Molecular Modeling At The Atomic Scale

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications.

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.

Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.

This is an introduction to molecular and atomistic modeling techniques applied to fracture and deformation of solids, focusing on a variety of brittle, ductile, geometrically confined and biological materials. The overview includes computational methods and techniques operating at the atomic scale, and describes how these techniques can be used to model cracks and other deformation mechanisms. The book aims to make new molecular modeling techniques available to a wider community.

Atomic-Scale Modelling of Electrochemical Systems A comprehensive overview of atomistic computational electrochemistry, discussing methods, implementation, and state-of-the-art applications in the field The first book to review state-of-the-art computational and theoretical methods for modelling, understanding, and predicting the properties of electrochemical interfaces. This book presents a detailed description of the current methods, their background, limitations, and use for addressing the electrochemical interface and reactions. It also highlights several applications in electrocatalysis and electrochemistry. Atomic-Scale Modelling of Electrochemical Systems discusses different ways of including the electrode potential in the computational setup and fixed potential calculations within the framework of grand canonical density functional theory. It examines classical and quantum mechanical models for the solid-liquid interface and formation of an electrochemical double-layer using molecular dynamics and/or continuum descriptions. A thermodynamic description of the interface and reactions taking place at the interface as a function of the electrode potential is provided, as are novel ways to describe rates of heterogeneous electron transfer, proton-coupled electron transfer, and other electrocatalytic reactions. The book also covers multiscale modelling, where atomic level information is used for predicting experimental observables to enable direct comparison with experiments, to rationalize experimental results, and to predict the following electrochemical performance. Uniquely explains how to understand, predict, and optimize the properties and reactivity of electrochemical interfaces starting from the atomic scale Uses an engaging “tutorial style” presentation, highlighting a solid physicochemical background, computational implementation, and applications for different methods, including merits and limitations Bridges the gap between experimental electrochemistry and computational atomistic modelling Written by a team of experts within the field of computational electrochemistry and the wider computational condensed matter community, this book serves as an introduction to the subject for readers entering the field of atom-level electrochemical modeling, while also serving as an invaluable reference for advanced practitioners already working in the field.

The series Topics in Current Chemistry Collections presents critical reviews from the journal Topics in Current Chemistry organized in topical volumes. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. The chapters “Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions” and “Elucidating Solvation Structures for Rational Design of Multivalent Electrolytes—A Review” are available open access under a CC BY 4.0 License via link.springer.com.

Design of new molecular materials is emerging as a new interdisciplinary research field. Corresponding reports are scattered in literature, and this book constitutes one of the first attempts to overview ongoing research efforts. It provides basic information, as well as the details of theory and examples of its application, to experimentalists and theoreticians interested in modeling molecular properties and putting into practice rational design of new materials.

This book is a practical, easy to use guide for readers with limited experience of molecular modelling. It will provide students at the undergraduate and early postgraduate chemistry level with a similar entry to modelling. The needs of independent readers are catered for by the inclusion of instructions for acquiring and setting up a suitable computer. Unlike many other textbooks in this field, the authors avoid extensive discussion around complex mathematical foundations behind the methods, choosing instead to provide the reader with the choice of methods themselves. To further these aims of the book, compact discs are included that provide a comprehensive suite of modelling software and datasets. The continuing interest of the pharmaceutical industry in molecular modelling in early stage drug design is recognized by the inclusion of chapters Medicinal Chemistry and Drug Discovery. There is a chapter on modelling of the solid state, a subject that is also of importance for pharma, where problems due to polymorphism in the crystalline forms of drugs are often encountered in the later design stages.