Download or read book Quantum Mechanical Simulation Methods for Studying Biological Systems written by Dominique Bicout and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is now generally agreed that a deeper understanding of biological processes requires a multi-disciplinary approach employing the tools of biology, chemistry, and physics. Such understanding involves study of biomacromolecules and their functions, which includes how they interact, their reactions, and how information is transmitted between them. This volume is devoted to quantum mechanical simulation techniques, which have developed rapidly in recent years. It covers quantum mechanical calculations of large systems, molecular dynamics combining quantum and classical algorithms, quantum dynamical simulations, and electron and proton transfer processes in proteins and in solutions.

Download or read book QUANTUM MECHANICAL SIMULATION METHODS written by Collectif and published by . This book was released on 1996-02 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer Science & Business Media. This book was released on 2013-07-17 with total page 809 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Download or read book Quantum Simulations of Materials and Biological Systems written by Jun Zeng and published by Springer Science & Business Media. This book was released on 2012-07-26 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantum Simulations of Materials and Biological Systems features contributions from leading world experts in the fields of density functional theory (DFT) and its applications to material and biological systems. The recent developments of correlation functionals, implementations of Time-dependent algorithm into DFTB+ method are presented. The applications of DFT method to large materials and biological systems such as understanding of optical and electronic properties of nanoparticles, X-ray structure refinement of proteins, the catalytic process of enzymes and photochemistry of phytochromes are detailed. In addition, the book reviews the recent developments of methods for protein design and engineering, as well as ligand-based drug design. Some insightful information about the 2011 International Symposium on Computational Sciences is also provided. Quantum Simulations of Materials and Biological Systems is aimed at faculties and researchers in the fields of computational physics, chemistry and biology, as well as at the biotech and pharmaceutical industries.

Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 1997-11-30 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: 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.

Download or read book Computer Simulations in Molecular Biology written by Hiqmet Kamberaj and published by Springer Nature. This book was released on 2023-07-31 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.

Download or read book Theoretical Physics for Biological Systems written by Paola Lecca and published by CRC Press. This book was released on 2019-01-30 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.

Download or read book Biomolecular Simulations written by Luca Monticelli and published by Humana Press. This book was released on 2012-10-04 with total page 702 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Multi scale Quantum Models for Biocatalysis written by Darrin M. York and published by Springer. This book was released on 2010-10-28 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.

Download or read book Semiclassical Molecular Dynamics Simulation Method written by Hiroki Nakamura and published by World Scientific Publishing Company. This book was released on 2024-11-30 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Various quantum mechanical effects such as nonadiabatic transition, tunneling, and interference phenomena play crucial roles in chemical and biological systems. Semiclassical molecular dynamics is an attempt to properly treat these effects in computational simulations, and this book presents and explains how this may be achieved with the use of new methods and theoretical frameworks developed by the authors. This semiclassical approach could provide a powerful step forward to tackle and clarify the quantum dynamics in large chemical and biological systems, which is currently not feasible by the full quantum mechanical methods.

Download or read book Biomolecular Simulations written by Luca Monticelli and published by Humana Press. This book was released on 2012-10-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computational Modeling And Simulations Of Biomolecular Systems written by Benoit Roux and published by World Scientific. This book was released on 2021-08-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).

Download or read book Multiscale Modeling and Simulation in Science written by Björn Engquist and published by Springer Science & Business Media. This book was released on 2009-02-11 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most problems in science involve many scales in time and space. An example is turbulent ?ow where the important large scale quantities of lift and drag of a wing depend on the behavior of the small vortices in the boundarylayer. Another example is chemical reactions with concentrations of the species varying over seconds and hours while the time scale of the oscillations of the chemical bonds is of the order of femtoseconds. A third example from structural mechanics is the stress and strain in a solid beam which is well described by macroscopic equations but at the tip of a crack modeling details on a microscale are needed. A common dif?culty with the simulation of these problems and many others in physics, chemistry and biology is that an attempt to represent all scales will lead to an enormous computational problem with unacceptably long computation times and large memory requirements. On the other hand, if the discretization at a coarse level ignoresthe?nescale informationthenthesolutionwillnotbephysicallymeaningful. The in?uence of the ?ne scales must be incorporated into the model. This volume is the result of a Summer School on Multiscale Modeling and S- ulation in Science held at Boso ¤n, Lidingo ¤ outside Stockholm, Sweden, in June 2007. Sixty PhD students from applied mathematics, the sciences and engineering parti- pated in the summer school.

Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Download or read book Dynamics Structure and Function of Biological Macromolecules written by Oleg Jardetzky and published by IOS Press. This book was released on 2001 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: A collection of articles looking at modern structural biology, summarizing the applications of physical methods - such as x-ray diffraction, high resolution nuclear magnetic resonance and molecular dynamics - to the study of protein structure and dynamics. There is a review of contemporary thoughts within the field, looking at the mechanisms of alloateric transitions and allosteric control, the transmission of information within protein structures and the role of dynamics in determining the specificity of protein - ligand interactions. There is also a look at future innovations.