Download or read book Long Time Scale Computer Simulations of Proteins written by Peter Eastman and published by . This book was released on 2000 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Bridging the Time Scales written by Peter Nielaba and published by Springer Science & Business Media. This book was released on 2007-10-13 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: The behaviour of many complex materials extends over time- and lengthscales well beyond those that can normally be described using standard molecular dynamics or Monte Carlo simulation techniques. As progress is coming more through refined simulation methods than from increased computer power, this volume is intended as both an introduction and a review of all relevant modern methods that will shape molecular simulation in the forthcoming decade. Written as a set of tutorial reviews, the book will be of use to specialists and nonspecialists alike.
Download or read book Computer Simulations in Condensed Matter From Materials to Chemical Biology Volume 2 written by Mauro Ferrario and published by Springer. This book was released on 2007-04-16 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt: This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 2 offers surveys on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology, including supercooled liquids, spin glasses, colloids, polymers, liquid crystals, biological membranes and folding proteins.
Download or read book The Development of Accurate Force Fields for Protein Simulation written by Yuanfang Jiao and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer simulations have provided a wealth of information concerning a wide range of systems. The precision of computer simulation results depends on the degree of sampling (time scales) achieved, while the accuracy of the results (given sufficient sampling) depends on the quality of force field used. A force field provides a description of the energy for a system of interest. Recently, we have been developing a Kirkwood Buff (KB) force field for molecular dynamics simulations of biological systems. This force field is based on the KB Theory of solutions, emphasizing the accurate description of intermolecular interactions, and reasonably reproducing a range of other physical properties from experiment. In this approach simulation results in terms of KB integrals can be directly compared with experimental data through a KB analysis of the solution properties. The approach therefore provides a simple and clear method to test the capability of a force field. Here we firstly studied a series of alcohol-water mixtures in an attempt to validate the transferability and additivity of the force field. A general fluctuation theory was applied to investigate the properties of these systems, and to compare with computer simulation results. The possible effects of cosolvents on peptides and proteins were then investigated using N-methylacetamide as model for the peptide backbone and urea as cosolvent. A possible explanation for the urea denaturation of protein structure was provided using a thermodynamics point of view involving transfer free energies and preferential interactions obtained from the KB integrals. Finally, potentials for protein backbone and sidechain torsions were developed by fitting to quantum mechanical calculations and NMR data. Simulations of a variety of peptides and proteins in aqueous solutions were then performed to demonstrate the overall reliability of the force field.
Download or read book Molecular Dynamics written by Ben Leimkuhler and published by Springer. This book was released on 2015-05-18 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.
Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer. This book was released on 1995-08-18 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Download or read book Computer Simulations of Protein Folding written by Atipat Rojnuckarin and published by . This book was released on 1998 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Recent Developments In Theoretical Studies Of Proteins written by Ron Elber and published by World Scientific. This book was released on 1996-10-16 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experts provide a unique and broad perspective of the theoretical tools available today to analyze protein structure and function. Topics at the frontier of computational biophysics, such as dynamics and thermodynamics of proteins, reaction path studies, optimization techniques, analytical theories of protein folding, sequence alignment algorithms and electrostatics of proteins are discussed in a pedagogical and complete way. Those entering the field will find the book to be a useful introduction. It will also serve as a complementary text to existing ones that focus on just one of the above subjects.
Download or read book Bayesian Statistics and Single molecule Trajectories written by Daniel L. Ensign and published by Stanford University. This book was released on 2010 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian statistics is a powerful method for inference--possibly the uniquely correct method for inference. As described herein, when applied to a few degrees of freedom from single molecule trajectories, Bayesian statistics yield useful insights into rates, states, and motions.
Download or read book Protein Misfolding written by Rossen Donev and published by Academic Press. This book was released on 2020-01-13 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Misfolding, Volume 118, covers the wide spectrum of diseases and disorders that are attributed to protein misfolding, including degenerative and neurodegenerative, cardiovascular, renal, glaucoma, cancer, cystic fibrosis, Gaucher's disease, and many others. Specific chapters cover Mass spectrometric approaches for profiling protein folding and stability, Biomembranes, a key player in protein misfolding, how Genetic and environmental factors interact to disrupt proteostasis and trigger protein misfolding diseases, Formation of oligomers and large amorphous aggregates by intrinsically disordered proteins, Protein misfolding in ER stress with applications to cardiovascular and renal disease, and much more. - Integrates methods for studying protein misfolding, factors that trigger this process and its role in a wide spectrum of diseases and disorders - Contains timely chapters written by well-renowned authorities in their field - Provides data that is well supported by a number of high quality illustrations, figures and tables, and targets a very wide audience of specialists, researchers and students
Download or read book Computational Chemistry Reviews Of Current Trends Vol 9 written by Jerzy Leszczynski and published by World Scientific. This book was released on 2005-05-30 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vast progress in the area of computational chemistry has been achieved in the last decade. Theoretical methods such as quantum mechanics, molecular dynamics and statistical mechanics have been successfully used to characterize chemical systems and to design new materials, drugs and chemicals. The reviews presented in this volume discuss the current advances in computational methodologies and their applications. The areas covered include materials science, nanotechnology, inorganic and biological systems. The major thrust of the book is to bring timely overviews of new findings and methods applied in the rapidly changing field of computational chemistry.
Download or read book Advances in Protein and Peptide Sciences written by Ben M. Dunn and published by Bentham Science Publishers. This book was released on 2013-10-30 with total page 911 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein and Peptide Sciences is a book series focused on leading-edge research on the structure, physical properties, and functions of proteins and peptides. The series presents highly cited contributions first published in the journal Current Protein and Peptide Science. Authors of these contributions have updated their work with new experimental data and references following their initial research. Each volume highlights a number of important topics in current research in the field of protein and peptide chemistry and molecular biology, including membrane proteins and their interactions with ligands, computational methods, and proteins in disease and biotechnology.
Download or read book Computational Chemistry written by Jerzy Leszczynski and published by World Scientific. This book was released on 2005 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Vast progress in the area of computational chemistry has been achieved in the last decade. Theoretical methods such as quantum mechanics, molecular dynamics and statistical mechanics have been successfully used to characterize chemical systems and to design new materials, drugs and chemicals. The reviews presented in this volume discuss the current advances in computational methodologies and their applications. The areas covered include materials science, nanotechnology, inorganic and biological systems. The major thrust of the book is to bring timely overviews of new findings and methods applied in the rapidly changing field of computational chemistry."--BOOK JACKET.
Download or read book Computer Simulations in Condensed Matter From Materials to Chemical Biology Volume 1 written by Mauro Ferrario and published by Springer. This book was released on 2007-03-09 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Amyloid Prions and Other Protein Aggregates Part B written by and published by Elsevier. This book was released on 2006-10-06 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability of polypeptides to form alternatively folded, polymeric structures such as amyloids and related aggregates is being increasingly recognized as a major new frontier in protein research. This new volume of Methods in Enzymology along with Part C (volume 413) on Amyloid, Prions and other Protein Aggregates continue in the tradition of the first volume (309) in containing detailed protocols and methodological insights, provided by leaders in the field, into the latest methods for investigating the structures, mechanisms of formation, and biological activities of this important class of protein assemblies. - Presents detailed protocols - Includes troubleshooting tips - Provides coverage on structural biology, computational methods, and biology
Download or read book Computer Simulations in Molecular Biology written by Hiqmet Kamberaj and published by Springer Nature. This book was released on 2023-07-31 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.
