Download or read book Quantitative Biology Dynamics of Living Systems written by Noriko Hiroi and published by Frontiers Media SA. This book was released on 2017-07-24 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the emergence of Systems Biology, there is a greater realization that the whole behavior of a living system may not be simply described as the sum of its elements. To represent a living system using mathematical principles, practical quantities with units are required. Quantities are not only the bridge between mathematical description and biological observations; they often stand as essential elements similar to genome information in genetics. This important realization has greatly rejuvenated research in the area of Quantitative Biology. Because of the increased need for precise quantification, a new era of technological development has opened. For example, spatio-temporal high-resolution imaging enables us to track single molecule behavior in vivo. Clever artificial control of experimental conditions and molecular structures has expanded the variety of quantities that can be directly measured. In addition, improved computational power and novel algorithms for analyzing theoretical models have made it possible to investigate complex biological phenomena. This research topic is organized on two aspects of technological advances which are the backbone of Quantitative Biology: (i) visualization of biomolecules, their dynamics and function, and (ii) generic technologies of model optimization and numeric integration. We have also included articles highlighting the need for new quantitative approaches to solve some of the long-standing cell biology questions. In the first section on visualizing biomolecules, four cutting-edge techniques are presented. Ichimura et al. provide a review of quantum dots including their basic characteristics and their applications (for example, single particle tracking). Horisawa discusses a quick and stable labeling technique using click chemistry with distinct advantages compared to fluorescent protein tags. The relatively small physical size, stability of covalent bond and simple metabolic labeling procedures in living cells provides this type of technology a potential to allow long-term imaging with least interference to protein function. Obien et al. review strategies to control microelectrodes for detecting neuronal activity and discuss techniques for higher resolution and quality of recordings using monolithic integration with on-chip circuitry. Finally, the original research article by Amariei et al. describes the oscillatory behavior of metabolites in bacteria. They describe a new method to visualize the periodic dynamics of metabolites in large scale cultures populations. These four articles contribute to the development of quantitative methods visualizing diverse targets: proteins, electrical signals and metabolites. In the second section of the topic, we have included articles on the development of computational tools to fully harness the potential of quantitative measurements through either calculation based on specific model or validation of the model itself. Kimura et al. introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental data. They present four examples: transcriptional regulation, bacterial chemotaxis, morphogenesis of tissues and organs, and cell cycle regulation. The original research article by Sumiyoshi et al. presents a general methodology to accelerate stochastic simulation efforts. They introduce a method to achieve 130 times faster computation of stochastic models by applying GPGPU. The strength of such accelerated numerical calculation are sometimes underestimated in biology; faster simulation enables multiple runs and in turn improved accuracy of numerical calculation which may change the final conclusion of modeling study. This also highlights the need to carefully assess simulation results and estimations using computational tools.
Download or read book Quantitative Biology written by Brian Munsky and published by MIT Press. This book was released on 2018-08-21 with total page 729 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
Download or read book Quantitative Biology written by Michael E. Wall and published by CRC Press. This book was released on 2012-08-25 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative methods are revolutionizing modern molecular and cellular biology. Groundbreaking technical advances are fueling the rapid expansion in our ability to observe, as seen in multidisciplinary studies that integrate theory, computation, experimental assays, and the control of microenvironments. Integrating new experimental and theoretical methods, Quantitative Biology: From Molecular to Cellular Systems gives both new and established researchers a solid foundation for starting work in this field. The book is organized into three sections: Fundamental Concepts covers bold ideas that inspire novel approaches in modern quantitative biology. It offers perspectives on evolutionary dynamics, system design principles, chance and memory, and information processing in biology. Methods describes recently developed or improved techniques that are transforming biological research. It covers experimental methods for studying single-molecule biochemistry, small-angle scattering from biomolecules, subcellular localization of proteins, and single-cell behavior. It also describes theoretical methods for synthetic biology and modeling random variations among cells. Molecular and Cellular Systems focuses on specific biological systems where modern quantitative biology methods are making an impact. It incorporates case studies of biological systems for which new concepts or methods are increasing our understanding. Examples include protein kinase at the molecular level, the genetic switch of phage lambda at the regulatory system level, and Escherichia coli chemotaxis at the cellular level. In short, Quantitative Biology presents practical tools for the observation, modeling, design, and manipulation of biological systems from the molecular to the cellular levels.
Download or read book Dynamics of Biological Systems written by Michael Small and published by CRC Press. This book was released on 2011-08-25 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: From the spontaneous rapid firing of cortical neurons to the spatial diffusion of disease epidemics, biological systems exhibit rich dynamic behaviour over a vast range of time and space scales. Unifying many of these diverse phenomena, Dynamics of Biological Systems provides the computational and mathematical platform from which to understand the underlying processes of the phenomena. Through an extensive tour of various biological systems, the text introduces computational methods for simulating spatial diffusion processes in excitable media, such as the human heart, as well as mathematical tools for dealing with systems of nonlinear ordinary and partial differential equations, such as neuronal activation and disease diffusion. The mathematical models and computer simulations offer insight into the dynamics of temporal and spatial biological systems, including cardiac pacemakers, artificial electrical defibrillation, pandemics, pattern formation, flocking behaviour, the interaction of autonomous agents, and hierarchical and structured network topologies. Tools from complex systems and complex networks are also presented for dealing with real phenomenological systems. With exercises and projects in each chapter, this classroom-tested text shows students how to apply a variety of mathematical and computational techniques to model and analyze the temporal and spatial phenomena of biological systems. MATLAB® implementations of algorithms and case studies are available on the author’s website.
Download or read book Models of Life written by Kim Sneppen and published by Cambridge University Press. This book was released on 2014-10-02 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of current models of biological systems, reflecting the major advances that have been made over the past decade.
Download or read book An Introduction to Systems Biology written by Uri Alon and published by CRC Press. This book was released on 2006-07-07 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.
Download or read book Physical Models of Living Systems written by Philip Nelson and published by Macmillan Higher Education. This book was released on 2014-12-20 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written for intermediate-level undergraduates pursuing any science or engineering major, Physical Models of Living Systems helps students develop many of the competencies that form the basis of the new MCAT2015. The only prerequisite is first-year physics. With the more advanced "Track-2" sections at the end of each chapter, the book can be used in graduate-level courses as well.
Download or read book Quantitative Fundamentals of Molecular and Cellular Bioengineering written by K. Dane Wittrup and published by MIT Press. This book was released on 2020-01-07 with total page 593 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive presentation of essential topics for biological engineers, focusing on the development and application of dynamic models of biomolecular and cellular phenomena. This book describes the fundamental molecular and cellular events responsible for biological function, develops models to study biomolecular and cellular phenomena, and shows, with examples, how models are applied in the design and interpretation of experiments on biological systems. Integrating molecular cell biology with quantitative engineering analysis and design, it is the first textbook to offer a comprehensive presentation of these essential topics for chemical and biological engineering. The book systematically develops the concepts necessary to understand and study complex biological phenomena, moving from the simplest elements at the smallest scale and progressively adding complexity at the cellular organizational level, focusing on experimental testing of mechanistic hypotheses. After introducing the motivations for formulation of mathematical rate process models in biology, the text goes on to cover such topics as noncovalent binding interactions; quantitative descriptions of the transient, steady state, and equilibrium interactions of proteins and their ligands; enzyme kinetics; gene expression and protein trafficking; network dynamics; quantitative descriptions of growth dynamics; coupled transport and reaction; and discrete stochastic processes. The textbook is intended for advanced undergraduate and graduate courses in chemical engineering and bioengineering, and has been developed by the authors for classes they teach at MIT and the University of Minnesota.
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 2012-02-12 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.
Download or read book The Dynamics of Biological Systems written by Arianna Bianchi and published by Springer Nature. This book was released on 2019-10-02 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book presents nine mini-courses from a summer school, Dynamics of Biological Systems, held at the University of Alberta in 2016, as part of the prestigious seminar series: Séminaire de Mathématiques Supérieures (SMS). It includes new and significant contributions in the field of Dynamical Systems and their applications in Biology, Ecology, and Medicine. The chapters of this book cover a wide range of mathematical methods and biological applications. They - explain the process of mathematical modelling of biological systems with many examples, - introduce advanced methods from dynamical systems theory, - present many examples of the use of mathematical modelling to gain biological insight - discuss innovative methods for the analysis of biological processes, - contain extensive lists of references, which allow interested readers to continue the research on their own. Integrating the theory of dynamical systems with biological modelling, the book will appeal to researchers and graduate students in Applied Mathematics and Life Sciences.
Download or read book Frontiers in Computational and Systems Biology written by Jianfeng Feng and published by Springer Science & Business Media. This book was released on 2010-06-14 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological and biomedical studies have entered a new era over the past two decades thanks to the wide use of mathematical models and computational approaches. A booming of computational biology, which sheerly was a theoretician’s fantasy twenty years ago, has become a reality. Obsession with computational biology and theoretical approaches is evidenced in articles hailing the arrival of what are va- ously called quantitative biology, bioinformatics, theoretical biology, and systems biology. New technologies and data resources in genetics, such as the International HapMap project, enable large-scale studies, such as genome-wide association st- ies, which could potentially identify most common genetic variants as well as rare variants of the human DNA that may alter individual’s susceptibility to disease and the response to medical treatment. Meanwhile the multi-electrode recording from behaving animals makes it feasible to control the animal mental activity, which could potentially lead to the development of useful brain–machine interfaces. - bracing the sheer volume of genetic, genomic, and other type of data, an essential approach is, ?rst of all, to avoid drowning the true signal in the data. It has been witnessed that theoretical approach to biology has emerged as a powerful and st- ulating research paradigm in biological studies, which in turn leads to a new - search paradigm in mathematics, physics, and computer science and moves forward with the interplays among experimental studies and outcomes, simulation studies, and theoretical investigations.
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. - Logical information flow aids understanding of basic building blocks of life through disease phenotypes - Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns - Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation - Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
Download or read book An Introduction to Computational Systems Biology written by Karthik Raman and published by CRC Press. This book was released on 2021-05-30 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling Covers a broad spectrum of modelling, from static networks to dynamic models and constraint-based models Thoughtful exercises to test and enable understanding of concepts State-of-the-art chapters on exciting new developments, like community modelling and biological circuit design Emphasis on coding and software tools for systems biology Companion website featuring lecture videos, figure slides, codes, supplementary exercises, further reading, and appendices: https://ramanlab.github.io/SysBioBook/ An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.
Download or read book The Dynamics of Living Systems written by Thomas Lecuit and published by Collège de France. This book was released on 2020-11-16 with total page 32 pages. Available in PDF, EPUB and Kindle. Book excerpt: How can we explain the fundamental paradox of living matter, which combines stability and robustness of form with constant internal dynamics? It is not only the genetic information contained in every cell, but also numerous stochastic biomolecular processes that are at work in morphogenesis. In addition, the shaping of an organism is driven by mechanical forces that operate within and between cells, across tissues and organs. The dynamics of morphogenesis is a self-organized process that emerges from biological control and physical constraints at all scales. Its study is currently bringing together a fast-growing interdisciplinary community that observes, analyses and models living organisms.
Download or read book Biological Systems Nonlinear Dynamics Approach written by Jorge Carballido-Landeira and published by Springer. This book was released on 2019-04-29 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book collects recent advances in the field of nonlinear dynamics in biological systems. Focusing on medical applications as well as more fundamental questions in biochemistry, it presents recent findings in areas such as control in chemically driven reaction-diffusion systems, electrical wave propagation through heart tissue, neural network growth, chiral symmetry breaking in polymers and mechanochemical pattern formation in the cytoplasm, particularly in the context of cardiac cells. It is a compilation of works, including contributions from international scientists who attended the “2nd BCAM Workshop on Nonlinear Dynamics in Biological Systems,” held at the Basque Center for Applied Mathematics, Bilbao in September 2016. Embracing diverse disciplines and using multidisciplinary approaches – including theoretical concepts, simulations and experiments – these contributions highlight the nonlinear nature of biological systems in order to be able to reproduce their complex behavior. Edited by the conference organizers and featuring results that represent recent findings and not necessarily those presented at the conference, the book appeals to applied mathematicians, biophysicists and computational biologists.
Download or read book Quantitative Imaging in Cell Biology written by and published by Academic Press. This book was released on 2014-06-25 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume, number 123, of Methods in Cell Biology looks at methods for quantitative imaging in cell biology. It covers both theoretical and practical aspects of using optical fluorescence microscopy and image analysis techniques for quantitative applications. The introductory chapters cover fundamental concepts and techniques important for obtaining accurate and precise quantitative data from imaging systems. These chapters address how choice of microscope, fluorophores, and digital detector impact the quality of quantitative data, and include step-by-step protocols for capturing and analyzing quantitative images. Common quantitative applications, including co-localization, ratiometric imaging, and counting molecules, are covered in detail. Practical chapters cover topics critical to getting the most out of your imaging system, from microscope maintenance to creating standardized samples for measuring resolution. Later chapters cover recent advances in quantitative imaging techniques, including super-resolution and light sheet microscopy. With cutting-edge material, this comprehensive collection is intended to guide researchers for years to come. Covers sections on model systems and functional studies, imaging-based approaches and emerging studies Chapters are written by experts in the field Cutting-edge material
Download or read book Systems Biology of Cell Signaling written by James Ferrell and published by Garland Science. This book was released on 2021-09-28 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: How can we understand the complexity of genes, RNAs, and proteins and the associated regulatory networks? One approach is to look for recurring types of dynamical behavior. Mathematical models prove to be useful, especially models coming from theories of biochemical reactions such as ordinary differential equation models. Clever, careful experiments test these models and their basis in specific theories. This textbook aims to provide advanced students with the tools and insights needed to carry out studies of signal transduction drawing on modeling, theory, and experimentation. Early chapters summarize the basic building blocks of signaling systems: binding/dissociation, synthesis/destruction, and activation/inactivation. Subsequent chapters introduce various basic circuit devices: amplifiers, stabilizers, pulse generators, switches, stochastic spike generators, and oscillators. All chapters consistently use approaches and concepts from chemical kinetics and nonlinear dynamics, including rate-balance analysis, phase plane analysis, nullclines, linear stability analysis, stable nodes, saddles, unstable nodes, stable and unstable spirals, and bifurcations. This textbook seeks to provide quantitatively inclined biologists and biologically inclined physicists with the tools and insights needed to apply modeling and theory to interesting biological processes. Key Features: Full-color illustration program with diagrams to help illuminate the concepts Enables the reader to apply modeling and theory to the biological processes Further Reading for each chapter High-quality figures available for instructors to download
