.kobe-u.ac.jp/ keywords: protein structure prediction, comparative modeling, fold recognition, ab initio, CASP 1. 40 X... 03] § 3 PSI-BLAST PSI-BLAST IMPALA[Schaffer 99] [Wang 04] 3 2 § 1 ab initio ab initio ab ...

  

Source: Takada, Shoji - Department of Biophysics, Kyoto University

 

Collection: Chemistry ; Biotechnology

 
2 A MOLECULAR AND QUANTUM MECHANICAL STUDY OF INDOLE-3-ACETIC ACID
 

Summary:  , PM3) and ab initio (about fifteen DFT and RHF basis sets). Bond length matrix mxn (m = number... structure was optimized using various methods. In general, ab initio bond lengths are closer to experimental... of ab initio and also methods of the same level of ...

  

Source: Ferreira, Márcia M. C. - Instituto de Química, Universidade Estadual de Campinas

 

Collection: Chemistry

 
3 New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy
 

Summary:  the protein molecule is decomposed into amino-acid-based fragments that are properly capped. Ab initio... New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation... are made of the computed ab initio energies with ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
4 246 List Of Abbreviations List Of Abbreviations
 

Summary:  246 List Of Abbreviations List Of Abbreviations AIEMP Ab Initio Embedding Model Potential AIMP Ab... Initio Model Potential AFM Antiferromagnetic ANO Atomic Natural Orbital CASCI Complete Active Space... -Reference Configuration Interaction OF Overlapping Fragment OF1 Overlapping ...

  

Source: Groningen, Rijksuniversiteit - Centre for Ecological and Evolutionary Studies, Department of Marine Benthic Ecology and Evolution,

 

Collection: Biology and Medicine ; Environmental Sciences and Ecology

 
5 Nasir Mahmood1, TJ Brunette2 and Oliver Brock1 1 -Robotics and Biology Laboratory, Technical University Berlin, Germany
 

Summary:  adaptive exploration-exploitation mechanism. An Attempt to Unite Homology Modeling and Ab Initio Structure... Prediction Homologs Fragments PDB Amino Acids MotifsFolds BEETS Strategy ­ Adaptive Balancing of Exploitation... will be increased. Homologs Fragments PDB Amino Acid MotifsFolds exploitation ...

  

Source: 

 

Collection: Engineering ; Computer Technologies and Information Sciences

 
6 BMRB is a member of the wwPDB BMRB collaborates with
 

Summary:  Jobs ! Entry processing involves 4 stages " Preparation (1 job) " Ab initio (1 job per 25 structures... = prepare.log output = prepare_$(ENTRYID).out error = prepare_$(ENTRYID).err queue #12;Ab initio (From... #12;Ab initio ! Run at CHTC " Able to fall back to ...

  

Source: Liblit, Ben - Department of Computer Sciences, University of Wisconsin at Madison

 

Collection: Computer Technologies and Information Sciences

 
7 Molecular fractionation with conjugate caps for full quantum mechanical calculation of proteinmolecule interaction energy
 

Summary:  calculated ab initio. Specifically, we decompose the protein into amino acid-based fragments whose ends... between the molecule and the capped protein fragments that can be obtained by ab initio calculations... mechanical ab ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
8 Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with molecules
 

Summary:  curves are computed using the MFCC method at various ab initio levels for a number of interaction... obtained from the corresponding full system ab initio calculations for both peptide/water systems... number of atoms in proteins, the standard quantum chemistry or ab ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
9 Modeling the dissociation and ionization of a sputtered organic molecule
 

Summary:  molecular dynamics and ab initio calculations to gain insight into the ionization and fragmentation... , the fragmentation of TPN via the ejection of a phenyl radical is energetically possible. Ab initio calculations also... principles. Nevertheless classical MD can ...

  

Source: Garrison, Barbara J.- Department of Chemistry, Pennsylvania State University

 

Collection: Chemistry ; Materials Science

 
10 March 11, 2004 22:38 WSPC/178-JTCC 00089 Journal of Theoretical and Computational Chemistry
 

Summary:  the water molecule and individual protein fragments are then calculated using desired ab initio methods... , No. 1 (2004) 43­49 c World Scientific Publishing Company FULL AB INITIO COMPUTATION OF PROTEIN... (ab initio) calculation of interaction ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
11 Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins
 

Summary:  * level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed... -were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface... relative to ab initio energy differences between ...

  

Source: Ponder, Jay - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biotechnology ; Biology and Medicine

 
12 COMMUNICATIONS Quantum mechanical map for protein-ligand binding with application
 

Summary:  -based fragments that are properly capped. The present MFCC ab initio calculation enables us to obtain... -based fragments.6,7 In this Communication, we report benchmark ab initio computation of interaction energies... fragment, and the three di- ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
13 The linearly scaling 3D fragment method for large scale electronic structure calculations
 

Summary:  . The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method... . This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while... , to study the properties of nanostructures, one needs to do ...

  

Source: Bailey, David H. - National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory; Meza, Juan C. - Computational Research Division, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
14 22842294 Nucleic Acids Research, 2008, Vol. 36, No. 7 Published online 20 February 2008 doi:10.1093/nar/gkn064
 

Summary:  .1093/nar/gkn064 Empirical comparison of ab initio repeat finding programs Surya Saha1,2,3 , Susan Bridges1... repetitive elements in an ab initio manner, i.e. without using prior sequence data. Here we present... the results of side-by-side evaluations of six of the most widely used ab ...

  

Source: Ray, David - Department of Biochemistry and Molecular Biology, Mississippi State University

 

Collection: Environmental Sciences and Ecology

 
15 INSTITUTE OF PHYSICS PUBLISHING MEASUREMENT SCIENCE AND TECHNOLOGY Meas. Sci. Technol. 16 (2005) 296301 doi:10.1088/0957-0233/16/1/039
 

Summary:  ) 296­301 doi:10.1088/0957-0233/16/1/039 High-throughput and data mining with ab initio methods Dane... 2004 Published 16 December 2004 Online at stacks.iop.org/MST/16/296 Abstract Accurate ab initio methods... in computer speed and ab initio algorithms have now ...

  

Source: Curtarolo, Stefano - Department of Mechanical Engineering and Materials Science, Duke University

 

Collection: Materials Science

 
16 Publications 1. Optical limiting properties of CdS nanowires, Muthukumar Sai, J. Reppert, C.S. Sandeep, S.
 

Summary:  -methylaniline in the S0 and S1 states studied by ab initio calculations and resonant two-photon ionization spectroscopy W... structure and vibrations of p-diaminobenzene studied by ab initio calculations. W.B.Tzeng and K.Narayanan, J... , C6D5NHD and C6D5ND2 in the S1 state by ab ...

  

Source: Preyer, Norris - Department of Physics and Astronomy, College of Charleston

 

Collection: Physics

 
17 Recursive Protein Structure Jianlin Cheng, PhD
 

Summary:  ;Template-Free (Ab Initio) Modeling Dill & Chan, 1997 Protein Structure Space Native Structure #12;Template... Structure Template-based modeling (GDT-TS = 0.34) Template-based + Ab Initio (GDT-TS = 0.39) #12;Native... Structure Template-based modeling (GDT-TS = 0.34) Template-based + ...

  

Source: Cheng, Jianlin Jack - Department of Computer Science, University of Missouri-Columbia

 

Collection: Computer Technologies and Information Sciences

 
18 Gilles Zerah Large scale parallel ab initio electronic structure
 

Summary:  Gilles Z´erah Large scale parallel ab initio electronic structure calculations with the LOBPCG... ¸cois Bottin St´ephane Le Roux Andrew Knyazev We present an implementation in the ab initio plane-wave code... . Leroux, A. Knyazev, G. Zerah, Large scale ab initio ...

  

Source: Knyazev, Andrew - Department of Mathematics, University of Colorado at Denver

 

Collection: Mathematics

 
19 Noncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method: Theory and Application to Nucleobase Oligomers
 

Summary:  be generated from a set of ab initio calculations on each unique isolated fragment.91 The Q-CHEM implementation... fragments and an ab initio region, the total electric field Fai-total acting on an effective fragment... on the effective ...

  

Source: Herbert, John - Department of Chemistry, Ohio State University; Krylov, Anna I. - Department of Chemistry, University of Southern California

 

Collection: Chemistry

 
20 A linear scaling three dimensional fragment method for large scale electronic structure calculations
 

Summary:  Laboratory, Berkeley, CA 94720 (Dated: January 18, 2008) Abstract We present a novel linear scaling ab initio... to parallelize, and produces essentially the same results as the direct ab initio method, while it could... of theoretical ab initio calculations on these ...

  

Source: Meza, Juan C. - Computational Research Division, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences


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21 Linear-scaling three-dimensional fragment method for large-scale electronic structure calculations Lin-Wang Wang, Zhengji Zhao,* and Juan Meza
 

Summary:  present a linear scaling ab initio total energy electronic structure calculation method, which is simple... to implement, easily to parallelize, and produces essentially the same results as the direct ab initio method... complex nanostructures. This trend calls for a corresponding set of theoretical ...

  

Source: Meza, Juan C. - Computational Research Division, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
22 Ab initio Protein Structure Prediction Using Pathway Models Xin Yuan, Yu Shao, and Christopher Bystroff
 

Summary:  " (Karplus et al., 2003). Fragment library simulations have had perhaps the broadest success in ab initio... 1 1 Ab initio Protein Structure Prediction Using Pathway Models Xin Yuan, Yu Shao, and Christopher... Bystroff Department of Biology, Rensselaer Polytechnic Institute, Troy, NY12180 ...

  

Source: Bystroff, Chris - Department of Biology, Rensselaer Polytechnic Institute

 

Collection: Biotechnology ; Biology and Medicine

 
23 Physica B 325 (2003) 172183 Energies and stabilities of sodium chloride clusters
 

Summary:  agreement with the calculations by previous empirical potentials and ab initio method. This indicates... ; Sodium chloride; Ab initio calculations 1. Introduction Since the properties of sodium chloride clusters... potential models and advanced ab initio calculations. ...

  

Source: Wang, Yayu - Department of Physics, Tsinghua University

 

Collection: Physics ; Materials Science

 
24 images/logoetsf Introduction Electron Energy Loss Spectroscopy Applications: Nanotubes and Graphene Perspectives
 

Summary:  Perspectives Ab Initio calculations of electronic excitations Carbon Nanotubes and Graphene layer systems... Theoretical Spectroscopy Facility (ETSF) Strasbourg, 27 August 2008 Ab Initio calculations of electronic... 3 Applications: Nanotubes and Graphene 4 Perspectives Ab ...

  

Source: Botti, Silvana - Laboratoire des Solides Irradiés, École Polytechnique

 

Collection: Materials Science

 
25 Ab initio potentials for the S,,3 Pj...rare gas dimers: Implementation
 

Summary:  Ab initio potentials for the S,,3 Pj...­rare gas dimers: Implementation for elastic and inelastic... states are calculated ab initio using an unrestricted CCSD T level of theory and extended correlation... , whose validity is verified by the direct ab initio ...

  

Source: Krems, Roman - Department of Chemistry, University of British Columbia

 

Collection: Physics ; Chemistry

 
26 Treating Hydrogen Bonding in Ab Initio Calculation of Biopolymers
 

Summary:  Treating Hydrogen Bonding in Ab Initio Calculation of Biopolymers YE MEI,1 EMILIA L. WU,2 K. L. HAN... , and dipole moment are compared with those from the standard full system ab initio calculations. The result... in practical ab initio calculation of proteins. Our ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
27 List of Publications of H. Bernhard Schlegel 1. Wolfe, S.; Schlegel, H. B.; Whangbo, M. -H.; Bernardi, F.; On the origin of the Bohlmann bands.
 

Summary:  .; Wolfe, S.; Mislow, K.; Ab initio molecular orbital calculations on silaethylene H2Si=CH2... -3370. 8. Schlegel, H. B.; Wolfe, S.; Bernardi, F.; Ab initio computation of force constants. I. The second... .; Ab initio computation of force constants. II. The estimation ...

  

Source: Schlegel, H. Bernhard - Department of Chemistry, Wayne State University

 

Collection: Chemistry

 
28 Ab Initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure
 

Summary:  Ab Initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering... and new fold categories. For a few targets (T0110 is probably the best example), the ab initio method... proteins, ab initio protein structure assembly becomes ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University; Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Biology and Medicine ; Biotechnology ; Chemistry

 
29 IOP PUBLISHING JOURNAL OF PHYSICS: CONDENSED MATTER J. Phys.: Condens. Matter 20 (2008) 294203 (8pp) doi:10.1088/0953-8984/20/29/294203
 

Summary:  be implemented easily using an existing ab initio code; (3) since the fragment wavefunction calculations... are independent for different fragments, it can be parallelized easily; (4) it can be applied to ab initio methods... -dimensional fragment ...

  

Source: Meza, Juan C. - Computational Research Division, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
30 Protein Structure Analysis Iosif Vaisman
 

Summary:  Protein Structure Analysis Iosif Vaisman 2009 BINF 731 Protein Modeling Methods · Ab initio methods... · Energy-based methods · Knowledge-based methods Protein Modeling Methods · Ab initio methods: solution... molecular simulation · Knowledge-based methods: homology modeling fold recogniion ...

  

Source: Vaisman, Iosif - Bioinformatics and Computational Biology Program, School of Computational Sciences, George Mason University

 

Collection: Biotechnology

 
31 CS 374 Abhishek Rathod Prof. Serafim Batzoglou 12/02/2005
 

Summary:  CS 374 Abhishek Rathod Prof. Serafim Batzoglou 12/02/2005 Ab initio protein structure prediction... .1146/annurev.biophys.30.1.173 Abstract: Homology-based comparative modeling, Fold recognition and Ab initio... reviews features of current ab initio methods like ...

  

Source: Batzoglou, Serafim - Department of Computer Science, Stanford University

 

Collection: Biotechnology ; Computer Technologies and Information Sciences

 
32 Theoretical method for full ab initio calculation of DNARNAligand interaction energy
 

Summary:  Theoretical method for full ab initio calculation of DNAÕRNA­ligand interaction energy Xi H. Chen... from the full system ab initio calculations. The current study extends the application of the MFCC... method to ab initio calculations for DNA­ or RNA­ligand ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
33 A divide-and-conquer linear scaling three dimensional fragment method for large scale electronic structure calculations
 

Summary:  an existing ab initio code; (3) Since the fragment wavefunction calculations are independent for different... fragments, it can be parallelized 3 #12;easily; (4) It is applicable to ab initio methods other than DFT. II... dimensional fragment ...

  

Source: Lee, Jason R. - Data Intensive Distributed Computing Group, Distributed Systems Department, National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
34 Introduction Protein structure prediction is one of the classic problems from computational
 

Summary:  for Bioinformatics, Hamburg University, Germany mahmood@zbh.uni-hamburg.de State of the art In ab Initio or de novo... sequence. The biased moves our search method makes are made by selection from a fragment library generated... by chopping up 7000+ structures (which have sequence identity less than 50%) into ~2.0 million ...

  

Source: 

 

Collection: Engineering ; Computer Technologies and Information Sciences

 
35 Introduction Protein structure prediction is one of the classic problems from computational
 

Summary:  Center for Bioinformatics, Hamburg University, Germany mahmood@zbh.uni-hamburg.de State of the art In ab... Initio or de novo protein modelling, one seeks to build 3D protein models from scratch rather than... by selection from a fragment library generated by chopping up 7000+ structures (which have sequence identity

  

Source: 

 

Collection: Engineering ; Computer Technologies and Information Sciences

 
36 Multi-Laser-Beam Open-Atmosphere Surface Coating Techniques Based on Precursor Excitation, Photodissociation and Controlled Cooling
 

Summary:  .) for fast diamond growth; (2) Theoretically (ab initio, molecular dynamics and continuum models) investigate... -Lung Tsai, "Calculation of Thermophysical Properties of CO2 Gas Using an Ab Initio Potential Model... , "Ab Initio Calculations of Infrared Absorption ...

  

Source: Ragsdell, Kenneth M. - Design Engineering Center, University of Missouri-Rolla

 

Collection: Engineering

 
37 Liste de publications 13. "Acetone-water complexes at MRCI level using localized orbitals: n-* and -* electronic
 

Summary:  , 451, 141-146. 12. "Large systems at ab initio multireference level: a cheap treatment thanks... of Na+ complexation, and attachment sites from the dissociation of Na+ -bound heterodimers and ab initio... to a division into fragments" BESSAC F., HOYAU S., MAYNAU D. J. Chem. Phys. 2005, ...

  

Source: Giraud, Olivier - Laboratoire de Physique Théorique, Université Paul Sabatier

 

Collection: Physics

 
38 An adiabatic model for the photodissociation of CH3SH in the first ultraviolet absorption band
 

Summary:  ­4 of the CH3S fragment than does the ab initio surface. This coin- cides more nearly with experiment than... . The effective valence shell Hamiltonian (H ab initio many-body perturbation technique is used to calculate... are performed, one in which the ground state is represented by a ...

  

Source: Butler, Laurie J. - Department of Chemistry, University of Chicago

 

Collection: Chemistry

 
39 Photoinduced dynamics in protonated aromatic amino acid G. Grgoire3
 

Summary:  with high level ab initio calculations, have shed light on the role of the different electronic states... in the excited state calculations. Excited states ab-initio calculations6,10,12,13 have shown the very important... figure 2) and ab-initio calculations have been the key to understand the possible ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
40 Nearly Deterministic Methods for Optimising Protein Geometry Gundolf Schenk, Andrew Torda
 

Summary:  self consistency within this framework. State of the art Methods for ab initio protein structure... protein fragments, ·each with 5-7 amino acid types + 10-14 dihedral angles from backbone. ·assigns a fixed... number of class weights (typically 150-300) to each fragment. Structure Generation With this ...

  

Source: Kurtz, Stefan - Center for Bioinformatics, Universität Hamburg

 

Collection: Computer Technologies and Information Sciences


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41 Molecular Caps for Full Quantum Mechanical Computation of PeptideWater Interaction Energy
 

Summary:  in biological molecules like proteins or polypeptides, standard ab initio meth- ods1­3 that include entire... that the MFCC approach is capable of giving excellent ab initio energies com- pared to the full system ab initio... quantum mechanical fashion using varies ...

  

Source: Zhang, John Z.H. - Department of Chemistry, New York University

 

Collection: Chemistry

 
42 Electron delocalization in mixed-valence Keggin polyoxometalates. Ab initio calculation of the local e ective
 

Summary:  Electron delocalization in mixed-valence Keggin polyoxometalates. Ab initio calculation... -valence polyoxometalates reduced by two electrons. For that purpose, we extract from valence-spectroscopy ab initio... will calculate the transfer parameters t and t 0 by using very accurate ab ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
43 Ab Initio/IGLO/NMR Investigation of nido-C4B7H11 Configurations: Structural Assignment of the Three Known Isomers and Reconfirmation of Empirical Carbon Placement Patterns
 

Summary:  Ab Initio/IGLO/NMR Investigation of nido-C4B7H11 Configurations: Structural Assignment of the Three... Angeles, California, 90089-1661 ReceiVed June 1, 1995X The ab initio/IGLO/NMR method has been successfully... avoiding carbon-carbon connections. Introduction In this paper we demonstrate that the ...

  

Source: Rizzo, Robert C. - Department of Applied Mathematics and Statistics, SUNY at Stony Brook

 

Collection: Chemistry ; Biology and Medicine

 
44 AUGUSTUS as ab initio method Mario Stanke
 

Summary:  AUGUSTUS as ab initio method Mario Stanke Institut f¨ur Mikrobiologie und Genetik Universit¨at G... ¨ottingen Germany AUGUSTUS as ab initio method ­ p.1/8 #12;Application Flow Input: DNA sequence s AUGUSTUS... algorithm This parse defines the predicted gene structure (only CDS, 1 transcript). AUGUSTUS as ...

  

Source: Foissac, Sylvain - Centre de Regulació Genòmica, Barcelona

 

Collection: Biotechnology

 
45 AUGUSTUS as dual-Genome-based Method
 

Summary:  ­ p.9/10 #12;Accuracy on 31 Test Regions AUGUSTUS ab initio + mouse genome AUGUSTUS Gene Sensitivity... on the peptide level 4. process the DIALIGN fragment pairs and make hints from them 5. AUGUSTUS predicts genes... on s using the hints from 4. AUGUSTUS as dual-Genome-based Method ­ p.2/10 #12;DIALIGN Alignment ...

  

Source: Foissac, Sylvain - Centre de Regulació Genòmica, Barcelona

 

Collection: Biotechnology

 
46 This journal is c The Royal Society of Chemistry 2011 Mol. BioSyst. Cite this: DOI: 10.1039/c1mb05207a
 

Summary:  into four different categories: (1) ab initio, or sequence only, (2) clustering, (3) template based and (4... the basis for each category and briefly discuss some implementations. Ab initio methods The distinguishing... feature of ab initio approaches is that they ...

  

Source: Cheng, Jianlin Jack - Department of Computer Science, University of Missouri-Columbia

 

Collection: Computer Technologies and Information Sciences

 
47 Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa)
 

Summary:  Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa) Department... Street, London, WC1E 6BT, United Kingdom Received 23 October 2003; accepted 13 November 2003 Ab initio... calculations of the melting properties of copper in the pressure range 0­100 GPa are reported. The ...

  

Source: Alfè, Dario - Departments of Earth Sciences & Physics and Astronomy, University College London

 

Collection: Physics ; Geosciences

 
48 Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa)
 

Summary:  Ab initio melting curve of copper by the phase coexistence approach L. Vocadloa) Department... Street, London, WC1E 6BT, United Kingdom Received 23 October 2003; accepted 13 November 2003 Ab initio... calculations of the melting properties of copper in the pressure range 0­100 GPa are reported. The ...

  

Source: Price, G. David - Department Earth Sciences, University College London; Voèadlo, Lidunka - Department Earth Sciences, University College London

 

Collection: Chemistry ; Geosciences ; Materials Science

 
49 Parametrization and validation of a force field for liquid-crystal forming molecules D. L. Cheung,1,2
 

Summary:  or crystallography. Ab initio calculations can also be used. In principle, such calculations can achieve a high level... between the ab initio energies and the fitted energies to below 0.0019 eV2 . III. COMPUTATIONAL METHOD A... . Ab initio calculations Structural and ...

  

Source: Wilson, Mark R. - Department of Chemistry, University of Durham

 

Collection: Chemistry

 
50 Relationships between bridging oxygen 17 O quadrupolar coupling
 

Summary:  have performed ab initio calculations on the model cluster OH 3Si­O­Si OH 3 with lithium or sodium... ­9 have shown that ab initio quantum chemical calculations can be a powerful tool for researchers trying... to connect measured 17 O NMR parameters to structural features. Indeed, the Tossell group's ...

  

Source: Grandinetti, Philip J.- Department of Chemistry, Ohio State University

 

Collection: Chemistry ; Materials Science

 
51 Prospects for ab initio Protein Structural Genomics Kim T. Simons, Charlie Strauss and David Baker*
 

Summary:  Prospects for ab initio Protein Structural Genomics Kim T. Simons, Charlie Strauss and David Baker... of the ROSETTA method for ab initio protein structure prediction. Models were generated for two independently... protein. These results suggest that ab initio ...

  

Source: Baker, David - Center for Nanotechnology and NanoTechnology & Department of Biochemistry, University of Washington at Seattle

 

Collection: Chemistry ; Biotechnology

 
52 TOUCHSTONE: A Unified Approach to Protein Structure Jeffrey Skolnick,1* Yang Zhang,1
 

Summary:  that spans the range from homology modeling to ab initio folding to all protein targets in CASP5. Using our... at least weakly threading templates are pooled and incorporated into ab initio folding. Often, TOUCHSTONE... analogous templates. When ab initio folding is ...

  

Source: Kihara, Daisuke - Department of Biological Sciences, Purdue University; Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Biology and Medicine ; Biotechnology ; Chemistry

 
53 An Overview of Protein Structure Prediction: From Homology to Ab Initio
 

Summary:  An Overview of Protein Structure Prediction: From Homology to Ab Initio Final Project For Bioc218... , comparative modeling, threading or fold recognition, and Ab Initio prediction, is described. The accuracy... ) homology modeling, 2) threading or fold recognition, and 3) Ab ...

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
54 Nearly Deterministic Methods for Optimising Protein Geometry Gundolf Schenk, Andrew Torda
 

Summary:  self consistency within this framework. State of the art Methods for ab initio protein structure... protein fragments, ·each with 5-7 amino acid types + 10-14 dihedral angles from backbone. ·assigns a fixed... number of class weights (typically 150-300) to each fragment. Structure Generation With this ...

  

Source: Kurtz, Stefan - Center for Bioinformatics, Universität Hamburg

 

Collection: Computer Technologies and Information Sciences

 
55 J. Am. Chem. SOC.1992, 114, 4265-4268 4265 allyl alcohol vs that of acrolein). Alternatively, one could argue
 

Summary:  translational energy is calculated upon separation of the fragments. Ab initio trajectories (6) Helgaker, T... studied the dynamics of the fragmentation of pro- tonated formaldehydeat the ab initio level. Our... -16-6. Dynamics of the Reaction CH20H+-+ CHO+ + H2. ...

  

Source: Helgaker, Trygve - Department of Chemistry, Universitetet i Oslo

 

Collection: Physics ; Chemistry

 
56 proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Improving threading algorithms for remote
 

Summary:  ­template alignments, for example, models built by (chunk-)TASSER simulations27,28 or models obtained from ab initio... such as threading or ab initio structure prediction. FTCOM requires the Ca coordinates of full length models... the input struc- tures. Alternatively, given a set of arbitrarily generated ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
57 Predicting Interresidue Contacts Using Templates and Pathways
 

Summary:  potentials then were used to evaluate these templates. An ab initio method based on the target contact... and ab initio methods were combined to produce accurate, protein-like contact maps. Pathways sometimes... targets are dis- cussed. Also included is a brief update on the quality of fully automated ...

  

Source: Bystroff, Chris - Department of Biology, Rensselaer Polytechnic Institute

 

Collection: Biotechnology ; Biology and Medicine

 
58 Empirical limits for template-based protein structure prediction: the CASP5 example
 

Summary:  , template-based methods have intrinsic limitations, suggesting that other method- ologies, such as ab initio... reconstruct the protein of interest. The first class is usually known as ab initio approaches [1]; the second... of the sequence alignment problem, and can implicitly tell us to what extent ...

  

Source: Moreira, Bruno Contreras - Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

 

Collection: Biotechnology

 
59 Z .Chemical Physics 232 1998 321328 Towards quantitative diatomics-in-molecules model for the water
 

Summary:  to a multicenter charge distribution in the polyatomic molecule are required. The results of new ab initio... for the point-by-point comparison of DIM and ab initio results showing the efficiency of the present model. q... as the Fourier trans- forms of velocity­velocity autocorrelation functions. The ...

  

Source: Apkarian, V. Ara - Department of Chemistry, University of California, Irvine

 

Collection: Chemistry

 
60 roteins are the workhorses of life. These polymers, comprised of 20 natu-
 

Summary:  prediction: homology modeling, threading, and ab initio folding. In homology modeling,6 the query sequence... structure must already exist. With ab initio fold- ing, we attempt to fold a protein from a random... threading algorithm for protein structure prediction that can also be applied to ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine


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61 1. Score function: Unlike most Monte Carlo methods we do not use
 

Summary:  to be announced) with our threading and ab initio servers. We are now working to refine solvation and hydrogen... - · ( ) (2) 1 , 1 1 | )( fragmentsN fragments classes seq i x slvstruct i N i N j jfj cstat f... method makes two kinds of moves: 1) biased moves made by drawing a fragment ...

  

Source: 

 

Collection: Engineering ; Computer Technologies and Information Sciences

 
62 Linear Scaling 3D Fragment Method for Large-scale Electronic Structure Calculations
 

Summary:  (LS3DF) method that uses a novel decomposition and patching scheme to do ab initio density functional... code portfolio for large-scale ab initio simulations. 1 Introduction Nanostructures such as quantum... functions. To address these and other issues, what is needed is a direct atomistic ...

  

Source: Lee, Jason R. - Data Intensive Distributed Computing Group, Distributed Systems Department, National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory; Meza, Juan C. - Computational Research Division, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
63 Halide adsorption on single-crystal silver substrates: dynamic
 

Summary:  Halide adsorption on single-crystal silver substrates: dynamic simulations and ab initio density... potential with input from ab-initio DFT slab calculations: Surface Solution Lateral potential on surface #12

  

Source: Rikvold, Per Arne - Department of Physics, Florida State University

 

Collection: Physics

 
64 Princeton Institute for Computational Science (PICSciE) Colloquium: Materials Properties from ab-initio Simulations
 

Summary:  Princeton Institute for Computational Science (PICSciE) Colloquium: Materials Properties from ab-initio... , using ab-initio, quantum simulations, in particular first principles molecular dynamics and Quantum

  

Source: Singh, Jaswinder Pal - Department of Computer Science, Princeton University

 

Collection: Computer Technologies and Information Sciences

 
65 University of Maryland Symposium on Theoretical Chemistry 15 April 2009, 9:00 AM
 

Summary:  Speakers Joel Bowman (Emory University) "Ab initio-based full dimensional water dimer and trimer potentials... and on towards a general ab initio potential for water" Kenneth Jordan (University of Pittsburgh) Millard

  

Source: Krylov, Anna I. - Department of Chemistry, University of Southern California

 

Collection: Chemistry

 
66 Theoretical Sensitivity of the C(3 S) Rate Constant: The
 

Summary:  theory (MPCT) based on a full ab initio potential energy surface fitted with q1 2, 5 kernels... is obtained in a subset of three models: the ACCSA method with PME-SO or ab initio PESs and the QCT method... /product channel is computed as the average of the ab initio ...

  

Source: Honvault, Pascal - L’Institut UTINAM, Université de Franche-Comté

 

Collection: Chemistry

 
67 1. Phys.: Condens. Malter 7 (1995)577-584. Printed in the UK Structuralpropertiesof siliconclusters: an empirical
 

Summary:  the ab initio molecular dynamics relaxes ions and electrons simultaneously, the calculations become too... different from the ab initio results [12]. Consequently the experimental results on clusters cannot... ,asfollow. Comparing the bond angle distribution of silicon clusters obtained from SW-potential and ...

  

Source: Gong, Xingao - Department of Physics, Fudan University

 

Collection: Materials Science ; Physics

 
68 CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.CSAR Focus, Edition 4, January 2000.44444 TTTTTurururururing Pring Pring Pring Pring Probes the Earobes the Ear
 

Summary:  . Parameter-free ab initio techniques based on density functional theory (DFT) have recently made enormous... unnecessary.With ab initio molecular-dynamics methods (Car- Parrinello)4 , this is true for both liquids... , January 2000.66666 Figure 2 compares our ab ...

  

Source: Alfè, Dario - Departments of Earth Sciences & Physics and Astronomy, University College London

 

Collection: Physics ; Geosciences

 
69 A MOLECULAR AND QUANTUM MECHANICAL STUDY OF INDOLE-3-ACETIC ACID
 

Summary:  , MNDO, AM1, PM3) and ab initio (about twenty DFT, RHF and B3LYP basis sets). Bond length matrix mxn (m... from crystal structure was optimized using various methods. In general, ab initio bond lengths... similar basis sets of ab initio and also methods of the same ...

  

Source: Ferreira, Márcia M. C. - Instituto de Química, Universidade Estadual de Campinas

 

Collection: Chemistry

 
70 Nuclear Structure and Reactions (Quantum Monte Carlo, Lanczos Methods, Density Functional Methods), June 6 10
 

Summary:  and new challenges in ab initio nuclear structure and nuclear reactions" 2:00 pm Bira van Kolck "Harmonic... EFT: trapped atoms and nucleons" Tuesday, June 7 10:00 am Bruce Barrett "Ab initio shell model... systems: nuclei and the unitary Fermi gas" Thursday, June 9 10:00 am Stefano Gandolfi ...

  

Source: Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group - Neutron Beta Decay Time Reversal Invariance Test

 

Collection: Physics

 
71 and Ion Processes ELSEVIER International Journal of Mass Spectrometry and lon Processes 167/168 (1997) 637-647
 

Summary:  spectroscopy. Vibrational assignments are based on ab initio calculations by taking into account complexation... of the tetrahedral monomer. © 1997 Elsevier Science B.V. © 1997 Elsevier Science B.V. Keywords: Ab initio studies... - scopy [17-23] and ab initio ...

  

Source: Nizkorodov, Sergey - Department of Chemistry, University of California, Irvine

 

Collection: Chemistry

 
72 Nitrosative Adenine Deamination. A Quantum Mechanical Study of the Decomposition Pathways of Adeninediazonium Ion.
 

Summary:  the adeninediazonium ion, 2, and its product of dediazoniation, 3. In the course of our ab initio studies of DNA base... -products of adenine deamination. Three pathways for fragmentation of 5 by loss of two HCN molecules and one proton

  

Source: Glaser, Rainer - Department of Chemistry, University of Missouri-Columbia

 

Collection: Chemistry

 
73 J. Phys. Chem. 1990, 94, 3995-4000 Ab Initio Study of Stretch-Bend Coupling in HOOH
 

Summary:  J. Phys. Chem. 1990, 94, 3995-4000 Ab Initio Study of Stretch-Bend Coupling in HOOH 3995 Coral... University, Ithaca, New York 14853 (Received: September 25, 1989) Ab initio calculations are used... are obtained by fitting the ab initio data and are found to be ...

  

Source: Ezra, Gregory S.- Department of Chemistry and Chemical Biology, Cornell University

 

Collection: Chemistry

 
74 Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio
 

Summary:  Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio Folding... The ab initio folding problem can be divided into two sequential tasks of approximately equal... backbones on side-chain prediction for folds generated ab initio, ...

  

Source: California at Davis, University of - Computer Science Department, Computer Science Theory Laboratory; Huang, Enoch S. - Bioinformatics Program, Boston University; Levitt, Michael - Department of Structural Biology, Stanford University; Ponder, Jay - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine ; Biotechnology ; Computer Technologies and Information Sciences

 
75 From kp to atomic calculations applied to semiconductor heterostructures
 

Summary:  , it appears necessary to use ab initio calculations in order to provide either input parameters for k... .2 is an example of using ab initio parameters to start k····p calculations with piezoelectric coefficients. Then... ab initio calculations: (InAs (Ref. 4), ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
76 Benchmarking of TASSER in the Ab Initio Limit Jose M. Borreguero and Jeffrey Skolnick*
 

Summary:  Benchmarking of TASSER in the Ab Initio Limit Jose M. Borreguero and Jeffrey Skolnick* Center... related protein in the database of solved protein structures, the PDB. Under these conditions, ab initio... performance on proteomes, the TASSER structure prediction algo- rithm is benchmarked in the ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
77 All-Atom Ab Initio Folding of a Diverse Set of Proteins
 

Summary:  Structure Article All-Atom Ab Initio Folding of a Diverse Set of Proteins Jae Shick Yang,1 William... problems in bio- physics. Here, we show successful all-atom ab initio folding of a representative diverse... a few crucial energetic terms. INTRODUCTION Ab initio ...

  

Source: Skolnick, Jeff - Center for the Study of Systems Biology, Georgia Institute of Technology

 

Collection: Chemistry ; Biology and Medicine

 
78 Reshma P.Shetty1, Paul I.W.de Bakker2,3, Mark A.DePristo and Tom L.Blundell
 

Summary:  with backbone ¯exibility, fragments are remodelled ab initio as described above with the additional restraint... clashes. An unexpected ®nding of this work is that inclusion of side chain atoms during ab initio fragment... is described for simultaneously modelling ...

  

Source: de Bakker, Paul - Division of Genetics, Brigham and Women's Hospital, Harvard University

 

Collection: Biology and Medicine

 
79 BIOINFORMATICS Vol. 00 no. 00 2007
 

Summary:  . (2003). Ab initio con- struction of polypeptide fragments: efficient generation of accurate... fragments from known proteins, research has also been conducted on constructing structural fragments with ab... initio methods, and such methods ...

  

Source: Waterloo, University of - Computer Graphics Lab.

 

Collection: Computer Technologies and Information Sciences

 
80 Rosetta in CASP4: Progress in Ab Initio Protein Structure Richard Bonneau,1
 

Summary:  Rosetta in CASP4: Progress in Ab Initio Protein Structure Prediction Richard Bonneau,1 Jerry Tsai,1... Laboratory, Los Alamos, New Mexico ABSTRACT Rosetta ab initio protein structure predictions in CASP4 were... considerably more con- sistent and more accurate than previous ab ...

  

Source: Baker, David - Center for Nanotechnology and NanoTechnology & Department of Biochemistry, University of Washington at Seattle

 

Collection: Chemistry ; Biotechnology


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81 PetaScale Calculations of the Electronic Structures of Nanostructures with Hundreds of Thousands of Processors
 

Summary:  widely used ab initio method in material simulations. It accounts for 75% of the NERSC allocation time... and semiconductor systems, it covers a current gap in DOE's material science code portfolio for ab initio ultrascale... functions, etc. Thus, what needed here is a direct atomistic ...

  

Source: Meza, Juan C. - Computational Research Division, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
82 Protein Science (1998), 7: 1998-2003. Cambridge University Press. Printed in the USA. Copyright 1998 The Protein Society
 

Summary:  of Medicine, Saint Louis, Missouri 63110; e-mail:ponder@dasher.wustl.edu. Abstract For successful ab initio... in an average coordinate RMS error of 4.38 Å. Keywords: ab initio folding; distance geometry; energy functions... and methods Generation of ab initio ...

  

Source: Huang, Enoch S. - Bioinformatics Program, Boston University; Ponder, Jay - Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis

 

Collection: Biology and Medicine ; Biotechnology

 
83 All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins A. D. MacKerell, Jr.,*,, D. Bashford,, M. Bellott,, R. L. Dunbrack, Jr.,, J. D. Evanseck,,
 

Summary:  surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized... the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes... demonstrate that use of ab initio structural and ...

  

Source: Li, Yaohang - Department of Computer Science, Old Dominion University; Straub, John E. - Department of Chemistry, Boston University

 

Collection: Chemistry ; Computer Technologies and Information Sciences

 
84 A New O(N) Method for Petascale Nanoscience Simulations Zhengji Zhao, Juan Meza, and Lin-Wang Wang
 

Summary:  energy, biomedical imaging, and other novel materials. To fully explore these ideas, petascale ab initio... materials simulations will be required. We have developed a new linear scaling 3 dimensional fragment (LS3DF... into fragments and solve each fragment independently), and then ...

  

Source: Lawrence Berkeley National Laboratory, Computational Research Division, Distributed Systems Department, Data Intensive Distributed Computing Group

 

Collection: Computer Technologies and Information Sciences

 
85 Prorein Science (1998). 7:1998-2003.CambridgeUniversityPress.Printed in the USA Copyright 0 1998TheProteinSociety
 

Summary:  ,1998; ACCEPTEDJune I, 1998) Abstract For successful ab initio protein structure prediction, a method is needed... these restraints resulted in an average coordinate RMS error of 4.38 A. Keywords: ab initio folding; distance... . So-called "ab initio" computationalap- ...

  

Source: Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biotechnology ; Biology and Medicine

 
86 Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations
 

Summary:  -dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based... thousands to tens of thousands of atoms that can be accurately simulated only by ab initio self... . The above questions can be answered by ab ...

  

Source: Bailey, David H. - National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory; Lee, Jason R. - Data Intensive Distributed Computing Group, Distributed Systems Department, National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory

 

Collection: Computer Technologies and Information Sciences

 
87 Ab Initio Classical Trajectory Study of the Fragmentation of C3H4 Dications on the Singlet and Triplet Surfaces
 

Summary:  Ab Initio Classical Trajectory Study of the Fragmentation of C3H4 Dications on the Singlet... , 2010 Ab initio molecular dynamics have been used to examine the fragmentation of allene, propyne... dissociation event. Summary Ab ...

  

Source: Schlegel, H. Bernhard - Department of Chemistry, Wayne State University

 

Collection: Chemistry

 
88 ELECTRONIC STRUCTURE AND SPECTROSCOPY IN THE GAS AND CONDENSED PHASE: METHODOLOGY AND APPLICATIONS.
 

Summary:  region is modeled with an ab initio method. The effec- tive fragments are the spectator molecules... cost is O(N2 ) for the system with N effective fragments, plus the cost of the ab initio computation... fragment and the ab ...

  

Source: Krylov, Anna I. - Department of Chemistry, University of Southern California

 

Collection: Chemistry

 
89 Rachel Kolodny Department of Structural Biology and
 

Summary:  fragments. Our approach has the advantages of ab initio methods since we are able to enumerate all candidate... to progress in recent years (Bonneau and Baker 2001; Moult et al. 2003), successful ab initio protein... structures, these methods can be divided into ab ...

  

Source: California at Davis, University of - Computer Science Department, Computer Science Theory Laboratory; Guibas, Leonidas J. - Department of Computer Science, Stanford University; NONE

 

Collection: Biology and Medicine ; Biotechnology ; Computer Technologies and Information Sciences

 
90 Dissociation of acetone radical cation (CH3COCH3 d): An ab initio direct classical trajectory studyw
 

Summary:  Dissociation of acetone radical cation (CH3COCH3 1d - CH3CO1 þCH3 d): An ab initio direct classical... radical cation (CH3COCH3 1d - CH3CO1 þ CH3 d) has been studied by ab initio direct classical trajectory... . Heinrich et al.10 have used RRKM studies on an ab ...

  

Source: Schlegel, H. Bernhard - Department of Chemistry, Wayne State University

 

Collection: Chemistry

 
91 Protein Structure Prediction Jayanthi Sourirajan
 

Summary:  is predicted using Ab-initio prediction. #12;Secondary structure prediction The secondary structure... recognition or threading and 3) Ab-initio method. All these methods involve searching the database... structure is predicted through ab-initio predictions. Template selection and alignment accuracy have a large

  

Source: Bejerano, Gill - Departments of Computer Science & Developmental Biology, Stanford University

 

Collection: Computer Technologies and Information Sciences ; Biology and Medicine

 
92 Dipole moment of water molecules in narrow pores Christoph Dellago a, Mor M. Naor b
 

Summary:  , University of Iowa, Iowa City, IA 52242, USA Abstract We use ab initio molecular dynamics simulation... phase. Here we use density functional theory based ab initio molecular dynamics simulation to calculate... in the interior of a narrow pore taken from our ab ...

  

Source: Dellago, Christoph - Institute for Experimental Physics, Universität Wien

 

Collection: Physics ; Materials Science

 
93 BioMed Central Page 1 of 16
 

Summary:  identities ranging from 50% to 10% to the nearest related protein with known structure. Using our ab initio... 2 of 16 (page number not for citation purposes) ling, fold recognition, and ab initio prediction... structure is used to create the initial or seed model. In the ab ...

  

Source: Levitt, Michael - Department of Structural Biology, Stanford University; Samudrala, Ram - Department of Microbiology, University of Washington at Seattle

 

Collection: Biology and Medicine ; Biotechnology

 
94 ccsd-00003024,version3-4Mar2005 EPJ manuscript No.
 

Summary:  -J+V model for the chain subsystem of the Sr14Cu24O41 has been extracted from ab-initio calculations... by Majumdar and Gosh [15] and Haldane [16]. We recently showed, using ab initio calculation, that the origin... periodic approximation. The next section will describe the ab-initio methods used in the ...

  

Source: Ecole Polytechnique, Centre de mathématiques

 

Collection: Mathematics

 
95 Theor Chim Acta (1994) 89:157-168 Theoretica Chimica Acta
 

Summary:  and accurate determination of minimum energy reaction-paths for small polyatomic molecules using ab initio... , energy gradients and force-constants, V, G and F, can be routinely calculated by ab initio molecular... for the reaction coordinates, s. Such a potential describes - within the validity of the ...

  

Source: Helgaker, Trygve - Department of Chemistry, Universitetet i Oslo

 

Collection: Physics ; Chemistry

 
96 Polymers near Metal Surfaces: Selective Adsorption and Global Conformations L. Delle Site,1
 

Summary:  .g., production of compact disks). We combine ab initio calculations for the interaction of fragments of bisphenol... to metal surfaces. We first describe the ab initio part of our work. Then we introduce the coarse... near a Ni surface. Our motivation to perform ab ...

  

Source: Alavi, Ali - Department of Chemistry, University of Cambridge

 

Collection: Chemistry

 
97 Connecting the Protein Structure Universe by Using Sparse Recurring Fragments
 

Summary:  ,b is the BLOSUM62 score for amino acids a,b. Scoring the Fragment alignments Given a fragment size r, the scores... domain structures. Structure 5, 1093-1108. Pedersen, J. T., and Moult, J. (1995). Ab initio structure... 1 Connecting the Protein Structure Universe by Using Sparse ...

  

Source: Friedberg, Iddo - Departments of Microbiology and Computer Science, Miami University (Ohio)

 

Collection: Computer Technologies and Information Sciences ; Biotechnology

 
98 Volume 173,number 2,3 CHEMICAL PHYSICS LETTERS 5October1990 Integration of the classical equations of motion
 

Summary:  for calculating classical trajectories on molecular ab initio potential energy surfaces is presented... be obtained from ab initio electronic structure calculations [ 11.The traditional approach is to calculate... -order Taylor expansions of the ab initio surface. The ...

  

Source: Helgaker, Trygve - Department of Chemistry, Universitetet i Oslo

 

Collection: Physics ; Chemistry

 
99 A Theoretical Model for Indirect Dissociative Electron Attachment Iwona Anusiewicz,,, Monika Sobczyk,, Joanna Berdys-Kochanska,, Piotr Skurski,, and
 

Summary:  ab initio electronic structure methods, the neutral and Figure 3. Illustrative plots of the neutral... now examine several applications of this model and compare its predictions with the fully ab initio... -sugar-phosphate fully ab initio neutral and lowest adiabatic ...

  

Source: Simons, Jack - Department of Chemistry, University of Utah

 

Collection: Chemistry

 
100 Multiphoton ionization photoelectron spectroscopy of acetaldehyde via the A~ 1
 

Summary:  , and to identify useful routes for preparing state-selected ions. Ab initio calculations of neutral and cation... . Inconsistencies in the literature are discussed in light of the photoelectron spectra and ab initio results... function. C. Ab initio calculations of ...

  

Source: Anderson, Scott L. - Department of Chemistry, University of Utah

 

Collection: Energy Storage, Conversion and Utilization ; Materials Science ; Chemistry


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