Stochastic Dynamics Of Reacting Biomolecules

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Stochastic Dynamics of Reacting Biomolecules

Werner Ebeling,Lutz Schimansky-Geier,Yuri M Romanovsky
Stochastic Dynamics of Reacting Biomolecules Book PDF

Author : Werner Ebeling,Lutz Schimansky-Geier,Yuri M Romanovsky
Publisher : World Scientific
Page : 344 pages
File Size : 40,9 Mb
Release : 2003-01-29
Category : Science
ISBN : 9789814487498

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Stochastic Dynamics of Reacting Biomolecules by Werner Ebeling,Lutz Schimansky-Geier,Yuri M Romanovsky Pdf

This is a book about the physical processes in reacting complex molecules, particularly biomolecules. In the past decade scientists from different fields such as medicine, biology, chemistry and physics have collected a huge amount of data about the structure, dynamics and functioning of biomolecules. Great progress has been achieved in exploring the structure of complex molecules. However, there is still a lack of understanding of the dynamics and functioning of biological macromolecules. In particular this refers to enzymes, which are the basic molecular machines working in living systems. This book contributes to the exploration of the physical mechanisms of these processes, focusing on critical aspects such as the role of nonlinear excitations and of stochastic effects. An extensive range of original results has been obtained in the last few years by the authors, and these results are presented together with a comprehensive survey of the state of the art in the field. Contents:Introduction to the Reaction Theory and Cluster Dynamics of Enzymes (W Ebeling, A Netrebko & Yu Romanovsky)Tools of Stochastic Dynamics (L Schimansky-Geier & P Talkner)Motion of Test Particles in a 2-D Potential Landscape (O A Chichigina, A V Netrebko & N V Netrebko)Microscopic Simulations of Activation and Dissociation (W Ebeling, V Yu Podlipchuk, M G Sapeshinsky & A A Valuev)Excitations on Rings of Molecules (A Chetverikov, W Ebeling, M Jenssen & Yu Romanovsky)Fermi Resonance and Kramers Problem in 2-D Force Field (S V Kroo, A V Netrebko, Yu M Romanovsky & L Schimansky-Geier)Molecular Scissors. Cluster Model of Acetylcholinesterase (A Yu Chikishev, S V Kroo, A V Netrebko, N V Netrebko & Yu Romanovsky)Dynamics of Proton Transfer in the Active Site of Chymotrypsin (A Yu Chikishev, B A Grishanin & E V Shuvalova)On the Damping of Cluster Oscillations in Protein Molecules (A Yu Chikishev, A V Netrebko & Yu M Romanovsky)Protein Dynamics and New Approaches to the Molecular Mechanisms of Protein Functioning (K V Shaitan) Readership: Researchers and graduate students in physics, biophysics, molecular biology and the life sciences; experts on nonlinear dynamics and the stochastic process in molecular systems and biomolecules. Keywords:Stochastic Dynamics;Reacting Complex Molecules;Biomolecules;Enzymatic Reactions;Molecular Dynamics;Nonlinear Excitations;Resonances

IUTAM Symposium on Nonlinear Stochastic Dynamics and Control

W.Q. Zhu,Y.K. Lin,G. Q. Cai
IUTAM Symposium on Nonlinear Stochastic Dynamics and Control Book PDF

Author : W.Q. Zhu,Y.K. Lin,G. Q. Cai
Publisher : Springer Science & Business Media
Page : 328 pages
File Size : 42,8 Mb
Release : 2011-03-07
Category : Science
ISBN : 9789400707320

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IUTAM Symposium on Nonlinear Stochastic Dynamics and Control by W.Q. Zhu,Y.K. Lin,G. Q. Cai Pdf

Non-linear stochastic systems are at the center of many engineering disciplines and progress in theoretical research had led to a better understanding of non-linear phenomena. This book provides information on new fundamental results and their applications which are beginning to appear across the entire spectrum of mechanics. The outstanding points of these proceedings are Coherent compendium of the current state of modelling and analysis of non-linear stochastic systems from engineering, applied mathematics and physics point of view. Subject areas include: Multiscale phenomena, stability and bifurcations, control and estimation, computational methods and modelling. For the Engineering and Physics communities, this book will provide first-hand information on recent mathematical developments. The applied mathematics community will benefit from the modelling and information on various possible applications.

Stochastic Dynamics in Computational Biology

Stefanie Winkelmann,Christof Schütte
Stochastic Dynamics in Computational Biology Book PDF

Author : Stefanie Winkelmann,Christof Schütte
Publisher : Springer Nature
Page : 284 pages
File Size : 40,5 Mb
Release : 2021-01-04
Category : Mathematics
ISBN : 9783030623876

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Stochastic Dynamics in Computational Biology by Stefanie Winkelmann,Christof Schütte Pdf

The aim of this book is to provide a well-structured and coherent overview of existing mathematical modeling approaches for biochemical reaction systems, investigating relations between both the conventional models and several types of deterministic-stochastic hybrid model recombinations. Another main objective is to illustrate and compare diverse numerical simulation schemes and their computational effort. Unlike related works, this book presents a broad scope in its applications, from offering a detailed introduction to hybrid approaches for the case of multiple population scales to discussing the setting of time-scale separation resulting from widely varying firing rates of reaction channels. Additionally, it also addresses modeling approaches for non well-mixed reaction-diffusion dynamics, including deterministic and stochastic PDEs and spatiotemporal master equations. Finally, by translating and incorporating complex theory to a level accessible to non-mathematicians, this book effectively bridges the gap between mathematical research in computational biology and its practical use in biological, biochemical, and biomedical systems.

Stochastic Dynamics for Systems Biology

Christian Mazza,Michel Benaim
Stochastic Dynamics for Systems Biology Book PDF

Author : Christian Mazza,Michel Benaim
Publisher : CRC Press
Page : 274 pages
File Size : 55,5 Mb
Release : 2016-04-19
Category : Mathematics
ISBN : 9781466514942

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Stochastic Dynamics for Systems Biology by Christian Mazza,Michel Benaim Pdf

Stochastic Dynamics for Systems Biology is one of the first books to provide a systematic study of the many stochastic models used in systems biology. The book shows how the mathematical models are used as technical tools for simulating biological processes and how the models lead to conceptual insights on the functioning of the cellular processing

Biomolecular Structure and Dynamics

G. Vergoten,T. Theophanides
Biomolecular Structure and Dynamics Book PDF

Author : G. Vergoten,T. Theophanides
Publisher : Springer Science & Business Media
Page : 327 pages
File Size : 54,7 Mb
Release : 2012-12-06
Category : Science
ISBN : 9789401154840

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Biomolecular Structure and Dynamics by G. Vergoten,T. Theophanides Pdf

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.

Computational Chemistry: Reviews Of Current Trends, Vol. 9

Jerzy Leszczynski
Computational Chemistry Reviews Of Current Trends Vol 9 Book PDF

Author : Jerzy Leszczynski
Publisher : World Scientific
Page : 258 pages
File Size : 51,5 Mb
Release : 2005-05-30
Category : Science
ISBN : 9789814481397

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Computational Chemistry: Reviews Of Current Trends, Vol. 9 by Jerzy Leszczynski Pdf

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.

Computational Chemistry

Jerzy Leszczynski
Computational Chemistry Book PDF

Author : Jerzy Leszczynski
Publisher : World Scientific
Page : 260 pages
File Size : 45,5 Mb
Release : 2005
Category : Computers
ISBN : 9789812560971

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Computational Chemistry by Jerzy Leszczynski Pdf

"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.

Statistical Thermodynamics And Stochastic Theory Of Nonequilibrium Systems

Ebeling Werner,Sokolov Igor
Statistical Thermodynamics And Stochastic Theory Of Nonequilibrium Systems Book PDF

Author : Ebeling Werner,Sokolov Igor
Publisher : World Scientific Publishing Company
Page : 344 pages
File Size : 53,9 Mb
Release : 2005-09-23
Category : Science
ISBN : 9789813104631

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Statistical Thermodynamics And Stochastic Theory Of Nonequilibrium Systems by Ebeling Werner,Sokolov Igor Pdf

This book presents both the fundamentals and the major research topics in statistical physics of systems out of equilibrium. It summarizes different approaches to describe such systems on the thermodynamic and stochastic levels, and discusses a variety of areas including reactions, anomalous kinetics, and the behavior of self-propelling particles.

Cellular Oscillatory Mechanisms

Miguel Maroto,Nick Monk
Cellular Oscillatory Mechanisms Book PDF

Author : Miguel Maroto,Nick Monk
Publisher : Springer Science & Business Media
Page : 166 pages
File Size : 52,9 Mb
Release : 2008-12-19
Category : Medical
ISBN : 9780387097947

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Cellular Oscillatory Mechanisms by Miguel Maroto,Nick Monk Pdf

Oscillatory dynamics are a central feature of a wide range of biological processes. This text fully explores cellular oscillations, focusing particularly on elucidating the basic mechanisms that underlie these oscillations.

Biodiversity

Oscar Grillo
Biodiversity Book PDF

Author : Oscar Grillo
Publisher : BoD – Books on Demand
Page : 382 pages
File Size : 44,7 Mb
Release : 2014-05-14
Category : Science
ISBN : 9789535113157

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Biodiversity by Oscar Grillo Pdf

The current world biodiversity consists of an inestimable amount of living forms, that at all levels, from genes to biomes, from individuals to populations, from species to communities, are in constant pursuit of the best strategies to react to the natural and anthropic environmental changes. The arrangement of new and dynamic ecosystems balanced by the formation and the vanishing of species, is the direct consequence of these changes. This book contains comprehensive overviews and original studies focused on ecological and ecosystem functioning studies, hazards and conservation management, assessment of environmental variables affecting species diversity, also considering species richness and distribution, in order to identify the best management strategies to face and solve the conservation problems.

Stochastic Chemical Reaction Systems in Biology

Hong Qian,Hao Ge
Stochastic Chemical Reaction Systems in Biology Book PDF

Author : Hong Qian,Hao Ge
Publisher : Springer Nature
Page : 364 pages
File Size : 40,5 Mb
Release : 2021-10-18
Category : Mathematics
ISBN : 9783030862527

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Stochastic Chemical Reaction Systems in Biology by Hong Qian,Hao Ge Pdf

This book provides an introduction to the analysis of stochastic dynamic models in biology and medicine. The main aim is to offer a coherent set of probabilistic techniques and mathematical tools which can be used for the simulation and analysis of various biological phenomena. These tools are illustrated on a number of examples. For each example, the biological background is described, and mathematical models are developed following a unified set of principles. These models are then analyzed and, finally, the biological implications of the mathematical results are interpreted. The biological topics covered include gene expression, biochemistry, cellular regulation, and cancer biology. The book will be accessible to graduate students who have a strong background in differential equations, the theory of nonlinear dynamical systems, Markovian stochastic processes, and both discrete and continuous state spaces, and who are familiar with the basic concepts of probability theory.

Terahertz Biomedical Science and Technology

Joo-Hiuk Son
Terahertz Biomedical Science and Technology Book PDF

Author : Joo-Hiuk Son
Publisher : CRC Press
Page : 382 pages
File Size : 53,5 Mb
Release : 2014-06-13
Category : Medical
ISBN : 9781466570443

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Terahertz Biomedical Science and Technology by Joo-Hiuk Son Pdf

A number of applications including scientific spectroscopy, security screening, and medical imaging have benefitted from the development and utilization of new and emerging terahertz (THz) generation and detection techniques. Exploring recent discoveries and the advancements of biological behaviors through THz spectroscopy and imaging and the development of THz medical techniques, Terahertz Biomedical Science and Technology contains contributions from scientists and researchers in the terahertz biomedical field and is exclusively dedicated to new and emerging terahertz biomedical research and applications. This text offers an assessment of terahertz technology, and provides a compilation of fundamental biological studies conducted using terahertz waves. It introduces THz electromagnetic waves as a new tool for convergent studies, includes laser-based generation techniques and solid-state devices, contains a number of detectors, and discusses high-field generation methods. The material covers recent advancements in terahertz imaging for medical applications—most specifically in cancer diagnosis—reviewing the current status of the THz imaging technique for diagnosing cancers, and exploring the potential medical applications of THz radiation. It also considers the development of future medical applications using terahertz technology. Summarizes the recent progress made in THz waveguides, which are absolutely essential in the development of THz endoscopes Describes the dynamic imaging of drug absorption in skin, exploiting the sensitivity of THz waves to pharmaceutical materials Explores the principle and applications of THz molecular imaging techniques using nanoparticle probes Scientists and engineers involved in biological research and medical applications using optical techniques, as well as graduate students and instructors in optics, physics, electrical engineering, biology, chemistry, and medicine can benefit from this text which highlights new and emerging biomedical studies utilizing novel THz wave techniques.

Statistical Physics of Biomolecules

Daniel M. Zuckerman
Statistical Physics of Biomolecules Book PDF

Author : Daniel M. Zuckerman
Publisher : CRC Press
Page : 366 pages
File Size : 45,8 Mb
Release : 2010-06-02
Category : Mathematics
ISBN : STANFORD:36105215510137

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Statistical Physics of Biomolecules by Daniel M. Zuckerman Pdf

It is essential for modern students of molecular behavior to understand the physics at the heart of modern molecular science, but traditional presentations of this material are often difficult to penetrate. This volume brings down to earth some of the most intimidating but important theories of molecular biophysics. Students build understanding by focusing on topics such as probability theory, low-dimensional models, and the simplest molecular systems. The book's accessible development of equilibrium and dynamical statistical physics makes this a valuable text for students with limited physics and chemistry backgrounds.

Frontiers of Quantum Chemistry

Marek J. Wójcik,Hiroshi Nakatsuji,Bernard Kirtman,Yukihiro Ozaki
Frontiers of Quantum Chemistry Book PDF

Author : Marek J. Wójcik,Hiroshi Nakatsuji,Bernard Kirtman,Yukihiro Ozaki
Publisher : Springer
Page : 512 pages
File Size : 53,7 Mb
Release : 2017-11-06
Category : Science
ISBN : 9789811056512

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Frontiers of Quantum Chemistry by Marek J. Wójcik,Hiroshi Nakatsuji,Bernard Kirtman,Yukihiro Ozaki Pdf

The purpose of this book is to convey to the worldwide scientific community the rapid and enthusiastic progress of state-of-the-art quantum chemistry. Quantum chemistry continues to grow with remarkable success particularly due to rapid progress in supercomputers. The usefulness of quantum chemistry is almost limitless. Its application covers not only physical chemistry but also organic and inorganic chemistry, physics, and life sciences. This book deals with all of these topics. Frontiers of Quantum Chemistry is closely related to the symposium of the same name held at Kwansei Gakuin University at Nishinomiya, Japan, in November 2015. The book's contributors, however, include not only invited speakers at the symposium but also many other distinguished scientists from wide areas of quantum chemistry around the world.

Dynamics and Kinetics in Structural Biology

Keith Moffat,Eaton E. Lattman
Dynamics and Kinetics in Structural Biology Book PDF

Author : Keith Moffat,Eaton E. Lattman
Publisher : John Wiley & Sons
Page : 292 pages
File Size : 47,7 Mb
Release : 2024-01-03
Category : Science
ISBN : 9781119696285

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Dynamics and Kinetics in Structural Biology by Keith Moffat,Eaton E. Lattman Pdf

Understand the latest experimental tools in structural biology with this pioneering work Structural biology seeks to understand the chemical mechanisms and functions of biological molecules, such as proteins, based on their atomic structures. Until recently, these structures have been studied only statically, using procedures which deliberately freeze atomic motion. However, freezing eliminates the rapid structural motions so essential to biological activity and function; the molecules are inactive. But with the recent development of X-ray free electron laser (XFEL) sources, efforts to conduct dynamic experiments have expanded using the principles of dynamics and kinetics to capture active biological molecules as they function. Dynamics and Kinetics in Structural Biology promotes the development of these experiments and their successful application. It grounds readers in the foundational principles of dynamics and kinetics; proceeds through extended discussions of experimental procedures, data analysis techniques; and explores experimental frontiers in structural dynamics. The book will aid researchers to gather and interpret cutting-edge data on the dynamic structure of biological molecules, under conditions where they retain their biological functions. Dynamics and Kinetics in Structural Biology offers readers: Authorship by founding figures in the field In-depth presentation of time-resolved X-ray crystallography, solution scattering, and more A pioneering contribution to a rapidly developing field of study Dynamics and Kinetics in Structural Biology is essential reading for graduate students, scientists, researchers and industry professionals engaged in structural studies of biological systems. Industry professionals considering dynamic studies in the development of new product lines will also benefit.