On Metastability And Markov State Models For Non Stationary Molecular Dynamics
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On Metastability And Markov State Models For Non Stationary Molecular Dynamics
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Author : Péter Koltai
language : en
Publisher:
Release Date : 2016
On Metastability And Markov State Models For Non Stationary Molecular Dynamics written by Péter Koltai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Metastability And Markov State Models In Molecular Dynamics
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Author : Christof Schütte
language : en
Publisher: American Mathematical Soc.
Release Date : 2013-12-26
Metastability And Markov State Models In Molecular Dynamics written by Christof Schütte and has been published by American Mathematical Soc. this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-26 with Mathematics categories.
Applications in modern biotechnology and molecular medicine often require simulation of biomolecular systems in atomic representation with immense length and timescales that are far beyond the capacity of computer power currently available. As a consequence, there is an increasing need for reduced models that describe the relevant dynamical properties while at the same time being less complex. In this book the authors exploit the existence of metastable sets for constructing such a reduced molecular dynamics model, the so-called Markov state model (MSM), with good approximation properties on the long timescales. With its many examples and illustrations, this book is addressed to graduate students, mathematicians, and practical computational scientists wanting an overview of the mathematical background for the ever-increasing research activity on how to construct MSMs for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecular sensors to molecular aggregation. This book bridges the gap between mathematical research on molecular dynamics and its practical use for realistic molecular systems by providing readers with tools for performing in-depth analysis of simulation and data-analysis methods. Titles in this series are co-published with the Courant Institute of Mathematical Sciences at New York University.
Machine Learning Meets Quantum Physics
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Author : Kristof T. Schütt
language : en
Publisher: Springer Nature
Release Date : 2020-06-03
Machine Learning Meets Quantum Physics written by Kristof T. Schütt and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-06-03 with Science categories.
Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.
Generalisierte Markov Modellierung
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Author : Bernhard Reuter
language : de
Publisher: Springer-Verlag
Release Date : 2020-03-16
Generalisierte Markov Modellierung written by Bernhard Reuter and has been published by Springer-Verlag this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-16 with Mathematics categories.
Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zustände ermöglichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der für das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschränkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzuklären. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu führt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1–40)-Peptids durch und modelliert diese. Der Autor: Bernhard Reuter forscht in der Gruppe Methoden der Medizininformatik an der Eberhard-Karls-Universität Tübingen und der Gruppe Computational Molecular Design am Zuse Institut Berlin. Ein Schwerpunkt seiner Forschung ist die Simulation und Modellierung biomolekularer Nichtgleichgewichtssysteme. Er entwickelt u.a. datenbasierte Methoden zur Modellierung biomolekularer Nichtgleichgewichtsprozesse.
An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation
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Author : Gregory R. Bowman
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-12-02
An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation written by Gregory R. Bowman 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 2013-12-02 with Science categories.
The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Stochastic Dynamics Out Of Equilibrium
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Author : Giambattista Giacomin
language : en
Publisher: Springer
Release Date : 2019-06-30
Stochastic Dynamics Out Of Equilibrium written by Giambattista Giacomin and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-30 with Mathematics categories.
Stemming from the IHP trimester "Stochastic Dynamics Out of Equilibrium", this collection of contributions focuses on aspects of nonequilibrium dynamics and its ongoing developments. It is common practice in statistical mechanics to use models of large interacting assemblies governed by stochastic dynamics. In this context "equilibrium" is understood as stochastically (time) reversible dynamics with respect to a prescribed Gibbs measure. Nonequilibrium dynamics correspond on the other hand to irreversible evolutions, where fluxes appear in physical systems, and steady-state measures are unknown. The trimester, held at the Institut Henri Poincaré (IHP) in Paris from April to July 2017, comprised various events relating to three domains (i) transport in non-equilibrium statistical mechanics; (ii) the design of more efficient simulation methods; (iii) life sciences. It brought together physicists, mathematicians from many domains, computer scientists, as well as researchers working at the interface between biology, physics and mathematics. The present volume is indispensable reading for researchers and Ph.D. students working in such areas.
The Theory Of Critical Phenomena
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Author :
language : en
Publisher: Oxford University Press
Release Date : 1992-06-11
The Theory Of Critical Phenomena written by and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1992-06-11 with Science categories.
The successful calculation of critical exponents for continuous phase transitions is one of the main achievements of theoretical physics over the last quarter-century. This was achieved through the use of scaling and field-theoretic techniques which have since become standard equipment in many areas of physics, especially quantum field theory. This book provides a thorough introduction to these techniques. Continuous phase transitions are introduced, then the necessary statistical mechanics is summarized, followed by standard models, some exact solutions and techniques for numerical simulations. The real-space renormalization group and mean-field theory are then explained and illustrated. The final chapters cover the Landau-Ginzburg model, from physical motivation, through diagrammatic perturbation theory and renormalization to the renormalization group and the calculation of critical exponents above and below the critical temperature.
Innovations In Biomolecular Modeling And Simulations
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Author : Tamar Schlick
language : en
Publisher: Royal Society of Chemistry
Release Date : 2012-05-24
Innovations In Biomolecular Modeling And Simulations written by Tamar Schlick and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-05-24 with Science categories.
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.
Computer Simulations In Condensed Matter From Materials To Chemical Biology Volume 1
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Author : Mauro Ferrario
language : en
Publisher: Springer
Release Date : 2007-03-09
Computer Simulations In Condensed Matter From Materials To Chemical Biology Volume 1 written by Mauro Ferrario and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-03-09 with Science categories.
This comprehensive collection of lectures by leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. Volume 2 is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems.
Free Energy Computations
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Author : Tony Lelivre
language : en
Publisher: World Scientific
Release Date : 2010
Free Energy Computations written by Tony Lelivre and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Science categories.
This monograph provides a general introduction to advanced computational methods for free energy calculations, from the systematic and rigorous point of view of applied mathematics. Free energy calculations in molecular dynamics have become an outstanding and increasingly broad computational field in physics, chemistry and molecular biology within the past few years, by making possible the analysis of complex molecular systems. This work proposes a new, general and rigorous presentation, intended both for practitioners interested in a mathematical treatment, and for applied mathematicians interested in molecular dynamics.