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Computer Simulation And Data Analysis In Molecular Biology And Biophysics
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Book Synopsis Computer Simulation and Data Analysis in Molecular Biology and Biophysics by : Victor Bloomfield
Download or read book Computer Simulation and Data Analysis in Molecular Biology and Biophysics written by Victor Bloomfield and published by Springer Science & Business Media. This book was released on 2009-06-05 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.
Book Synopsis Computer Simulations in Molecular Biology by : Hiqmet Kamberaj
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.
Book Synopsis Mathematical Modeling of Biological Systems, Volume I by : Andreas Deutsch
Download or read book Mathematical Modeling of Biological Systems, Volume I written by Andreas Deutsch and published by Springer Science & Business Media. This book was released on 2007-06-15 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume I of this two-volume, interdisciplinary work is a unified presentation of a broad range of state-of-the-art topics in the rapidly growing field of mathematical modeling in the biological sciences. The chapters are thematically organized into the following main areas: cellular biophysics, regulatory networks, developmental biology, biomedical applications, data analysis and model validation. The work will be an excellent reference text for a broad audience of researchers, practitioners, and advanced students in this rapidly growing field at the intersection of applied mathematics, experimental biology and medicine, computational biology, biochemistry, computer science, and physics.
Book Synopsis Computational Biochemistry and Biophysics by : Oren M. Becker
Download or read book Computational Biochemistry and Biophysics written by Oren M. Becker and published by CRC Press. This book was released on 2001-02-09 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret b
Book Synopsis Data Analysis in Biochemistry and Biophysics by : Magar Mager
Download or read book Data Analysis in Biochemistry and Biophysics written by Magar Mager and published by Elsevier. This book was released on 2012-12-02 with total page 516 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data Analysis in Biochemistry and Biophysics describes the techniques how to derive the most amount of quantitative and statistical information from data gathered in enzyme kinetics, protein-ligand equilibria, optical rotatory dispersion, chemical relaxation methods. This book focuses on the determination and analysis of parameters in different models that are used in biochemistry, biophysics, and molecular biology. The Michaelis-Menten equation can explain the process to obtain the maximum amount of information by determining the parameters of the model. This text also explains the fundamentals present in hypothesis testing, and the equation that represents the statistical aspects of a linear model occurring frequently in this field of testing. This book also analyzes the ultraviolet spectra of nucleic acids, particularly, to establish the composition of melting regions of nucleic acids. The investigator can use the matrix rank analysis to determine the spectra to substantiate systems whose functions are not known. This text also explains flow techniques and relaxation methods associated with rapid reactions to determine transient kinetic parameters. This book is suitable for molecular biologists, biophysicists, physiologists, biochemists, bio- mathematicians, statisticians, computer programmers, and investigators involved in related sciences
Book Synopsis Numerical Computer Methods, Part E by :
Download or read book Numerical Computer Methods, Part E written by and published by Elsevier. This book was released on 2004-06-02 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: The contributions in this volume emphasize analysis of experimental data and analytical biochemistry, with examples taken from biochemistry. They serve to inform biomedical researchers of the modern data analysis methods that have developed concomitantly with computer hardware. Selected Contents: A practical approach to interpretation of SVD results; modeling of oscillations in endocrine networks with feedback; quantifying asynchronous breathing; sample entropy; wavelet modeling and processing of nasal airflow traces
Book Synopsis Computational Modeling And Simulations Of Biomolecular Systems by : Benoit Roux
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).
Book Synopsis Computational Modeling of Biological Systems by : Nikolay V Dokholyan
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 2012-02-10 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.
Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick
Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
Book Synopsis Statistical Modeling and Machine Learning for Molecular Biology by : Alan Moses
Download or read book Statistical Modeling and Machine Learning for Molecular Biology written by Alan Moses and published by CRC Press. This book was released on 2017-01-06 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: • Assumes no background in statistics or computers • Covers most major types of molecular biological data • Covers the statistical and machine learning concepts of most practical utility (P-values, clustering, regression, regularization and classification) • Intended for graduate students beginning careers in molecular biology, systems biology, bioengineering and genetics
Book Synopsis Guide to Biomolecular Simulations by : Oren M. Becker
Download or read book Guide to Biomolecular Simulations written by Oren M. Becker and published by Springer Science & Business Media. This book was released on 2006-06-26 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures. The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.
Book Synopsis Modelling in Molecular Biology by : Gabriel Ciobanu
Download or read book Modelling in Molecular Biology written by Gabriel Ciobanu and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents new mathematical and computational models as well as statistical methods for the solution of fundamental problems in the biosciences. Describes how to find regularities among empirical data, as well as conceptual models and theories.
Book Synopsis Computational Science – ICCS 2009 by : Gabrielle Allen
Download or read book Computational Science – ICCS 2009 written by Gabrielle Allen and published by Springer. This book was released on 2009-05-21 with total page 920 pages. Available in PDF, EPUB and Kindle. Book excerpt: “There is something fascinating about science. One gets such wholesale returns of conjecture out of such a tri?ing investment of fact. ” Mark Twain, Life on the Mississippi The challenges in succeeding with computational science are numerous and deeply a?ect all disciplines. NSF’s 2006 Blue Ribbon Panel of Simulation-Based 1 Engineering Science (SBES) states ‘researchers and educators [agree]: com- tational and simulation engineering sciences are fundamental to the security and welfare of the United States. . . We must overcome di?culties inherent in multiscale modeling, the development of next-generation algorithms, and the design. . . of dynamic data-driven application systems. . . We must determine better ways to integrate data-intensive computing, visualization, and simulation. - portantly,wemustoverhauloureducationalsystemtofostertheinterdisciplinary study. . . The payo?sformeeting these challengesareprofound. ’The International Conference on Computational Science 2009 (ICCS 2009) explored how com- tational sciences are not only advancing the traditional hard science disciplines, but also stretching beyond, with applications in the arts, humanities, media and all aspects of research. This interdisciplinary conference drew academic and industry leaders from a variety of ?elds, including physics, astronomy, mat- matics,music,digitalmedia,biologyandengineering. Theconferencealsohosted computer and computational scientists who are designing and building the - ber infrastructure necessary for next-generation computing. Discussions focused on innovative ways to collaborate and how computational science is changing the future of research. ICCS 2009: ‘Compute. Discover. Innovate. ’ was hosted by the Center for Computation and Technology at Louisiana State University in Baton Rouge.
Book Synopsis Computer Analysis of Genetic Macromolecules by : N. A. Kolchanov
Download or read book Computer Analysis of Genetic Macromolecules written by N. A. Kolchanov and published by World Scientific. This book was released on 1994 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular biology and genetics are fast-growing fields with significant results and findings being reported virtually every day. Raw data from the wet lab accumulate at an astonishing rate, making it necessary to analyze the biological data with the use of computers. This book reveals how the current challenges of molecular biology and genetics are met with computer and mathematical treatments. A combined effort of the Computational Genetics and Biophysics Group (Supercomputer Computations Research Institute, USA), the Theoretical Molecular Genetics (Russian Academy of Sciences, Russia) and the Bioinformatics Group (Consiglio Nazionale delle Ricerche, Italy), many of these findings are firsthand discoveries made by these groups. The book emphasizes the fundamental principles of the structural-functional organization of the 3 major classes of genetic macromolecules: DNA, RNA and proteins. It also introduces universally applicable theoretical principles into the enormous realm of raw data and develops an integrative, theoretical computer approach to the analysis of these macromolecules to gain insights into the complexities of their function and evolution.
Book Synopsis Using R for Numerical Analysis in Science and Engineering by : Victor A. Bloomfield
Download or read book Using R for Numerical Analysis in Science and Engineering written by Victor A. Bloomfield and published by CRC Press. This book was released on 2018-09-03 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: Instead of presenting the standard theoretical treatments that underlie the various numerical methods used by scientists and engineers, Using R for Numerical Analysis in Science and Engineering shows how to use R and its add-on packages to obtain numerical solutions to the complex mathematical problems commonly faced by scientists and engineers. This practical guide to the capabilities of R demonstrates Monte Carlo, stochastic, deterministic, and other numerical methods through an abundance of worked examples and code, covering the solution of systems of linear algebraic equations and nonlinear equations as well as ordinary differential equations and partial differential equations. It not only shows how to use R’s powerful graphic tools to construct the types of plots most useful in scientific and engineering work, but also: Explains how to statistically analyze and fit data to linear and nonlinear models Explores numerical differentiation, integration, and optimization Describes how to find eigenvalues and eigenfunctions Discusses interpolation and curve fitting Considers the analysis of time series Using R for Numerical Analysis in Science and Engineering provides a solid introduction to the most useful numerical methods for scientific and engineering data analysis using R.
Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo
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 810 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.
Book Synopsis Multivariate Methods of Representing Relations in R for Prioritization Purposes by : Wayne L. Myers
Download or read book Multivariate Methods of Representing Relations in R for Prioritization Purposes written by Wayne L. Myers and published by Springer Science & Business Media. This book was released on 2012-03-24 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph is multivariate, multi-perspective and multipurpose. We intend to be innovatively integrative through statistical synthesis. Innovation requires capacity to operate in ways that are not ordinary, which means that conventional computations and generic graphics will not meet the needs of an adaptive approach. Flexible formulation and special schematics are essential elements that must be manageable and economical.
