Advanced Mechanical Models of DNA Elasticity

Advanced Mechanical Models of DNA Elasticity
Author: Yakov M Tseytlin
Publisher: Academic Press
Total Pages: 318
Release: 2016-04-08
Genre: Science
ISBN: 0128020369

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

Statistical Physics of DNA

Statistical Physics of DNA
Author: Nikos Theodorakopoulos
Publisher: World Scientific Publishing Company
Total Pages: 0
Release: 2019-11-13
Genre: DNA
ISBN: 9789811209536

The stability of the DNA double helix is contingent on fine-tuning a number of physicochemical control parameters. Varying any one of them leads to separation of the two strands, in what constitutes a rare physical example of a thermodynamic phase transition in a one-dimensional system. The present book aims at providing a self-contained account of the statistical physics of cooperative processes in DNA, e.g. thermal and mechanical dissociation, force-induced melting, equilibria of hairpin-like secondary structures. In addition, the book presents some fundamental aspects of DNA elasticity, as observed in key experiments, old and new. The latter include some recently published scattering data on apparently soft, short DNA chains and their interpretation in terms of local structural defects (permanent bends, "kinky DNA", after the original Crick-Klug hypothesis). The development of mathematical models used (Kratky-Porod polymer chain, Poland-Scheraga and Peyrard-Bishop-Dauxois models of DNA melting) emphasizes the use of realistic parameters and the relevance of practical numerical methods for comparing with experimental data. Accordingly, a large number of specially produced figures has been included. The presentation is at the level of an advanced undergraduate or introductory graduate course. An extra chapter provides the necessary mathematical background on elasticity of model polymer chains.

Mechanics of Elastic Biomolecules

Mechanics of Elastic Biomolecules
Author: W.A. Linke
Publisher: Springer Science & Business Media
Total Pages: 223
Release: 2012-12-06
Genre: Science
ISBN: 9401001472

A representative cross-section of elastic biomolecules is covered in this volume, which combines seventeen contributions from leading research groups. State-of-the-art molecular mechanics experiments are described dealing with the elasticity of DNA and nucleoprotein complexes, titin and titin-like proteins in muscle, as well as proteins of the cytoskeleton and the extracellular matrix. The book speaks particularly to cell biologists, biophysicists, or bioengineers, and to senior researchers and graduate students alike, who are interested in recent advances in single-molecule technology (optical tweezers technique, atomic force microscopy), EM imaging, and computer simulation approaches to study nanobiomechanics. The findings discussed here have redefined our view of the role mechanical signals play in cellular functions and have greatly helped improve our understanding of biological elasticity in general.

Physical and Numerical Models in Knot Theory

Physical and Numerical Models in Knot Theory
Author: Jorge Alberto Calvo
Publisher: World Scientific
Total Pages: 642
Release: 2005
Genre: Mathematics
ISBN: 9812703462

The physical properties of knotted and linked configurations in space have long been of interest to mathematicians. More recently, these properties have become significant to biologists, physicists, and engineers among others. Their depth of importance and breadth of application are now widely appreciated and valuable progress continues to be made each year. This volume presents several contributions from researchers using computers to study problems that would otherwise be intractable. While computations have long been used to analyze problems, formulate conjectures, and search for special structures in knot theory, increased computational power has made them a staple in many facets of the field. The volume also includes contributions concentrating on models researchers use to understand knotting, linking, and entanglement in physical and biological systems. Topics include properties of knot invariants, knot tabulation, studies of hyperbolic structures, knot energies, the exploration of spaces of knots, knotted umbilical cords, studies of knots in DNA and proteins, and the structure of tight knots. Together, the chapters explore four major themes: physical knot theory, knot theory in the life sciences, computational knot theory, and geometric knot theory.

IUTAM Symposium on Interaction between Dynamics and Control in Advanced Mechanical Systems

IUTAM Symposium on Interaction between Dynamics and Control in Advanced Mechanical Systems
Author: Dick H. van Campen
Publisher: Springer Science & Business Media
Total Pages: 458
Release: 2012-12-06
Genre: Technology & Engineering
ISBN: 9401157782

During the last decades, applications of dynamical analysis in advanced, often nonlinear, engineering systems have been evolved in a revolutionary way. In this context one can think of applications in aerospace engineering like satellites, in naval engineering like ship motion, in mechanical engineering like rotating machinery, vehicle systems, robots and biomechanics, and in civil engineering like earthquake dynamics and offshore technology. One could continue with this list for a long time. The application of advanced dynamics in the above fields has been possible due to the use of sophisticated computational techniques employing powerful concepts of nonlinear dynamics. These concepts have been and are being developed in mathematics, mechanics and physics. It should be remarked that careful experimental studies are vitally needed to establish the real existence and observability of the predicted dynamical phenomena. The interaction between nonlinear dynamics and nonlinear control in advanced engineering systems is becoming of increasing importance because of several reasons. Firstly, control strategies in nonlinear systems are used to obtain desired dynamic behaviour and improved reliability during operation, Applications include power plant rotating machinery, vehicle systems, robotics, etc. Terms like motion control, optimal control and adaptive control are used in this field of interest. Since mechanical and electronic components are often necessary to realize the desired action in practice, the engineers use the term mechatronics to indicate this field. If the desired dynamic behaviour is achieved by changing design variables (mostly called system parameters), one can think of fields like control of chaos.

Nonlinear Dynamics of Nanobiophysics

Nonlinear Dynamics of Nanobiophysics
Author: Slobodan Zdravković
Publisher: Springer Nature
Total Pages: 369
Release: 2022-12-07
Genre: Science
ISBN: 9811953236

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.

Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems

Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems
Author: Alexander A. Golovin
Publisher: Springer Science & Business Media
Total Pages: 356
Release: 2006
Genre: Mathematics
ISBN: 9781402043543

Nano-science and nano-technology are rapidly developing scientific and technological areas that deal with physical, chemical and biological processes that occur on nano-meter scale – one millionth of a millimeter. Self-organization and pattern formation play crucial role on nano-scales and promise new, effective routes to control various nano-scales processes. This book contains lecture notes written by the lecturers of the NATO Advanced Study Institute "Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems" that took place in St Etienne de Tinee, France, in the fall 2004. They give examples of self-organization phenomena on micro- and nano-scale as well as examples of the interplay between phenomena on nano- and macro-scales leading to complex behavior in various physical, chemical and biological systems. They discuss such fascinating nano-scale self-organization phenomena as self-assembly of quantum dots in thin solid films, pattern formation in liquid crystals caused by light, self-organization of micro-tubules and molecular motors, as well as basic physical and chemical phenomena that lead to self-assembly of the most important molecule on the basis of which most of living organisms are built – DNA. A review of general features of all pattern forming systems is also given. The authors of these lecture notes are the leading experts in the field of self-organization, pattern formation and nonlinear dynamics in non-equilibrium, complex systems.

The Mathematics and Mechanics of Biological Growth

The Mathematics and Mechanics of Biological Growth
Author: Alain Goriely
Publisher: Springer
Total Pages: 651
Release: 2017-05-29
Genre: Mathematics
ISBN: 038787710X

This monograph presents a general mathematical theory for biological growth. It provides both a conceptual and a technical foundation for the understanding and analysis of problems arising in biology and physiology. The theory and methods are illustrated on a wide range of examples and applications. A process of extreme complexity, growth plays a fundamental role in many biological processes and is considered to be the hallmark of life itself. Its description has been one of the fundamental problems of life sciences, but until recently, it has not attracted much attention from mathematicians, physicists, and engineers. The author herein presents the first major technical monograph on the problem of growth since D’Arcy Wentworth Thompson’s 1917 book On Growth and Form. The emphasis of the book is on the proper mathematical formulation of growth kinematics and mechanics. Accordingly, the discussion proceeds in order of complexity and the book is divided into five parts. First, a general introduction on the problem of growth from a historical perspective is given. Then, basic concepts are introduced within the context of growth in filamentary structures. These ideas are then generalized to surfaces and membranes and eventually to the general case of volumetric growth. The book concludes with a discussion of open problems and outstanding challenges. Thoughtfully written and richly illustrated to be accessible to readers of varying interests and background, the text will appeal to life scientists, biophysicists, biomedical engineers, and applied mathematicians alike.

Bifurcations of Equilibria in DNA Elasticity

Bifurcations of Equilibria in DNA Elasticity
Author:
Publisher:
Total Pages: 110
Release: 2007
Genre: Bifurcation theory
ISBN:

DNA molecules in the familiar double helical B form are treated here as though they have rod-like structures obtained by stacking the nearly planar base pairs comprising them one on top of another with each rotated by approximately one-tenth of a full turn with respect to its immediate predecessor in the stack. As each base in a base pair is attached to the sugar-phosphate backbone chain of one of the two DNA strands that have come together to form the Watson-Crick structure, and each phosphate group in a backbone chain bears one electronic charge, two such charges are associated with each base pair. Thus, each base pair is subject to not only the elastic forces and moments exerted on it by its neighboring base pairs but also to remote electrostatic forces that, because they are only partially screened out by positively charged counter ions, can render the molecule's equilibrium configurations sensitive to changes in the concentration c of salt in the medium. The observation that the step from one base pair to the next can be one of several distinct types, each having its own mechanical properties that depend on the nucleotide composition of the step, and the assumption that a base pair is rigid, led to the development of a theory of sequence dependent DNA elasticity [Coleman, Olson, and Swigon, J. Chem. Phys. 118, 7127-7140, (2003)]. The theory of DNA molecules in aqueous solution developed here is based on but goes beyond that theory. It takes into account the intramolecular electrostatic interactions of the negatively charged phosphate groups in the molecule and the impenetrability of the DNA molecule for cases in which the electrostatic repulsive forces do not suffice to avoid self penetration. The theory permits one to calculate equilibrium configurations, to determine their stability, and to study the dependence of them on salt concentration and on all kinds of end conditions. When the intramolecular electrostatic forces are taken into account, the equations of mechanical equilibrium for a DNA molecule with N+1 base pairs are a system of mu*N non-linear equations, where mu, the number of kinematical variables describing the relative displacement and orientation of adjacent base pairs is in general 6; it reduces to 3 when base-pair steps are assumed to be inextensible and non-shearable. An efficient numerically stable computational scheme is here presented for solving those equations and determining the mechanical stability of the calculated equilibrium configurations. That scheme is employed to compute and analyze bifurcation diagrams in which c is the bifurcation parameter and to show that, for an intrinsically curved molecule, small changes in c can have a strong effect on stable equilibrium configurations. Cases are presented in which self-contact must be taken into account even though the intramolecular electrostatic forces of repulsion are strong.