Master Equation Models Of Macromolecular Dynamics From Atomistic Simulation
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Master Equation Models Of Macromolecular Dynamics From Atomistic Simulation
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Author : John D. Chodera
language : en
Publisher:
Release Date : 2006
Master Equation Models Of Macromolecular Dynamics From Atomistic Simulation written by John D. Chodera and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with categories.
This dissertation is concerned with the construction, validation, and use of master equation models for the study of macromolecular conformational dynamics. The master equation formalism is a powerful tool for describing the dynamics of a system that can be characterized by a discrete-state, continuous-time Markov process. Once constructed from a large quantities of short trajectories, the evolution of experimentally measurable dynamical observables can be computed and compared with experiment. Additionally, information not yet directly accessible to experiment but which may be useful in aiding understanding or the generation of novel hypotheses, such as folding pathways, transiently populated conformations, and mean first passage times, can also be easily obtained. We demonstrate that a master equation model constructed from short trajectories can describe slow conformational dynamics for a solvated alanine peptide over long times, propose a number of tests to tell whether a model constructed from short trajectories will adequately describe dynamics over long times, and describe an algorithm for the automatic construction of these models from simulation data. While the focus here is on protein folding and dynamics, these techniques are very general, and can be broadly applied to problems in biomolecular dynamics.
New Algorithms For Macromolecular Simulation
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Author : Benedict Leimkuhler
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-03-22
New Algorithms For Macromolecular Simulation written by Benedict Leimkuhler and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-03-22 with Computers categories.
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.
Extending The Time Scale In Atomistic Simulations
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Author : Sanket Sarkar
language : en
Publisher:
Release Date : 2011
Extending The Time Scale In Atomistic Simulations written by Sanket Sarkar and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Abstract: Materials properties depend on processes that take place on a variety of time scales. These range from atomic vibrations or dislocation-mediated slip processes, which have typical time scales of hundreds of femtoseconds (fs) to hundreds of picoseconds (ps), to diffusion, which may take place on the order of seconds or longer. This disparity in time scales leads to difficulties when trying to model slower processes where individual atomic motions may be important, such as diffusion controlled boundary migration and dislocation climb. A straightforward molecular dynamics (MD) approach, with a typical time step of 1 fs, would require an enormous computation time to adequately capture these processes. This work presents a novel method, called Diffusive Molecular Dynamics (DMD), which can capture the diffusion time scale while retaining the atomic spatial resolution by coarse-graining over atomic vibrations and evolving a site-probability representation of atomic density clouds. DMD solves master equation on a moving atomic grid. It combines long-range elastic effects and short- range atomic interactions simultaneously with gradient thermodynamics.
Molecular Dynamics
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Author : Lichang Wang
language : en
Publisher: BoD – Books on Demand
Release Date : 2012-04-11
Molecular Dynamics written by Lichang Wang and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-04-11 with Computers categories.
Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines
Computational Molecular Dynamics Challenges Methods Ideas
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Author : Peter Deuflhard
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
Computational Molecular Dynamics Challenges Methods Ideas written by Peter Deuflhard and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Mathematics categories.
On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.
Comparisons Between Integral Equation Theory And Molecular Dynamics Simulations For Atomistic Models Of Polyethylene Liquids
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Author :
language : en
Publisher:
Release Date : 1999
Comparisons Between Integral Equation Theory And Molecular Dynamics Simulations For Atomistic Models Of Polyethylene Liquids written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1999 with categories.
Molecular dynamics (MD) simulations were performed on dense liquids of polyethylene chains of 24 and 66 united atom CH2 units. A series of models was studied ranging in atomistic detail from coarse-grained, freely-jointed, tangent site chains to realistic, overlapping site models subjected to bond angle restrictions and torsional potentials. These same models were also treated with the self-consistent, polymer reference interaction site model (PRISM) theory. The intramolecular and total structure factors, as well as, the intermolecular radial distribution functions g(r) and direct correlation functions C(r) were obtained from theory and simulation. Angular correlation functions were also simulation obtained from the MD simulations. Comparisons between theory and reveal that PRISM theory works well for computing the intermolecular structure of coarse-grained chain models, but systematically underpredicts the extent of intermolecular packing as more atomistic details are introduced into the model. A consequence of g(r) having insufficient structure is that the theory yields an isothermal compressibility that progressively becomes larger, relative to the simulations, as overlapping the PRISM sites and angular restrictions are introduced into the model. We found that theory could be considerably improved by adding a tail function to C(r) beyond the effective hard core diameter. The range of this tail function was determined by requiring the theory to yield the correct compressibility.
Dynamics And Transport In Macromolecular Networks
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Author : Li-Tang Yan
language : en
Publisher: John Wiley & Sons
Release Date : 2024-04-08
Dynamics And Transport In Macromolecular Networks written by Li-Tang Yan and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-04-08 with Technology & Engineering categories.
Comprehensive knowledge on concepts and experimental advancement, as well as state-of-the-art computational tools and techniques for simulation and theory Dynamics and Transport in Macromolecular Networks: Theory, Modeling, and Experiments provides a unique introduction to the currently emerging, highly interdisciplinary field of those transport processes that exhibit various dynamic patterns and even anomalous behaviors of dynamics, investigating concepts and experimental advancement, as well as state-of-the-art computational tools and techniques for the simulation of macromolecular networks and the transport behavior in them. The detailed text begins with discussions on the structural organization of various macromolecular networks, then moves on to review and consolidate the latest research advances and state-of-the-art tools and techniques for the experimental and theoretical studies of the transport in macromolecular networks. In so doing, the text extracts and emphasizes common principles and research advancement from many different disciplines while providing up-to-date coverage of this new field of research. Written by highly experienced and internationally renowned specialists in various disciplines, such as polymer, soft matter, chemistry, biophysics, and more, Dynamics and Transport in Macromolecular Networks covers sample topics such as: Modeling (visco)elasticity macromolecular and biomacromolecular networks, covering statistical and elastic models and permanent biomacromolecular networks Focus on controlled degradation in modeling reactive hydrogels, covering mesoscale modeling of reactive polymer networks and modeling crosslinking due to hydrosilylation reaction Dynamic bonds in associating polymer networks, covering segmental and chain dynamics and phase-separated aggregate dynamics Direct observation of polymer reptation in entangled solutions and junction fluctuations in crosslinked networks, covering tube width fluctuations and dynamic fluctuations of crosslinks A much-needed overview of developments and scientific findings in the transport behaviors in macromolecular networks, Dynamics and Transport in Macromolecular Networks is a highly valuable resource for chemists, physicists, and other scientists and engineers working in fields related to macromolecular network systems, both theoretically and experimentally.
Rotational Isomeric State Models In Macromolecular Systems
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Author : Matthias Rehan
language : en
Publisher: Springer
Release Date : 2006-05-09
Rotational Isomeric State Models In Macromolecular Systems written by Matthias Rehan and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-05-09 with Technology & Engineering categories.
Over the past 40 years, RIS models for hundreds of polymer structures have been developed, and now the RIS approach is available in several software packages. However, users are often faced with the time-consuming task of finding the appropriate RIS parameters among the literature. This book facilitates this task by providing a comprehensive overview of the models available. It reviews the literature from the very first applications to the end of 1994, comprises synthetic as well as naturally occuring macromolecules, and tabulates all the pertinent features of published models. It will thus help readers, even those new to this method, to take advantage of this computationally efficient way of assessing the conformational properties of macromolecular systems.
Molecular Dynamics Simulation
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Author : J. M. Haile
language : en
Publisher: Wiley-Interscience
Release Date : 1992-06-05
Molecular Dynamics Simulation written by J. M. Haile and has been published by Wiley-Interscience this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992-06-05 with Technology & Engineering categories.
"Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes
Molecular Dynamics Simulation
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Author : Kun Zhou
language : en
Publisher: Elsevier
Release Date : 2022-02-14
Molecular Dynamics Simulation written by Kun Zhou and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-14 with Technology & Engineering categories.
Molecular Dynamic Simulation: Fundamentals and Applications explains the fundamentals of MD simulation and explores recent developments in advanced modeling approaches based on the MD method. The improvements in efficiency and accuracy delivered by this new research are explained to help readers apply them to a wide range of tasks. Details of the implementation of MD simulation are illustrated by presenting the applications of MD simulation in various aspects of materials study including mechanical, thermal, mass transportation, and absorption/desorption problems. Innovative methods of using MD to explore the mechanics of nano/micromaterials, and for the characterization of crystalline, amorphous and liquid materials are also presented. The rich research experience of the authors in molecular dynamic simulation will ensure that readers are provided with both an in-depth understanding of this method and clear technical guidance.