Modelling In Molecular Biology

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Biological Modeling and Simulation

Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262303396
Total Pages : 403 pages
Book Rating : 4.2/5 (623 download)

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Book Synopsis Biological Modeling and Simulation by : Russell Schwartz

Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.

Mathematical Modeling in Systems Biology

Author : Brian P. Ingalls
Publisher : MIT Press
ISBN 13 : 0262545829
Total Pages : 423 pages
Book Rating : 4.2/5 (625 download)

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Book Synopsis Mathematical Modeling in Systems Biology by : Brian P. Ingalls

Download or read book Mathematical Modeling in Systems Biology written by Brian P. Ingalls and published by MIT Press. This book was released on 2022-06-07 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.

Discrete and Topological Models in Molecular Biology

Author : Nataša Jonoska
Publisher : Springer Science & Business Media
ISBN 13 : 3642401937
Total Pages : 522 pages
Book Rating : 4.6/5 (424 download)

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Book Synopsis Discrete and Topological Models in Molecular Biology by : Nataša Jonoska

Download or read book Discrete and Topological Models in Molecular Biology written by Nataša Jonoska and published by Springer Science & Business Media. This book was released on 2013-12-23 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.

Modelling in Molecular Biology

Author : Gabriel Ciobanu
Publisher : Springer Science & Business Media
ISBN 13 : 364218734X
Total Pages : 311 pages
Book Rating : 4.6/5 (421 download)

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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 311 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.

Mathematical Models in Molecular Cellular Biology

Author : Lee A. Segel
Publisher : CUP Archive
ISBN 13 : 9780521229258
Total Pages : 776 pages
Book Rating : 4.2/5 (292 download)

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Book Synopsis Mathematical Models in Molecular Cellular Biology by : Lee A. Segel

Download or read book Mathematical Models in Molecular Cellular Biology written by Lee A. Segel and published by CUP Archive. This book was released on 1980 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interest in theoretical biology is rapidly growing and this 1981 book attempts to make the theory more accessible to experimentalists. Its primary purpose is to demonstrate to experimental molecular and cellular biologists the possible usefulness of mathematical models. Biologists with a basic command of calculus should be able to learn from the book what assumptions are implied by various types of equations, to understand in broad outline a number of major theoretical concepts, and to be aware of some of the difficulties connected with analytical and numerical solutions of mathematical problems. Thus they should be able to appreciate the significance of theoretical papers in their fields and to communicate usefully with theoreticians in the course of their work.

Molecular Modeling and Simulation

Author : Tamar Schlick
Publisher : Springer Science & Business Media
ISBN 13 : 0387224645
Total Pages : 669 pages
Book Rating : 4.3/5 (872 download)

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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

Computer Modelling in Molecular Biology

Author : Julia M. Goodfellow
Publisher : John Wiley & Sons
ISBN 13 : 3527615326
Total Pages : 259 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Computer Modelling in Molecular Biology by : Julia M. Goodfellow

Download or read book Computer Modelling in Molecular Biology written by Julia M. Goodfellow and published by John Wiley & Sons. This book was released on 2008-07-11 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book supplies an application-oriented introduction to molecular simulation techniques used to study a wide range of problems in molecular biology. Each chapter focuses in detail on one kind of application, including the scientific background, the appropriate methodology and the relationship to experimental results. The book contains many areas of interest to basic and industrial scientists, including: - flexibility of peptides - protein-peptide interactions - ion translocation across membranes - modelling protein and nucleic acid conformations - stability of mutant proteins - modelling conformational transitions Currently the only up-to-date compilation available, this book enables readers to get an overview of the methods and how they are used in various specialized applications without having to search for them in a large number of papers in different journals.

Molecular Modeling of Proteins

Author : Andreas Kukol
Publisher : Humana Press
ISBN 13 : 9781493954919
Total Pages : 474 pages
Book Rating : 4.9/5 (549 download)

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Book Synopsis Molecular Modeling of Proteins by : Andreas Kukol

Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.

Modeling Dynamic Phenomena in Molecular and Cellular Biology

Author : Lee A. Segel
Publisher : Cambridge University Press
ISBN 13 : 9780521274777
Total Pages : 326 pages
Book Rating : 4.2/5 (747 download)

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Book Synopsis Modeling Dynamic Phenomena in Molecular and Cellular Biology by : Lee A. Segel

Download or read book Modeling Dynamic Phenomena in Molecular and Cellular Biology written by Lee A. Segel and published by Cambridge University Press. This book was released on 1984-03-30 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dynamic development of various processes is a central problem of biology and indeed of all the sciences. The mathematics describing that development is, in general, complicated, because the models that are realistic are usually nonlinear. Consequently many biologists may not notice a possible application of theory. They may be unable to decide whether a particular model captures the essence of a system, or to appreciate that analysis of a model can reveal important aspects of biological problems and may even describe in detail how a system works. The aim of this textbook is to remedy the situation by adopting a general approach to model analysis and applying it several times to problems (drawn primarily from molecular and cellular biology) of gradually increasing biological and mathematical complexity. Although material of considerable sophistication is included, little mathematical background is required - only some exposure to elementary calculus; appendixes supply the necessary mathematics and the author concentrates on concepts rather than techniques. He also emphasizes the role of computers in giving a full picture of model behavior and complementing more qualitative analysis. Some problems suitable for computer analysis are also included. This is a class-tested textbook suitable for a one-semester course for advanced undergraduate and beginning graduate students in biology or applied mathematics. It can also be used as a source book for teachers and a reference for specialists.

Mathematical Models in Biology

Author : Leah Edelstein-Keshet
Publisher : SIAM
ISBN 13 : 9780898719147
Total Pages : 629 pages
Book Rating : 4.7/5 (191 download)

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Book Synopsis Mathematical Models in Biology by : Leah Edelstein-Keshet

Download or read book Mathematical Models in Biology written by Leah Edelstein-Keshet and published by SIAM. This book was released on 1988-01-01 with total page 629 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical Models in Biology is an introductory book for readers interested in biological applications of mathematics and modeling in biology. A favorite in the mathematical biology community, it shows how relatively simple mathematics can be applied to a variety of models to draw interesting conclusions. Connections are made between diverse biological examples linked by common mathematical themes. A variety of discrete and continuous ordinary and partial differential equation models are explored. Although great advances have taken place in many of the topics covered, the simple lessons contained in this book are still important and informative. Audience: the book does not assume too much background knowledge--essentially some calculus and high-school algebra. It was originally written with third- and fourth-year undergraduate mathematical-biology majors in mind; however, it was picked up by beginning graduate students as well as researchers in math (and some in biology) who wanted to learn about this field.

Statistical Modeling and Machine Learning for Molecular Biology

Author : Alan Moses
Publisher : CRC Press
ISBN 13 : 1482258609
Total Pages : 281 pages
Book Rating : 4.4/5 (822 download)

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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

Molecular Modeling at the Atomic Scale

Author : Ruhong Zhou
Publisher : CRC Press
ISBN 13 : 1466562951
Total Pages : 392 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Molecular Modeling at the Atomic Scale by : Ruhong Zhou

Download or read book Molecular Modeling at the Atomic Scale written by Ruhong Zhou and published by CRC Press. This book was released on 2014-08-21 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.

Biological Modeling and Simulation

Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262195844
Total Pages : 403 pages
Book Rating : 4.2/5 (621 download)

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Book Synopsis Biological Modeling and Simulation by : Russell Schwartz

Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Author : Victor Bloomfield
Publisher : Springer Science & Business Media
ISBN 13 : 1441900837
Total Pages : 325 pages
Book Rating : 4.4/5 (419 download)

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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.

Mathematical Models in Biology

Author : Valeria Zazzu
Publisher : Springer
ISBN 13 : 3319234978
Total Pages : 207 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis Mathematical Models in Biology by : Valeria Zazzu

Download or read book Mathematical Models in Biology written by Valeria Zazzu and published by Springer. This book was released on 2015-11-26 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy. The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content useful as it addresses existing challenges in identifying the gaps between mathematical modeling and biological research. The shared solutions will aid and promote further collaboration between life sciences and mathematics.

Molecular Modeling and Prediction of Bioactivity

Author : Klaus Gundertofte
Publisher : Springer Science & Business Media
ISBN 13 : 1461541417
Total Pages : 490 pages
Book Rating : 4.4/5 (615 download)

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Book Synopsis Molecular Modeling and Prediction of Bioactivity by : Klaus Gundertofte

Download or read book Molecular Modeling and Prediction of Bioactivity written by Klaus Gundertofte and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: Much of chemistry, molecular biology, and drug design, are centered around the relationships between chemical structure and measured properties of compounds and polymers, such as viscosity, acidity, solubility, toxicity, enzyme binding, and membrane penetration. For any set of compounds, these relationships are by necessity complicated, particularly when the properties are of biological nature. To investigate and utilize such complicated relationships, henceforth abbreviated SAR for structure-activity relationships, and QSAR for quantitative SAR, we need a description of the variation in chemical structure of relevant compounds and biological targets, good measures of the biological properties, and, of course, an ability to synthesize compounds of interest. In addition, we need reasonable ways to construct and express the relationships, i. e. , mathematical or other models, as well as ways to select the compounds to be investigated so that the resulting QSAR indeed is informative and useful for the stated purposes. In the present context, these purposes typically are the conceptual understanding of the SAR, and the ability to propose new compounds with improved property profiles. Here we discuss the two latter parts of the SARlQSAR problem, i. e. , reasonable ways to model the relationships, and how to select compounds to make the models as "good" as possible. The second is often called the problem of statistical experimental design, which in the present context we call statistical molecular design, SMD. 1.

Molecular Modeling

Author : Hans-Dieter Höltje
Publisher : John Wiley & Sons
ISBN 13 : 3527614761
Total Pages : 206 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Molecular Modeling by : Hans-Dieter Höltje

Download or read book Molecular Modeling written by Hans-Dieter Höltje and published by John Wiley & Sons. This book was released on 2008-07-11 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experienced experts in molecular modeling, this books describes the basics to the extent that is necessary if one wants to be able to reliably judge the results from molecular modeling calculations. Its main objective is the description of the various pitfalls to be avoided. Without unnecessary overhead it leads the reader from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules. A textbook for beginners as well as an invaluable reference for all those dealing with molecular modeling in their daily work!