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| Author | : Christopher Bernido |
| Publisher | : American Institute of Physics |
| Total Pages | : 234 |
| Release | : 2008-06-25 |
| Genre | : Mathematics |
| ISBN | : |
Conference Location and Date: Jagna, Bohol, Philippines, 3-5 January 2008
| 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.
| Author | : Yann von Hansen |
| Publisher | : |
| Total Pages | : 248 |
| Release | : 2013 |
| Genre | : |
| ISBN | : |
| Author | : Werner Ebeling |
| Publisher | : World Scientific |
| Total Pages | : 343 |
| Release | : 2003-01-29 |
| Genre | : Science |
| ISBN | : 981448749X |
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.
| Author | : Norbert Schaudinnus |
| Publisher | : |
| Total Pages | : |
| Release | : 2015 |
| Genre | : |
| ISBN | : |
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
| Author | : Edward J. O'Reilly |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2014 |
| Genre | : |
| ISBN | : |
| 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).
| Author | : |
| Publisher | : |
| Total Pages | : 256 |
| Release | : 2014 |
| Genre | : |
| ISBN | : |
| Author | : G. Vergoten |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 327 |
| Release | : 2012-12-06 |
| Genre | : Science |
| ISBN | : 9401154848 |
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.
| 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.
