Download or read book Theoretical and in Silico Modeling of Biological Systems written by Bogdan Barz and published by . This book was released on 2009 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis describes four distinct studies (involving a variety of concepts and methods from the physical sciences) of complex biological systems and processes that cover a wide range of time and length scales (extending from the molecular to the multi-cellular level), namely: 1) identification of near-native structures from a large set of in silico predicted structures for a given target protein by probing the stability of the structures against simulated heating using Molecular Dynamics (MD) simulations; 2) all atom MD simulation study of protein-cell membrane interactions designed to elucidate the relation between the conformational structure of the GP41 fusion peptide of HIV-1 virus and the density of the lipid membrane; 3) calculation of the potential of mean force for water transport through single wall carbon nanotubes from nonequilibrium MD simulations; and 4) development and application of a novel computational method, referred to as the cellular particle dynamics (CPD) method, for the simulation of the dynamics of multicellular systems.

Download or read book Theoretical Models in Biology written by Glenn Rowe and published by Oxford University Press. This book was released on 1994 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book surveys the state of the art in theoretical and computer modeling for biological sciences. Using both mathematical and stochastic computer models of biological systems, the author focuses in particular on three central topics: the origin of life, the immune system, and memory in the brain. Throughout the book, the author emphasizes how the power of modern computers is allowing researchers in theoretical biology to break free of the constraints on modeling that were imposed by the traditional differential equation approach. Unique in its emphasis on modeling and computer simulation, Theoretical Models in Biology: The Origin of Life, the Immune System, and the Brain will be welcomed by students and researchers of mathematical biology.

Download or read book In Silico Simulation of Biological Processes written by Gregory R. Bock and published by John Wiley & Sons. This book was released on 2003-07-07 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over recent decades vast amounts of biological data have been accumulated. However, it is becoming increasingly difficult to apply traditional theoretical methods to the formulation of coherent pictures of cell and organ function because it is no longer possible for a human theorist to integrate all of the available information. Instead, computer technologies must now be used to perform this integration. This book brings together contributions from many different fields to summarize the current status of computer-assisted modelling of biological processes. The initial chapters deal with fundamental developments in hardware, software and mathematics that underlie current approaches to biological modelling. Next, different approaches to collating data on gene structure and function are presented. These databases form a vital resource for any investigator trying to construct an integrated picture of particular biological systems. Cell signalling systems form a particularly complicated aspect of all cellular function and are important both in the understanding of basic cellular processes and in selecting targets for drugs. Recent approaches to integrating data on cell signalling into computer models are covered. Further chapters build on these approaches to show how computerized models of intact cells can be developed. Finally, approaches to the computer modelling of whole organs such as the heart are presented. The role of computer modelling in drug design is the subject of the final chapter and is also touched on throughout the discussions.

Download or read book Systems Biological Approaches in Infectious Diseases written by Helena I. Boshoff and published by Springer Science & Business Media. This book was released on 2007-01-15 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book brings together the various fields of functional genomics and systems biology that provide information on metabolic function. There is special emphasis on the identification of drug targets. The book includes practical examples from the various "omic" sciences as well as theoretical examples of how integrated knowledge of these sciences can be applied to drug discovery. It is of interest to researchers in the pharmaceutical drug discovery environment.

Download or read book Foundations of Theoretical Approaches in Systems Biology written by Alberto Marin-Sanguino and published by Frontiers Media SA. This book was released on 2019-01-11 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: If biology in the 20th century was characterized by an explosion of new technologies and experimental methods, that of the 21st has seen an equally exuberant proliferation of mathematical and computational methods that attempt to systematize and explain the abundance of available data. As we live through the consolidation of a new paradigm where experimental data goes hand in hand with computational analysis, we contemplate the challenge of fusing these two aspects of the new biology into a consistent theoretical framework. Whether systems biology will survive as a field or be washed away by the tides of future fads will ultimately depend on its success to achieve this type of synthesis. The famous quote attributed to Kurt Lewin comes to mind: "there is nothing more practical than a good theory". This book presents a wide assortment of articles on systems biology in an attempt to capture the variety of current methods in systems biology and show how they can help to find answers to the challenges of modern biology.

Download or read book Modeling Dynamic Biological Systems written by Bruce Hannon and published by Springer. This book was released on 2014-07-05 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many biologists and ecologists have developed models that find widespread use in theoretical investigations and in applications to organism behavior, disease control, population and metapopulation theory, ecosystem dynamics, and environmental management. This book captures and extends the process of model development by concentrating on the dynamic aspects of these processes and by providing the tools such that virtually anyone with basic knowledge in the Life Sciences can develop meaningful dynamic models. Examples of the systems modeled in the book range from models of cell development, the beating heart, the growth and spread of insects, spatial competition and extinction, to the spread and control of epidemics, including the conditions for the development of chaos. Key features: - easy-to-learn and easy-to-use software - examples from many subdisciplines of biology, covering models of cells, organisms, populations, and metapopulations - no prior computer or programming experience required Key benefits: - learn how to develop modeling skills and system thinking on your own rather than use models developed by others - be able to easily run models under alternative assumptions and investigate the implications of these assumptions for the dynamics of the biological system being modeled - develop skills to assess the dynamics of biological systems

Download or read book Systems Biology written by Aleš Prokop and published by Springer Science & Business Media. This book was released on 2013-08-28 with total page 569 pages. Available in PDF, EPUB and Kindle. Book excerpt: Growth in the pharmaceutical market has slowed down – almost to a standstill. One reason is that governments and other payers are cutting costs in a faltering world economy. But a more fundamental problem is the failure of major companies to discover, develop and market new drugs. Major drugs losing patent protection or being withdrawn from the market are simply not being replaced by new therapies – the pharmaceutical market model is no longer functioning effectively and most pharmaceutical companies are failing to produce the innovation needed for success. This multi-authored new book looks at a vital strategy which can bring innovation to a market in need of new ideas and new products: Systems Biology (SB). Modeling is a significant task of systems biology. SB aims to develop and use efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of biological systems, such as the networks of metabolites comprise signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes. SB involves a series of operational protocols used for performing research, namely a cycle composed of theoretical, analytic or computational modeling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.

Download or read book Theoretical and Applied Aspects of Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer. This book was released on 2018-06-21 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

Download or read book Contextualizing Systems Biology written by Martin Döring and published by Springer. This book was released on 2015-12-18 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collective monograph aims at contributing to an improved understanding of the epistemic presumptions, sociocultural implications and historically backgrounds of the newly emerging and currently expanding approach of systems biology. In doing so, it offers empirically grounded, valuable and reflexive information about a paradigmatic shift in the biosciences for a wide range of scientists working in the interdisciplinary areas of systems biology, synthetic biology, molecular biology, biology, the philosophy of science, the sociology of science and scientific knowledge, science and technology studies, technology assessment and the like. The authors of this monograph share the theoretical methodological premise that science is a culturally and socially embedded practice which characterizes our culture as a scientific one and at the same time draws its innovative potential from its socio-cultural context. This dialectic relationship lies at the heart of the current development of systems biology which is conceived as a so-called successor of ‘-omics’ research and triggered by high-throughput information technologies. At the same time a need for a holistic conceptualization of complex biological processes emerges. The title Contextualizing Systems Biology suggests that this book analyzes the development and advent of systems biology from different theoretical and methodological perspectives. We investigate a variety of contexts ranging from the analysis of cognitive contexts (such as basic theoretical concepts) to regulative contexts (policies) to the concrete application of a systems biology in the socio-scientific context of a European research project. In empirically analyzing these different and interrelated layers and dimensions of systems biology, the scope of the book goes beyond present attempts to investigate the advent of new approaches in the biological sciences as it frames and assesses systems biology from an interdisciplinary and integrated perspective.

Download or read book In Silico Systems Biology written by Maria Victoria Schneider and published by Humana Press. This book was released on 2013-05-29 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology can now be considered an established and fundamental field in life sciences. It has moved from the identification of molecular 'parts lists' for living organisms towards synthesising information from different 'omics'-based approaches to generate and test new hypotheses about how biological systems work. In In Silico Systems Biology: Methods and Protocols, expert researchers in the field detail a practical set of chapters based often on actual materials used and develop for face-to-face training with examples and case studies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step workflows, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, In Silico Systems Biology: Methods and Protocols seeks to aid scientists in the further study of network biology and mathematical models of biological systems.

Download or read book A Systems Theoretic Approach to Systems and Synthetic Biology I Models and System Characterizations written by Vishwesh V. Kulkarni and published by Springer. This book was released on 2014-07-03 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume I provides a panoramic view that illustrates the potential of such mathematical methods in systems and synthetic biology. Recent advances in systems and synthetic biology have clearly demonstrated the benefits of a rigorous and systematic approach rooted in the principles of systems and control theory - not only does it lead to exciting insights and discoveries but it also reduces the inordinately lengthy trial-and-error process of wet-lab experimentation, thereby facilitating significant savings in human and financial resources. In Volume I, some of the leading researchers in the field of systems and synthetic biology demonstrate how systems and control theoretic concepts and techniques can be useful, or should evolve to be useful, in order to understand how biological systems function. As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.

Download or read book Introduction to Systems Biology written by Sangdun Choi and published by Springer Science & Business Media. This book was released on 2008-05-17 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Download or read book Cambridge Healthtech Institute s Fourth Annual In Silico Biology Conference Modeling Systems Biology for Research and Target Prioritization written by and published by . This book was released on 2002 with total page 8 pages. Available in PDF, EPUB and Kindle. Book excerpt: In silico biology, the computer aided analysis of biological systems, is a relatively young research area. It first has been coined in the late 1990's and emerged from Theoretical and Computational Biology. As in other fields before, biology experiences an increased use of systems mathematics and computer simulation. With the human genome sequence available, with an exponentially growing number of completely sequenced genomes from various model organisms and with expression and proteomic data at hand, the research paradigm is shifted towards systems analysis and simulation. Computer aided modeling of complex biomolecules and assemblies are already routinely performed. Nowadays, theoretical description and computer simulation of cellular components in larger intra- and inter-cellular networks is of growing importance. Together with classic biological and clinical experiments as well as data from functional genomics, in silico biology will take the leading role in the analysis of biological systems.

Download or read book A Systems Theoretic Approach to Systems and Synthetic Biology II Analysis and Design of Cellular Systems written by Vishwesh V. Kulkarni and published by Springer. This book was released on 2014-07-03 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume II contains chapters contributed by leading researchers in the field of systems and synthetic biology that concern modeling physiological processes and bottom-up constructions of scalable biological systems. The modeling problems include characterisation and synthesis of memory, understanding how homoeostasis is maintained in the face of shocks and relatively gradual perturbations, understanding the functioning and robustness of biological clocks such as those at the core of circadian rhythms, and understanding how the cell cycles can be regulated, among others. Some of the bottom-up construction problems investigated in Volume II are as follows: How should biomacromolecules, platforms, and scalable architectures be chosen and synthesised in order to build programmable de novo biological systems? What are the types of constrained optimisation problems encountered in this process and how can these be solved efficiently? As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.

Download or read book In Silico Drug Discovery and Design written by Claudio N. Cavasotto and published by CRC Press. This book was released on 2015-08-06 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design. Its main aims are to introduce the theoretical framework and algorithms, discuss the range of validity, strengths and limita

Download or read book Biological Systems Complexity and Artificial Life written by Jacques Ricard and published by Bentham Science Publishers. This book was released on 2014-05-06 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: The exponential increase in computing power in the late twentieth century has allowed researchers to gather, process and analyze large volumes of information and construct rational paradigms of systems. Life sciences are no exception and computing advances have led to the birth of fields such as functional genomics and bioinformatics and facilitated an expansion of our understanding of biological systems. Biological Systems: Complexity and Artificial Life is an essential primer on systems biology for biologists and researchers having a multidisciplinary background. The volume covers a variety of theoretical models explaining biological processes. The book starts with an introductory chapter on the classical molecular biology paradigm and progresses towards concepts related to enzyme kinetics, non equilibrium dynamics, cellular thermodynamics, molecular motion in cells and more. The book concludes with a philosophical note on the concept of the biological system.

Download or read book Modeling Biological Systems written by James W. Haefner and published by Springer Science & Business Media. This book was released on 2005-12-05 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: I Principles 1 1 Models of Systems 3 1. 1 Systems. Models. and Modeling . . . . . . . . . . . . . . . . . . . . 3 1. 2 Uses of Scientific Models . . . . . . . . . . . . . . . . . . . . . . . . 4 1. 3 Example: Island Biogeography . . . . . . . . . . . . . . . . . . . . . 6 1. 4 Classifications of Models . . . . . . . . . . . . . . . . . . . . . . . . 10 1. 5 Constraints on Model Structure . . . . . . . . . . . . . . . . . . . . . 12 1. 6 Some Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1. 7 Misuses of Models: The Dark Side . . . . . . . . . . . . . . . . . . . 13 1. 8 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2 The Modeling Process 17 2. 1 Models Are Problems . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2. 2 Two Alternative Approaches . . . . . . . . . . . . . . . . . . . . . . 18 2. 3 An Example: Population Doubling Time . . . . . . . . . . . . . . . . 24 2. 4 Model Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 2. 5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 3 Qualitative Model Formulation 32 3. 1 How to Eat an Elephant . . . . . . . . . . . . . . . . . . . . . . . . . 32 3. 2 Forrester Diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 3. 3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 3. 4 Errors in Forrester Diagrams . . . . . . . . . . . . . . . . . . . . . . 44 3. 5 Advantages and Disadvantages of Forrester Diagrams . . . . . . . . . 44 3. 6 Principles of Qualitative Formulation . . . . . . . . . . . . . . . . . . 45 3. 7 Model Simplification . . . . . . . . . . . . . . . . . . . . . . . . . . 47 3. 8 Other Modeling Problems . . . . . . . . . . . . . . . . . . . . . . . . 49 viii Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3. 9 Exercises 53 4 Quantitative Model Formulation: I 4. 1 From Qualitative to Quantitative . . . . . . . . . . . . . . . . . Finite Difference Equations and Differential Equations 4. 2 . . . . . . . . . . . . . . . . 4. 3 Biological Feedback in Quantitative Models . . . . . . . . . . . . . . . . . . . . . . . . . . 4. 4 Example Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4. 5 Exercises 5 Quantitative Model Formulation: I1 81 . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 1 Physical Processes 81 . . . . . . . . . . . . . . . 5. 2 Using the Toolbox of Biological Processes 89 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 3 Useful Functions 96 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 4 Examples 102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5. 5 Exercises 104 6 Numerical Techniques 107 . . . . . . . . . . . . . . . . . . . . . . . 6. 1 Mistakes Computers Make 107 . . . . . . . . . . . . . . . . . . . . . . . . . . 6. 2 Numerical Integration 110 . . . . . . . . . . . . . . . . 6. 3 Numerical Instability and Stiff Equations 115 . . . . . . . . . . . . . .