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Author: K. Dane Wittrup
Publisher: Garland Science
ISBN: 9780815341390
Category : Science
Languages : en
Pages : 550
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Book Description
Author: K. Dane Wittrup
Publisher: Garland Science
ISBN: 9780815341390
Category : Science
Languages : en
Pages : 550
Get Book Here
Book Description
Author: David A. Case
Publisher: University of California, San Francisco
ISBN:
Category : Computers
Languages : en
Pages : 1016
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Book Description
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term Amber is also used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools23, a collection of freely available programs mostly under the GPL license, and Amber22, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber22 represents a significant change from the most recent previous version, Amber20. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Author: Alberto Podjarny
Publisher: Royal Society of Chemistry
ISBN: 1849732663
Category : Science
Languages : en
Pages : 373
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Book Description
The binding of small ligands to biological molecules is central to most aspects of biological function. The past twenty years has seen the development of an increasing armoury of biophysical methods that not only detect such binding, but also provide varying degrees of information about the kinetics, thermodynamics and structural aspects of the process. These methods have received increasing attention with the growth in more rational approaches to drug discovery and design. This book reviews the latest advances in the application of biophysics to the study of ligand binding. It provides a complete overview of current techniques to identify ligands, characterise their binding sites and understand their binding mechanisms. Particular emphasis is given to the combined use of different techniques and their relative strengths and weaknesses. Consistency in the way each technique is described makes it easy for readers to select the most suitable protocol for their research. The introduction explains why some techniques are more suitable than others and emphasizes the possible synergies between them. The following chapters, all written by a specialist in the particular technique, focus on each method individually. The book finishes by describing how several complimentary techniques can be used together for maximum effectiveness. This book is suitable for biomolecular scientists at graduate or post-doctoral level in academia and industry. Biologists and chemists will also find it a useful introduction to the techniques available.
Author: Domitilla Del Vecchio
Publisher: Princeton University Press
ISBN: 1400850509
Category : Science
Languages : en
Pages : 287
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Book Description
This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu
Author: K. Dane Wittrup
Publisher: MIT Press
ISBN: 0262042657
Category : Science
Languages : en
Pages : 593
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Book Description
A comprehensive presentation of essential topics for biological engineers, focusing on the development and application of dynamic models of biomolecular and cellular phenomena. This book describes the fundamental molecular and cellular events responsible for biological function, develops models to study biomolecular and cellular phenomena, and shows, with examples, how models are applied in the design and interpretation of experiments on biological systems. Integrating molecular cell biology with quantitative engineering analysis and design, it is the first textbook to offer a comprehensive presentation of these essential topics for chemical and biological engineering. The book systematically develops the concepts necessary to understand and study complex biological phenomena, moving from the simplest elements at the smallest scale and progressively adding complexity at the cellular organizational level, focusing on experimental testing of mechanistic hypotheses. After introducing the motivations for formulation of mathematical rate process models in biology, the text goes on to cover such topics as noncovalent binding interactions; quantitative descriptions of the transient, steady state, and equilibrium interactions of proteins and their ligands; enzyme kinetics; gene expression and protein trafficking; network dynamics; quantitative descriptions of growth dynamics; coupled transport and reaction; and discrete stochastic processes. The textbook is intended for advanced undergraduate and graduate courses in chemical engineering and bioengineering, and has been developed by the authors for classes they teach at MIT and the University of Minnesota.
Author: Vasudevan Ramesh
Publisher: John Wiley & Sons
ISBN: 1119483964
Category : Science
Languages : en
Pages : 576
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Book Description
An essential guide to biomolecular and bioanalytical techniques and their applications Biomolecular and Bioanalytical Techniques offers an introduction to, and a basic understanding of, a wide range of biophysical techniques. The text takes an interdisciplinary approach with contributions from a panel of distinguished experts. With a focus on research, the text comprehensively covers a broad selection of topics drawn from contemporary research in the fields of chemistry and biology. Each of the internationally reputed authors has contributed a single chapter on a specific technique. The chapters cover the specific technique’s background, theory, principles, technique, methodology, protocol and applications. The text explores the use of a variety of analytical tools to characterise biological samples. The contributors explain how to identify and quantify biochemically important molecules, including small molecules as well as biological macromolecules such as enzymes, antibodies, proteins, peptides and nucleic acids. This book is filled with essential knowledge and explores the skills needed to carry out the research and development roles in academic and industrial laboratories. A technique-focused book that bridges the gap between an introductory text and a book on advanced research methods Provides the necessary background and skills needed to advance the research methods Features a structured approach within each chapter Demonstrates an interdisciplinary approach that serves to develop independent thinking Written for students in chemistry, biological, medical, pharmaceutical, forensic and biophysical sciences, Biomolecular and Bioanalytical Techniques is an in-depth review of the most current biomolecular and bioanalytical techniques in the field.
Author: John J. Correia
Publisher: Academic Press
ISBN: 0080554946
Category : Science
Languages : en
Pages : 996
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Book Description
Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in Methods in Cell Biology is devoted to biophysical techniques in vitro and their applications to cellular biology. Biophysical Tools for Biologists covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval. - Describes techniques in the context of important biological problems - Delineates critical steps and potential pitfalls for each method - Includes full-color plates to illustrate techniques
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1436
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Book Description
Author: Thomas M. Nordlund
Publisher: CRC Press
ISBN: 1351801171
Category : Science
Languages : en
Pages : 870
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Book Description
Praise for the prior edition "The author has done a magnificent job... this book is highly recommended for introducing biophysics to the motivated and curious undergraduate student." ―Contemporary Physics "a terrific text ... will enable students to understand the significance of biological parameters through quantitative examples―a modern way of learning biophysics." ―American Journal of Physics "A superb pedagogical textbook... Full-color illustrations aid students in their understanding" ―Midwest Book Review This new edition provides a complete update to the most accessible yet thorough introduction to the physical and quantitative aspects of biological systems and processes involving macromolecules, subcellular structures, and whole cells. It includes two brand new chapters covering experimental techniques, especially atomic force microscopy, complementing the updated coverage of mathematical and computational tools. The authors have also incorporated additions to the multimedia component of video clips and animations, as well as interactive diagrams and graphs. Thomas Nordlund is professor emeritus in the Department of Physics at The University of Alabama at Birmingham. He is an elected fellow of the American Physical Society and has been studying biomolecular dynamics for over thirty years. Peter M. Hoffmann is a professor in the Department of Physics and Astronomy at Wayne State University in Detroit, Michigan, where he founded the biomedical physics program. He has been involved in soft matter and biophysics research for twenty-five years, and earned his PhD in materials science and engineering from Johns Hopkins University.
Author: György Keserü
Publisher: John Wiley & Sons
ISBN: 352733582X
Category : Medical
Languages : en
Pages : 360
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Book Description
This practical reference for medicinal and pharmaceutical chemists combines the theoretical background with modern methods as well as applications from recent lead finding and optimization projects. Divided into two parts on the thermodynamics and kinetics of drug-receptor interaction, the text provides the conceptual and methodological basis for characterizing binding mechanisms for drugs and other bioactive molecules. It covers all currently used methods, from experimental approaches, such as ITC or SPR, right up to the latest computational methods. Case studies of real-life lead or drug development projects are also included so readers can apply the methods learned to their own projects. Finally, the benefits of a thorough binding mode analysis for any drug development project are summarized in an outlook chapter written by the editors.
