Stochastic Dynamics and Energetics of Biomolecular Systems

Stochastic Dynamics and Energetics of Biomolecular Systems
Author: Artem Ryabov
Publisher: Springer
Total Pages: 127
Release: 2015-11-28
Genre: Science
ISBN: 3319271881

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.

Computational Modeling And Simulations Of Biomolecular Systems

Computational Modeling And Simulations Of Biomolecular Systems
Author: Benoit Roux
Publisher: World Scientific
Total Pages: 209
Release: 2021-08-23
Genre: Computers
ISBN: 9811232776

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).

Stochastic and Infinite Dimensional Analysis

Stochastic and Infinite Dimensional Analysis
Author: Christopher C. Bernido
Publisher: Birkhäuser
Total Pages: 304
Release: 2016-08-10
Genre: Mathematics
ISBN: 3319072455

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.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Author: Adam Liwo
Publisher: Springer
Total Pages: 849
Release: 2018-12-19
Genre: Technology & Engineering
ISBN: 3319958437

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.

Let Us Use White Noise

Let Us Use White Noise
Author: Takeyuki Hida
Publisher: World Scientific
Total Pages: 230
Release: 2017-03-10
Genre: Mathematics
ISBN: 9813220953

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.

Molecular Quantum Dynamics

Molecular Quantum Dynamics
Author: Fabien Gatti
Publisher: Springer Science & Business Media
Total Pages: 281
Release: 2014-04-09
Genre: Science
ISBN: 3642452906

This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book "Molecular Quantum Dynamics" offers them an accessible introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.

Methods And Applications Of White Noise Analysis In Interdisciplinary Sciences

Methods And Applications Of White Noise Analysis In Interdisciplinary Sciences
Author: Christopher C Bernido
Publisher: World Scientific
Total Pages: 202
Release: 2014-11-27
Genre: Mathematics
ISBN: 9814569135

Analysis, modeling, and simulation for better understanding of diverse complex natural and social phenomena often require powerful tools and analytical methods. Tractable approaches, however, can be developed with mathematics beyond the common toolbox. This book presents the white noise stochastic calculus, originated by T Hida, as a novel and powerful tool in investigating physical and social systems. The calculus, when combined with Feynman's summation-over-all-histories, has opened new avenues for resolving cross-disciplinary problems. Applications to real-world complex phenomena are further enhanced by parametrizing non-Markovian evolution of a system with various types of memory functions. This book presents general methods and applications to problems encountered in complex systems, scaling in industry, neuroscience, polymer physics, biophysics, time series analysis, relativistic and nonrelativistic quantum systems.

The Geography of Networks and R&D Collaborations

The Geography of Networks and R&D Collaborations
Author: Thomas Scherngell
Publisher: Springer Science & Business Media
Total Pages: 382
Release: 2014-01-20
Genre: Business & Economics
ISBN: 3319026992

The geography of networks and R&D collaborations, in particular the spatial dimension of interactions between organisations performing joint R&D, have attracted a burst of attention in the last decade, both in the scientific study of the networks and in the policy sector. The volume is intended to bring together a selection of articles providing novel theoretical and empirical insights into the geographical dynamics of such networks and R&D collaborations, using new, systematic data sources and employing cutting-edge spatial analysis and spatial econometric techniques. It comprises a section on analytic advances and methodology and two thematic sections on structure and spatial characteristics of R&D networks and the impact of R&D networks and policy implications. The edited volume provides a collection of high-level research contributions with an aim to contribute to the recent debate in economic geography and regional science on how the structure of formal and informal networks modifies and influences the spatial and temporal diffusion of knowledge.

Metastability and Markov State Models in Molecular Dynamics

Metastability and Markov State Models in Molecular Dynamics
Author: Christof Schütte
Publisher: American Mathematical Soc.
Total Pages: 141
Release: 2013-12-26
Genre: Mathematics
ISBN: 0821843591

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.