Stochastic Dynamics And Energetics Of Biomolecular Systems
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Author |
: Artem Ryabov |
Publisher |
: Springer |
Total Pages |
: 127 |
Release |
: 2015-11-28 |
ISBN-10 |
: 9783319271880 |
ISBN-13 |
: 3319271881 |
Rating |
: 4/5 (80 Downloads) |
Synopsis Stochastic Dynamics and Energetics of Biomolecular Systems by : Artem Ryabov
This thesis both broadens and deepens our understanding of the Brownian world. It addresses new problems in diffusion theory that have recently attracted considerable attention, both from the side of nanotechnology and from the viewpoint of pure academic research. The author focusses on the difussion of interacting particles in restricted geometries and under externally controlled forces. These geometries serve, for example, to model ion transport through narrow channels in cell membranes or a Brownian particle diffusing in an optical trap, now a paradigm for both theory and experiment. The work is exceptional in obtaining explicit analytically formulated answers to such realistic, experimentally relevant questions. At the same time, with its detailed exposition of the problems and a complete set of references, it presents a clear and broadly accessible introduction to the domain. Many of the problem settings and the corresponding exact asymptotic laws are completely new in diffusion theory.
Author |
: Benoit Roux |
Publisher |
: World Scientific |
Total Pages |
: 209 |
Release |
: 2021-08-23 |
ISBN-10 |
: 9789811232770 |
ISBN-13 |
: 9811232776 |
Rating |
: 4/5 (70 Downloads) |
Synopsis Computational Modeling And Simulations Of Biomolecular Systems by : Benoit Roux
This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).
Author |
: Domitilla Del Vecchio |
Publisher |
: Princeton University Press |
Total Pages |
: 287 |
Release |
: 2014-10-26 |
ISBN-10 |
: 9781400850501 |
ISBN-13 |
: 1400850509 |
Rating |
: 4/5 (01 Downloads) |
Synopsis Biomolecular Feedback Systems by : Domitilla Del Vecchio
This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu
Author |
: W.F. van Gunsteren |
Publisher |
: Springer Science & Business Media |
Total Pages |
: 633 |
Release |
: 2013-11-27 |
ISBN-10 |
: 9789401711203 |
ISBN-13 |
: 9401711208 |
Rating |
: 4/5 (03 Downloads) |
Synopsis Computer Simulation of Biomolecular Systems by : W.F. van Gunsteren
The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...
Author |
: Gregory A. Voth |
Publisher |
: CRC Press |
Total Pages |
: 492 |
Release |
: 2008-09-22 |
ISBN-10 |
: 9781420059564 |
ISBN-13 |
: 1420059564 |
Rating |
: 4/5 (64 Downloads) |
Synopsis Coarse-Graining of Condensed Phase and Biomolecular Systems by : Gregory A. Voth
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.
Author |
: Bernold Fiedler |
Publisher |
: Springer Science & Business Media |
Total Pages |
: 816 |
Release |
: 2012-12-06 |
ISBN-10 |
: 9783642565892 |
ISBN-13 |
: 3642565891 |
Rating |
: 4/5 (92 Downloads) |
Synopsis Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems by : Bernold Fiedler
Presenting very recent results in a major research area, this book is addressed to experts and non-experts in the mathematical community alike. The applied issues range from crystallization and dendrite growth to quantum chaos, conveying their significance far into the neighboring disciplines of science.
Author |
: Christof Schütte |
Publisher |
: American Mathematical Soc. |
Total Pages |
: 141 |
Release |
: 2013-12-26 |
ISBN-10 |
: 9780821843598 |
ISBN-13 |
: 0821843591 |
Rating |
: 4/5 (98 Downloads) |
Synopsis Metastability and Markov State Models in Molecular Dynamics by : Christof Schütte
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.
Author |
: G. Vergoten |
Publisher |
: Springer Science & Business Media |
Total Pages |
: 327 |
Release |
: 2012-12-06 |
ISBN-10 |
: 9789401154840 |
ISBN-13 |
: 9401154848 |
Rating |
: 4/5 (40 Downloads) |
Synopsis Biomolecular Structure and Dynamics by : G. Vergoten
Biomolecular Structure and Dynamics describes recent fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The book provides a broad perspective of the current theoretical aspects and recent experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could fruitfully collaborate.
Author |
: David A. Case |
Publisher |
: University of California, San Francisco |
Total Pages |
: 998 |
Release |
: 2022-04-28 |
ISBN-10 |
: |
ISBN-13 |
: |
Rating |
: 4/5 ( Downloads) |
Synopsis Amber 2022 by : David A. Case
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools22, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Author |
: Andrey B. Rubin |
Publisher |
: John Wiley & Sons |
Total Pages |
: 833 |
Release |
: 2017-07-13 |
ISBN-10 |
: 9781119160274 |
ISBN-13 |
: 1119160278 |
Rating |
: 4/5 (74 Downloads) |
Synopsis Compendium of Biophysics by : Andrey B. Rubin
The most thorough coverage of biophysics available, in a handy, easy-to-read volume, perfect as a reference for experienced engineers or as a textbook for the novice. Following up on his first book, Fundamentals of Biophysics, the author, a well-known scientist in this area, builds on that foundation by offering the biologist or scientist an advanced, comprehensive coverage of biophysics. Structuring the book into four major parts, he thoroughly covers the biophysics of complex systems, such as the kinetics and thermodynamic processes of biological systems, in the first part. The second part is dedicated to molecular biophysics, such as biopolymers and proteins, and the third part is on the biophysics of membrane processes. The final part is on photobiological processes. This ambitious work is a must-have for the veteran biologist, scientist, or chemist working in this field, and for the novice or student, who is interested in learning about biophysics. It is an emerging field, becoming increasingly more important, the more we learn about and develop the science. No library on biophysics is complete without this text and its precursor, both available from Wiley-Scrivener.