Stochastic and Quantum Dynamics of Biomolecular Systems PDF Download
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Author: Christopher Bernido
Publisher: American Institute of Physics
ISBN:
Category : Mathematics
Languages : en
Pages : 234
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Book Description
Conference Location and Date: Jagna, Bohol, Philippines, 3-5 January 2008
Author: Christopher Bernido
Publisher: American Institute of Physics
ISBN:
Category : Mathematics
Languages : en
Pages : 234
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Book Description
Conference Location and Date: Jagna, Bohol, Philippines, 3-5 January 2008
Author: Benoit Roux
Publisher: World Scientific
ISBN: 9811232776
Category : Computers
Languages : en
Pages : 209
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Book Description
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: Christopher C. Bernido
Publisher: Birkhäuser
ISBN: 3319072455
Category : Mathematics
Languages : en
Pages : 304
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Book Description
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.
Author: Takeyuki Hida
Publisher: World Scientific
ISBN: 9813220953
Category : Mathematics
Languages : en
Pages : 230
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Book Description
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.
Author: Christopher C Bernido
Publisher: World Scientific
ISBN: 9814569135
Category : Mathematics
Languages : en
Pages : 202
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Book Description
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.
Author: Thomas Scherngell
Publisher: Springer Science & Business Media
ISBN: 3319026992
Category : Business & Economics
Languages : en
Pages : 382
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Book Description
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.
Author: W.F. van Gunsteren
Publisher: Springer Science & Business Media
ISBN: 9401711208
Category : Technology & Engineering
Languages : en
Pages : 633
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Book Description
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
ISBN: 1420059564
Category : Science
Languages : en
Pages : 492
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Book Description
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: Fabien Gatti
Publisher: Springer Science & Business Media
ISBN: 3642452906
Category : Science
Languages : en
Pages : 281
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Book Description
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.
Author: Oleg Jardetzky
Publisher: IOS Press
ISBN: 9781586030322
Category : Biomolecules
Languages : en
Pages : 212
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Book Description
A collection of articles looking at modern structural biology, summarizing the applications of physical methods - such as x-ray diffraction, high resolution nuclear magnetic resonance and molecular dynamics - to the study of protein structure and dynamics. There is a review of contemporary thoughts within the field, looking at the mechanisms of alloateric transitions and allosteric control, the transmission of information within protein structures and the role of dynamics in determining the specificity of protein - ligand interactions. There is also a look at future innovations.
