Methods For Increasing Model Accuracy And Simulation Time Scales Of Biological Processes With Molecular Dynamics
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Methods For Increasing Model Accuracy And Simulation Time Scales Of Biological Processes With Molecular Dynamics
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Author : Koon Heng Ivan Teo
language : en
Publisher:
Release Date : 2016
Methods For Increasing Model Accuracy And Simulation Time Scales Of Biological Processes With Molecular Dynamics written by Koon Heng Ivan Teo 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.
Molecular Modeling At The Atomic Scale
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Author : Ruhong Zhou
language : en
Publisher: CRC Press
Release Date : 2014-08-21
Molecular Modeling At The Atomic Scale written by Ruhong Zhou and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-08-21 with Science categories.
Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.
Lengthening The Timescale Reach Of Molecular Dynamics
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Author :
language : en
Publisher:
Release Date : 2012
Lengthening The Timescale Reach Of Molecular Dynamics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Biomolecular Simulations
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Author : Luca Monticelli
language : en
Publisher: Humana Press
Release Date : 2016-05-01
Biomolecular Simulations written by Luca Monticelli and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-05-01 with Computers categories.
This Methods in Molecular Biology volume reviews common methods used in molecular modeling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques."
Molecular Simulation Studies In Material And Biological Sciences
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Author : Kholmirzo Kholmurodov
language : en
Publisher: Nova Publishers
Release Date : 2007
Molecular Simulation Studies In Material And Biological Sciences written by Kholmirzo Kholmurodov and has been published by Nova Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Science categories.
Book & CD. Computer molecular simulations of complex multi-particle systems play a fascinating role in fundamental physics, biochemical and life sciences. Having an increasingly significant impact on many applied industries, especially in modern biophysical and nanotechnological areas, molecular simulation provides a set of tools for predicting many functional properties of molecular systems. The chemical, pharmaceutical, materials and related industries -- all share the computer molecular simulation methods. The molecular simulation studies cover different fields of either biological processes -- protein folding and electron densities of DNA and proteins, or thin film formations and surface-cluster phenomena in nanoelectronics, synthetic copolymers and biopolymer design in biochemistry, so on. Practically all of the world's present supercomputers and many specially developed high performance computing clusters over the world are performing molecular simulations or are aimed on these needs. This book presents leading international research in this dynamic field.
Molecular Simulations And Biomembranes
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Author : Mark S. P. Sansom
language : en
Publisher: Royal Society of Chemistry
Release Date : 2010
Molecular Simulations And Biomembranes written by Mark S. P. Sansom 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 2010 with Science categories.
The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.
Efficient Sampling Of Protein Conformational Dynamics And Prediction Of Mutation Effects
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Author : Hongbin Wan
language : en
Publisher:
Release Date : 2019
Efficient Sampling Of Protein Conformational Dynamics And Prediction Of Mutation Effects written by Hongbin Wan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; however, MD simulations are typically limited to the microsecond timescale, whereas biological motions can take seconds or longer. Because of this, it remains extremely challenging to restrain simulations using ensemble-averaged experimental observables. Among various approaches to elucidate the kinetics of molecular simulations, Markov State Models (MSMs) have proven their ability to extract both kinetic and thermodynamic properties of long-timescale motions using ensembles of shorter MD simulation trajectories. In this dissertation, we have implemented an MSM path-entropy method, based on the idea of maximum-caliber, to efficiently predict the changes in protein folding behavior upon mutation. Next, we explore the accuracy of different MSM estimators applied to trajectory data obtained by adaptive seeding, in which new rounds of short MD simulations are collected from states of interest, and propose a simple method to build accurate models by population re-weighting of the transition count matrix. Finally, we explore ways to reconcile simulated ensembles with Hydrogen/Deuterium exchange (HDX) protection measurements, by constructing multi-ensemble Markov State Models (MEMMs) from biased MD simulations, and reconciling these predictions against the experimental data using the BICePs (Bayesian Inference of Conformational Populations) algorithm. We apply this approach to model the native-state conformational ensemble of apomyoglobin at neutral pH.
Bridging The Time Scales
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Author : Peter. Nielaba
language : en
Publisher:
Release Date : 2014-01-15
Bridging The Time Scales written by Peter. Nielaba and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-01-15 with categories.
Computational Modeling Of Biological Systems
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Author : Nikolay V Dokholyan
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-02-12
Computational Modeling Of Biological Systems written by Nikolay V Dokholyan 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 2012-02-12 with Science categories.
Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.
Accelerating Molecular Dynamics Simulations With High Performance Reconfigurable Systems
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Author : Shihchin Chiu
language : en
Publisher:
Release Date : 2011
Accelerating Molecular Dynamics Simulations With High Performance Reconfigurable Systems written by Shihchin Chiu 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: Molecular Dynamics (MD) simulation plays an important role in understanding functionally important phenomena of biological processes. Many of such events, however, occur on time scales beyond the capabilities of modern computers. Hence, accelerating MD simulations becomes one of critical challenges in the current study of Computational Biology and Chemistry. For the past several years, various implementations and efficient algorithms have been developed toward this goal. Of these, accelerating MD with Field Programmable Gate Arrays (FPGAs) has been shown to be a viable candidate for improved MD cost/performance. Given the intense competition from multi-core and GPUs, there is now a question whether MD on High Performance Reconfigurable Computing (HPRC) can be competitive. The goal of this research is to create an FPGA-based MD system to achieve substantial speedup over production MD software without compromising simulation quality. In one part of the study, we systematically explore and evaluate the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, equation complexity, and various other optimizations. We find that the FPGAs' Block RAM (BRAM) architecture makes them well suited to support unusually fine-grained intervals. This leads to a reduction in other logic and a proportional increase in performance. In the other part, we present the first FPGA study of the filtering of particle pairs having nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, six force pipelines running at nearly 200 MHz can fit on the FPGA. This results in a 26x per core speedup for the nonbonded short-range force. The resulting integrated system is likely to make FPGAs highly competitive for MD.