The Statistical Mechanics of Free and Protein-bound DNA by Monte Carlo Simulation PDF Download
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Author: Luke Czapla
Publisher:
ISBN:
Category : DNA-protein interactions
Languages : en
Pages : 126
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Book Description
There are many challenges involved in the simulation of DNA. In this work, novel Monte Carlo techniques are developed and applied to understanding the biophysical properties of DNA. A coarse-grained model is applied to feasibly simulate long DNA chains of hundreds to thousands of base pairs, using a reduced base-pair step representation of the DNA. Using this model, a canonical Monte Carlo simulation of DNA is developed to characterize the structure and flexibility of double-helical DNA. By applying a unique algorithm for generating uncorrelated DNA conformations a priori, limitations of the original Metropolis Monte Carlo algorithm are avoided. Furthermore, there is developing experimental evidence that non-specifically associating proteins that induce DNA bending modulate the in-vivo flexibility of DNA. To investigate the effect of these proteins, a grand canonical Monte Carlo simulation technique is developed, extending the model of free DNA to incorporate non-specific protein-DNA interactions. In this technique, DNA chains are simulated with varying numbers of bound proteins. Ubiquitous DNA architectural proteins such as the prokaroytic nucleoid protein HU and the eukaryotic HMG-box proteins are investigated with this technique. By incorporating structural information from the protein-DNA complexes currently available in the Nucleic Acid Database, models of these DNA-binding proteins are constructed and used in this method. The results predict an enhancement of DNA flexibility due to non-specific binding of these proteins, and calculations of the cyclization (ring-closure) properties and force-extension responses of protein-bound DNA chains compared to free DNA chains are presented. In addition, the effects of these proteins on the topological properties of closed circular DNA and on the looping properties of DNA constrained by binding to the Lac repressor protein assembly are characterized in large-scale parallel simulations. Coordination of protein binding on circular and looped DNA and induction of negative supercoiling of DNA by DNA architectural proteins is predicted, with important biological implications for chromosome organization and transcription regulation.
Author: Luke Czapla
Publisher:
ISBN:
Category : DNA-protein interactions
Languages : en
Pages : 126
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Book Description
There are many challenges involved in the simulation of DNA. In this work, novel Monte Carlo techniques are developed and applied to understanding the biophysical properties of DNA. A coarse-grained model is applied to feasibly simulate long DNA chains of hundreds to thousands of base pairs, using a reduced base-pair step representation of the DNA. Using this model, a canonical Monte Carlo simulation of DNA is developed to characterize the structure and flexibility of double-helical DNA. By applying a unique algorithm for generating uncorrelated DNA conformations a priori, limitations of the original Metropolis Monte Carlo algorithm are avoided. Furthermore, there is developing experimental evidence that non-specifically associating proteins that induce DNA bending modulate the in-vivo flexibility of DNA. To investigate the effect of these proteins, a grand canonical Monte Carlo simulation technique is developed, extending the model of free DNA to incorporate non-specific protein-DNA interactions. In this technique, DNA chains are simulated with varying numbers of bound proteins. Ubiquitous DNA architectural proteins such as the prokaroytic nucleoid protein HU and the eukaryotic HMG-box proteins are investigated with this technique. By incorporating structural information from the protein-DNA complexes currently available in the Nucleic Acid Database, models of these DNA-binding proteins are constructed and used in this method. The results predict an enhancement of DNA flexibility due to non-specific binding of these proteins, and calculations of the cyclization (ring-closure) properties and force-extension responses of protein-bound DNA chains compared to free DNA chains are presented. In addition, the effects of these proteins on the topological properties of closed circular DNA and on the looping properties of DNA constrained by binding to the Lac repressor protein assembly are characterized in large-scale parallel simulations. Coordination of protein binding on circular and looped DNA and induction of negative supercoiling of DNA by DNA architectural proteins is predicted, with important biological implications for chromosome organization and transcription regulation.
Author: Ivet Bahar
Publisher: Garland Science
ISBN: 1351815016
Category : Science
Languages : en
Pages : 337
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Book Description
Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.
Author: Goodfellow
Publisher: CRC Press
ISBN: 9780849371196
Category : Medical
Languages : en
Pages : 224
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Book Description
Molecular dynamics is an important technique with applications in many areas, including drug design, protein engineering, macromolecular structure determination, and molecular recognition. This book concentrates on these exciting applications while briefly summarizing the essential mathematical background. Using standard molecular dynamics and related algorithms, results are presented on protein, carbohydrate, and nucleotide modeling and dynamics. Chapters covering relatively new applications, such as simulated annealing protocol and the free energy perturbation method, are also included. Molecular biologists, biochemists, and researchers in structural molecular biology, chemistry, crystallography, and computer modelling will find this book a useful reference resource.
Author: Igor Kulić
Publisher:
ISBN:
Category :
Languages : en
Pages : 149
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Book Description
Author: Kirill Kuzanyan
Publisher: John Wiley & Sons
ISBN: 1119841704
Category : Science
Languages : en
Pages : 275
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Book Description
Helicities in Geophysics, Astrophysics, and Beyond Helicities play essential roles in numerous geophysical, astrophysical, and magnetohydrodynamic phenomena, thus are studied from various disciplinary viewpoints. Helicities in Geophysics, Astrophysics, and Beyond draws together experts from different research fields to present an interdisciplinary and integrated approach to helicity studies. This synthesis advances understanding of the fundamental physical processes underlying various helicity-related phenomena. Volume highlights include: Concise introduction to fundamental properties of helicities Recent developments and achievements in helicity studies Perspectives from different fields including geophysics, space physics, solar physics, plasma physics, atmospheric and nonlinear sciences A cohesive mathematical, physical, observational, experimental, and numerical strategy for helicity studies A synthesized framework for the application of helicity to real-world problems The American Geophysical Union promotes discovery in Earth and space science for the benefit of humanity. Its publications disseminate scientific knowledge and provide resources for researchers, students, and professionals.
Author: Igor Kulić
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: David P. Landau
Publisher: Cambridge University Press
ISBN: 9780521653664
Category : Mathematics
Languages : en
Pages : 402
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Book Description
This book describes all aspects of Monte Carlo simulation of complex physical systems encountered in condensed-matter physics and statistical mechanics, as well as in related fields, such as polymer science and lattice gauge theory. The authors give a succinct overview of simple sampling methods and develop the importance sampling method. In addition they introduce quantum Monte Carlo methods, aspects of simulations of growth phenomena and other systems far from equilibrium, and the Monte Carlo Renormalization Group approach to critical phenomena. The book includes many applications, examples, and current references, and exercises to help the reader.
Author:
Publisher:
ISBN:
Category : Chemistry
Languages : en
Pages : 2668
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Book Description
Author: Victor A. Bloomfield
Publisher: Sterling Publishing Company
ISBN: 9780935702491
Category : Science
Languages : en
Pages : 854
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Book Description
Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.
Author: David P. Landau
Publisher: Springer Science & Business Media
ISBN: 3540265651
Category : Science
Languages : en
Pages : 287
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Book Description
Over ?fteen years ago, because of the tremendous increase in the power and utility of computer simulations, The University of Georgia formed the ?rst institutional unit devoted to the use of simulations in research and teaching: The Center for Simulational Physics. As the international simulations c- munityexpandedfurther,wesensedaneedforameetingplaceforbothex- riencedsimulatorsandneophytestodiscussnewtechniquesandrecentresults in an environment which promoted lively discussion. As a consequence, the Center for Simulational Physics established an annual workshop on Recent DevelopmentsinComputerSimulationStudiesinCondensedMatterPhysics. This year’s workshop was the seventeenth in this series, and the continued interest shown by the scienti?c community demonstrates quite clearly the useful purpose that these meetings have served. The latest workshop was held at The University of Georgia, February 16–20, 2004, and these proce- ings provide a “status report” on a number of important topics. This volume is published with the goal of timely dissemination of the material to a wider audience. We wish to o?er a special thanks to IBM and to SGI for partial support of this year’s workshop. This volume contains both invited papers and contributed presentations on problems in both classical and quantum condensed matter physics. We hope that each reader will bene?t from specialized results as well as pro?t from exposure to new algorithms, methods of analysis, and conceptual dev- opments.
