Experts provide a unique and broad perspective of the theoretical tools available today to analyze protein structure and function. Topics at the frontier of computational biophysics, such as dynamics and thermodynamics of proteins, reaction path studies, optimization techniques, analytical theories of protein folding, sequence alignment algorithms and electrostatics of proteins are discussed in a pedagogical and complete way. Those entering the field will find the book to be a useful introduction. It will also serve as a complementary text to existing ones that focus on just one of the above subjects.
A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times. The book’s exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book: Offers an introduction to the topic that combines theory, simulation and analysis Presents a guide written by authors that are well-known and highly regarded leaders in their fields Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed. Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.
Deformable objects are ubiquitous in the world surrounding us, on all levels from micro to macro. The need to study such shapes and model their behavior arises in a wide spectrum of applications, ranging from medicine to security. In recent years, non-rigid shapes have attracted growing interest, which has led to rapid development of the field, where state-of-the-art results from very different sciences - theoretical and numerical geometry, optimization, linear algebra, graph theory, machine learning and computer graphics, to mention several - are applied to find solutions. This book gives an overview of the current state of science in analysis and synthesis of non-rigid shapes. Everyday examples are used to explain concepts and to illustrate different techniques. The presentation unfolds systematically and numerous figures enrich the engaging exposition. Practice problems follow at the end of each chapter, with detailed solutions to selected problems in the appendix. A gallery of colored images enhances the text. This book will be of interest to graduate students, researchers and professionals in different fields of mathematics, computer science and engineering. It may be used for courses in computer vision, numerical geometry and geometric modeling and computer graphics or for self-study.
This book constitutes the refereed proceedings of the 5th International Conference on Scale Space and PDE Methods in Computer Vision, Scale-Space 2005, held in Hofgeismar, Germany in April 2005. The 53 revised full papers presented were carefully reviewed and selected from 79 submissions. The papers are organized in topical sections on novel linear spaces, image features, deep structure, image processing, medical applications, contours, tensors, non-linear filters, and motion.
Numerical Geometry of Images examines computational methods and algorithms in image processing. It explores applications like shape from shading, color-image enhancement and segmentation, edge integration, offset curve computation, symmetry axis computation, path planning, minimal geodesic computation, and invariant signature calculation. In addition, it describes and utilizes tools from mathematical morphology, differential geometry, numerical analysis, and calculus of variations. Graduate students, professionals, and researchers with interests in computational geometry, image processing, computer graphics, and algorithms will find this new text / reference an indispensable source of insight of instruction.
Arrangements of curves constitute fundamental structures that have been intensively studied in computational geometry. Arrangements have numerous applications in a wide range of areas – examples include geographic information systems, robot motion planning, statistics, computer-assisted surgery and molecular biology. Implementing robust algorithms for arrangements is a notoriously difficult task, and the CGAL arrangements package is the first robust, comprehensive, generic and efficient implementation of data structures and algorithms for arrangements of curves. This book is about how to use CGAL two-dimensional arrangements to solve problems. The authors first demonstrate the features of the arrangement package and related packages using small example programs. They then describe applications, i.e., complete standalone programs written on top of CGAL arrangements used to solve meaningful problems – for example, finding the minimum-area triangle defined by a set of points, planning the motion of a polygon translating among polygons in the plane, computing the offset polygon, finding the largest common point sets under approximate congruence, constructing the farthest-point Voronoi diagram, coordinating the motion of two discs moving among obstacles in the plane, and performing Boolean operations on curved polygons. The book contains comprehensive explanations of the solution programs, many illustrations, and detailed notes on further reading, and it is supported by a website that contains downloadable software and exercises. It will be suitable for graduate students and researchers involved in applied research in computational geometry, and for professionals who require worked-out solutions to real-life geometric problems. It is assumed that the reader is familiar with the C++ programming-language and with the basics of the generic-programming paradigm.
A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times. The book’s exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book: Offers an introduction to the topic that combines theory, simulation and analysis Presents a guide written by authors that are well-known and highly regarded leaders in their fields Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed. Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.
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