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RSC Biomolecular Sciences
Innovations in Biomolecular Modeling and Simulations
Edited by
Tamar Schlick
Tamar Schlick
New York University, USA
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Volume
1
Hardback ISBN:
978-1-84973-461-5
PDF ISBN:
978-1-84973-504-9
No. of Pages:
380
Published online:
24 May 2012
Published in print:
01 May 2012
About this book
The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
Innovations in Biomolecular Modeling and Simulations, The Royal Society of Chemistry, 2012.
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Digital access
$216.00
Print format
Innovations in Biomolecular Modeling and Simulations
$216.00
Table of contents
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Chapter 1: Personal Perspectivep3-7ByHarold A. ScheragaHarold A. ScheragaSearch for other works by this author on:
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Chapter 2: Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminiscesp8-19ByLisa PollackLisa PollackBeckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-ChampaignUrbana, Illinois 61801US[email protected]Search for other works by this author on:
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Chapter 3: Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Modelp23-50ByC. M. Baker;C. M. BakerUniversity of Maryland BaltimoreDepartment of Pharmaceutical Sciences, School of Pharmacy20 Penn St, Baltimore, MD 2101USA[email protected]Search for other works by this author on:E. Darian;E. DarianUniversity of Maryland BaltimoreDepartment of Pharmaceutical Sciences, School of Pharmacy20 Penn St, Baltimore, MD 2101USA[email protected]Search for other works by this author on:A. D. MacKerell JrA. D. MacKerell JrUniversity of Maryland BaltimoreDepartment of Pharmaceutical Sciences, School of Pharmacy20 Penn St, Baltimore, MD 2101USA[email protected]Search for other works by this author on:
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Chapter 4: Integral Equation Theory of Biomolecules and Electrolytesp51-86ByTyler Luchko;Tyler LuchkoDepartment of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University PiscatawayNJ 08854, USA[email protected]Search for other works by this author on:In Suk Joung;In Suk JoungDepartment of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University PiscatawayNJ 08854, USA[email protected]Search for other works by this author on:David A. CaseDavid A. CaseDepartment of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University PiscatawayNJ 08854, USA[email protected]Search for other works by this author on:
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Chapter 5: Molecular Simulation in the Energy Biosciencesp87-114ByXiaolin Cheng;Xiaolin ChengUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Jerry M. Parks;Jerry M. ParksUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Loukas Petridis;Loukas PetridisUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Benjamin Lindner;Benjamin LindnerUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Roland Schulz;Roland SchulzUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Hao-Bo Guo;Hao-Bo GuoUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Goundla Srinivas;Goundla SrinivasUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:Jeremy C. SmithJeremy C. SmithUT/ORNL Center for Molecular BiophysicsOak Ridge National LaboratoryP. O. Box 2008 Oak RidgeTN 37831USADepartment of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee, M407 Walters Life Sciences1414 Cumberland AvenueKnoxville TN 37996USA[email protected]Search for other works by this author on:
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Chapter 6: Enhancing the Capacity of Molecular Dynamics Simulations with Trajectory Fragmentsp117-137ByAlfredo E. Cardenas;Alfredo E. CardenasInstitute for Computational Engineering and SciencesSearch for other works by this author on:Ron ElberRon ElberInstitute for Computational Engineering and SciencesDepartment of Chemistry and BiochemistryUniversity of Texas at Austin1 University Station C0200, Austin, Texas 78712USA[email protected]; [email protected]Search for other works by this author on:
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Chapter 7: Computing Reaction Rates in Bio-molecular Systems Using Discrete Macro-statesp138-206ByEric Darve;Eric DarveInstitute for Computational and Mathematical EngineeringMechanical Engineering DepartmentStanford UniversityLomita Mall, Stanford CA 94305USA[email protected]Search for other works by this author on:Ernest RyuErnest RyuInstitute for Computational and Mathematical EngineeringSearch for other works by this author on:
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Chapter 8: Challenges in Applying Monte Carlo Sampling to Biomolecular Systemsp207-216ByM. MezeiM. MezeiMount Sinai School of Medicine, Department of Structural and Chemical BiologyOne Gustave L. Levy Pl.New York, NY 10029USA[email protected]Search for other works by this author on:
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Chapter 9: Coarse-grain Protein Modelsp219-248ByN. Ceres;N. CeresBases Moléculaires et Structurales des Systèmes InfectieuxUniversité Lyon1/CNRSUMR 5086, IBCP, 7 Passage du Vercors, 69367, LyonFrance[email protected]Search for other works by this author on:R. LaveryR. LaveryBases Moléculaires et Structurales des Systèmes InfectieuxUniversité Lyon1/CNRSUMR 5086, IBCP, 7 Passage du Vercors, 69367, LyonFrance[email protected]Search for other works by this author on:
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Chapter 10: Generalised Multi-level Coarse-grained Molecular Simulation and its Application to Myosin-V Movementp249-271ByWilliam R. Taylor;William R. TaylorDivision of Mathematical BiologyMRC National Institute for Medical ResearchThe Ridgeway, Mill Hill, London NW7 1AAU.K[email protected]Search for other works by this author on:Zoe KatsimitsouliaZoe KatsimitsouliaDivision of Mathematical BiologyMRC National Institute for Medical ResearchThe Ridgeway, Mill Hill, London NW7 1AAU.K[email protected]Search for other works by this author on:
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Chapter 11: Top-down Mesoscale Models and Free Energy Calculations of Multivalent Protein-Protein and Protein-Membrane Interactions in Nanocarrier Adhesion and Receptor Traffickingp272-292ByJin Liu;Jin LiuDepartment of Bioengineering, University of PennsylvaniaPhiladelphia, PA 19104, USASearch for other works by this author on:Neeraj J. Agrawal;Neeraj J. AgrawalDepartment of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphia, PA 19104, USASearch for other works by this author on:David M. Eckmann;David M. EckmannDepartment of Bioengineering, University of PennsylvaniaPhiladelphia, PA 19104, USADepartment of Anesthesiology and Critical Care, University of PennsylvaniaPhiladelphia, PA 19104, USASearch for other works by this author on:Portonovo S. Ayyaswamy;Portonovo S. AyyaswamyDepartment of Mechanical Engineering and Applied Mechanics, University of PennsylvaniaPhiladelphia, PA 19104, USA[email protected]Search for other works by this author on:Ravi RadhakrishnanRavi RadhakrishnanDepartment of Bioengineering, University of PennsylvaniaPhiladelphia, PA 19104, USASearch for other works by this author on:
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Chapter 12: Studying Proteins and Peptides at Material Surfacesp293-320ByJun Feng;Jun FengDepartment of Biology and BiochemistryUniversity of HoustonHouston, TX 77204-5001USASearch for other works by this author on:Gillian C. Lynch;Gillian C. LynchDepartment of Chemistry and Institute for Molecular DesignUniversity of Houston, HoustonTX 77204-5003USA[email protected]Search for other works by this author on:B. Montgomery PettittB. Montgomery PettittDepartment of Biology and BiochemistryUniversity of HoustonHouston, TX 77204-5001USADepartment of Chemistry and Institute for Molecular DesignUniversity of Houston, HoustonTX 77204-5003USA[email protected]Search for other works by this author on:
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Chapter 13: Multiscale Design: From Theory to Practicep321-344ByJ. Fish;J. FishDepartment of Civil Engineering and Engineering MechanicsColumbia UniversityWest 120th Street, 10027, New YorkUSASearch for other works by this author on:V. Filonova;V. FilonovaDepartment of Civil Engineering and Engineering MechanicsColumbia UniversityWest 120th Street, 10027, New YorkUSASearch for other works by this author on:Z. YuanZ. YuanSearch for other works by this author on:
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