Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures.

The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.

Some of the topics covered include:

• diffusion of free particles on the basis of the Langevin equation

•the separation of time, length and angular scales;

• the fundamental Fokker-Planck and Smoluchowski equations derived for interacting particles

• friction of spheres and rods, and hydrodynamic interaction of spheres (including three body interactions)

• diffusion, sedimentation, critical phenomena and phase separation kinetics

• experimental light scattering results.

For universities and research departments in industry this textbook makes vital reading.

Computational methods impact all aspects of modern drug discovery and most notably these methods move rapidly from academic exercises to becoming drugs in clinical trials.

This insightful book represents the experience and understanding of the global experts in the field and spotlights both the structural and medicinal chemistry aspects of drug design. The need to 'encode' the factors that determine adsorption, distribution, metabolism, excretion and toxicology are explored, as they remain the critical issues in this area of research. This indispensable resource provides the reader with:

A rich understanding of modern approaches to docking; A comparison and critical evaluation of state-of-the-art methods; Details on harnessing computational methods for both analysis and prediction; An insight into prediction potencies and protocols for unbiased evaluations of docking and scoring algorithms; Critical reviews of current fragment based methods with perceptive applications to kinases.

Addressing a wide range of uses of protein structures for drug discovery the Editors have created an essential reference for professionals in the pharmaceutical industry and moreover an indispensable core text for all graduate level courses covering molecular interactions and drug discovery.

Computational Studies of RNA and DNA includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.

The systems and problems studied include:

• Accurate calculations of base pairing energies
• Electronic properties of nucleic acids and electron transfer, through various types of nucleic acid
• Calculating DNA elasticity

This book is ideally suited to academics and researchers in organic and computational chemistry as well as biochemistry and particularly those interested in the molecular modelling of nucleic acids.

Besides the state-of-the art science, the book also provides introductory information to non-specialists to enter and understand this field.

• simulation methodology
• the treatment of electrostatics
• protein structure refinement
• the combined experimental and theoretical approaches to the study of very large biological systems
• applications and methodology involved in the study of protein folding
• applications and methodology associated with structure-based design. <

This volume sets out to present a coherent account of the concepts that underlay different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.

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This book brings about the confluence of various concepts and tools to address significant problems of our time in physical biology and adjacent disciplines. The volume is structured to provide a broad perspective on current state-of-the-art methods and concepts at the heart of chemical and biological behavior, covering the topics of visualization; theory and computation for complexity; macromolecular function, protein folding, and protein misfolding; molecular recognition; and systems integration from cells to consciousness. The scope of tools is wide-ranging, spanning imaging, crystallography, microfluidics, single-molecule spectroscopy, and synthetic probe targeting, either molecular or by metallic particles. The perspectives are from the point of view of world leaders in physics, chemistry, and biology; and they define potential new frontiers at the interface of these disciplines, including physical, systems, and synthetic biology.

Contents: The Preoccupations of 21st-Century Biology (D Baltimore); Physical Biology: 4D Visualization of Complexity (A H Zewail); The Challenge of Quasi-Regular Structures in Biology (R D Kornberg); The Future of Biological X-ray Analysis (D C Rees); Biology by the Numbers (R Phillips); The Neurobiology of Consciousness (C Koch & F Mormann); Precision Measurements in Biology (S R Quake); Symmetry Breaking, Delocalization and Dynamics in Electron Transfer Systems (N S Hush); and other papers.

This best-selling volume presents the principles and applications of physical chemistry as they are used to solve problems in biology and medicine. The First Law; the Second Law; free energy and chemical equilibria; free energy and physical Equilibria; molecular motion and transport properties; kinetics: rates of chemical reactions; enzyme kinetics; the theory and spectroscopy of molecular structures and interactions: molecular distributions and statistical thermodynamics; and macromolecular structure and X-ray diffraction. For anyone interested in physical chemistry as it relates to problems in biology and medicine.

This highly respected book emphasizes rational theory and its consequences to demonstrate the underlying unity of PCH, which allows diverse phenomena to be described in physically and mathematically similar ways. Physicochemical Hydrodynamics communicates the fundamentals while, at the same time, conveying the importance of applications of PCH to a variety of fields, including: mechanical, chemical, and environmental engineering; materials science, biotechnology, microfluidics, and fluid aspects of nanotechnology. Numerous illustrations, analogies, and examples highlight the text and help to clarify and solidify students’ and professionals’ understanding of the material.

This book offers the most up-to-date look at the theory and techniques used in the study of the physical chemistry of biological and biochemical molecules. Ken van Holde is one of the leading experts in biophysical chemistry and a well-known author (he is coauthor of an introductory biochemistry book). Comprehensive coverage of all physical techniques currently used by practicing biochemists, including. Up-to-date treatment of NMR and X-ray diffraction. Comprehensive coverage of other types of spectroscopy.

This easy-to-read volume, designed to bring users to a functional level of literacy in the use, practice, appreciation and execution of physical chemistry principles and methods is designed to promote understanding. The text presents all the theories and equations relevant to classical thermodynamics, quantum mechanics and bonding, spectroscopy, statistical mechanics, kinetics and dynamics. For individuals interested in mastering the basic principles and methods of physical chemistry, including chemical engineers.