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Computational Biology of Transcription Factor Binding

by Istvan Ladunga

Through great experimental difficulty, we've witnessed rapid, crucial developments at the intersection of computational biology, experimental technology, and statistics through which the vital process of transcriptional regulation can be further examined. In Computational Biology of Transcription Factor Binding, experts in the field examine the basic principles and provide detailed guidance for the computational analyses and biological interpretations of transcription factor binding, while disclosing critical practical information and caveats that are missing from many research publications. The volume serves not only computational biologists but experimentalists as well, who may want to better understand how to design and execute experiments and to communicate more effectively with computational biologists, computer scientists, and statisticians. Written for the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results in the lab. Authoritative and easy to use, Computational Biology of Transcription Factor Binding guides scientists working in this area and demands not only new experiments but also the re-annotation of existing experimental data and computational predictions leading to important ongoing, major paradigm changes for us all.

Computational Biomechanics for Medicine

by Poul M.F. Nielsen Karol Miller

Mathematical modelling and computer simulation have proved tremendously successful in engineering. One of the greatest challenges for mechanists is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, biomedical sciences, and medicine. The proposed workshop will provide an opportunity for computational biomechanics specialists to present and exchange opinions on the opportunities of applying their techniques to computer-integrated medicine. For example, continuum mechanics models provide a rational basis for analysing biomedical images by constraining the solution to biologically reasonable motions and processes. Biomechanical modelling can also provide clinically important information about the physical status of the underlying biology, integrating information across molecular, tissue, organ, and organism scales. The main goal of this workshop is to showcase the clinical and scientific utility of computational biomechanics in computer-integrated medicine.

Computational Biomechanics for Medicine

by Poul M.F. Nielsen Karol Miller Adam Wittek

One of the greatest challenges for mechanists is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, biomedical sciences, and medicine. The proposed workshop will provide an opportunity for computational biomechanics specialists to present and exchange opinions on the opportunities of applying their techniques to computer-integrated medicine. These are peer-reviewed proceedings of the workshop affiliated to a major international research conference (Medical Image Computing and Computer Assisted Intervention MICCAI 2010 in Beijing) dedicated to research in the field of medical image computing and computer assisted medical interventions. The list of subjects covered include: medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, injury mechanism analysis, implant and prostheses design, medical robotics.

Computational Cancer Biology

by Mathukumalli Vidyasagar

This brief introduces people with a basic background in probability theory to various problems in cancer biology that are amenable to analysis using methods of probability theory and statistics. The title mentions "cancer biology" and the specific illustrative applications reference cancer data but the methods themselves are more broadly applicable to all aspects of computational biology. Aside from providing a self-contained introduction to basic biology and to cancer, the brief describes four specific problems in cancer biology that are amenable to the application of probability-based methods. The application of these methods is illustrated by applying each of them to actual data from the biology literature. After reading the brief, engineers and mathematicians should be able to collaborate fruitfully with their biologist colleagues on a wide variety of problems.

Computational Colour Science Using MATLAB

by Caterina Ripamonti Vien Cheung Stephen Westland

Computational Colour Science Using MATLAB 2nd Edition offers a practical, problem-based approach to colour physics. The book focuses on the key issues encountered in modern colour engineering, including efficient representation of colour information, Fourier analysis of reflectance spectra and advanced colorimetric computation. Emphasis is placed on the practical applications rather than the techniques themselves, with material structured around key topics. These topics include colour calibration of visual displays, computer recipe prediction and models for colour-appearance prediction.Each topic is carefully introduced at three levels to aid student understanding. First, theoretical ideas and background information are discussed, then explanations of mathematical solutions follow and finally practical solutions are presented using MATLAB. The content includes:A compendium of equations and numerical data required by the modern colour and imaging scientist.Numerous examples of solutions and algorithms for a wide-range of computational problems in colour science.Example scripts using the MATLAB programming language.This 2nd edition contains substantial new and revised material, including three innovative chapters on colour imaging, psychophysical methods, and physiological colour spaces; the MATLAB toolbox has been extended with a professional, optimized, toolbox to go alongside the current teaching toolbox; and a java toolbox has been added which will interest users who are writing web applications and/or applets or mobile phone applications.Computational Colour Science Using MATLAB 2nd Edition is an invaluable resource for students taking courses in colour science, colour chemistry and colour physics as well as technicians and researchers working in the area. In addition, it acts a useful reference for professionals and researchers working in colour dependent industries such as textiles, paints, print & electronic imaging.Review from First Edition:"...highly recommended as a concise introduction to the practicalities of colour science..." (Color Technology, 2004)

Computational Continuum Mechanics

by Ahmed A. Shabana

This updated text presents the theory of continuum mechanics using computational methods. The text covers a broad range of topics including general problems of large rotation and large deformations and the development and limitations of finite element formulations in solving such problems. Dr. Shabana introduces theories on motion kinematics, strain, forces, and stresses, and goes on to discuss linear and nonlinear constitutive equations, including viscoelastic and plastic constitutive models. General nonlinear continuum mechanics theory is used to develop small and large finite element formulations which correctly describe rigid body motion for use in engineering applications. This second edition features a new chapter that focuses on computational geometry and finite element analysis. This book is ideal for graduate and undergraduate students, professionals, and researchers who are interested in continuum mechanics.

Computational Developmental Psychology

by Thomas R. Shultz

An overview of the emerging discipline of computational developmental psychology, emphasizing the use of constructivist neural networks.

Computational Fluid Dynamics for Engineers

by Mikael Mortensen Love Håkansson Ronnie Andersson Bengt Andersson Berend Van Wachem Rahman Sudiyo

Computational fluid dynamics, CFD, has become an indispensable tool for many engineers. This book gives an introduction to CFD simulations of turbulence, mixing, reaction, combustion and multiphase flows. The emphasis on understanding the physics of these flows helps the engineer to select appropriate models to obtain reliable simulations. Besides presenting the equations involved, the basics and limitations of the models are explained and discussed. The book combined with tutorials, project and power-point lecture notes (all available for download) forms a complete course. The reader is given hands-on experience of drawing, meshing and simulation. The tutorials cover flow and reactions inside a porous catalyst, combustion in turbulent non-premixed flow, and multiphase simulation of evaporation spray respectively. The project deals with design of an industrial-scale selective catalytic reduction process and allows the reader to explore various design improvements and apply best practice guidelines in the CFD simulations.

Computational Gasdynamics

by Culbert B. Laney

Numerical methods are indispensable tools in the analysis of complex fluid flows. This book focuses on computational techniques for high-speed gas flows, especially gas flows containing shocks and other steep gradients. The book decomposes complicated numerical methods into simple modular parts, showing how each part fits and how each method relates to or differs from others. The text begins with a review of gasdynamics and computational techniques. Next come basic principles of computational gasdynamics. The last two parts cover basic techniques and advanced techniques. Senior and graduate level students, especially in aerospace engineering, as well as researchers and practising engineers, will find a wealth of invaluable information on high-speed gas flows in this text.

Computational Inorganic and Bioinorganic Chemistry

by Robert A. Scott Edward I. Solomon R. Bruce King

Over the past several decades there have been major advances in our ability to computationally evaluate the electronic structure of inorganic molecules, particularly transition metal systems. This advancement is due to the Moore's Law increase in computing power as well as the impact of density functional theory (DFT) and its implementation in commercial and freeware programs for quantum chemical calculations. Improved pure and hybrid density functionals are allowing DFT calculations with accuracy comparable to high-level Hartree-Fock treatments, and the results of these calculations can now be evaluated by experiment.When calculations are correlated to, and supported by, experimental data they can provide fundamental insight into electronic structure and its contributions to physical properties and chemical reactivity. This interplay continues to expand and contributes to both improved value of experimental results and improved accuracy of computational predictions.The purpose of this EIC Book is to provide state-of-the-art presentations of quantum mechanical and related methods and their applications, written by many of the leaders in the field. Part 1 of this volume focuses on methods, their background and implementation, and their use in describing bonding properties, energies, transition states and spectroscopic features. Part 2 focuses on applications in bioinorganic chemistry and Part 3 discusses inorganic chemistry, where electronic structure calculations have already had a major impact. This addition to the EIC Book series is of significant value to both experimentalists and theoreticians, and we anticipate that it will stimulate both further development of the methodology and its applications in the many interdisciplinary fields that comprise modern inorganic and bioinorganic chemistry.This volume is also available as part of Encyclopedia of Inorganic Chemistry, 5 Volume Set.This set combines all volumes published as EIC Books from 2007 to 2010, representing areas of key developments in the field of inorganic chemistry published in the Encyclopedia of Inorganic Chemistry. Find out more.

Computational Methods for Electromagnetic Phenomena: Electrostatics in Solvation, Scattering, and Electron Transport

by Wei Cai

A unique and comprehensive graduate text and reference on numerical methods for electromagnetic phenomena, from atomistic to continuum scales, in biology, optical-to-micro waves, photonics, nanoelectronics and plasmas. The state-of-the-art numerical methods described include: * Statistical fluctuation formulae for the dielectric constant * Particle-Mesh-Ewald, Fast-Multipole-Method and image-based reaction field method for long-range interactions * High-order singular/hypersingular (Nyström collocation/Galerkin) boundary and volume integral methods in layered media for Poisson-Boltzmann electrostatics, electromagnetic wave scattering and electron density waves in quantum dots * Absorbing and UPML boundary conditions * High-order hierarchical Nédélec edge elements * High-order discontinuous Galerkin (DG) and Yee finite difference time-domain methods * Finite element and plane wave frequency-domain methods for periodic structures * Generalized DG beam propagation method for optical waveguides * NEGF(Non-equilibrium Green's function) and Wigner kinetic methods for quantum transport * High-order WENO and Godunov and central schemes for hydrodynamic transport * Vlasov-Fokker-Planck and PIC and constrained MHD transport in plasmas

Computational Methods for Microstructure-Property Relationships

by Dennis Dimiduk Somnath Ghosh

Computational Methods for Microstructure-Property Relationships introduces state-of-the-art advances in computational modeling approaches for materials structure-property relations. Written with an approach that recognizes the necessity of the engineering computational mechanics framework, this volume provides balanced treatment of heterogeneous materials structures within the microstructural and component scales. Encompassing both computational mechanics and computational materials science disciplines, this volume offers an analysis of the current techniques and selected topics important to industry researchers, such as deformation, creep and fatigue of primarily metallic materials. Researchers, engineers and professionals involved with predicting performance and failure of materials will find Computational Methods for Microstructure-Property Relationships a valuable reference.

Computational Methods for Plasticity

by D. Peric E. A. de Souza Neto D. R. Owen

The subject of computational plasticity encapsulates the numerical methods used for the finite element simulation of the behaviour of a wide range of engineering materials considered to be plastic - i.e. those that undergo a permanent change of shape in response to an applied force. Computational Methods for Plasticity: Theory and Applications describes the theory of the associated numerical methods for the simulation of a wide range of plastic engineering materials; from the simplest infinitesimal plasticity theory to more complex damage mechanics and finite strain crystal plasticity models. It is split into three parts - basic concepts, small strains and large strains. Beginning with elementary theory and progressing to advanced, complex theory and computer implementation, it is suitable for use at both introductory and advanced levels. The book:Offers a self-contained text that allows the reader to learn computational plasticity theory and its implementation from one volume.Includes many numerical examples that illustrate the application of the methodologies described.Provides introductory material on related disciplines and procedures such as tensor analysis, continuum mechanics and finite elements for non-linear solid mechanics.Is accompanied by purpose-developed finite element software that illustrates many of the techniques discussed in the text, downloadable from the book's companion website.This comprehensive text will appeal to postgraduate and graduate students of civil, mechanical, aerospace and materials engineering as well as applied mathematics and courses with computational mechanics components. It will also be of interest to research engineers, scientists and software developers working in the field of computational solid mechanics.

Computational Methods for Sensor Material Selection

by Charles J. Taylor Margaret A. Ryan M. L. Homer Mario Blanco Joseph R. Stetter Abhijit V. Shevade

Chemical vapor sensing arrays have grown in popularity over the past two decades, finding applications for tasks such as process control, environmental monitoring, and medical diagnosis. This is the first in-depth analysis of the process of choosing materials and components for these "electronic noses", with special emphasis on computational methods. For a view of component selection with an experimental perspective, readers may refer to the complementary volume of Integrated Microanalytical Systems entitled "Combinatorial Methodologies for Sensor Materials."

Computational Methods in Lanthanide and Actinide Chemistry

by Michael Dolg

The f-elements and their compounds often possess an unusually complex electronic structure, governed by the high number of electronic states arising from open f-shells as well as large relativistic and electron correlation effects. A correct theoretical description of these elements poses the highest challenges to theory. Computational Methods in Lanthanide and Actinide Chemistry summarizes state-of-the-art electronic structure methods applicable for quantum chemical calculations of lanthanide and actinide systems and presents a broad overview of their most recent applications to atoms, molecules and solids. The book contains sixteen chapters, written by leading experts in method development as well as in theoretical investigations of f-element systems. Topics covered include: * Relativistic configuration interaction calculations for lanthanide and actinide anions * Study of actinides by relativistic coupled cluster methods * Relativistic all-electron approaches to the study of f- element chemistry * Relativistic pseudopotentials and their applications * Gaussian basis sets for lanthanide and actinide elements * Applied computational actinide chemistry This book will serve as a comprehensive reference work for quantum chemists and computational chemists, both those already working in, and those planning to enter the field of quantum chemistry for f-elements. Experimentalists will also find important information concerning the capabilities of modern quantum chemical methods to assist in the interpretation or even to predict the outcome of their experiments.

Computational Modeling of Biological Systems

by Nikolay V Dokholyan

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.

Computational Modeling of Signaling Networks

by Xuedong Liu Meredith D. Betterton

Signaling networks are composed of numerous signaling pathways and each has its own intricate component parts. Signaling outputs are dynamic, extraordinarily complex and yet highly specific. In, Computational Modeling of Signaling Networks: Methods and Protocols, expert researchers in the field provide key techniques to study signaling networks. Focusing on Systems of ODEs, parameterization of signaling models, signaling pathways, mass-action kinetics and ODEs, and how to use modeling to plan experiments. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Computational Modeling of Signaling Networks: Methods and Protocols aids scientists in continuing study of how signaling networks behave in space and time to generate specific biological responses and how those responses impact biology and medicine.

Computational Models for Polydisperse Particulate and Multiphase Systems

by Daniele L. Marchisio Rodney O. Fox

Providing a clear description of the theory of polydisperse multiphase flows, with emphasis on the mesoscale modelling approach and its relationship with microscale and macroscale models, this all-inclusive introduction is ideal whether you are working in industry or academia. Theory is linked to practice through discussions of key real-world cases (particle/droplet/bubble coalescence, break-up, nucleation, advection and diffusion and physical- and phase-space), providing valuable experience in simulating systems that can be applied to your own applications. Practical cases of QMOM, DQMOM, CQMOM, EQMOM and ECQMOM are also discussed and compared, as are realizable finite-volume methods. This provides the tools you need to use quadrature-based moment methods, choose from the many available options, and design high-order numerical methods that guarantee realizable moment sets. In addition to the numerous practical examples, MATLAB scripts for several algorithms are also provided, so you can apply the methods described to practical problems straight away.

Computational Models of the Auditory System

by Arthur N. Popper Richard R. Fay Ray Meddis Enrique Lopez-Poveda

This volume, Computational Models of the Auditory, will have at its unifying theme a systems approach where the focus will be on studies whose intent is to contribute to the big picture of hearing. In effect, the work covered in this volume, and the volume itself, will build a global model of audition. The chapters will, rather than focusing on details of individual components of the hearing system, address the concerns of readers and researchers who want to know how the system works as a whole.

The Computational Neurobiology of Reaching and Pointing: A Foundation for Motor Learning

by Reza Shadmehr Steven P. Wise

This book presents an introduction to the computational neurobiology of reaching and pointing--with emphasis on motor learning in primates--based on an eclectic selection of topics.

Computational Neuroscience of Drug Addiction

by Serge H. Ahmed Boris Gutkin

Drug addiction remains one of the most important public health problems in western societies and is a rising concern for developing nations. Over the past 3 decades, experimental research on the neurobiology and psychology of drug addiction has generated a torrent of exciting data, from the molecular up to the behavioral levels. As a result, a new and pressing challenge for addiction research is to formulate a synthetic theoretical framework that goes well beyond mere scientific eclectism to deepen our understanding of drug addiction and to foster our capacity to prevent and to cure drug addiction. Intrigued by the apparent irrational behavior of drug addicts, researchers from a wide range of scientific disciplines have formulated a plethora of theoretical schemes over the years to understand addiction. However, most of these theories and models are qualitative in nature and are formulated using terms that are often ill-defined. As a result, the empirical validity of these models has been difficult to test rigorously, which has served to generate more controversy than clarity. In this context, as in other scientific fields, mathematical and computational modeling should contribute to the development of more testable and rigorous models of addiction.

Computational Ocean Acoustics

by Henrik Schmidt Michael B. Porter Finn B. Jensen William A. Kuperman

Senior level/graduate level text/reference presenting state-of-the- art numerical techniques to solve the wave equation in heterogeneous fluid-solid media. Numerical models have become standard research tools in acoustic laboratories, and thus computational acoustics is becoming an increasingly important branch of ocean acoustic science. The first edition of this successful book, written by the recognized leaders of the field, was the first to present a comprehensive and modern introduction to computational ocean acoustics accessible to students. This revision, with 100 additional pages, completely updates the material in the first edition and includes new models based on current research. It includes problems and solutions in every chapter, making the book more useful in teaching (the first edition had a separate solutions manual). The book is intended for graduate and advanced undergraduate students of acoustics, geology and geophysics, applied mathematics, ocean engineering or as a reference in computational methods courses, as well as professionals in these fields, particularly those working in government (especially Navy) and industry labs engaged in the development or use of propagating models.

Computational Organic Chemistry

by Steven M. Bachrach

The Second Edition demonstrates how computational chemistry continues to shed new light on organic chemistryThe 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 chemistryPericyclic reactionsDiradicals and carbenesOrganic reactions of anionsSolution-phase organic chemistryOrganic reaction dynamicsThe 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.

Computational Pharmaceutical Solid State Chemistry

by Yuriy A. Abramov

Recent trends within the pharmaceutical industry through the Quality by Design initiatives have seen a greater emphasis on the development of a molecular-scale understanding in the development of efficient manufacturing processes for active pharmaceutical ingredients (APIs) and their formulation into drug products. This book examines the state-of-the-art computational approaches to guide solid form experiments to optimize the physical and chemical properties of API related to its stability, bioavailability and formulatability. The book is intended to be used as a professional reference to researchers in Pharmaceutical industry and in academia and potentially as a text book reference for undergraduate, graduate and postgraduate students in the field of Computational Chemistry, Solid State Chemistry, Pharmaceutical Science and Material Science.

Computational Pharmaceutics

by Juergen Siepmann Dennis Douroumis Alfred Fahr Defang Ouyang Sean C. Smith Vladimir Torchilin Martin J. Snowden

Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems. The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems. Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field. This book is included in the Advances in Pharmaceutical Technology book series.

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