Download or read book A Nonlinear Model for DNA Dynamics written by and published by . This book was released on 1989 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this paper the thermal equilibrium number of solitons in DNA as a function of absolute temperature and the number of base pairs is calculated. These calculations are effected by modeling DNA as a Toda lattice with parameters chosen to match experimentally measured properties of DNA. It is found that a significant number of solitons is generated at physiological temperature. 23 refs., 2 figs.
Download or read book Nonlinear Models for DNA Dynamics written by V. Muto and published by . This book was released on 1988 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nonlinear Physics of DNA written by Ludmila V. Yakushevich and published by John Wiley & Sons. This book was released on 2006-01-24 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first edition of this book was the first on the physics of DNA to go beyond the simple (simplified) 'linear' approach, and it has since been found that the inclusion of nonlinear effects leads to a significantly improved interpretation of experimental data. This new edition naturally retains this approach, but has been completely revised, updated and expanded to cover recent developments. Beginning with introductory chapters on DNA structure and dynamics, the book also includes a comparison between linear and nonlinear approaches to the DNA molecule, a chapter devoted to the statistics of nonlinear excitations of DNA, and examples for the interpretation of experimental data on the dynamics of DNA in terms of nonlinear theory. Essential reading for researchers in biophysics and nonlinear physics, allowing biologists, chemists and physicists to continue developing new and improved techniques of investigating the DNA molecule.
Download or read book Role of Disorder on the Dynamics of a Nonlinear Model for DNA Thermal Denaturation written by and published by . This book was released on 1990 with total page 11 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dynamics of thermal denaturation of DNA is a good example in which nonlinearity coexits with disorder. The amplitude of the motions is so high that bonds break and the base sequence is inhomogeneous since it contains the genetic code. Using a simple nonlinear model, we study the role of local inhomogeneities or of extended disorder on the dynamics of the localized excitations and on the denaturation rate by numerical simulations at constrained temperature. Approximate analytical results are obtained for the trapping of the breatherlike excitations by isolated defects and the statistical mechanics of the disordered molecule. 17 refs., 4 figs.
Download or read book Nonlinear Discrete Models for DNA Dynamics written by and published by . This book was released on 1989 with total page 12 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this paper we report the investigations on a problem related to DNA dynamics: thermal generation of localized pulses that are called solitons. The thermal generation of solitons in circular homogeneous DNA is investigated by calculating the number of solitons as a function of the absolute temperature. These calculations are effected by using two different models for the DNA molecule. In both models the parameters are chosen to match experimentally measured properties of the molecule. We find that a significant number of solitons is generated at physiological temperatures, and a T13 law is followed at low temperatures. 20 refs., 2 figs.
Download or read book Mathematical Models of Non Linear Excitations Transfer Dynamics and Control in Condensed Systems and Other Media written by Ludmilla A. Uvarova and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: The articles in this book are derived from the Third International Conference of the same name, held June 29-July 3, 1998. Topics include: nonlinear exaltations in condensed systems, evolution of complex systems, dynamics and structure of molecular and biomolecular systems, mathematical models of transfer processes in nonlinear systems and numerical modeling and algorithms.
Download or read book Advanced Mechanical Models of DNA Elasticity written by Yakov M Tseytlin and published by Academic Press. This book was released on 2016-04-08 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advanced Mechanical Models of DNA Elasticity includes coverage on 17 different DNA models and the role of elasticity in biological functions with extensive references. The novel advanced helicoidal model described reflects the direct connection between the molecule helix structure and its specific properties, including nonlinear features and transitions. It provides an introduction to the state of the field of DNA mechanics, known and widely used models with their short analysis, as well as coverage on experimental methods and data, the influence of electrical, magnetic, ionic conditions on the persistence length, and dynamics with viscosity influence. It then addresses the need to understand the nature of the non-linear overstretching transition of DNA under force and why DNA has a negative twist-stretch coupling. Includes coverage of 17 contemporary models of DNA mechanics with analysis Provides comparison of DNA and RNA mechanical features Covers advances in experimental techniques including AFM, X-ray, and optical tweezers Contains extensive references for further reading
Download or read book Stochastic Nonlinear Models of DNA Breathing at a Defect written by Ciprian Ionut Duduiala and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Deoxyribonucleic acid (DNA) is a long polymer consisting of two chains of bases, in which the genetic information is stored. A base from one chain has a corresponding base on the other chain which together form a so-called base-pair. Molecular-dynamics simulations of a normal DNA duplex show that breathing events – the temporary opening of one or more base-pairs – typically occur on the microsecond time-scale. Using the molecular dynamics package AMBER, we analyse, for different twist angles in the range 30-40 degrees of twist, a 12 basepair DNA duplex solvated in a water box, which contains the ’rogue’ base difluorotoluene (F) in place of a thymine base (T). This replacement makes breathing occur on the nanosecond time-scale. The time spent simulating such large systems, as well as the variation of breathing length and frequency with helical twist, determined us to create a simplified model, which is capable to predict with accuracy the DNA behaviour. Starting from a nonlinear Klein-Gordon lattice model and adding noise and damping to our system, we obtain a new mesoscopic model of the DNA duplex, close to that observed in experiments and all-atom MD simulations. Defects are considered in the inter-chain interactions as well as in the along-chain interactions. The system parameters are fitted to AMBER data using the maximum likelihood method. This model enables us to discuss the role of the fluctuation-dissipation relations in the derivation of reduced (mesoscopic) models, the differences between the potential of mean force and the potential energies used in Klein-Gordon lattices and how breathing can be viewed as competition between the along-chain elastic energy, the inter-chain binding energy and the entropy term of the system’s free energy. Using traditional analysis methods, such as principal component analysis, data autocorrelation, normal modes and Fourier transform, we compare the AMBER and SDE simulations to emphasize the strength of the proposed model. In addition, the Fourier transform of the trajectory of the A-F base-pair suggests that DNA is a self-organised system and our SDE model is also capable of preserving this behaviour. However, we reach the conclusion that the critical DNA behaviour needs further investigations, since it might offer some information about bubble nucleation and growth and even about DNA transcription and replication.
Download or read book Nonlinear Dynamics of Nanobiophysics written by Slobodan Zdravković and published by Springer Nature. This book was released on 2022-12-07 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights important aspects of nonlinear dynamics of biophysical nanosystems, such as DNA, alpha helix, and microtubules. It presents the differences between the linear and nonlinear models in these molecules and includes interesting chapters on Soliton dynamics of the DNA molecule. This book is meant not only for researchers but also for both graduate and undergraduate students. Chapters include derivations, detailed explanations, and exercises for students. Therefore, the book is convenient to be used as a textbook in suitable courses.
Download or read book Simple Models of Non linear DNA Dynamics written by and published by . This book was released on 1994 with total page 48 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nonlinear Physics of DNA written by Ludmila V. Yakushevich and published by Wiley-VCH. This book was released on 2004-07-02 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first edition of this book was the first on the physics of DNA to go beyond the simple (simplified) 'linear' approach, and it has since been found that the inclusion of nonlinear effects leads to a significantly improved interpretation of experimental data. This new edition naturally retains this approach, but has been completely revised, updated and expanded to cover recent developments. Beginning with introductory chapters on DNA structure and dynamics, the book also includes a comparison between linear and nonlinear approaches to the DNA molecule, a chapter devoted to the statistics of nonlinear excitations of DNA, and examples for the interpretation of experimental data on the dynamics of DNA in terms of nonlinear theory. Essential reading for researchers in biophysics and nonlinear physics, allowing biologists, chemists and physicists to continue developing new and improved techniques of investigating the DNA molecule.
Download or read book Journal of Nonlinear Mathematical Physics Vol 14 written by and published by atlantis press. This book was released on with total page 647 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Nonlinear Science at the Dawn of the 21st Century written by P.L. Christiansen and published by Springer. This book was released on 2008-01-11 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nonlinear science is by now a well established field of research at the interface of many traditional disciplines and draws on the theoretical concepts developed in physics and mathematics. The present volume gathers the contributions of leading scientists to give the state of the art in many areas strongly influenced by nonlinear research, such as superconduction, optics, lattice dynamics, biology and biomolecular dynamics. While this volume is primarily intended for researchers working in the field care, has been taken that it will also be of benefit to graduate students or nonexpert scientist wishing to familiarize themselves with the current status of research.
Download or read book Nonlinear Dynamics in Biological Systems written by Jorge Carballido-Landeira and published by Springer. This book was released on 2016-07-20 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied mathematicians, biophysicists, and computational biologists.
Download or read book Future Directions of Nonlinear Dynamics in Physical and Biological Systems written by P.L. Christiansen and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: Early in 1990 a scientific committee was formed for the purpose of organizing a high-level scientific meeting on Future Directions of Nonlinear Dynamics in Physical and Biological Systems, in honor of Alwyn Scott's 60th birthday (December 25, 1991). As preparations for the meeting proceeded, they were met with an unusually broad-scale and high level of enthusiasm on the part of the international nonlinear science community, resulting in a participation by 168 scientists from 23 different countries in the conference, which was held July 23 to August 11992 at the Laboratory of Applied Mathematical Physics and the Center for Modelling, Nonlinear Dynamics and Irreversible Thermodynamics (MIDIT) of the Technical University of Denmark. During the meeting about 50 lectures and 100 posters were presented in 9 working days. The contributions to this present volume have been grouped into the following chapters: 1. Integrability, Solitons, and Coherent Structures 2. Nonlinear Evolution Equations and Diffusive Systems 3. Chaotic and Stochastic Dynamics 4. Classical and Quantum Lattices and Fields 5. Superconductivity and Superconducting Devices 6. Nonlinear Optics 7. Davydov Solitons and Biomolecular Dynamics 8. Biological Systems and Neurophysics. AI Scott has made early and fundamental contributions to many of these different areas of nonlinear science. They form an important subset of the total number of the papers and posters presented at the meeting. Other papers from the meeting are being published in a special issue of Physica D Nonlinear Phenomena.
Download or read book Nonlinear Dynamics written by M. Daniel and published by Alpha Science Int'l Ltd.. This book was released on 2000 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contributed articles presented at the International Conference on Nonlinear Dynamics: Integrability and Chaos held at Bharathidasan University during 12-16 Feb., 1998. In honor of Prof. M. Lakshmanan.
Download or read book Complex Population Dynamics Nonlinear Modeling In Ecology Epidemiology And Genetics written by Bernd Blasius and published by World Scientific. This book was released on 2007-09-24 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of review articles is devoted to the modeling of ecological, epidemiological and evolutionary systems. Theoretical mathematical models are perhaps one of the most powerful approaches available for increasing our understanding of the complex population dynamics in these natural systems. Exciting new techniques are currently being developed to meet this challenge, such as generalized or structural modeling, adaptive dynamics or multiplicative processes. Many of these new techniques stem from the field of nonlinear dynamics and chaos theory, where even the simplest mathematical rule can generate a rich variety of dynamical behaviors that bear a strong analogy to biological populations.
