Tight Binding Methods For Overdamped Brownian Motion And Their Application To Molecular Motors PDF Download
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| Author | : Thi Thanh Phuong Nguyen |
| Publisher | : |
| Total Pages | : 131 |
| Release | : 2017 |
| Genre | : |
| ISBN | : |
Download Tight-binding Methods for Overdamped Brownian Motion and Their Application to Molecular Motors Book in PDF, ePub and Kindle
Biomolecular motors are molecules that transform energy to perform physiological functions. The operation of molecular motors has a number of interesting physical properties that have attracted a great deal of investigation. One of the most compelling theories describes molecular motors as Brownian motion on a multidimensional free-energy potential landscape. Approximation methods are required to be able to compare this theory with experimental results. In this thesis, we develop two tight-binding methods to systematically transform the continuous equation describing Brownian motion on a potential with deep wells to a much simpler discrete master equation that can be used to facilitate comparison with experiments. Both methods are based on an expansion in a basis of localized states. One of them, the generalized Wannier-state method, exploits the periodicity of the system to define localized states in terms of Bloch eigenfunctions. The other method, analogous to the atomic-orbital approach of quantum mechanics, defines localized states in terms of the eigenfunctions of local metastable potentials around individual wells. For simplicity, we focus on the tight-coupling regime where the average diffusion dynamics on the multidimensional potential landscape can be approximated by the diffusion along a one-dimensional coupling channel. We show that the tight-binding methods connect the master equation to properties of the potential landscape and allow the regime of validity of the master equation to be determined. Thus, in contrast to more phenomenological treatments, our work provides a link between discrete master equations and an underlying theory of molecular motor operation. Finally, applying our method to particular model potentials, we find that the theory predicts qualitatively different discrete operation for molecular motors in different regimes that could be observed in current single-molecule experiments.
| Author | : José Antonio Fornés |
| Publisher | : Springer Nature |
| Total Pages | : 198 |
| Release | : 2021-02-04 |
| Genre | : Science |
| ISBN | : 3030649571 |
Download Principles of Brownian and Molecular Motors Book in PDF, ePub and Kindle
Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Biomolecular motors are proteins able of converting chemical energy into mechanical motion and force. Because of their dimension, the many small parts that make up molecular motors must operate at energies only a few times greater than those of the thermal baths. The description of molecular motors must be stochastic in nature. Their actions are often described in terms of Brownian Ratchets mechanisms. In order to describe the principles used in their movement, we need to use the tools that theoretical physics give us. In this book we centralize on the some physical mechanisms of molecular motors.
| Author | : José Antonio Fornés |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2021 |
| Genre | : |
| ISBN | : 9783030649586 |
Download Principles of Brownian and Molecular Motors Book in PDF, ePub and Kindle
Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Biomolecular motors are proteins able of converting chemical energy into mechanical motion and force. Because of their dimension, the many small parts that make up molecular motors must operate at energies only a few times greater than those of the thermal baths. The description of molecular motors must be stochastic in nature. Their actions are often described in terms of Brownian Ratchets mechanisms. In order to describe the principles used in their movement, we need to use the tools that theoretical physics give us. In this book we centralize on the some physical mechanisms of molecular motors.
| Author | : Martin Reichelsdorfer |
| Publisher | : |
| Total Pages | : 99 |
| Release | : 2010 |
| Genre | : |
| ISBN | : |
Download On Brownian Motion of Asymmetric Particles Book in PDF, ePub and Kindle
| Author | : Jan A. Freund |
| Publisher | : Springer |
| Total Pages | : 512 |
| Release | : 2008-01-11 |
| Genre | : Science |
| ISBN | : 3540453962 |
Download Stochastic Processes in Physics, Chemistry, and Biology Book in PDF, ePub and Kindle
The theory of stochastic processes originally grew out of efforts to describe Brownian motion quantitatively. Today it provides a huge arsenal of methods suitable for analyzing the influence of noise on a wide range of systems. The credit for acquiring all the deep insights and powerful methods is due ma- ly to a handful of physicists and mathematicians: Einstein, Smoluchowski, Langevin, Wiener, Stratonovich, etc. Hence it is no surprise that until - cently the bulk of basic and applied stochastic research was devoted to purely mathematical and physical questions. However, in the last decade we have witnessed an enormous growth of results achieved in other sciences - especially chemistry and biology - based on applying methods of stochastic processes. One reason for this stochastics boom may be that the realization that noise plays a constructive rather than the expected deteriorating role has spread to communities beyond physics. Besides their aesthetic appeal these noise-induced, noise-supported or noise-enhanced effects sometimes offer an explanation for so far open pr- lems (information transmission in the nervous system and information p- cessing in the brain, processes at the cell level, enzymatic reactions, etc.). They may also pave the way to novel technological applications (noise-- hanced reaction rates, noise-induced transport and separation on the na- scale, etc.). Key words to be mentioned in this context are stochastic r- onance, Brownian motors or ratchets, and noise-supported phenomena in excitable systems.
| Author | : A. I?U. Grosberg |
| Publisher | : World Scientific |
| Total Pages | : 347 |
| Release | : 2011 |
| Genre | : Technology & Engineering |
| ISBN | : 9812839224 |
Download Giant Molecules Book in PDF, ePub and Kindle
?? Giant molecules are important in our everyday life. But, as pointed out by the authors, they are also associated with a culture. What Bach did with the harpsichord, Kuhn and Flory did with polymers. We owe a lot of thanks to those who now make this music accessible ??Pierre-Gilles de GennesNobel Prize laureate in Physics(Foreword for the 1st Edition, March 1996)This book describes the basic facts, concepts and ideas of polymer physics in simple, yet scientifically accurate, terms. In both scientific and historic contexts, the book shows how the subject of polymers is fascinating, as it is behind most of the wonders of living cell machinery as well as most of the newly developed materials. No mathematics is used in the book beyond modest high school algebra and a bit of freshman calculus, yet very sophisticated concepts are introduced and explained, ranging from scaling and reptations to protein folding and evolution. The new edition includes an extended section on polymer preparation methods, discusses knots formed by molecular filaments, and presents new and updated materials on such contemporary topics as single molecule experiments with DNA or polymer properties of proteins and their roles in biological evolution.
| Author | : John J. Kasianowicz |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 46 |
| Release | : 2002-07-31 |
| Genre | : Science |
| ISBN | : 9781402006975 |
Download Structure and Dynamics of Confined Polymers Book in PDF, ePub and Kindle
Polymers are essential to biology because they can have enough stable degrees of freedom to store the molecular code of heredity and to express the sequences needed to manufacture new molecules. Through these they perform or control virtually every function in life. Although some biopolymers are created and spend their entire career in the relatively large free space inside cells or organelles, many biopolymers must migrate through a narrow passageway to get to their targeted destination. This suggests the questions: How does confining a polymer affect its behavior and function? What does that tell us about the interactions between the monomers that comprise the polymer and the molecules that confine it? Can we design and build devices that mimic the functions of these nanoscale systems? The NATO Advanced Research Workshop brought together for four days in Bikal, Hungary over forty experts in experimental and theoretical biophysics, molecular biology, biophysical chemistry, and biochemistry interested in these questions. Their papers collected in this book provide insight on biological processes involving confinement and form a basis for new biotechnological applications using polymers. In his paper Edmund DiMarzio asks: What is so special about polymers? Why are polymers so prevalent in living things? The chemist says the reason is that a protein made of N amino acids can have any of 20 different kinds at each position along the chain, resulting in 20 N different polymers, and that the complexity of life lies in this variety.
| Author | : Kim Sneppen |
| Publisher | : Cambridge University Press |
| Total Pages | : 328 |
| Release | : 2005-08-25 |
| Genre | : Science |
| ISBN | : 9780521844192 |
Download Physics in Molecular Biology Book in PDF, ePub and Kindle
This book, first published in 2005, is a discussion for advanced physics students of how to use physics to model biological systems.
| Author | : William Bialek |
| Publisher | : Princeton University Press |
| Total Pages | : 653 |
| Release | : 2012-12-17 |
| Genre | : Science |
| ISBN | : 1400845572 |
Download Biophysics Book in PDF, ePub and Kindle
A physicist's guide to the phenomena of life Interactions between the fields of physics and biology reach back over a century, and some of the most significant developments in biology—from the discovery of DNA's structure to imaging of the human brain—have involved collaboration across this disciplinary boundary. For a new generation of physicists, the phenomena of life pose exciting challenges to physics itself, and biophysics has emerged as an important subfield of this discipline. Here, William Bialek provides the first graduate-level introduction to biophysics aimed at physics students. Bialek begins by exploring how photon counting in vision offers important lessons about the opportunities for quantitative, physics-style experiments on diverse biological phenomena. He draws from these lessons three general physical principles—the importance of noise, the need to understand the extraordinary performance of living systems without appealing to finely tuned parameters, and the critical role of the representation and flow of information in the business of life. Bialek then applies these principles to a broad range of phenomena, including the control of gene expression, perception and memory, protein folding, the mechanics of the inner ear, the dynamics of biochemical reactions, and pattern formation in developing embryos. Featuring numerous problems and exercises throughout, Biophysics emphasizes the unifying power of abstract physical principles to motivate new and novel experiments on biological systems. Covers a range of biological phenomena from the physicist's perspective Features 200 problems Draws on statistical mechanics, quantum mechanics, and related mathematical concepts Includes an annotated bibliography and detailed appendixes
| Author | : Federico Toschi |
| Publisher | : Springer Nature |
| Total Pages | : 309 |
| Release | : 2019-09-25 |
| Genre | : Science |
| ISBN | : 3030233707 |
Download Flowing Matter Book in PDF, ePub and Kindle
This open access book, published in the Soft and Biological Matter series, presents an introduction to selected research topics in the broad field of flowing matter, including the dynamics of fluids with a complex internal structure -from nematic fluids to soft glasses- as well as active matter and turbulent phenomena. Flowing matter is a subject at the crossroads between physics, mathematics, chemistry, engineering, biology and earth sciences, and relies on a multidisciplinary approach to describe the emergence of the macroscopic behaviours in a system from the coordinated dynamics of its microscopic constituents. Depending on the microscopic interactions, an assembly of molecules or of mesoscopic particles can flow like a simple Newtonian fluid, deform elastically like a solid or behave in a complex manner. When the internal constituents are active, as for biological entities, one generally observes complex large-scale collective motions. Phenomenology is further complicated by the invariable tendency of fluids to display chaos at the large scales or when stirred strongly enough. This volume presents several research topics that address these phenomena encompassing the traditional micro-, meso-, and macro-scales descriptions, and contributes to our understanding of the fundamentals of flowing matter. This book is the legacy of the COST Action MP1305 “Flowing Matter”.
