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Combining Simulations Theory And Experiments Into Multiscale Models Of Biological Events
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Book Synopsis Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events by : Fabio Trovato
Download or read book Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events written by Fabio Trovato and published by Frontiers Media SA. This book was released on 2022-01-11 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Physical Virology by : Urs F. Greber
Download or read book Physical Virology written by Urs F. Greber and published by Springer. This book was released on 2019-07-17 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores a new challenge in virology: to understand how physical properties of virus particles (virions) and viruses (infected cells) affect the course of an infection. Insights from the emerging field of physical virology will contribute to understanding of the physical nature of viruses and cells, and will open new ways for anti-viral interference. Nine chapters and an editorial written by physicists, chemists, biologists and computational experts describe how virions serve as trail blazers in uncharted territory of cells. The authors outline how particles change in composition as they interact with host cells. Such virus dynamics are crucial for virus entry into cells and infection. It influences the modern concepts of virus-host interactions, viral lineages and evolution. The volume gives numerous up-to-date examples of modern virology and provides a fascinating read for researchers, clinicians and students in the field of infectious diseases.
Book Synopsis Hybrid Biomolecular Modeling by : Slavica Jonic
Download or read book Hybrid Biomolecular Modeling written by Slavica Jonic and published by Frontiers Media SA. This book was released on 2019-01-24 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.
Book Synopsis Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems by : Tamiki Komatsuzaki
Download or read book Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems written by Tamiki Komatsuzaki and published by John Wiley & Sons. This book was released on 2011-07-07 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: This series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. Volume 145 in the series continues to report recent advances with significant, up-to-date chapters by internationally recognized researchers.
Book Synopsis Multiscale Analysis and Nonlinear Dynamics by : Misha Meyer Pesenson
Download or read book Multiscale Analysis and Nonlinear Dynamics written by Misha Meyer Pesenson and published by John Wiley & Sons. This book was released on 2013-09-13 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since modeling multiscale phenomena in systems biology and neuroscience is a highly interdisciplinary task, the editor of the book invited experts in bio-engineering, chemistry, cardiology, neuroscience, computer science, and applied mathematics, to provide their perspectives. Each chapter is a window into the current state of the art in the areas of research discussed and the book is intended for advanced researchers interested in recent developments in these fields. While multiscale analysis is the major integrating theme of the book, its subtitle does not call for bridging the scales from genes to behavior, but rather stresses the unifying perspective offered by the concepts referred to in the title. It is believed that the interdisciplinary approach adopted here will be beneficial for all the above mentioned fields.
Book Synopsis Multiscale Modeling of Cancer by : Vittorio Cristini
Download or read book Multiscale Modeling of Cancer written by Vittorio Cristini and published by Cambridge University Press. This book was released on 2010-09-09 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical modeling, analysis and simulation are set to play crucial roles in explaining tumor behavior, and the uncontrolled growth of cancer cells over multiple time and spatial scales. This book, the first to integrate state-of-the-art numerical techniques with experimental data, provides an in-depth assessment of tumor cell modeling at multiple scales. The first part of the text presents a detailed biological background with an examination of single-phase and multi-phase continuum tumor modeling, discrete cell modeling, and hybrid continuum-discrete modeling. In the final two chapters, the authors guide the reader through problem-based illustrations and case studies of brain and breast cancer, to demonstrate the future potential of modeling in cancer research. This book has wide interdisciplinary appeal and is a valuable resource for mathematical biologists, biomedical engineers and clinical cancer research communities wishing to understand this emerging field.
Book Synopsis Advances in data-driven approaches and modeling of complex systems by : Mohd Hafiz Mohd
Download or read book Advances in data-driven approaches and modeling of complex systems written by Mohd Hafiz Mohd and published by Frontiers Media SA. This book was released on 2023-06-27 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments by : Dennis R. Salahub
Download or read book Multiscale Dynamics Simulations: Nano and Nano-bio Systems in Complex Environments written by Dennis R. Salahub and published by Royal Society of Chemistry. This book was released on 2021-10-01 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on key methodological breakthroughs in the field, this book provides newcomers with a comprehensive menu of multiscale modelling options.
Book Synopsis Dynamics of Systems on the Nanoscale by : Ilia A. Solov'yov
Download or read book Dynamics of Systems on the Nanoscale written by Ilia A. Solov'yov and published by Springer Nature. This book was released on 2022-06-03 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the structure formation and dynamics of animate and inanimate matter on the nanometre scale. This is a new interdisciplinary field known as Meso-Bio-Nano (MBN) science that lies at the intersection of physics, chemistry, biology and material science. Special attention in the book is devoted to investigations of the structure, properties and dynamics of complex MBN systems by means of photonic, electronic, heavy particle and atomic collisions. This includes problems of fusion and fission, fragmentation, surfaces and interfaces, reactivity, nanoscale phase and morphological transitions, irradiation-driven transformations of complex molecular systems, collective electron excitations, radiation damage and biodamage, channeling phenomena and many more. Emphasis in the book is placed on the theoretical and computational physics research advances in these areas and related state-of-the-art experiments. Particular attention in the book is devoted to the utilization of advanced computational techniques and high-performance computing in studies of the dynamics of systems.
Book Synopsis Multiscale Dynamics Simulations by : Dennis R. Salahub
Download or read book Multiscale Dynamics Simulations written by Dennis R. Salahub and published by Royal Society of Chemistry. This book was released on 2021-09-24 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past decade, great strides have been taken in developing methodologies that can treat more and more complex nano- and nano-bio systems embedded in complex environments. Multiscale Dynamics Simulations covers methods including DFT/MM-MD, DFTB and semi-empirical QM/MM-MD, DFT/MMPOL as well as Machine-learning approaches to all of the above. Focusing on key methodological breakthroughs in the field, this book provides newcomers with a comprehensive menu of multiscale modelling options so that they can better chart their course in the nano/bio world.
Book Synopsis Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 by : Mauro Ferrario
Download or read book Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 written by Mauro Ferrario and published by Springer. This book was released on 2007-03-09 with total page 712 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive collection of lectures by leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. Volume 2 is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems.
Book Synopsis Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 2 by : Mauro Ferrario
Download or read book Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 2 written by Mauro Ferrario and published by Springer. This book was released on 2007-04-16 with total page 592 pages. Available in PDF, EPUB and Kindle. Book excerpt: This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 2 offers surveys on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology, including supercooled liquids, spin glasses, colloids, polymers, liquid crystals, biological membranes and folding proteins.
Book Synopsis Mathematics of Bioinformatics by : Matthew He
Download or read book Mathematics of Bioinformatics written by Matthew He and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematics of Bioinformatics: Theory, Methods, and Applications provides a comprehensive format for connecting and integrating information derived from mathematical methods and applying it to the understanding of biological sequences, structures, and networks. Each chapter is divided into a number of sections based on the bioinformatics topics and related mathematical theory and methods. Each topic of the section is comprised of the following three parts: an introduction to the biological problems in bioinformatics; a presentation of relevant topics of mathematical theory and methods to the bioinformatics problems introduced in the first part; an integrative overview that draws the connections and interfaces between bioinformatics problems/issues and mathematical theory/methods/applications.
Book Synopsis Experiments and Simulations: A Pas de Deux to Unravel Biological Function by : Massimiliano Bonomi
Download or read book Experiments and Simulations: A Pas de Deux to Unravel Biological Function written by Massimiliano Bonomi and published by Frontiers Media SA. This book was released on 2022-01-19 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modeling of Microscale Transport in Biological Processes by : Sid Becker
Download or read book Modeling of Microscale Transport in Biological Processes written by Sid Becker and published by Academic Press. This book was released on 2016-12-27 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling of Microscale Transport in Biological Processes provides a compendium of recent advances in theoretical and computational modeling of biotransport phenomena at the microscale. The simulation strategies presented range from molecular to continuum models and consider both numerical and exact solution method approaches to coupled systems of equations. The biological processes covered in this book include digestion, molecular transport, microbial swimming, cilia mediated flow, microscale heat transfer, micro-vascular flow, vesicle dynamics, transport through bio-films and bio-membranes, and microscale growth dynamics. The book is written for an advanced academic research audience in the fields of engineering (encompassing biomedical, chemical, biological, mechanical, and electrical), biology and mathematics. Although written for, and by, expert researchers, each chapter provides a strong introductory section to ensure accessibility to readers at all levels. Features recent developments in theoretical and computational modeling for clinical researchers and engineers Furthers researcher understanding of fluid flow in biological media and focuses on biofluidics at the microscale Includes chapters expertly authored by internationally recognized authorities in the fundamental and applied fields that are associated with microscale transport in living media
Book Synopsis Computational Methods for Understanding Riboswitches by :
Download or read book Computational Methods for Understanding Riboswitches written by and published by Academic Press. This book was released on 2015-02-24 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers computational methods and applications in RNA structure and dynamics Contains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands.
Book Synopsis Stochastic Models for In-silico Event-based Biological Network Simulation by : Preetam Ghosh
Download or read book Stochastic Models for In-silico Event-based Biological Network Simulation written by Preetam Ghosh and published by ProQuest. This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The multi-scale biological system model is a new research direction to capture the dynamic measurements of complex biological systems. The current statistical thermodynamic models can not scale to this challenge due to the explosion of state-spaces of the system, where a biological organ may have billions of cells, each with millions of molecule types and each type may have a few million molecules. We seek to propose a phenomenological theory that will require a smaller number of state variables to address this multi-scaling problem. Discrete Markov statistical process is used to understand the system dynamics in the networking community for a long time. In this dissertation, we focus more specifically on a composite system by combining the state variables in the time-space domain as events, and determine the immediate dynamics between the events by using statistical analysis or simulation methods. In our approach the space-time behavior of the cell dynamics is captured by discrete state variables, where an event is a combined process of a large number of state transitions between a set of state variables. The execution time of these state transitions to manifest the event outcome is a random variable called event-holding time. The underlying assumption is that it will be possible to segregate the complete system state-space into a disjoint set of independent events and events can be executed simultaneously without any interaction once the execution conditions are satisfied (removal of resource bottleneck, collision). In this dissertation, we present the event-time models for some biological functions that will be incorporated in the discrete-event based stochastic simulator. In particular, we present analytical models for the molecular transport event in cells considering charged/non-charged macromolecules. We show, that molecular transport event completion time can be approximated by an exponential distribution. Next we present stochastic models for biochemical reactions in the cell (that can be extended to reactions occurring in the cell cytoplasm, membrane or nucleus). We show that the reaction completion time follows an exponential distribution when one of the reactant molecules enter the cell one at a time, whereas, it follows a gamma distribution when a batch of the reactant molecules enter the cell. We also present stochastic models for the protein-DNA binding and protein-ligand docking events and show that both these events have an exponentially distributed event completion time. We also validate each of the models presented in the dissertation with experimental findings reported in the literature. Finally, we present a markov chain based stochastic biochemical system simulator which can give us the dynamics of more complex events and can be used to improve the scalability of the discrete-event based stochastic simulator. We propose to successfully demonstrate this technique by modeling the complete dynamics of one Salmonella cell.
