Computational Methods For Macromolecules

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Computational Methods for Macromolecules: Challenges and Applications

Tamar Schlick,Hin H. Gan

Author : Tamar Schlick,Hin H. Gan
Publisher : Springer Science & Business Media
Page : 504 pages
File Size : 53,8 Mb
Release : 2012-12-06
Category : Mathematics
ISBN : 9783642560804

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Computational Methods for Macromolecules: Challenges and Applications by Tamar Schlick,Hin H. Gan Pdf

This special volume collects invited articles by participants of the Third International Workshop on Methods for Macromolecular Modeling, Courant Institute of Mathematical Sciences, Oct. 12-14, 2000. Leading developers of methods for biomolecular simulations review advances in Monte Carlo and molecular dynamics methods, free energy computational methods, fast electrostatics (particle-mesh Ewald and fast multipole methods), mathematics, and molecular neurobiology, nucleic acid simulations, enzyme reactions, and other essential applications in biomolecular simulations. A Perspectives article by the editors assesses the directions and impact of macromolecular modeling research, including genomics and proteomics. These reviews and original papers by applied mathematicians, theoretical chemists, biomedical researchers, and physicists are of interest to interdisciplinary research students, developers and users of biomolecular methods in academia and industry.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Adam Liwo

Author : Adam Liwo
Publisher : Springer
Page : 851 pages
File Size : 46,5 Mb
Release : 2018-12-19
Category : Technology & Engineering
ISBN : 9783319958439

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo Pdf

This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Computer Analysis of Genetic Macromolecules

N. A. Kolchanov,Hwa A. Lim

Author : N. A. Kolchanov,Hwa A. Lim
Publisher : World Scientific
Page : 590 pages
File Size : 55,5 Mb
Release : 1994
Category : Science
ISBN : 9810213786

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Computer Analysis of Genetic Macromolecules by N. A. Kolchanov,Hwa A. Lim Pdf

Molecular biology and genetics are fast-growing fields with significant results and findings being reported virtually every day. Raw data from the wet lab accumulate at an astonishing rate, making it necessary to analyze the biological data with the use of computers. This book reveals how the current challenges of molecular biology and genetics are met with computer and mathematical treatments. A combined effort of the Computational Genetics and Biophysics Group (Supercomputer Computations Research Institute, USA), the Theoretical Molecular Genetics (Russian Academy of Sciences, Russia) and the Bioinformatics Group (Consiglio Nazionale delle Ricerche, Italy), many of these findings are firsthand discoveries made by these groups. The book emphasizes the fundamental principles of the structural-functional organization of the 3 major classes of genetic macromolecules: DNA, RNA and proteins. It also introduces universally applicable theoretical principles into the enormous realm of raw data and develops an integrative, theoretical computer approach to the analysis of these macromolecules to gain insights into the complexities of their function and evolution.

Computational Methods in Transport

Frank Graziani

Author : Frank Graziani
Publisher : Springer Science & Business Media
Page : 539 pages
File Size : 41,6 Mb
Release : 2006-02-17
Category : Computers
ISBN : 9783540281252

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Computational Methods in Transport by Frank Graziani Pdf

Thereexistawiderangeofapplicationswhereasigni?cantfractionofthe- mentum and energy present in a physical problem is carried by the transport of particles. Depending on the speci?capplication, the particles involved may be photons, neutrons, neutrinos, or charged particles. Regardless of which phenomena is being described, at the heart of each application is the fact that a Boltzmann like transport equation has to be solved. The complexity, and hence expense, involved in solving the transport problem can be understood by realizing that the general solution to the 3D Boltzmann transport equation is in fact really seven dimensional: 3 spatial coordinates, 2 angles, 1 time, and 1 for speed or energy. Low-order appro- mations to the transport equation are frequently used due in part to physical justi?cation but many in cases, simply because a solution to the full tra- port problem is too computationally expensive. An example is the di?usion equation, which e?ectively drops the two angles in phase space by assuming that a linear representation in angle is adequate. Another approximation is the grey approximation, which drops the energy variable by averaging over it. If the grey approximation is applied to the di?usion equation, the expense of solving what amounts to the simplest possible description of transport is roughly equal to the cost of implicit computational ?uid dynamics. It is clear therefore, that for those application areas needing some form of transport, fast, accurate and robust transport algorithms can lead to an increase in overall code performance and a decrease in time to solution.

Equilibria and Kinetics of Biological Macromolecules

Prof. Jan Hermans,Barry Lentz

Author : Prof. Jan Hermans,Barry Lentz
Publisher : John Wiley & Sons
Page : 411 pages
File Size : 50,6 Mb
Release : 2013-10-22
Category : Science
ISBN : 9781118733776

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Equilibria and Kinetics of Biological Macromolecules by Prof. Jan Hermans,Barry Lentz Pdf

Progressively builds a deep understanding of macromolecular behavior Based on each of the authors' roughly forty years of biophysics research and teaching experience, this text instills readers with a deep understanding of the biophysics of macromolecules. It sets a solid foundation in the basics by beginning with core physical concepts such as thermodynamics, quantum chemical models, molecular structure and interactions, and water and the hydrophobic effect. Next, the book examines statistical mechanics, protein-ligand binding, and conformational stability. Finally, the authors address kinetics and equilibria, exploring underlying theory, protein folding, and stochastic models. With its strong emphasis on molecular interactions, Equilibria and Kinetics of Biological Macromolecules offers new insights and perspectives on proteins and other macromolecules. The text features coverage of: Basic theory, applications, and new research findings Related topics in thermodynamics, quantum mechanics, statistical mechanics, and molecular simulations Principles and applications of molecular simulations in a dedicated chapter and interspersed throughout the text Macromolecular binding equilibria from the perspective of statistical mechanics Stochastic processes related to macromolecules Suggested readings at the end of each chapter include original research papers, reviews and monographs, enabling readers to explore individual topics in greater depth. At the end of the text, ten appendices offer refreshers on mathematical treatments, including probability, computational methods, Poisson equations, and defining molecular boundaries. With its classroom-tested pedagogical approach, Equilibria and Kinetics of Biological Macromolecules is recommended as a graduate-level textbook for biophysics courses and as a reference for researchers who want to strengthen their understanding of macromolecular behavior.

Computational Methods for Three-Dimensional Microscopy Reconstruction

Gabor T. Herman,Joachim Frank

Author : Gabor T. Herman,Joachim Frank
Publisher : Springer Science & Business Media
Page : 275 pages
File Size : 41,8 Mb
Release : 2014-01-29
Category : Mathematics
ISBN : 9781461495215

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Computational Methods for Three-Dimensional Microscopy Reconstruction by Gabor T. Herman,Joachim Frank Pdf

Approaches to the recovery of three-dimensional information on a biological object, which are often formulated or implemented initially in an intuitive way, are concisely described here based on physical models of the object and the image-formation process. Both three-dimensional electron microscopy and X-ray tomography can be captured in the same mathematical framework, leading to closely-related computational approaches, but the methodologies differ in detail and hence pose different challenges. The editors of this volume, Gabor T. Herman and Joachim Frank, are experts in the respective methodologies and present research at the forefront of biological imaging and structural biology. Computational Methods for Three-Dimensional Microscopy Reconstruction will serve as a useful resource for scholars interested in the development of computational methods for structural biology and cell biology, particularly in the area of 3D imaging and modeling.

Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy

Jeffrey C. Hoch

Author : Jeffrey C. Hoch
Publisher : Springer Science & Business Media
Page : 457 pages
File Size : 50,8 Mb
Release : 2013-11-21
Category : Medical
ISBN : 9781475797947

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Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy by Jeffrey C. Hoch Pdf

This volume is the scientific chronicle of the NATO Advanced Research Workshop on Computational Aspects of the Study of Biological Macro molecules by Nuclear Magnetic Resonance Spectroscopy, which was held June 3-8, 1990 at Il Ciocco, near Barga, Italy. The use of computers in the study of biological macromolecules by NMR spectroscopy is ubiquitous. The applications are diverse, including data col lection, reduction, and analysis. Furthermore, their use is rapidly evolv ing, driven by the development of new experimental methods in NMR and molecular biology and by phenomenal increases in computational perfor mance available at reasonable cost. Computers no longer merely facilitate, but are now absolutely essential in the study of biological macromolecules by NMR, due to the size and complexity of the data sets that are obtained from modern experiments. The Workshop, and this proceedings volume, provide a snapshot of the uses of computers in the NMR of biomolecules. While by no means exhaustive, the picture that emerges illustrates both the· importance and the diversity of their application.

Macromolecular Crystallography Protocols

Sylvie Doublié

Author : Sylvie Doublié
Publisher : Unknown
Page : 128 pages
File Size : 48,6 Mb
Release : 2007
Category : Electronic
ISBN : 1280832622

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Macromolecular Crystallography Protocols by Sylvie Doublié Pdf

In the decade since the publication of the first edition of "Crystallographic Methods and Protocols", the field has seen several major developments that have both accelerated the pace of structure determination and made crystallography accessible to a broader range of investigators. "Volume I, Preparation and Crystallization of Macromolecules" is dedicated to the crystallization and ways to increase the odds of obtaining crystals in macromolecules, while "Volume 2, Structure Determination" covers both computational methods for characterizing crystals and solving structures.

Computational Biochemistry and Biophysics

Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe

Author : Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe
Publisher : CRC Press
Page : 527 pages
File Size : 50,5 Mb
Release : 2001-02-09
Category : Medical
ISBN : 9780203903827

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Computational Biochemistry and Biophysics by Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe Pdf

Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret b

Interacting Macromolecules

John Cann

Author : John Cann
Publisher : Elsevier
Page : 262 pages
File Size : 48,9 Mb
Release : 2012-12-02
Category : Science
ISBN : 9780323158657

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Interacting Macromolecules by John Cann Pdf

Interacting Macromolecules: The Theory and Practice of Their Electrophoresis, Ultracentrifugation, and Chromatography reviews advances in theory and practice concerning the electrophoresis, ultracentrifugation, and chromatography of interacting macromolecules. The principles of mass transport of non-interacting systems are discussed, along with the weak electrolyte moving-boundary theory and analytical solution of approximate transport equations for certain types of interactions. Computer computations on ligand-mediated association-dissociation reactions are also presented. This book is comprised of six chapters and begins with a survey of the principles of electrophoresis and ultracentrifugation of non-reacting systems before proceeding with a detailed treatment of the mass transport of reversibly reacting macromolecules. A conservation equation is derived for a solution containing a single macromolecular ion. The following chapters explore the weak-electrolyte moving-boundary theory; the analytical Solution of approximate conservation equations; and numerical solution of exact conservation equations. The formulation of the numerical computation for ligand-mediated association-dissociation reactions is described, together with a code for sedimentation calculations. The final chapter summarizes the procedures and precautions required to assure accurate interpretation of sedimentation and electrophoretic patterns in terms of the thermodynamic and molecular parameters characterizing the reactions exhibited by biological macromolecules. The more common analytical applications of ultracentrifugation, electrophoresis, and chromatography are also outlined. This monograph is intended for molecular biologists and graduate students.

Nuclear Magnetic Resonance of Biological Macromolecules, Part C

Anonim

Author : Anonim
Publisher : Academic Press
Page : 672 pages
File Size : 49,6 Mb
Release : 2005-04-20
Category : Science
ISBN : 0121827992

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Nuclear Magnetic Resonance of Biological Macromolecules, Part C by Anonim Pdf

The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences. Nuclear Magnetic Resonance of Biological Macromolecules, Part C is written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules. * One of the most highly respected publications in the field of biochemistry since 1955 * Frequently consulted, and praised by researchers and reviewers alike * Truly an essential publication for anyone in any field of the life sciences

Macromolecular Crystallography

Maria Armenia Carrondo,Paola Spadon

Author : Maria Armenia Carrondo,Paola Spadon
Publisher : Springer
Page : 208 pages
File Size : 43,7 Mb
Release : 2011-12-01
Category : Science
ISBN : 9789400725300

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Macromolecular Crystallography by Maria Armenia Carrondo,Paola Spadon Pdf

This volume is a collection of the contributions presented at the 42nd Erice Crystallographic Course whose main objective was to train the younger generation on advanced methods and techniques for examining structural and dynamic aspects of biological macromolecules. The papers review the techniques used to study protein assemblies and their dynamics, including X-ray diffraction and scattering, electron cryo-electron microscopy, electro nanospray mass spectrometry, NMR, protein docking and molecular dynamics. A key theme throughout the book is the dependence of modern structural science on multiple experimental and computational techniques, and it is the development of these techniques and their integration that will take us forward in the future.

Nanomaterial Interactions with Plant Cellular Mechanisms and Macromolecules and Agricultural Implications

Jameel M. Al-Khayri,Lina M. Alnaddaf,S. Mohan Jain

Author : Jameel M. Al-Khayri,Lina M. Alnaddaf,S. Mohan Jain
Publisher : Springer Nature
Page : 509 pages
File Size : 51,5 Mb
Release : 2023-01-01
Category : Science
ISBN : 9783031208782

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Nanomaterial Interactions with Plant Cellular Mechanisms and Macromolecules and Agricultural Implications by Jameel M. Al-Khayri,Lina M. Alnaddaf,S. Mohan Jain Pdf

This book focuses on the recent progress of nanotechnology with emphasis on the interaction between nanoparticles and plants on the cellular level. It is devoted to understanding the pathways of nanomaterials entry into plant cell and their influence on cellular organelle processes and influence on crop yield. It consists of 16 chapters grouped in 3 parts: Part I Cellular mechanisms, Part II Cellular macromolecules, and Part III Implications of nanomaterials. Chapters present the plant response to nanomaterial applications including morphological, physiochemical, and anatomical changes and their effect on plant growth and productivity. The book discusses the mechanisms of absorbance and translocation of nanoparticles and their interaction with the plant cellular biochemical compounds and organelles. It presents the current perspective of nanomaterials influence on cellular processes which include photosynthesis, photorespiration and pigment synthesis and accumulation. In addition, it provides current understanding of the impact of nanomaterials on cellular macromolecules including carbohydrates, lipids, nucleic acids, proteins, hormones, and antioxidant defense activities. Collectively, these processes and biochemical compounds have implications on crop yield. Chapters are written by globally recognized scientists and subjected to a rigorous review process to ensure quality presentation and scientific precision. Chapter begins with an introduction that covers similar contexts and includes a detailed discussion of the topic accompanied by high-quality color images, diagrams, and relevant details and concludes with recommendations for future study directions. Chapter "Impact of Nanomaterials on Plant Secondary Metabolism" is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Numerical Techniques for Global Atmospheric Models

Peter H. Lauritzen,Christiane Jablonowski,Mark A. Taylor,Ramachandran D. Nair

Author : Peter H. Lauritzen,Christiane Jablonowski,Mark A. Taylor,Ramachandran D. Nair
Publisher : Springer Science & Business Media
Page : 570 pages
File Size : 52,7 Mb
Release : 2011-03-29
Category : Mathematics
ISBN : 9783642116407

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Numerical Techniques for Global Atmospheric Models by Peter H. Lauritzen,Christiane Jablonowski,Mark A. Taylor,Ramachandran D. Nair Pdf

This book surveys recent developments in numerical techniques for global atmospheric models. It is based upon a collection of lectures prepared by leading experts in the field. The chapters reveal the multitude of steps that determine the global atmospheric model design. They encompass the choice of the equation set, computational grids on the sphere, horizontal and vertical discretizations, time integration methods, filtering and diffusion mechanisms, conservation properties, tracer transport, and considerations for designing models for massively parallel computers. A reader interested in applied numerical methods but also the many facets of atmospheric modeling should find this book of particular relevance.

In-Silico Approaches to Macromolecular Chemistry

Minu Elizabeth Thomas,Jince Thomas,Sabu Thomas,Haya Kornweitz

Author : Minu Elizabeth Thomas,Jince Thomas,Sabu Thomas,Haya Kornweitz
Publisher : Elsevier
Page : 628 pages
File Size : 42,8 Mb
Release : 2023-02-28
Category : Science
ISBN : 9780323909969

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In-Silico Approaches to Macromolecular Chemistry by Minu Elizabeth Thomas,Jince Thomas,Sabu Thomas,Haya Kornweitz Pdf

Computational approaches offer researchers unique insights into the structure, characteristics, and properties of macromolecules. However, with applications across a broad range of areas, various methods have been developed for exploring macromolecules in in silico; therefore, it can be difficult for researchers to select the most appropriate method for their specific needs. Covering both biopolymers and synthetic polymers, In-Silico Approaches to Macromolecular Chemistry familiarizes readers with the theoretical tools and software appropriate for such studies. In addition to providing essential background knowledge on both computational tools and macromolecules, the book presents in-depth studies of in silico macromolecule chemistry, discusses and compares these with experimental studies, and highlights the future potential for such approaches. Written by specialists in their respective fields, this book helps students, researchers, and industry professionals gain a clear overview of the field, and furnishes them with the knowledge needed to understand and select the most appropriate tools for conducting and analyzing computational studies. Highlights in silico studies of both bio and synthetic macromolecules in one book Supports both learners and experts though a combination of detailed guidance and perspectives on the future potential for in silico approaches to macromolecules Familiarizes readers with theoretical tools and software helping them select the best approach for their specific needs

Computational Methods For Macromolecules

Computational Methods for Macromolecules: Challenges and Applications by Tamar Schlick,Hin H. Gan Pdf

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo Pdf

Computer Analysis of Genetic Macromolecules by N. A. Kolchanov,Hwa A. Lim Pdf

Computational Methods in Transport by Frank Graziani Pdf

Equilibria and Kinetics of Biological Macromolecules by Prof. Jan Hermans,Barry Lentz Pdf

Computational Methods for Three-Dimensional Microscopy Reconstruction by Gabor T. Herman,Joachim Frank Pdf

Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy by Jeffrey C. Hoch Pdf

Macromolecular Crystallography Protocols by Sylvie Doublié Pdf

Computational Biochemistry and Biophysics by Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe Pdf

Interacting Macromolecules by John Cann Pdf

Nuclear Magnetic Resonance of Biological Macromolecules, Part C by Anonim Pdf

Macromolecular Crystallography by Maria Armenia Carrondo,Paola Spadon Pdf

Nanomaterial Interactions with Plant Cellular Mechanisms and Macromolecules and Agricultural Implications by Jameel M. Al-Khayri,Lina M. Alnaddaf,S. Mohan Jain Pdf

Numerical Techniques for Global Atmospheric Models by Peter H. Lauritzen,Christiane Jablonowski,Mark A. Taylor,Ramachandran D. Nair Pdf

In-Silico Approaches to Macromolecular Chemistry by Minu Elizabeth Thomas,Jince Thomas,Sabu Thomas,Haya Kornweitz Pdf

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