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Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition
by Yogambigai VelmuruguUsing a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins. Many cellular processes involve special proteins that bind to specific DNA sites with high affinity. How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms. The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually "stumbles" upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition. Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins.
Dynamics and Nonlinear Control of Integrated Process Systems
by Michael Baldea Prodromos DaoutidisPresenting a systematic model reduction and hierarchical controller design framework for broad classes of integrated process systems encountered in practice, this book first studies process systems with large material recycle and/or with small purge streams, followed by systems with energy integration. Step-by-step model reduction procedures are developed to derive nonlinear reduced models of the dynamics in each time scale. Hierarchical control architectures consisting of coordinated levels of control action in different time scales are proposed for each class of process systems considered to enforce stability, tracking performance and disturbance rejection. Numerous process applications are discussed in detail to illustrate the application of the methods and their potential to improve process operations. MATLAB codes are also presented to guide further application of the methods developed and facilitate practical implementations.
Dynamics and Predictability of Large-Scale High-Impact Weather and Climate Events (Special Publications of the International Union of Geodesy and Geophysics)
by Jianping Li Richard Swinbank Richard Grotjahn Hans VolkertBased largely on an International Commission on Dynamical Meteorology (ICDM) workshop, this timely volume, written by leading researchers in the field, covers a range of important research issues related to high-impact weather and extreme climate events. Dynamical linkages between these extremes and various atmospheric and ocean phenomena are examined, including Atlantic Multidecadal, North Atlantic, and Madden–Julian Oscillations; Annular Modes; tropical cyclones; and Asian monsoons. This book also examines the predictability of high-impact weather and extreme climate events on multiple time scales. Highlighting recent research and new advances in the field, this book enhances understanding of dynamical and physical processes associated with these events to help managers and policy makers make informed decisions to manage risk and prevent or mitigate disasters. It also provides guidance on future research directions in atmospheric science, meteorology, climate science, and weather forecasting, for experts and young scientists. Emphasises the predictability of extreme events, providing useful background information to help policymakers and managers plan for climate extremes and shorter-term forecasts of severe weather events. Provides a context for future research in the field of high-impact weather and climate extremes by compiling a wide variety of diagnostic and dynamical tools. Presents a less technical explanation of the dynamical processes involved in extreme weather events, making it accessible to a wider audience.
Dynamics and Stability of Continuous-Time Switched Linear Systems (Progress in Nonlinear Differential Equations and Their Applications #105)
by Mario Sigalotti Yacine Chitour Paolo MasonLinear switched systems are a fascinating field of research, with many theoretical questions arising from applications which require sophisticated mathematical tools for their resolution. This monograph presents a unified theoretical approach for the analysis of stability of continuous-time linear switched systems, organizing and optimizing results scattered throughout literature. Emphasis is placed on the development of a rigorous and complete mathematical theory. In addition to fundamental tools such as common Lyapunov functions, converse Lyapunov theorems, and maximal Lyapunov exponents, the concept of Barabanov norm is also discussed. While this is now well understood from a theoretical point of view, it has not received much attention in more application-focused settings, likely because this fundamental object was developed in the context of arbitrary switches but has no immediate equivalent for classes of switching signals subject to various constraints (dwell time, persistent excitation, etc.). One of the aims of this text is to bridge this gap as far as possible by explaining how the main features of Barabanov norms can be generalized for classes of constrained switchings. Throughout the text, the authors maintain a general point of view, rather than treating classes of switching signals separately, by developing an axiomatic approach and identifying structural properties of these classes that allow crucial aspects of the Barabanov norm to be extended. This monograph will be a valuable resource for mathematicians and control engineers interested in continuous-time switched linear systems, as well as a definitive reference for more experienced researchers.
Dynamics and Transport in Macromolecular Networks: Theory, Modelling, and Experiments
by Li-Tang YanDynamics and Transport in Macromolecular Networks Comprehensive knowledge on concepts and experimental advancement, as well as state-of-the-art computational tools and techniques for simulation and theory Dynamics and Transport in Macromolecular Networks: Theory, Modeling, and Experiments provides a unique introduction to the currently emerging, highly interdisciplinary field of those transport processes that exhibit various dynamic patterns and even anomalous behaviors of dynamics, investigating concepts and experimental advancement, as well as state-of-the-art computational tools and techniques for the simulation of macromolecular networks and the transport behavior in them. The detailed text begins with discussions on the structural organization of various macromolecular networks, then moves on to review and consolidate the latest research advances and state-of-the-art tools and techniques for the experimental and theoretical studies of the transport in macromolecular networks. In so doing, the text extracts and emphasizes common principles and research advancement from many different disciplines while providing up-to-date coverage of this new field of research. Written by highly experienced and internationally renowned specialists in various disciplines, such as polymer, soft matter, chemistry, biophysics, and more, Dynamics and Transport in Macromolecular Networks covers sample topics such as: Modeling (visco)elasticity macromolecular and biomacromolecular networks, covering statistical and elastic models and permanent biomacromolecular networks Focus on controlled degradation in modeling reactive hydrogels, covering mesoscale modeling of reactive polymer networks and modeling crosslinking due to hydrosilylation reaction Dynamic bonds in associating polymer networks, covering segmental and chain dynamics and phase-separated aggregate dynamics Direct observation of polymer reptation in entangled solutions and junction fluctuations in crosslinked networks, covering tube width fluctuations and dynamic fluctuations of crosslinks A much-needed overview of developments and scientific findings in the transport behaviors in macromolecular networks, Dynamics and Transport in Macromolecular Networks is a highly valuable resource for chemists, physicists, and other scientists and engineers working in fields related to macromolecular network systems, both theoretically and experimentally.
Dynamics and Vibrations: Progress in Nonlinear Analysis
by Davood Domairry Ganji Seyed Habibollah KachapiDynamical and vibratory systems are basically an application of mathematics and applied sciences to the solution of real world problems. Before being able to solve real world problems, it is necessary to carefully study dynamical and vibratory systems and solve all available problems in case of linear and nonlinear equations using analytical and numerical methods. It is of great importance to study nonlinearity in dynamics and vibration; because almost all applied processes act nonlinearly, and on the other hand, nonlinear analysis of complex systems is one of the most important and complicated tasks, especially in engineering and applied sciences problems. There are probably a handful of books on nonlinear dynamics and vibrations analysis. Some of these books are written at a fundamental level that may not meet ambitious engineering program requirements. Others are specialized in certain fields of oscillatory systems, including modeling and simulations. In this book, we attempt to strike a balance between theory and practice, fundamentals and advanced subjects, and generality and specialization. None of the books in this area have completely studied and analyzed nonlinear equation in dynamical and vibratory systems using the latest analytical and numerical methods, so that the user can solve the problems without the need of studying too many different references. Thereby in this book, by the use of the latest analytic, numeric laboratorial methods and using more than 300 references like books, papers and the researches done by the authors and by considering almost all possible processes and situation, new theories has been proposed to encounter applied problems in engineering and applied sciences. In this way, the user (bachelor's, master's and PhD students, university teachers and even in research centers in different fields of mechanical, civil, aerospace, electrical, chemical, applied mathematics, physics, and etc.) can encounter such systems confidently. In the different chapters of the book, not only are the linear and especially nonlinear problems with oscillatory form broadly discussed, but also applied examples are practically solved by the proposed methodology.
Dynamics at Solid State Surfaces and Interfaces
by Martin Wolf Hrvoje Petek Uwe BovensiepenThis two-volume work covers ultrafast structural and electronic dynamics of elementary processes at solid surfaces and interfaces, presenting the current status of photoinduced processes. Providing valuable introductory information for newcomers to this booming field of research, it investigates concepts and experiments, femtosecond and attosecond time-resolved methods, as well as frequency domain techniques.The whole is rounded off by a look at future developments.
Dynamics at Solid State Surfaces and Interfaces: Current Developments
by Martin Wolf Hrvoje Petek Uwe BovensiepenThis two-volume work covers ultrafast structural and electronic dynamics of elementary processes at solid surfaces and interfaces, presenting the current status of photoinduced processes. Providing valuable introductory information for newcomers to this booming field of research, it investigates concepts and experiments, femtosecond and attosecond time-resolved methods, as well as frequency domain techniques. The whole is rounded off by a look at future developments.
Dynamics at Solid State Surfaces and Interfaces: Volume 1 - Current Developments
by Martin Wolf Hrvoje Petek Uwe BovensiepenThis two-volume work covers ultrafast structural and electronic dynamics of elementary processes at solid surfaces and interfaces, presenting the current status of photoinduced processes. Providing valuable introductory information for newcomers to this booming field of research, it investigates concepts and experiments, femtosecond and attosecond time-resolved methods, as well as frequency domain techniques. The whole is rounded off by a look at future developments.
Dynamics in Engineering Practice (Applied and Computational Mechanics)
by Andrew P. Conkey Dara W. ChildsObserving that most books on engineering dynamics left students lacking and failing to grasp the general nature of dynamics in engineering practice, the authors of Dynamics in Engineering Practice, Eleventh Edition focused their efforts on remedying the problem. This text shows readers how to develop and analyze models to predict motion. While esta
Dynamics in Enzyme Catalysis
by Sharon Hammes-Schiffer Judith KlinmanChristopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond-Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.
Dynamics in Geometrical Confinement
by Friedrich KremerThis book describes the dynamics of low molecular weight and polymeric molecules when they are constrained under conditions of geometrical confinement. It covers geometrical confinement in different dimensionalities: (i) in nanometer thin layers or self supporting films (1-dimensional confinement) (ii) in pores or tubes with nanometric diameters (2-dimensional confinement) (iii) as micelles embedded in matrices (3-dimensional) or as nanodroplets. The dynamics under such conditions have been a much discussed and central topic in the focus of intense worldwide research activities within the last two decades. The present book discusses how the resulting molecular mobility is influenced by the subtle counterbalance between surface effects (typically slowing down molecular dynamics through attractive guest/host interactions) and confinement effects (typically increasing the mobility). It also explains how these influences can be modified and tuned, e. g. through appropriate surface coatings, film thicknesses or pore diameters. "Dynamics in Confinement" sums up the present state-of-the-art and introduces to the analytical methods of choice for the study of dynamics in nanometer-scale confinement.
Dynamics in Logistics
by Jürgen Pannek Herbert Kotzab Michael FreitagThese proceedings contain research papers presented at the 5th International Conference on Dynamics in Logistics, held in Bremen, Germany, February 2016. The conference is concerned with dynamic aspects of logistic processes and networks. The spectrum of topics reaches from modeling, planning and control of processes over supply chain management and maritime logistics to innovative technologies and robotic applications for cyber-physical production and logistic systems. The growing dynamic confronts the area of logistics with completely new challenges: it must become possible to describe, identify and analyze the process changes. Moreover, logistic processes and networks must be redevised to be rapidly and flexibly adaptable to continuously changing conditions. The book primarily addresses researchers and practitioners from the field of industrial engineering and logistics, but it may also be beneficial for graduate students.
Dynamics in Logistics
by Jürgen Pannek Herbert Kotzab Klaus-Dieter ThobenThis contributed volume brings together research papers presented at the 4th International Conference on Dynamics in Logistics, held in Bremen, Germany in February 2014. The conference focused on the identification, analysis and description of the dynamics of logistics processes and networks. Topics covered range from the modeling and planning of processes, to innovative methods like autonomous control and knowledge management, to the latest technologies provided by radio frequency identification, mobile communication, and networking. The growing dynamic poses wholly new challenges: logistics processes and networks must be(come) able to rapidly and flexibly adapt to constantly changing conditions. The book primarily addresses the needs of researchers and practitioners from the field of logistics, but will also be beneficial for graduate students.
Dynamics in Microwave Chemistry
by Kama Huang Xiaoqing Yang Huacheng ZhuThis book addresses microwave chemistry at both the physical and molecular level. Its main goal is to elaborate the highly complex scientific issues involved in the fundamental theory of microwave chemistry, and in industrialized applications in the near future.The book provides detailed insights into the characterization and measurement of dielectric properties under complex conditions, such as chemical reactions, high-temperature environments, etc. Considerable attention is paid to the theory of dynamics in microwave chemistry, from the view of both physical level and molecular level. Microwave-Material Interactions simulation is used for physical dynamical analysis, while a Microwave-Molecules Interactions methodology is proposed for molecular dynamical analysis. In turn, calculational examples are introduced for better description and validation, respectively. Lastly, the book proposes design strategies and calculational examples for large-scale application.Richly illustrated and including a wealth of worked-out examples, this book is ideal for all researchers, students and engineers who are just getting started in the dynamics of microwave chemistry.
Dynamics of Adsorptive Systems for Heat Transformation: Optimization Of Adsorber, Adsorbent And Cycle (SpringerBriefs in Applied Sciences and Technology)
by Angelo Freni Andrea Frazzica Alessio Sapienza Yuri AristovThis book investigates the adsorption dynamics of water, methanol, ethanol, and ammonia vapor on loose and consolidated adsorbent beds, as well as the impact of this aspect on the overall performance of adsorption systems for heat transformation. In particular, it presents the results of kinetic measurements made using the large temperature jump (LTJ) method, the most efficient way to study adsorption dynamics under realistic operating conditions for adsorptive heat transformers. The information provided is especially beneficial for all those working on the development of novel adsorbent materials and advanced adsorbers for heating and cooling applications. Today, technologies and systems based on adsorption heat transformation (AHT) processes offer a fascinating option for meeting the growing worldwide demand for air conditioning and space heating. Nevertheless, considerable efforts must still be made in order to enhance performance so as to effectively compete with commonly used electrical compression and absorption machines. For this purpose, intelligent design for adsorption units should above all focus on finding a convenient choice of adsorbent material by means of a comprehensive analysis that takes into account both thermodynamic and dynamic aspects. While the thermodynamic properties of the AHT cycle have been studied extensively, the dynamic optimization of AHT adsorbers is still an open issue. Several efforts have recently been made in order to analyze AHT dynamics, which greatly influence overall AHT performance.
Dynamics of Atmospheric Flight (Dover Books on Aeronautical Engineering)
by Bernard EtkinGeared toward upper-level undergrads, graduate students, and practicing engineers, this comprehensive treatment of the dynamics of atmospheric flight focuses especially on the stability and control of airplanes. An extensive set of numerical examples covers STOL airplanes, subsonic jet transports, hypersonic flight, stability augmentation, and wind and density gradients.The equations of motion receive a very full treatment, including the effects of the curvature and rotation of the Earth and distortional motion. Complete chapters are given to human pilots and handling qualities and to flight in turbulence, with numerical examples for a jet transport. Small-perturbation equations for longitudinal and lateral motion appear in convenient matrix forms, both in time-domain and Laplace transforms, dimensional and nondimensional.
Dynamics of Bacteria-Mucus Interactions (Methods in Molecular Biology #2942)
by Inka BrockhausenThis volume details the importance of bacteria in and around the human body, highlighting the bacteria that is harmless and pathogenic bacteria. Chapters guide readers through protocols on different bacteria&’s providing a better understand on they operate and how people can protect ourselves. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Dynamics of Bacteria-Mucus Interactions aims to be comprehensive guide for researchers in the field.
Dynamics of Biological Systems (Chapman & Hall/CRC Computational Biology Series)
by Michael SmallFrom the spontaneous rapid firing of cortical neurons to the spatial diffusion of disease epidemics, biological systems exhibit rich dynamic behaviour over a vast range of time and space scales. Unifying many of these diverse phenomena, Dynamics of Biological Systems provides the computational and mathematical platform from which to understand the
Dynamics of Blood Cell Suspensions in Microflows
by Annie Viallat and Manouk AbkarianBlood microcirculation is essential to our bodies for the successful supply of nutrients, waste removal, oxygen delivery, homeostasis, controlling temperature, wound healing, and active immune surveillance. This book provides a physical introduction to the subject and explores how researchers can successfully describe, understand, and predict behaviours of blood flow and blood cells that are directly linked to these important physiological functions. Using practical examples, this book explains how the key concepts of physics are related to blood microcirculation and underlie the dynamic behavior of red blood cells, leukocytes, and platelets. This interdisciplinary book will be a valuable reference for researchers and graduate students in biomechanics, fluid mechanics, biomedical engineering, biological physics, and medicine. Features: The first book to provide a physical perspective of blood microcirculation Draws attention to the potential of this physical approach for novel applications in medicine Edited by specialists in this field, with chapter contributions from subject area specialists
Dynamics of Bodies with Time-Variable Mass
by Livija CveticaninThis book deals with the problem of dynamics of bodies with time-variable mass and moment of inertia. Mass addition and mass separation from the body are treated. Both aspects of mass variation, continual and discontinual, are considered. Dynamic properties of the body are obtained applying principles of classical dynamics and also analytical mechanics. Advantages and disadvantages of both approaches are discussed. Dynamics of constant body is adopted, and the characteristics of the mass variation of the body is included. Special attention is given to the influence of the reactive force and the reactive torque. The vibration of the body with variable mass is presented. One and two degrees of freedom oscillators with variable mass are discussed. Rotors and the Van der Pol oscillator with variable mass are displayed. The chaotic motion of bodies with variable mass is discussed too. To support learning, some solved practical problems are included.
Dynamics of Cell Fate Decision Mediated by the Interplay of Autophagy and Apoptosis in Cancer Cells
by Iman TavassolyThis interdisciplinary thesis introduces a systems biology approach to study the cell fate decision mediated by autophagy. A mathematical model of interaction between Autophagy and Apoptosis in mammalian cells is proposed. In this dynamic model autophagy acts as a gradual response to stress (Rheostat) that delays the initiation of bistable switch of apoptosis to give the cells an opportunity to survive. The author shows that his dynamical model is consistent with existing quantitative measurements of time courses of autophagic responses to cisplatin treatment. To understand the function of this response in cancer cells, he has provided a systems biology experimental framework to study quantitative and dynamical aspects of autophagy in single cancer cells using live-cell imaging and quantitative fluorescence microscopy. This framework can provide new insights on function of autophagic response in cancer cells.
Dynamics of Chromatography: Principles and Theory
by J. Calvin GiddingsThis classic and bestselling landmark publication, originally published in 1965, examines the dynamic mechanisms, fundamental principles, and physical properties of various chromatographic procedures. It offers methods to characterize, identify, and predict chromatographic phenomena - providing strategies to select the most appropriate separation tools and techniques for specific applications in chemistry, physics, biology, and forensic and environmental science.Written by a world-renowned pioneer in the field, Dynamics of Chromatography contains many worked equations and real-world examples in gas and liquid chromatography. It includes numerous schematic figures for visualization of key concepts, introduces the means to control migration rate differences and zone spreading, and presents a detailed random-walk model for clarification of column processes. It also analyzes flow, diffusion, and kinetic events, stresses the link between theory and practice, and summarizes mathematical quantities and parameters.
Dynamics of Circle Mappings (IMPA Monographs)
by Pablo Guarino Edson de FariaThis book explores recent developments in the dynamics of invertible circle maps, a rich and captivating topic in one-dimensional dynamics. It focuses on two main classes of invertible dynamical systems on the circle: global diffeomorphisms and smooth homeomorphisms with critical points. The latter is the book's core, reflecting the authors' recent research interests.Organized into four parts and 14 chapters, the content covers rigid rotations, circle homeomorphisms, and the concept of rotation number in the first part. The second part delves into circle diffeomorphisms, presenting classical results. The third part introduces multicritical circle maps—smooth homeomorphisms of the circle with a finite number of critical points. The fourth and final part centers on renormalization theory, analyzing the fine geometric structure of orbits of multicritical circle maps. Complete proofs for several fundamental results in circle dynamics are provided throughout. The book concludes with a list of open questions.Primarily intended for graduate students and young researchers in dynamical systems, this book is also suitable for mathematicians from other fields with an interest in the subject. Prerequisites include familiarity with the content of a standard graduate course in real analysis, along with some understanding of ergodic theory and dynamical systems. Basic knowledge of complex analysis is needed for specific chapters.
Dynamics of Civil Structures, Vol. 2: Proceedings of the 42nd IMAC, A Conference and Exposition on Structural Dynamics 2024 (Conference Proceedings of the Society for Experimental Mechanics Series)
by Matthew Whelan P. Scott Harvey Fernando MoreuDynamics of Civil Structures, Volume 2: Proceedings of the 42nd IMAC, A Conference and Exposition on Structural Dynamics, 2024, the second volume of ten from the Conference brings together contributions to this important area of research and engineering. The collection presents early findings and case studies on fundamental and applied aspects of the Dynamics of Civil Structures, including papers on: Structural Vibration Dynamics of Bridges, Buildings, and Infrastructure Systems Innovative Sensors and Measurement Techniques for Structural Applications Structural Control and Vibration Mitigation Human Induced Vibrations and Human-Structure Interaction Modal Identification of Structural Systems Human Health Monitoring Using Structural Sensing Field Monitoring of Vibrations