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Author: M. Reza Rahimi Tabar Publisher: Springer ISBN: 3030184722 Category : Science Languages : en Pages : 290
Book Description
This book focuses on a central question in the field of complex systems: Given a fluctuating (in time or space), uni- or multi-variant sequentially measured set of experimental data (even noisy data), how should one analyse non-parametrically the data, assess underlying trends, uncover characteristics of the fluctuations (including diffusion and jump contributions), and construct a stochastic evolution equation? Here, the term "non-parametrically" exemplifies that all the functions and parameters of the constructed stochastic evolution equation can be determined directly from the measured data. The book provides an overview of methods that have been developed for the analysis of fluctuating time series and of spatially disordered structures. Thanks to its feasibility and simplicity, it has been successfully applied to fluctuating time series and spatially disordered structures of complex systems studied in scientific fields such as physics, astrophysics, meteorology, earth science, engineering, finance, medicine and the neurosciences, and has led to a number of important results. The book also includes the numerical and analytical approaches to the analyses of complex time series that are most common in the physical and natural sciences. Further, it is self-contained and readily accessible to students, scientists, and researchers who are familiar with traditional methods of mathematics, such as ordinary, and partial differential equations. The codes for analysing continuous time series are available in an R package developed by the research group Turbulence, Wind energy and Stochastic (TWiSt) at the Carl von Ossietzky University of Oldenburg under the supervision of Prof. Dr. Joachim Peinke. This package makes it possible to extract the (stochastic) evolution equation underlying a set of data or measurements.
Author: M. Reza Rahimi Tabar Publisher: Springer ISBN: 3030184722 Category : Science Languages : en Pages : 290
Book Description
This book focuses on a central question in the field of complex systems: Given a fluctuating (in time or space), uni- or multi-variant sequentially measured set of experimental data (even noisy data), how should one analyse non-parametrically the data, assess underlying trends, uncover characteristics of the fluctuations (including diffusion and jump contributions), and construct a stochastic evolution equation? Here, the term "non-parametrically" exemplifies that all the functions and parameters of the constructed stochastic evolution equation can be determined directly from the measured data. The book provides an overview of methods that have been developed for the analysis of fluctuating time series and of spatially disordered structures. Thanks to its feasibility and simplicity, it has been successfully applied to fluctuating time series and spatially disordered structures of complex systems studied in scientific fields such as physics, astrophysics, meteorology, earth science, engineering, finance, medicine and the neurosciences, and has led to a number of important results. The book also includes the numerical and analytical approaches to the analyses of complex time series that are most common in the physical and natural sciences. Further, it is self-contained and readily accessible to students, scientists, and researchers who are familiar with traditional methods of mathematics, such as ordinary, and partial differential equations. The codes for analysing continuous time series are available in an R package developed by the research group Turbulence, Wind energy and Stochastic (TWiSt) at the Carl von Ossietzky University of Oldenburg under the supervision of Prof. Dr. Joachim Peinke. This package makes it possible to extract the (stochastic) evolution equation underlying a set of data or measurements.
Author: Domitilla Del Vecchio Publisher: Princeton University Press ISBN: 1400850509 Category : Science Languages : en Pages : 287
Book Description
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: Christof Schütte Publisher: American Mathematical Soc. ISBN: 0821843591 Category : Mathematics Languages : en Pages : 141
Book Description
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: Alessandro Abate Publisher: Springer ISBN: 331926916X Category : Computers Languages : en Pages : 256
Book Description
This book constitutes the thoroughly referred post-workshop proceedings of the 4th International Workshop on Hybrid Systems biology, HSB 2015, held as part of the Madrid Meet 2015 event, in Madrid, Spain in September 2015. The volume presents 13 full papers together with 2 abstracts of invited sessions from 18 submissions. The scope of the HSB workshop is the general area of dynamical models in Biology with an emphasis on hybrid approaches — by no means restricted to a narrow class of mathematical models — and taking advantage of techniques developed separately in different areas.
Author: Vasudevan Ramesh Publisher: John Wiley & Sons ISBN: 1119484014 Category : Science Languages : en Pages : 1045
Book Description
An essential guide to biomolecular and bioanalytical techniques and their applications Biomolecular and Bioanalytical Techniques offers an introduction to, and a basic understanding of, a wide range of biophysical techniques. The text takes an interdisciplinary approach with contributions from a panel of distinguished experts. With a focus on research, the text comprehensively covers a broad selection of topics drawn from contemporary research in the fields of chemistry and biology. Each of the internationally reputed authors has contributed a single chapter on a specific technique. The chapters cover the specific technique’s background, theory, principles, technique, methodology, protocol and applications. The text explores the use of a variety of analytical tools to characterise biological samples. The contributors explain how to identify and quantify biochemically important molecules, including small molecules as well as biological macromolecules such as enzymes, antibodies, proteins, peptides and nucleic acids. This book is filled with essential knowledge and explores the skills needed to carry out the research and development roles in academic and industrial laboratories. A technique-focused book that bridges the gap between an introductory text and a book on advanced research methods Provides the necessary background and skills needed to advance the research methods Features a structured approach within each chapter Demonstrates an interdisciplinary approach that serves to develop independent thinking Written for students in chemistry, biological, medical, pharmaceutical, forensic and biophysical sciences, Biomolecular and Bioanalytical Techniques is an in-depth review of the most current biomolecular and bioanalytical techniques in the field.
Author: Garegin A. Papoian Publisher: CRC Press ISBN: 1466576170 Category : Science Languages : en Pages : 430
Book Description
"The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Author: Bernold Fiedler Publisher: Springer Science & Business Media ISBN: 3642565891 Category : Mathematics Languages : en Pages : 816
Book Description
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: Gregory R. Bowman Publisher: Springer Science & Business Media ISBN: 9400776063 Category : Science Languages : en Pages : 148
Book Description
The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Author: M. Reza Rahimi Tabar
Author: M. Reza Rahimi Tabar
Author: Domitilla Del Vecchio
Author: Christof Schütte
Author: Alessandro Abate
Author: Arno Kwade
Author: Tamar Schlick
Author: Vasudevan Ramesh
Author: Garegin A. Papoian
Author: Bernold Fiedler
Author: Gregory R. Bowman