Download or read book Polymer Physics Experiments with Single DNA Molecules written by Douglas E. Smith and published by . This book was released on 1999 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Investigating Polymer Physics with Single Molecule Experiment and Brownian Dynamics Simulation written by Charles Martin Schroeder and published by . This book was released on 2004 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Theory and Experiments in Polymer Physics with Single Molecules of DNA written by Stephen Ronald Quake and published by . This book was released on 1994 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Studying Topologically Complex DNA at the Single molecule Level written by Wan Yuan Beatrice Soh and published by . This book was released on 2020 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over two decades ago, with advances in microfabrication techniques and fluorescence microscopy, single-molecule studies emerged as a powerful approach to investigate polymer dynamics at the molecular level. By providing a platform for the direct observation and precise manipulation of individual polymer molecules, single-molecule studies allow for the probing of microscopic interactions that give rise to the macroscopic properties of the polymer system. Single molecule studies have been widely used to investigate the static and dynamic properties of double-stranded deoxyribonucleic acid (DNA) as a model polymer. Such studies not only help to develop a fundamental understanding of key topics in polymer physics that cannot be easily accessed via traditional bulk experimental methods, but also facilitate the development of emerging DNA mapping and sequencing techniques. The majority of single-molecule studies to date have involved linear DNA molecules. It is known that topological constraints on the molecular level have a signicant influence on polymer dynamics. A nascent area in the field of polymer physics is the study of polymers with complex topologies. In this thesis, we present a series of single-molecule experiments and Brownian dynamics simulations used to investigate the polymer physics of topologically complex DNA. Specically, we focus on knotted polymers, ring polymers and catenated polymer networks. To investigate the impact of a knot on polymer dynamics, we employ a combined approach of single-molecule experiments and Brownian dynamics simulations. We study experimentally the steady-state behavior of knotted polymers in planar elongational fields and nd that the presence of a knot leads to a faster relaxation time and, accordingly, a shift in the coilstretch transition for the molecule. In consequence, the untying of a knot near the coilstretch transition can give rise to dramatic changes in chain conformation. We use Brownian dynamics simulations to study in detail the impact of the knot untying process on polymer dynamics in planar elongational fields and complement the simulations with experimental results. As a knot moves o the chain in an elongational field, the knot size changes due to the non-uniform tension prole along the chain and causes a change in the eective Weissenberg number, which in turn leads to a change in chain extension. With the use of simulations, we further investigate the knot untying process by probing the topological pathway of an untying knot. We study the distributions of knot conformational states and knot untying pathways on uniformly tensioned chains and chains subjected to elongational fields, and demonstrate that external fields can be used to influence how a knot unties from a chain. Next, we shift focus to ring polymers. We use single-molecule experiments to study the dynamics of self-entangled circular DNA. Our results demonstrate that ring polymers can self-entangle by forming self-threadings, and that such threadings can lead to a signicant slowdown in polymer dynamics. It seems counterintuitive that self-entanglements can arise in ring polymers, which lack chain ends. To delve into the physics of self-entanglements on circular chains, we implement a macroscopic system that allows for the direct visualization of chain conformation. We investigate the formation of self-entanglements on granular chains subjected to a tumbling motion, and use the well-studied self-entanglements on linear chains as a framework for interpreting self-entanglements on circular chains. We develop a method to characterize the self-entanglements on circular chains with known topological descriptors from knot theory and propose a general mechanism for the self-entanglement of circular chains. Finally, we consider the deformation dynamics of catenated DNA networks. A kinetoplast is a complex network of catenated DNA rings that resembles a two-dimensional polymeric system. We perform single-molecule experiments to study the deformation response of kinetoplasts in a planar elongational field. Our results demonstrate that kinetoplasts deform in a stagewise fashion and undergo transient deformation at large strains, as a result of conformational rearrangements from a metastable state. In contrast to linear polymers that display a coil-stretch transition, kinetoplasts do not exhibit an abrupt transition between the non-deformed and deformed states.

Download or read book Giant Molecules written by A. I?U. Grosberg and published by World Scientific. This book was released on 2011 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt: ?? 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.

Download or read book Studying Self entangled DNA at the Single Molecule Level written by Christopher Benjamin Renner and published by . This book was released on 2015 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Knots seem to be found every time one encounters long, stringy objects. At the macroscopic scale, knots are seen every day in shoelaces, tangled hair, or woven clothing, yet they also present themselves at the microscopic scale in long polymer molecules. Knots can be found often in DNA packaged within the viral capsid, occasionally in proteins, and during the transcription and replication of genomic DNA. Biological knots are similarly thought to change the dynamics of viral ejection, protein digestion, and translocation of biomolecules through nanopores. Despite the prevalence of knots in important biological polymers, to date, the physics of knots is only partially understood. DNA has become a well-accepted model system for investigating the physics of single polymer molecules due to its tremendous biological significance and useful experimental properties. Recent advances in microscopy and nanofabrication have enabled the real-time manipulation and imaging of single DNA molecules, facilitating fundamental studies concerning the physics of individual polymers. Leveraging these experimental techniques, this thesis aims to explore the changes knots can impart on the static and dynamic properties of single DNA molecules. We first demonstrate a mechanism for the previously observed phenomenon of the compression and self-knotting of a single DNA molecule in the presence of an electric field. We then use this mechanism to study the process of stretching complex DNA knots in an extensional field. These knots dramatically alter the way DNA stretches in two ways: an initially arrested state and a subsequently slowed stretching phase. Our work consists of the first experimental support of these phenomena, originally predicted by simulation and theory. We then develop theoretical arguments, shown to agree with simulation results, for the physics that govern the distribution of sizes of knots that stochastically occur on DNA molecules, and more broadly, all semiflexible polymers. We then extend our theory to the case where the entire DNA molecule is confined and elongated within a channel. Here, the complex non-monotonic behavior of the sizes of knots agrees with our modified theory. We finally present the results of dynamical simulations where knots on polymers interact with flows or forces. We first examine the behavior of a knot along a polymer extended by extensional flow. The flow may cause a knot to be swept off a polymer molecule, and the motion of a knot is consistent with a model. Different families of knots display different rates of motion, and we explain this difference with a simple topological mechanism. We then turn to examine the case of knots jamming on a polymer molecule extended with high tensile forces. A simple energy barrier hopping argument qualitatively explains the observed slowdown in dynamics of knots. We use these results to reexamine the problem of DNA knots jamming during nanopore translocation, and our results establish the potential for using knots to slow and control the rate of translocation by a ratcheting mechanism. The impact of this thesis is threefold. First, we have demonstrated a novel experimental platform capable of interrogating DNA knots, likely the most efficient of its kind. Second, we have established a theoretical framework for the size and probability of knotting in single molecules capable of directing experiments where these properties need to be controlled. Finally, we have shown how knotted topologies can be manipulated by external flows or forces, which have applications involving preconditioning molecules to unknotted states or the jamming of knotted molecules in nanopores.

Download or read book Mathematics of DNA Structure Function and Interactions written by Craig John Benham and published by Springer Science & Business Media. This book was released on 2009-07-30 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: Propelled by the success of the sequencing of the human and many related genomes, molecular and cellular biology has delivered significant scientific breakthroughs. Mathematics (broadly defined) continues to play a major role in this effort, helping to discover the secrets of life by working collaboratively with bench biologists, chemists and physicists. Because of its outstanding record of interdisciplinary research and training, the IMA was an ideal venue for the 2007-2008 IMA thematic year on Mathematics of Molecular and Cellular Biology. The kickoff event for this thematic year was a tutorial on Mathematics of Nucleic Acids, followed by the workshop Mathematics of Molecular and Cellular Biology, held September 15--21 at the IMA. This volume is dedicated to the memory of Nicholas R. Cozzarelli, a dynamic leader who fostered research and training at the interface between mathematics and molecular biology. It contains a personal remembrance of Nick Cozzarelli, plus 15 papers contributed by workshop speakers. The papers give an overview of state-of-the-art mathematical approaches to the understanding of DNA structure and function, and the interaction of DNA with proteins that mediate vital life processes.

Download or read book Single Molecule Sensing Beyond Fluorescence written by Warwick Bowen and published by Springer Nature. This book was released on 2022-03-01 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an interesting snapshot of recent advances in the field of single molecule nanosensing. The ability to sense single molecules, and to precisely monitor and control their motion is crucial to build a microscopic understanding of key processes in nature, from protein folding to chemical reactions. Recently a range of new techniques have been developed that allow single molecule sensing and control without the use of fluorescent labels. This volume provides an overview of recent advances that take advantage of micro- and nanoscale sensing technologies and provide the prospect for rapid future progress. The book endeavors to provide basic introductions to key techniques, recent research highlights, and an outlook on big challenges in the field and where it will go in future. It is a valuable contribution to the field of single molecule nanosensing and it will be of great interest to graduates and researchers working in this topic.

Download or read book Flexible Polymer Chains in Elongational Flow written by Tuan Q. Nguyen and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: The behavior of polymer solutions in simple shear flows has been the subject of considerable research in the past. On the other hand, reports on polymers in elongational flow have appeared comparatively recently in the literature. Elongational flow with an inherent low vorticity is known to be more effective in extending polymer chains than simple shear flow and thus is more interesting from the point of view of basic (molecular chain dynamics at high deformation) and applied polymer science (rheology, fiber extrusion, drag reduction, flow through porous media). Undoubtly, one landmark in the field of polymer dynamics in elongational flow was the notion of critical strain-rate for chain extension, initially put forward by A. Peterlin (1966) and later refined into the "coil-stretching" transition by P. G. de Gennes and H. Hinch (1974). In the two decades which followed, significant progress in the understanding of chain conformation in "strong" flow has been accomplished through a combination of advances in instrumentation, computation techniques and theoretical studies. As a result of the multidisciplinary nature of the field, information on polymer chains in "strong" flow is accessible only from reviews and research papers scattered in disparate scientific journals. An important objective of this book is to remedy that situation by providing the reader with up-to-date knowledge in a single volume. The editors therefore invited leading specialists to provide both fundamental and applied information on the multiple facets of chain deformation in elongational flow.

Download or read book Single molecule Studies of DNA Dynamics and Intermolecular Forces written by Rae Marie Robertson and published by . This book was released on 2007 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA molecules were used as a model system to investigate fundamental problems in polymer physics; namely, how molecular length, topology and concentration influence the dynamical properties of polymers. A set of DNA molecules suitable for polymer studies was prepared using molecular biology techniques. Video fluorescence microscopy and single-molecule tracking were used to determine self-diffusion coefficients of DNA molecules. Optical tweezers were used to measure the intermolecular forces confining entangled DNA molecules. Scaling of diffusion with molecular length was in agreement with the Zimm model for dilute solutions of linear and circular DNA, indicating that excluded volume effects are appreciable for both topologies. Scaling of diffusion with concentration was also determined for the four possible topological combinations of linear and circular molecules: linear DNA diffusing in a solution of linear DNA, linear DNA in circular DNA, circular in circular, and circular in linear. For lower concentrations molecular topology had little effect and scaling was in agreement with that of the Rouse model. As concentration was increased topology played a much larger role and scaling crossed over to that of the reptation model, predicted to describe the dynamics of entangled polymers. The notable exception was the strongly hindered diffusion observed for a circular molecule diffusing in an entangled linear solution, suggesting the importance of constraint release. Using a new experimental approach with optical tweezers, a tube-like field confining a single entangled molecule was measured, in accord with the key assumption of the reptation model. A time-dependent harmonic potential opposed displacement transverse to the molecular contour, and the force relaxations following displacement were composed of three distinct modes. A characteristic tube radius of the entangled solution was also determined, close to the classically predicted value. The dependence of the above findings on molecular topology and concentration was also investigated. In particular, for an entangled solution of circular DNA of the same length and concentration, the confining tube radius was 25% smaller and the longest relaxation time was ~3 times shorter than with linear DNA. For large displacements the confining force for circular DNA was also substantially lower and shorter range than that measured with linear DNA.

Download or read book Giant Molecules Here There And Everywhere 2nd Edition written by Alexander Y Grosberg and published by World Scientific. This book was released on 2010-09-24 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: “… 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 Gennes Nobel 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.

Download or read book Single Molecule Analysis written by Iddo Heller and published by Springer Nature. This book was released on 2023-11-13 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: This third edition volume expands on the previous editions with new discussions on the latest techniques and developments in the field. The chapters in this book are organized into four parts, and cover topics such as optical tweezers; single-molecule fluorescence tools; atomic force microscopy; magnetic tweezers; applications to virus protein shells, unfolding of proteins, nucleic acids, motor proteins, in vivo and in vitro; and protocols to establish specific surface interactions and perform force calibration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Single Molecule Analysis: Methods and Protocols, Third Edition is a valuable resource for all researchers who want to learn more about this exciting and still expanding field. Chapters 2, 7, 8, 9, 12, 18, and 19 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Download or read book Nano Micro Science and Technology in Biorheology written by Rio Kita and published by Springer. This book was released on 2015-06-09 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrating basic to applied science and technology in medicine, pharmaceutics, molecular biology, biomedical engineering, biophysics and irreversible thermodynamics, this book covers cutting-edge research of the structure and function of biomaterials at a molecular level. In addition, it examines for the first time studies performed at the nano- and micro scale. With innovative technologies and methodologies aiming to clarify the molecular mechanism and macroscopic relationship, Nano/Micro Science and Technology in Biorheology thoroughly covers the basic principles of these studies, with helpful step-by-step explanations of methodologies and insight into medical applications. Written by pioneering researchers, the book is a valuable resource for academics and industry scientists, as well as graduate students, working or studying in bio-related fields.

Download or read book Polymer Dynamics in Confined and Concentrated Media written by Ajey Krishnamurty Dambal and published by . This book was released on 2009 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Single Molecule Studies of Flexible Polymers Under Shear and Mixed Flows written by Rodrigo Esquivel Teixeira and published by . This book was released on 2005 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Biophysics for Beginners written by Helmut Schiessel and published by CRC Press. This book was released on 2013-12-20 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a new way of looking at living matter. It uses quantitative experimental and theoretical methods to open a new window for studying and understanding life processes. This textbook gives compact introductions to the basics of the field, including molecular cell biology and statistical physics. It then presents in-depth discussions of more advanced biophysics subjects, progressing to state-of-the-art experiments and their theoretical interpretations. The book is unique by offering a general introduction to biophysics, yet at the same time restricting itself to processes that occur inside the cell nucleus and that involve biopolymers (DNA, RNA, and proteins). This allows for an accessible read for beginners and a springboard for specialists who wish to continue their study in more detail.

Download or read book Polymer Physics written by Wenbing Hu and published by Springer Science & Business Media. This book was released on 2012-11-05 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: A molecular view on the fundamental issues in polymer physics is provided with an aim at students in chemistry, chemical engineering, condensed matter physics and material science courses. An updated translation by the author, a renowned Chinese chemist, it has been proven to be an effective source of learning for many years. Up-to-date developments are reflected throughout the work in this concise presentation of the topic. The author aims at presenting the subject in an efficient manner, which makes this particularly suitable for teaching polymer physics in settings where time is limited, without having to sacrifice the extensive scope that this topic demands.