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Adaptive Pseudo Time Methods For The Poisson Boltzmann Equation With Eulerian Solvent Excluded Surface
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Book Synopsis Adaptive Pseudo-time Methods for the Poisson-Boltzmann Equation with Eulerian Solvent Excluded Surface by : Benjamin Daniel Jones
Download or read book Adaptive Pseudo-time Methods for the Poisson-Boltzmann Equation with Eulerian Solvent Excluded Surface written by Benjamin Daniel Jones and published by . This book was released on 2021 with total page 58 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties, such as exponential nonlinear term, strong singularity by the source terms, and complex dielectric interface. Recently, a pseudo-time ghost-fluid method (GFM) has been developed in [S. Ahmed Ullah and S. Zhao, Applied Mathematics and Computation, 380, 125267, (2020)], by analytically handling both nonlinearity and singular sources. The GFM interface treatment not only captures the discontinuity in the regularized potential and its flux across the molecular surface, but also guarantees the stability and efficiency of the time integration. However, the molecular surface definition based on the MSMS package is known to induce instability in some cases, and a nontrivial Lagrangian-to-Eulerian conversion is indispensable for the GFM finite difference discretization. In this paper, an Eulerian Solvent Excluded Surface (ESES) is implemented to replace the MSMS for defining the dielectric interface. The electrostatic analysis shows that the ESES free energy is more accurate than that of the MSMS, while being free of instability issues. Moreover, this work explores, for the first time in the PBE literature, adaptive time integration techniques for the pseudo-transient simulations. A major finding is that the time increment Delta t should become smaller as the time increases, in order to maintain the temporal accuracy. This is opposite to the common practice for the steady state convergence, and is believed to be due to the PBE nonlinearity and its time splitting treatment. Effective adaptive schemes have been constructed so that the pseudo-time GFM methods become more efficient than the constant Delta t ones.
Book Synopsis Hyperbolic Problems by : American Institute of Mathematical Sciences
Download or read book Hyperbolic Problems written by American Institute of Mathematical Sciences and published by . This book was released on 2014 with total page 1069 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Simulation Methods for Polymers by : Michael Kotelyanskii
Download or read book Simulation Methods for Polymers written by Michael Kotelyanskii and published by CRC Press. This book was released on 2004-03-01 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Flowing Matter written by Federico Toschi and published by Springer Nature. This book was released on 2019-09-25 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book, published in the Soft and Biological Matter series, presents an introduction to selected research topics in the broad field of flowing matter, including the dynamics of fluids with a complex internal structure -from nematic fluids to soft glasses- as well as active matter and turbulent phenomena. Flowing matter is a subject at the crossroads between physics, mathematics, chemistry, engineering, biology and earth sciences, and relies on a multidisciplinary approach to describe the emergence of the macroscopic behaviours in a system from the coordinated dynamics of its microscopic constituents. Depending on the microscopic interactions, an assembly of molecules or of mesoscopic particles can flow like a simple Newtonian fluid, deform elastically like a solid or behave in a complex manner. When the internal constituents are active, as for biological entities, one generally observes complex large-scale collective motions. Phenomenology is further complicated by the invariable tendency of fluids to display chaos at the large scales or when stirred strongly enough. This volume presents several research topics that address these phenomena encompassing the traditional micro-, meso-, and macro-scales descriptions, and contributes to our understanding of the fundamentals of flowing matter. This book is the legacy of the COST Action MP1305 “Flowing Matter”.
Book Synopsis An Introduction to Reservoir Simulation Using MATLAB/GNU Octave by : Knut-Andreas Lie
Download or read book An Introduction to Reservoir Simulation Using MATLAB/GNU Octave written by Knut-Andreas Lie and published by Cambridge University Press. This book was released on 2019-08-08 with total page 677 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents numerical methods for reservoir simulation, with efficient implementation and examples using widely-used online open-source code, for researchers, professionals and advanced students. This title is also available as Open Access on Cambridge Core.
Download or read book Amber 2021 written by David A. Case and published by University of California, San Francisco. This book was released on 2021-06-13 with total page 959 pages. Available in PDF, EPUB and Kindle. Book excerpt: Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools21, a collection of freely available programs mostly under the GPL license, and Amber20, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber20 represents a significant change from the most recent previous version, Amber18. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Author :Jordi Vil...-Guerau de Arellano Publisher :Cambridge University Press ISBN 13 :1107090946 Total Pages :283 pages Book Rating :4.1/5 (7 download)
Book Synopsis Atmospheric Boundary Layer by : Jordi Vil...-Guerau de Arellano
Download or read book Atmospheric Boundary Layer written by Jordi Vil...-Guerau de Arellano and published by Cambridge University Press. This book was released on 2015-06-04 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: Based on more than 20 years of research and lecturing, Jordi Vil...-Guerau de Arellano and his team's textbook provides an excellent introduction to the interactions between the atmosphere and the land for advanced undergraduate and graduate students and a reference text for researchers in atmospheric physics and chemistry, hydrology, and plant physiology. The combination of the book, which provides the essential theoretical concepts, and the associated interactive Chemistry Land-surface Atmosphere Soil Slab (CLASS) software, which provides hands-on practical exercises and allows students to design their own numerical experiments, will prove invaluable for learning about many aspects of the soil-vegetation-atmosphere system. This book has a modular and flexible structure, allowing instructors to accommodate it to their own learning-outcome needs.
Book Synopsis Fast Methods for Long-range Interactions in Complex Systems by : Godehard Sutmann
Download or read book Fast Methods for Long-range Interactions in Complex Systems written by Godehard Sutmann and published by Forschungszentrum Jülich. This book was released on 2011 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Nonequilibrium Molecular Dynamics by : Billy D. Todd
Download or read book Nonequilibrium Molecular Dynamics written by Billy D. Todd and published by Cambridge University Press. This book was released on 2017-03-10 with total page 371 pages. Available in PDF, EPUB and Kindle. Book excerpt: This coherent collection of theory, algorithms, and illustrative results presents the field of nonequilibrium molecular dynamics in detail.
Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel
Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer Science & Business Media. This book was released on 2007-08-16 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.
Book Synopsis Stochastic Methods in Fluid Mechanics by : Sergio Chibbaro
Download or read book Stochastic Methods in Fluid Mechanics written by Sergio Chibbaro and published by Springer Science & Business Media. This book was released on 2013-09-05 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since their first introduction in natural sciences through the work of Einstein on Brownian motion in 1905 and further works, in particular by Langevin, Smoluchowski and others, stochastic processes have been used in several areas of science and technology. For example, they have been applied in chemical studies, or in fluid turbulence and for combustion and reactive flows. The articles in this book provide a general and unified framework in which stochastic processes are presented as modeling tools for various issues in engineering, physics and chemistry, with particular focus on fluid mechanics and notably dispersed two-phase flows. The aim is to develop what can referred to as stochastic modeling for a whole range of applications.
Book Synopsis Fundamentals of Multiphase Flow by : Christopher E. Brennen
Download or read book Fundamentals of Multiphase Flow written by Christopher E. Brennen and published by Cambridge University Press. This book was released on 2005-04-18 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publisher Description
Book Synopsis Lattice-Gas Cellular Automata and Lattice Boltzmann Models by : Dieter A. Wolf-Gladrow
Download or read book Lattice-Gas Cellular Automata and Lattice Boltzmann Models written by Dieter A. Wolf-Gladrow and published by Springer. This book was released on 2004-10-19 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lattice-gas cellular automata (LGCA) and lattice Boltzmann models (LBM) are relatively new and promising methods for the numerical solution of nonlinear partial differential equations. The book provides an introduction for graduate students and researchers. Working knowledge of calculus is required and experience in PDEs and fluid dynamics is recommended. Some peculiarities of cellular automata are outlined in Chapter 2. The properties of various LGCA and special coding techniques are discussed in Chapter 3. Concepts from statistical mechanics (Chapter 4) provide the necessary theoretical background for LGCA and LBM. The properties of lattice Boltzmann models and a method for their construction are presented in Chapter 5.
Book Synopsis Electrostatics of Soft and Disordered Matter by : David S. Dean
Download or read book Electrostatics of Soft and Disordered Matter written by David S. Dean and published by CRC Press. This book was released on 2014-05-02 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recently, there has been a surge of activity to elucidate the behavior of highly charged soft matter and Coulomb fluids in general. Such systems are ubiquitous, especially in biological matter where the length scale and the strength of the interaction between highly charged biomolecules are governed by strong electrostatic effects. Several interesting limits have been discovered in the parameter space of highly charged many-particle Coulomb matter where analytical progress is possible and completely novel and unexpected results have been obtained. One of the challenges in highly charged matter is to correctly describe systems with finite coupling strength in the transition regime between weak and strong couplings. After studying the fluctuations of both, several theories have been developed that describe this experimentally highly relevant regime. At the same time, computer simulation algorithms and computing power have advanced to the level where all-ion simulations, including many-body and polarization effects, are possible; the new theories thus can be subjected to numerical confirmation. Another important question is the effect of the structural disorder on electrostatic interactions. It has recently been demonstrated, both theoretically and experimentally, that charge disorder can impose long-range interaction between charged or even uncharged surfaces. These interactions might become very significant in biological processes. Filling a void in the literature, this volume cross-pollinates different theoretical and simulation approaches with new experiments and ties together the low temperature, high coupling constant, and disorder parameters in a unified description of the electrostatic interactions, which largely determine the stability and conformations of most important biological macromolecules. With striking graphical illustrations, the book presents a unified view of the current advances in the field of Coulomb (bio)colloidal systems, building on previous literature that summarized the field over 20 years ago. Leading scientists in the field offer a detailed introduction to different modern methods in statistical physics of Coulomb systems. They detail various approaches to elucidate the behavior of strongly charged soft matter. They also provide experimental and theoretical descriptions of disorder effects in Coulomb systems, which have not been discussed in any other book.
Book Synopsis Principles of Multiscale Modeling by : Weinan E
Download or read book Principles of Multiscale Modeling written by Weinan E and published by Cambridge University Press. This book was released on 2011-07-07 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: A systematic discussion of the fundamental principles, written by a leading contributor to the field.
Book Synopsis Introduction to Tensor Analysis and the Calculus of Moving Surfaces by : Pavel Grinfeld
Download or read book Introduction to Tensor Analysis and the Calculus of Moving Surfaces written by Pavel Grinfeld and published by Springer Science & Business Media. This book was released on 2013-09-24 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook is distinguished from other texts on the subject by the depth of the presentation and the discussion of the calculus of moving surfaces, which is an extension of tensor calculus to deforming manifolds. Designed for advanced undergraduate and graduate students, this text invites its audience to take a fresh look at previously learned material through the prism of tensor calculus. Once the framework is mastered, the student is introduced to new material which includes differential geometry on manifolds, shape optimization, boundary perturbation and dynamic fluid film equations. The language of tensors, originally championed by Einstein, is as fundamental as the languages of calculus and linear algebra and is one that every technical scientist ought to speak. The tensor technique, invented at the turn of the 20th century, is now considered classical. Yet, as the author shows, it remains remarkably vital and relevant. The author’s skilled lecturing capabilities are evident by the inclusion of insightful examples and a plethora of exercises. A great deal of material is devoted to the geometric fundamentals, the mechanics of change of variables, the proper use of the tensor notation and the discussion of the interplay between algebra and geometry. The early chapters have many words and few equations. The definition of a tensor comes only in Chapter 6 – when the reader is ready for it. While this text maintains a consistent level of rigor, it takes great care to avoid formalizing the subject. The last part of the textbook is devoted to the Calculus of Moving Surfaces. It is the first textbook exposition of this important technique and is one of the gems of this text. A number of exciting applications of the calculus are presented including shape optimization, boundary perturbation of boundary value problems and dynamic fluid film equations developed by the author in recent years. Furthermore, the moving surfaces framework is used to offer new derivations of classical results such as the geodesic equation and the celebrated Gauss-Bonnet theorem.
Book Synopsis Free Energy Calculations by : Christophe Chipot
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie 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. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
