New Algorithms for Macromolecular Simulation
Contributor(s): Leimkuhler, Benedict [editor.1] | Chipot, Christophe [editor.1] | Elber, Ron [editor.1] | Laaksonen, Aatto [editor.1] | Mark, Alan [editor.1] | Schlick, Tamar [editor.1] | Sch�tte, Christoph [editor.1 ] | Skeel, Robert [editor.2 ] | SpringerLink (Online service)0.
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BookSeries: Lecture Notes in Computational Science and Engineering, 490.Berlin, Heidelberg : Springer Berlin Heidelberg, 2006. Description: XVI, 367 p. 85 illus., 8 illus. in color. online resource.Content type: text Media type: computer Carrier type: online resourceISBN: 9783540316183.Subject(s): Computer science | Computer simulation | Biomathematics | Physics | Biomedical engineering.1 | Computer Science.2 | Simulation and Modeling.2 | Mathematical and Computational Biology.2 | Theoretical, Mathematical and Computational Physics.2 | Biomedical Engineering.1DDC classification: 003.3 Online resources: Click here to access online | Item type | Current location | Call number | Status | Date due | Barcode | Item holds |
|---|---|---|---|---|---|---|
| PK Kelkar Library, IIT Kanpur | Available | EBK429 |
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.
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.
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