TY  - BOOK
AU  - Leimkuhler,Benedict
AU  - Chipot,Christophe
AU  - Elber,Ron
AU  - Laaksonen,Aatto
AU  - Mark,Alan
AU  - Schlick,Tamar
AU  - Schütte,Christoph
AU  - Skeel,Robert
ED  - SpringerLink (Online service)
TI  - New Algorithms for Macromolecular Simulation
T2  - Lecture Notes in Computational Science and Engineering,
SN  - 9783540316183
AV  - QA76.9.C65 
U1  - 003.3 23
PY  - 2006///
CY  - Berlin, Heidelberg
PB  - Springer Berlin Heidelberg
KW  - Computer science
KW  - Computer simulation
KW  - Biology
KW  - Mathematics
KW  - Mathematical physics
KW  - Biomedical engineering
KW  - Computer Science
KW  - Simulation and Modeling
KW  - Mathematical Biology in General
KW  - Mathematical and Computational Physics
KW  - Biomedical Engineering
N1  - Macromolecular Models: From Theories to Effective Algorithms -- Membrane Protein Simulations: Modelling a Complex Environment -- Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes -- Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach -- Learning to Align Sequences: A Maximum-Margin Approach -- Minimization of Complex Molecular Landscapes -- Overcoming Energetic and Time Scale Barriers Using the Potential Energy Surface -- The Protein Folding Problem -- Dynamical and Stochastic-Dynamical Foundations for Macromolecular Modelling -- Biomolecular Sampling: Algorithms, Test Molecules, and Metrics -- Approach to Thermal Equilibrium in Biomolecular Simulation -- The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method -- The Langevin Equation for Generalized Coordinates -- Metastability and Dominant Eigenvalues of Transfer Operators -- Computation of the Free Energy -- Free Energy Calculations in Biological Systems. How Useful Are They in Practice? -- Numerical Methods for Calculating the Potential of Mean Force -- Replica-Exchange-Based Free-Energy Methods -- Fast Electrostatics and Enhanced Solvation Models -- Implicit Solvent Electrostatics in Biomolecular Simulation -- New Distributed Multipole Metdhods for Accurate Electrostatics in Large-Scale Biomolecular Simulations -- Quantum-Chemical Models for Macromolecular Simulation -- Towards Fast and Reliable Quantum Chemical Modelling of Macromolecules -- Quantum Chemistry Simulations of Glycopeptide Antibiotics -- Panel Discussion
N2  - Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art
UR  - http://dx.doi.org/10.1007/3-540-31618-3
ER  -