Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Stochastic And Quantum Dynamics Of Biomolecular Systems
Download Stochastic And Quantum Dynamics Of Biomolecular Systems full books in PDF, epub, and Kindle. Read online Stochastic And Quantum Dynamics Of Biomolecular Systems ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Book Synopsis Stochastic and Quantum Dynamics of Biomolecular Systems by : Christopher Bernido
Download or read book Stochastic and Quantum Dynamics of Biomolecular Systems written by Christopher Bernido and published by American Institute of Physics. This book was released on 2008-06-25 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conference Location and Date: Jagna, Bohol, Philippines, 3-5 January 2008
Book Synopsis Stochastic Dynamics and Energetics of Biomolecular Systems by : Artem Ryabov
Download or read book Stochastic Dynamics and Energetics of Biomolecular Systems written by Artem Ryabov and published by Springer. This book was released on 2015-11-28 with total page 127 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Stochastic Dynamics in Biomolecular Systems by : Yann von Hansen
Download or read book Stochastic Dynamics in Biomolecular Systems written by Yann von Hansen and published by . This book was released on 2013 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Stochastic Dynamics Of Reacting Biomolecules by : Werner Ebeling
Download or read book Stochastic Dynamics Of Reacting Biomolecules written by Werner Ebeling and published by World Scientific. This book was released on 2003-01-29 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Stochastic Modeling of Biomolecular Systems Using the Data-driven Langevin Equation by : Norbert Schaudinnus
Download or read book Stochastic Modeling of Biomolecular Systems Using the Data-driven Langevin Equation written by Norbert Schaudinnus and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Zusammenfassung: Nowadays, molecular dynamics (MD) simulations are widely used to understand the dynamics of biomolecular systems.Although MD simulations provide a description in atomistic detail, they are limited with respect to both system size and simulation time for computational reasons.However, dynamics which take place on rather long time scales can often be captured along few collective coordinates.The data-driven Langevin Equation (dLE) is a systematic approach to capture dynamical information in this reduced space, establishing local field estimates from an underlying time series.These fields are in turn used to propagate dynamics.The dLE therefore relies on a clear timescale separation of a low-dimensional coordinate that enables to treat the remaining degrees of freedom as a stochastic bath.This thesis focuses on the characteristics and capabilities of the dLE approach. The property of the dLE to operate in a self-consistent manner can be applied to test the validity of the model assumptions.In particular, an important extension of the dLE is developed which accounts for inertia effects.This more generalized form of the dLE is shown to suitably recover the conformational dynamics of a small peptide system, showing a nontrivial dynamical behavior.Aside from establishing a technical guideline on how to construct a dLE model and verify its functionality, several promising applications are demonstrated.For instance, a dLE-based enhanced sampling scheme is introduced which facilitates to forecast the long-time behavior of a reduced system from short spatially overlapping trajectory samples
Book Synopsis Quantum Traits in the Dynamics of Biomolecular Systems by : Edward J. O'Reilly
Download or read book Quantum Traits in the Dynamics of Biomolecular Systems written by Edward J. O'Reilly and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Modeling And Simulations Of Biomolecular Systems by : Benoit Roux
Download or read book Computational Modeling And Simulations Of Biomolecular Systems written by Benoit Roux and published by World Scientific. This book was released on 2021-08-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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).
Book Synopsis Quantum Traits in the Dynamics of Biomolecular Systems by :
Download or read book Quantum Traits in the Dynamics of Biomolecular Systems written by and published by . This book was released on 2014 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Stochastic and Infinite Dimensional Analysis by : Christopher C. Bernido
Download or read book Stochastic and Infinite Dimensional Analysis written by Christopher C. Bernido and published by Birkhäuser. This book was released on 2016-08-10 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a collection of papers covering applications from a wide range of systems with infinitely many degrees of freedom studied using techniques from stochastic and infinite dimensional analysis, e.g. Feynman path integrals, the statistical mechanics of polymer chains, complex networks, and quantum field theory. Systems of infinitely many degrees of freedom create their particular mathematical challenges which have been addressed by different mathematical theories, namely in the theories of stochastic processes, Malliavin calculus, and especially white noise analysis. These proceedings are inspired by a conference held on the occasion of Prof. Ludwig Streit’s 75th birthday and celebrate his pioneering and ongoing work in these fields.
Book Synopsis Quantum Mechanical Simulation Methods for Studying Biological Systems by : Dominique Bicout
Download or read book Quantum Mechanical Simulation Methods for Studying Biological Systems written by Dominique Bicout and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is now generally agreed that a deeper understanding of biological processes requires a multi-disciplinary approach employing the tools of biology, chemistry, and physics. Such understanding involves study of biomacromolecules and their functions, which includes how they interact, their reactions, and how information is transmitted between them. This volume is devoted to quantum mechanical simulation techniques, which have developed rapidly in recent years. It covers quantum mechanical calculations of large systems, molecular dynamics combining quantum and classical algorithms, quantum dynamical simulations, and electron and proton transfer processes in proteins and in solutions.
Book Synopsis Biomolecular Structure and Dynamics by : G. Vergoten
Download or read book Biomolecular Structure and Dynamics written by G. Vergoten and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Quantum Processes in Biology by : José Antonio Fornés
Download or read book Quantum Processes in Biology written by José Antonio Fornés and published by Springer Nature. This book was released on with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Model Order Reduction for Stochastic Models of Biomolecular Systems with Time-scale Separation by : Narmada Kumari Herath
Download or read book Model Order Reduction for Stochastic Models of Biomolecular Systems with Time-scale Separation written by Narmada Kumari Herath and published by . This book was released on 2018 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomolecular systems often involve reactions that take place on different time-scales, giving rise to 'slow' and 'fast' system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In deterministic systems, methods to obtain such reduced-order models are well defined by the singular perturbation or averaging techniques. However, model reduction of stochastic systems remains an ongoing area of research. In particular, existing model reduction methods for stochastic models of biomolecular systems lack rigorous error quantifications between the full and reduced dynamics. Furthermore, they only provide approximations for the slow variable dynamics, making the application of such methods to biomolecular systems difficult since the variables of interest are typically mixed (i.e., they encompass both fast and slow variables). In this thesis, we consider biomolecular systems modeled using the chemical Langevin equation (CLE) and the Linear Noise Approximation (LNA). Specifically, we consider biomolecular systems with linear propensity functions modeled by the CLE and systems with arbitrary propensity functions modeled by the LNA. For these systems, we obtain reduced-order models that approximate both the slow and fast variables under time-scale separation conditions. In particular, with suitable assumptions, we prove that the moments of the reduced-order models converge to those of the full systems as the time-scale separation becomes large. Our results further provide a rigorous justification for the accuracy of the stochastic total quasi-steady state approximation (tQSSA). We then consider two applications of these reduced-order models. In the first application, we analyze the trade-offs between modularity and signal noise in biomolecular networks. In the second application, we consider the application of the reduced-order LNA developed in this work to obtain reduced-order stochastic models for gene-regulatory networks.
Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo
Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 849 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.
Book Synopsis Biomolecular Feedback Systems by : Domitilla Del Vecchio
Download or read book Biomolecular Feedback Systems written by Domitilla Del Vecchio and published by Princeton University Press. This book was released on 2014-10-26 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Let Us Use White Noise by : Takeyuki Hida
Download or read book Let Us Use White Noise written by Takeyuki Hida and published by World Scientific. This book was released on 2017-03-10 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: Why should we use white noise analysis? Well, one reason of course is that it fills that earlier gap in the tool kit. As Hida would put it, white noise provides us with a useful set of independent coordinates, parametrized by 'time'. And there is a feature which makes white noise analysis extremely user-friendly. Typically the physicist — and not only he — sits there with some heuristic ansatz, like e.g. the famous Feynman 'integral', wondering whether and how this might make sense mathematically. In many cases the characterization theorem of white noise analysis provides the user with a sweet and easy answer. Feynman's 'integral' can now be understood, the 'It's all in the vacuum' ansatz of Haag and Coester is now making sense via Dirichlet forms, and so on in many fields of application. There is mathematical finance, there have been applications in biology, and engineering, many more than we could collect in the present volume.Finally, there is one extra benefit: when we internalize the structures of Gaussian white noise analysis we will be ready to meet another close relative. We will enjoy the important similarities and differences which we encounter in the Poisson case, championed in particular by Y Kondratiev and his group. Let us look forward to a companion volume on the uses of Poisson white noise.The present volume is more than a collection of autonomous contributions. The introductory chapter on white noise analysis was made available to the other authors early on for reference and to facilitate conceptual and notational coherence in their work.
Book Synopsis Theoretical Physics for Biological Systems by : Paola Lecca
Download or read book Theoretical Physics for Biological Systems written by Paola Lecca and published by CRC Press. This book was released on 2019-01-30 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.
