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Author: Luca Monticelli
Publisher: Humana Press
ISBN: 9781627030168
Category : Science
Languages : en
Pages : 0
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Book Description
Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced. Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.
Author: Luca Monticelli
Publisher: Humana Press
ISBN: 9781627030168
Category : Science
Languages : en
Pages : 0
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Book Description
Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced. Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.
Author: Markus Reiher
Publisher: Springer Science & Business Media
ISBN: 3540380825
Category : Science
Languages : en
Pages : 368
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Book Description
With contributions by numerous experts
Author: Tadeusz Andruniów
Publisher:
ISBN: 9783030577223
Category :
Languages : en
Pages : 0
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Book Description
This book, a consecutive contribution to the series Challenges and Advances in Computational Chemistry and Physics, focuses on understanding the photoinduced processes in biological systems. Understanding and fine control of light fate in molecules is vital for the progress of society and environmental safety. Light induced changes of various physico-chemical and spectroscopic properties in nucleic acids and proteins is the basis of fundamental biological events such as vision, DNA photodamage or photosensing. The investigation of these processes is challenging to both theoretical and experimental studies. This volume encompasses the quantum mechanics/molecular mechanics theory in several subfields, including: advanced computational methods for nucleic acids and proteins systems; dynamics, spectroscopic and physico-chemical properties of biological photoreceptors; DNA photodamage. This book is of interest to readers in both fundamental and application-oriented research by overviewing recent achievements in computational modeling of excited states in nucleic acids and proteins.
Author: Jiali Gao
Publisher:
ISBN:
Category : Medical
Languages : en
Pages : 328
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Book Description
Combined quantum mechanical and molecular mechanical methods (QM/MM) is one of the most promising approaches for quantum mechanical calculations of chemical processes in solution and in enzymes. This book provides an in-depth survey of the methods and applications of these combined techniques in chemistry and biochemistry.
Author: Hai Lin
Publisher: American Chemical Society
ISBN: 0841299501
Category : Science
Languages : en
Pages : 163
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Book Description
Many chemical, physical, and biological processes occur in complex environments and span multiple scales in space and time. Combined (hybrid or integrated) quantum-mechanics/molecular-mechanics (QM/MM) is one family of multiscale algorithms for computer modeling these processes. First introduced in 1976, along with critical developments over the following decades, QM/MM is now a popular and powerful tool that helps scientists simultaneously capture the fundamental atomistic details and the overall big picture of these processes. Instead of providing a comprehensive survey of the QM/MM algorithms and their applications, QM/MM Methods focuses on explaining the key concepts in QM/MM methodology and how to interpret the results in applications. The author frequently uses small “toy” model systems to illustrate the fundamental principles, which can be easily generalized to large model systems. Unavoidably, formal proofs and many technical details are left out, for which readers are referred to the relevant literature. QM/MM Methods helps researchers enter the field with a good starting position, empowering them to ask the right questions in their QM/MM applications and select suitable algorithms to address them.
Author: Paolo Carloni
Publisher: John Wiley & Sons
ISBN: 3527605304
Category : Science
Languages : de
Pages : 294
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Book Description
Computational methods are transforming the work of chemical and pharmaceutical laboratories. Increasingly faster and more exact simulation algorithms have made quantum chemistry a valuable tool in the search for active substances. Written by a team of leading international quantum chemists, this book is aimed at both beginners as well as experienced users of quantum chemical methods. All commonly used quantum chemical methods are treated here, including Density Functional Theory, quantum and molecular mechanical approaches. Numerous examples illustrate the use of these methods for dealing with problems in pharmaceutical practice, whether the study of inhibitor binding, identifying the surface load of active substances or deriving molecular descriptors using quantum chemical tools. For anyone striving to stay ahead in this rapidly evolving field.
Author: Steven M. Bachrach
Publisher: John Wiley & Sons
ISBN: 1118291921
Category : Science
Languages : en
Pages : 653
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Book Description
The Second Edition demonstrates how computational chemistry continues to shed new light on organic chemistry The Second Edition of author Steven Bachrach’s highly acclaimed Computational Organic Chemistry reflects the tremendous advances in computational methods since the publication of the First Edition, explaining how these advances have shaped our current understanding of organic chemistry. Readers familiar with the First Edition will discover new and revised material in all chapters, including new case studies and examples. There’s also a new chapter dedicated to computational enzymology that demonstrates how principles of quantum mechanics applied to organic reactions can be extended to biological systems. Computational Organic Chemistry covers a broad range of problems and challenges in organic chemistry where computational chemistry has played a significant role in developing new theories or where it has provided additional evidence to support experimentally derived insights. Readers do not have to be experts in quantum mechanics. The first chapter of the book introduces all of the major theoretical concepts and definitions of quantum mechanics followed by a chapter dedicated to computed spectral properties and structure identification. Next, the book covers: Fundamentals of organic chemistry Pericyclic reactions Diradicals and carbenes Organic reactions of anions Solution-phase organic chemistry Organic reaction dynamics The final chapter offers new computational approaches to understand enzymes. The book features interviews with preeminent computational chemists, underscoring the role of collaboration in developing new science. Three of these interviews are new to this edition. Readers interested in exploring individual topics in greater depth should turn to the book’s ancillary website www.comporgchem.com, which offers updates and supporting information. Plus, every cited article that is available in electronic form is listed with a link to the article.
Author: Ross C. Walker
Publisher: John Wiley & Sons
ISBN: 1118670701
Category : Science
Languages : en
Pages : 368
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Book Description
Electronic Structure Calculations on Graphics Processing Units: From Quantum Chemistry to Condensed Matter Physics provides an overview of computing on graphics processing units (GPUs), a brief introduction to GPU programming, and the latest examples of code developments and applications for the most widely used electronic structure methods. The book covers all commonly used basis sets including localized Gaussian and Slater type basis functions, plane waves, wavelets and real-space grid-based approaches. The chapters expose details on the calculation of two-electron integrals, exchange-correlation quadrature, Fock matrix formation, solution of the self-consistent field equations, calculation of nuclear gradients to obtain forces, and methods to treat excited states within DFT. Other chapters focus on semiempirical and correlated wave function methods including density fitted second order Møller-Plesset perturbation theory and both iterative and perturbative single- and multireference coupled cluster methods. Electronic Structure Calculations on Graphics Processing Units: From Quantum Chemistry to Condensed Matter Physics presents an accessible overview of the field for graduate students and senior researchers of theoretical and computational chemistry, condensed matter physics and materials science, as well as software developers looking for an entry point into the realm of GPU and hybrid GPU/CPU programming for electronic structure calculations.
Author: Mark S. Gordon
Publisher: John Wiley & Sons
ISBN: 1119129249
Category : Science
Languages : en
Pages : 376
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Book Description
Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.
Author: Jörg Grunenberg
Publisher: John Wiley & Sons
ISBN: 3527643621
Category : Science
Languages : en
Pages : 421
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Book Description
Unique in its comprehensive coverage of not only theoretical methods but also applications in computational spectroscopy, this ready reference and handbook compiles the developments made over the last few years, from single molecule studies to the simulation of clusters and the solid state, from organic molecules to complex inorganic systems and from basic research to commercial applications in the area of environment relevance. In so doing, it covers a multitude of apparatus-driven technologies, starting with the common and traditional spectroscopic methods, more recent developments (THz), as well as rather unusual methodologies and systems, such as the prediction of parity violation, rare gas HI complexes or theoretical spectroscopy of the transition state. With its summarized results of so many different disciplines, this timely book will be of interest to newcomers to this hot topic while equally informing experts about developments in neighboring fields.
