Biophysics Books
Springer Fachmedien Wiesbaden 3D-Druck mit lebenden Zellen:
Book SynopsisDieses Buch setzt Impulse zur systematischen Validierung des Bioprintings und zur Etablierung dieser Technologie auch in nicht-medizinischen Anwendungsgebieten. Das dreidimensionale Drucken mit lebenden Zellen erlaubt die kontrollierte Zellimmobilisierung in 3D-Hydrogelgerüsten. In dieser Arbeit wird das Bioprinting erstmalig mit Zellkulturen höherer Pflanzen gezeigt. Für die Pflanzenzellbiotechnologie eröffnen sich damit Perspektiven beispielsweise hinsichtlich der Erzeugung von Gewebemodellen oder der strukturierten Zellimmobilisierung in industriellen Bioprozessen. Die Strömungsmodellierung im Druckprozess wird auf Basis von ausführlichen rheologischen Messungen der Bioink und der Analyse der Extrusionsgeschwindigkeit gezeigt. Die Darstellung der Ergebnisse im Nomogramm erlaubt eine systematische Optimierung des Druckprozesses.Table of ContentsStand der Forschung.- Material und Methoden.- Simulation und analytische Rechnung.- Ergebnisse und Diskussion.- Zusammenfassung und Ausblick.
£53.99
Springer Statistical Physics for Biological Matter
Book SynopsisThis book aims to cover a broad range of topics in statistical physics, including statistical mechanics (equilibrium and non-equilibrium), soft matter and fluid physics, for applications to biological phenomena at both cellular and macromolecular levels. It is intended to be a graduate level textbook, but can also be addressed to the interested senior level undergraduate. The book is written also for those involved in research on biological systems or soft matter based on physics, particularly on statistical physics.Typical statistical physics courses cover ideal gases (classical and quantum) and interacting units of simple structures. In contrast, even simple biological fluids are solutions of macromolecules, the structures of which are very complex. The goal of this book to fill this wide gap by providing appropriate content as well as by explaining the theoretical method that typifies good modeling, namely, the method of coarse-grained descriptions that extract the most salient features emerging at mesoscopic scales. The major topics covered in this book include thermodynamics, equilibrium statistical mechanics, soft matter physics of polymers and membranes, non-equilibrium statistical physics covering stochastic processes, transport phenomena and hydrodynamics. Generic methods and theories are described with detailed derivations, followed by applications and examples in biology. The book aims to help the readers build, systematically and coherently through basic principles, their own understanding of nonspecific concepts and theoretical methods, which they may be able to apply to a broader class of biological problems.Table of Contents1. Introduction : Biological Systems, and Physical ApproachesBring Physics to Life, Bring Life to Physics. Part A: Equilibrium Structures and Properties. 2. Basic Concepts of Relevant Thermodynamics. 2.1 The First Law and Thermodynamic Potentials. 2.2 The Second Law and Thermodynamic Variational Principles. 3. Basic Methods of Equilibrium Statistical Physics. 3.1 Boltzmann’s Entropy and Probability, Microcanonical Ensemble Theory. 3.2 Canonical Ensemble Theory. 3.3 The Gibbs Canonical Ensemble. 3.4 Grand Canonical Ensemble Theory. 4. Statistical Mechanics of Fluids and Solutions. 4.1 Phase-space Description of Fluids. 4.2 Fluids of Non-interacting Particles. 4.3 Fluids of Interacting Particles. 4.4 Extension to Solutions: Coarse-grained Descriptions. 5. The Coarse-grained Descriptions for Biological Complexes. 6. Water and Weak Electrostatic Interactions. 6.1 Thermodynamic Properties of Water. 6.2 The Interactions in Water. 6.3 Screened Coulomb Interaction. 7. Law of Chemical Forces: Transitions, Reactions and Self-assembly. 7.1 Law of Mass Action (LMA). 7.2 Self-Assembly. 8. Lattice and Ising Models. 8.1 Adsorption and Aggregation of Molecules. 8.2 Binary Mixtures. 8.3 1-D Ising Model and Applications. 9. Response, Fluctuations, Correlations, and Scatterings. 9.1 Linear Responses and Fluctuations: Fluctuation-Response Theorem. 9.2 Scatterings, Fluctuations, and Structures of Matter. 10. Mesoscopic model for Polymers: Flexible Chains. 10.1 Random Walk Model for a Flexible Chain. 10.2 A Flexible Chain under External Fields and Confinements. 10.3 Effects of Segmental Interactions. 10.4 Scaling Theory. 11. Mesoscopic model for Polymers: Semi-flexible Chain Model and Polyelectrolytes. 11.1 Worm-like chain model. 11.2 Fluctuations in nearly straight semi-flexible chains and the force-extension relation. 11.3 Polyelecrolytes. 12. Membranes and Elastic Surfaces. 12.1 Membrane Self-assembly and Transition. 12.2 Mesoscopic Model for Elastic Energies and Shapes. 12.3 Effects of Thermal Undulations. Part B: Non-equilibrium Phenomena. 13.Brownian Motions. 13.1 Brownian Motion/Diffusion Equation Theory. 13.2 Diffusive Transport in Cells. 13.3 Brownian Motion/Langevin Equation Theory. 14. Stochastic Processes, Markov Chains and Master Equations. 14.1 Markov Processes. 14.2 Master Equation. 15. Theory of Markov Processes & The Fokker-Planck Equations. 15.1 Fokker-Planck Equation (FPE). 15.2 The Langevin and Fokker-Planck Equations from Phenomenology and Effective Hamiltonian. 15.3 Solutions of Fokker-Planck Equations, Transition Probabilities and Correlation Functions. 16. The Mean-First Passage Times and Barrier Crossing Rates. 16.1 First Passage Time and Applications. 16.2 Rate Theory: Flux-over Population Method. 17. Dynamic Linear Responses and Time Correlation Functions. 17.1 Time-dependent Linear Response Theory. 17.2 Applications of the Fluctuation–dissipation Theorem. 18. Noise-induced Resonances: Stochastic Resonance and Resonant Activation, and Stochastic Ratchet. 18.1 Stochastic Resonance. 18.2 Resonant Activation (RA) and Stochastic Ratchet. 18.3 Stochastic ratchet. 19. Transport Phenomena and Fluid Dynamics. 19.1 Hydrodynamic Transport Equations. 19.2 Dynamics of Viscous Flow. 20. Dynamics of Polymers and Membranes in Fluids. 20.1 Dynamics of Flexible Polymers. 20.2 Dynamics of a Semiflexible Chain. 20.3 Dynamics of Membrane Undulation. 20.4 A Unified View. 21. Epilogue.
£67.49
Springer Verlag, Singapore Technology Innovation in Mechanical Engineering:
Book SynopsisThis book comprises select papers presented at the conference on Technology Innovation in Mechanical Engineering (TIME-2021). The book discusses the latest innovation and advanced research in the diverse field of Mechanical Engineering such as materials, manufacturing processes, evaluation of materials properties for the application in automotive, aerospace, marine, locomotive and energy sectors. The topics covered include advanced metal forming, Energy Efficient systems, Material Characterization, Advanced metal forming, bending, welding & casting techniques, Composite and Polymer Manufacturing, Intermetallics, Future generation materials, Laser Based Manufacturing, High-Energy Beam Processing, Nano materials, Smart Material, Super Alloys, Powder Metallurgy and Ceramic Forming, Aerodynamics, Biological Heat & Mass Transfer, Combustion & Propulsion, Cryogenics, Fire Dynamics, Refrigeration & Air Conditioning, Sensors and Transducers, Turbulent Flows, Reactive Flows, Numerical Heat Transfer, Phase Change Materials, Micro- and Nano-scale Transport, Multi-phase Flows, Nuclear & Space Applications, Flexible Manufacturing Technology & System, Non-Traditional Machining processes, Structural Strength and Robustness, Vibration, Noise Analysis and Control, Tribology. In addition, it discusses industrial applications and cover theoretical and analytical methods, numerical simulations and experimental techniques in the area of Mechanical Engineering. The book will be helpful for academics, including graduate students and researchers, as well as professionals interested in interdisciplinary topics in the areas of materials, manufacturing, and energy sectors.Table of ContentsBeacon Based Smart Shopping System Using IoT.- Cache Memory Design Analysis for Single Bit Architecture for Core Processor.- Impact of Acoustics Impingement on Proliferating Fires.- Analytical Study of Fluid Pressure Sensing Mechanism in Microchannel for Microfluidic Device.
£208.99
Springer Verlag, Singapore Radiation: An Energy Carrier
Book SynopsisThis book aims to explain radiation from a somewhat different aspect than its traditional image as something that is scary, dangerous, hazardous, and so on, to produce the correct understanding that radiation is carrying energy, and to convince readers that radiation is not "scary" but controllable and useful. As for radiation itself, many introductions or textbooks have been published, as in radiochemistry, radiobiology, and radiology. In most of them, the biological effects of radiation exposure are the main subjects, which often enhance the feeling that radiation is dangerous, and the effects produced by lower-dose exposure that are difficult to see are hardly discussed. The present volume mainly focuses on how radiation carries energy, how energy is absorbed in substances as absorbed doses (Gy) or dose equivalents (Sv), how damages or risks appear with the absorbed dose and why the effects of the exposure appear quite differently, depending on properties of the substances that were exposed.Table of ContentsTable of Contents Preface to English edition Preface Chapter 1 Radiation carries energy 1-1 Is radiation scary? 1-2 What is written in this book 1-2-1 Radiation is carries energy 1-2-2 All physical and chemical phenomena accompany energy transfer 1-2-3 “EQ (radiation) exposure” means energy deposition (absorption) or energy transfer from EQ to an object 1-2-4 Deposited or absorbed energy in unit mass or volume are quite different depending the kind of EQ. 1-2-5 Units related to radiation, exposure and radiation measurements 1-2-5-1 Energy and power carried/deposited by EQ (radiation) (J or eV and W) 1-2-5-2 Absorbed dose and dose rate 1-2-5-3 Intensity of EQ or radioactivity 1-2-6 Intensity and energy of EQ (radiation) 1-3 Energy release from a material (Black body radiation and EQ emission) 1-4 EQ sources in nature 1-5 Energy transfer in physical and chemical phenomena 1-6 Radioactive materials and artificial EQ (radiation) sources 1-7 Summary Chapter 2 Radiation (EQ: Energy Quantum) 2-1 Introduction 2-2 Radiation is consisting of EQ 2-3 Sources of EQ and their intensity 2-3-1 Sources 2-3-2 Characteristics of radioisotopes as EQ sources 2-3-3 Geometry of EQ sources (point, planner, volumetric and spatial sources) 2-3-3-1 Point and volumetric sources 2-3-3-2 Planner source 2-3-3-3 Spatial source 2-3-4 Air dose rate 2-4 Energy deposition (absorption) given by EQ exposure 2-5 Energy absorption in living beings exposed to EQ 2-5-1 External exposure 2-5-2 Internal exposure 2-5-3 Absorbed dose, dose rate and dose equivalent 2-5-4 Conversion of units related to EQ exposure (Bq, Gy, Sv and effective dose) 2-6 Shielding and decontamination 2-7 Effects of EQ exposure on a human body Chapter 3 Sources of Energetic Quanta (EQ) (Radiation Sources) 3-1 Radioisotopes 3-1-1 Stable isotopes and radioisotopes 3-1-2 Emission of EQ from radioactive isotopes (Disintegration of radioisotopes) 3-1-3 Radioactive isotopes in nature 3-1-4 EQ exposure of human body in nature 3-1-5 EQ emitted from 131-iodine and 137-cesium and their exposure effects 3-2 Radiation from the sun 3-3 Nuclear reactors 3-4 Release of FPs from the Fukushima power plant after the accident 3-5 Artificial EQ sources 3-5-1 Accelerators 3-5-2 X-ray Generator 3-5-3 Lasers Chapter 4. Irradiation effects of EQ on materials (inorganic- and organic-materials, and living beings) 4-1 Evaluation of the effects of EQ exposure 4-1-1 There is no critical dose to distinguish secure and insecure 4-1-2 Definite and stochastic (probabilistic) effects of exposure 4-1-3 Evaluation of the effects of low-dose exposure and reduction of exposure 4-2 Irradiation effects of EQ on materials 4-2-1 Effects of EQ exposure on inorganic materials 4-2-1-1 Irradiation effects of metals 4-2-1-1-1 Damages caused by nuclear collisions 4-2-1-1-2 Damage caused by electron excitation 4-2-1-2 Irradiation effects of covalent and ionic bonding materials 4-2-2 Irradiation effects of organic materials 4-2-3 Irradiation effects of living beings - from molecular levels in cells, tissues to individuals – 4-3 Resilience to EQ exposure and recovery 4-4 Absorbed does (deposited energy) and volume exposed to EQ Chapter 5 Reduction of exposure, Contamination and Decontamination 5-1 Introduction 5-2 Distribution of EQ sources and their removal 5-3 External and internal exposures 5-4 Reduction of exposure to a human body 5-5 Resilience 5-5-1 Where and how large area are damaged or influence by EQ exposure. 5-5-2 Recovery of damages and resilience 5-5 Short-term and long-term exposure Chapter 6 Detection and measurement of EQ 6-1 Introduction 6-2 Determination of type, intensity and energy of EQ 6-2-1 Measurements of intensities 6-2-2 Accuracy of intensity measurements 6-2-3 Measurements of EQ energy 6-2-4 Calorimetry 6-2-5 Intensity (radio activity) of EQ source 6-3 Absorbed dose measurement 6-4 Visualization of EQ source distribution 6-5 Absorbed dose equivalent -accuracy and assessment of effects of EQ exposure- 6-5-1 Consideration of exposed dose equivalent (Sv) to use for the assessment of the effects of EQ exposure 6-5-2 Accuracy and number of significant figures in EQ measurements Chapter 7 Utilization of EQ 7-1 Introduction 7-2 Sterilization or disinfection 7-3 Medical purposes 7-4 Utilization of EQ energy 7-5 Radiometric dating (14C dating) 7-5 Use of radioisotopes as tracers Chapter 8 Energy and the History of the Earth 8-1 Introduction 8-2 Changes in the global environment 8-3 Development and Evolution of Life Chapter 9 Energy use and radiation 9-1 Introduction 9-2 Sources of energy 9-3 There's no energy to use for free 9-3 Fossil fuels are originally solar energy 9-4 Risks associated with energy use Bibliography (a) Introductory (b) Radiation and Radioactivity (c) Radiation Biology (d) Radiation Physics, Radiochemistry (e) Radiation Measurements (f) Radiation Hormesis (g) Radiation Use Appendix: Q and A relating radiation (EQ) Radiation is explained in a simple form of Q & A, which also serves as summary. Q1: What is radioactivity? Q2: What is radiation? Q3: What is a radiation source? Q4: Is light and radiation the same ? Q5: What are particles that carry energy? Q6: What kind of particles and light (photons) are included in radiation (EQ)? Q7: How do EQ move? Q8: What does radiation exposure mean? Q9: What do following units related to EQ exposure mean and how they are different with each other? Count rates (cps, cpm, cph), Becquerel (Bq), Gray (Gy) and Siebert (Sv) Q10: Is the exposure of 20 mSv dangerous? Q11: Does the EQ exposure make objects (substances and/or living beings) radioactive? Q12: Does a substance exposed to EQ glow? Q13: What is internal and external exposures? What is the difference? Q14: What happens on radioactive materials ingested into a body?
£71.24
Springer Verlag, Singapore The Science of Soft Robots: Design, Materials and
Book SynopsisThe goal of this textbook is to equip readers with as structured knowledge of soft robotics as possible. Seeking to overcome the limitations of conventional robots by making them more flexible, gentle and adaptable, soft robotics has become one of the most active fields over the last decade. Soft robotics is also highly interdisciplinary, bringing together robotics, computer science, material science, biology, etc. After the introduction, the content is divided into three parts: Design of Soft Robots; Soft Materials; and Autonomous Soft Robots. Part I addresses soft mechanisms, biological mechanisms, and soft manipulation & locomotion. In Part II, the basics of polymer, biological materials, flexible & stretchable sensors, and soft actuators are discussed from a materials science standpoint. In turn, Part III focuses on modeling & control of continuum bodies, material intelligence, and information processing using soft body dynamics. In addition, the latest research results and cutting-edge research are highlighted throughout the book. Written by a team of researchers from highly diverse fields, the work offers a valuable textbook or technical guide for all students, engineers and researchers who are interested in soft robotics.Table of ContentsChapter 1: Introduction.- Chapter 2: Soft Mechanisms.- Chapter 3: Biological Mechanisms.- Chapter 4: Soft Manipulation and Locomotion.- Chapter 5: Basics of Polymer.- Chapter 6: Biological Material.- Chapter 7: Flexible and Stretchable Sensors.- Chapter 8: Soft Actuators.- Chapter 9: Modeling and Control of Continuum Body.- Chapter 10: Material Intelligence.- Chapter 11: Information Processing using Soft Body Dynamics.
£71.24
Springer Verlag, Singapore Nanofiltration Membrane for Water Purification
Book SynopsisThis book covers the basic and sustainable approach of nanofiltration membrane techniques along with their fabrication, characterization, separation mechanisms, and broad applications in the field of wastewater treatment. It provides a wide knowledge of nanofiltration technique to water purification audience concerning the recent development with various illustrations, methods and results for graduate students, scientists, academicians, researchers, and industrialists. Readers from wastewater and water purification will have a quick reference by exploring the research literature on the subject field with commercial value-added research applications of nanofiltration membrane.Table of Contents 1. Introduction and basic principle of Nanofiltration membrane Process.- 2. Synthesis and characterization of nanofiltration membrane.- 3. Pretreatments before the nanofiltration technique.- 4. Graphene oxide based nanofiltration membrane for wastewater treatment.- 5. Nano-filtration application in the textile industry for wastewater treatment.- 6. Dye removal from industrial water using nanofiltration membrane.- 7. Volatile organic compounds removal by nanofiltration from groundwater.- 8. Desalination through nanofiltration technique .- 9. Modified nanofiltration membrane for wastewater treatment.- 10. Performance of Ceramic Nanofiltration Membranes in Water Purification.- 11. Fouling Mechanisms in Nanofiltration Membranes.- 12. Nanofiltration Technology Applied for Peat and Wetland Saline Water.- 13. Removal of Pollutants from Wastewater through Nanofiltration: A review.
£104.49
Springer Verlag, Singapore NanoBioenergy: Application and Sustainability
Book SynopsisThis contributed volume presents new insight into sustainable possibilities of combination of nanomaterial and bioenergy production together. Biofuels as renewable energy sources have tremendous potential to replace fossil fuels in future energy scenario as biofuels production is likely to be advanced and novel research areas offers green alternative energy sources. continuous efforts are being made for the cost-effective production of biofuels worldwide to balance its techno-economy. In series of tremendous effort to improve biofuels production technologies, use of nanomaterials to improve biofuels production efficiency is highly emerging area with full scope to developed low cost, rapid technologies for biofuels production. The book covers the practical utility based properties of nanomaterial and bioenergy production together. It also discusses the recent advancements on various nanomaterial utility in biofuel production process along with its low cost application. It covers mega audiences, which include academician, researchers, and industries people. This book will be highly interesting for researchers and scientists as well as related industries.Table of ContentsAttached
£151.99
Springer Verlag, Singapore Optical Anisotropy of Biological Polycrystalline
Book SynopsisThis book highlights the analysis of new azimuth-independent methods of Stokes polarimetry and Mueller-matrixreconstruction of distributions of optical anisotropy parameters using spatial-frequency filtering of manifestations of phase (linear and circular birefringence) and amplitude (linear and circular dichroism) anisotropy for diagnosing changes in the orientational-phase structure of fibrillar networks of histological sections of biological tissues and polycrystalline films of biological fluids.Table of Contents Mueller-Matrix Modeling And Diagnostics Of Optically Anisotropic Biological Layers.- Materials And Method.- Mueller-Matrix Description Of The Optically Anisotropy Of Biological Layers.- Azimutally Invariant Mueller-Matrix Mapping Of Optically Anisotropic Networks Of Biological Tissues And Fluids.- Azimuthally Invariant Mueller-Matrix Reconstruction Of The Optical Anisotropy Parameters Of The Polycrystalline Structure Of Biological Tissues And Human Fluids.- Methods And Means Of Fourier-Stocks Polarimetry And Spatial-Frequency Filtering Of Phase Anisotropy Manifestations.
£999.99
Oxford University Press EVOLUTIONARY BIOMECHANICS OSEE P
Book SynopsisEvolutionary biomechanics is the study of evolution through the analysis of biomechanical systems. Its unique advantage is the precision with which physical constraints and performance can be predicted from first principles. Instead of reviewing the entire breadth of the biomechanical literature, a few key examples are explored in depth as vehicles for discussing fundamental concepts, analytical techniques, and evolutionary theory. Each chapter develops a conceptual theme, developing the underlying theory and techniques required for analyses in evolutionary biomechanics. Examples from terrestrial biomechanics, metabolic scaling, and bird flight are used to analyse how physics constrains the design space that natural selection is free to explore, and how adaptive evolution finds solutions to the trade-offs between multiple complex conflicting performance objectives.Evolutionary Biomechanics is suitable for graduate level students and professional researchers in the fields of biomechanicTrade ReviewThis is a scholarly volume that approaches a challenging subject in a straightforward and rigorous manner, which is illuminating without being overpowering...ideal for students who want both depth and a fascinating context. * Ian Carter, The Biologist *This volume provides for all. ... This is a great volume for undergraduates or postdoctoral researchers. * Christian Laurent, Quarterly Review of Biology *Table of Contents1. Themes ; 2. Selection ; 3. Constraint ; 4. Scaling ; 5. Phylogeny ; 6. Form and function in flight ; 7. Adaptation in avian wing design ; 8. Trade-offs: selection, phylogeny and constraint
£39.89
Taylor & Francis Ltd Structural and Morphological Evolution in MetalOrganic Films and Multilayers
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£58.89
Taylor & Francis Ltd Spike Timing Mechanisms and Function 53 Frontiers in Neuroscience
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Taylor & Francis Ltd Fluctuation Theory of Solutions
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£47.99
Taylor & Francis Ltd Chemical Physics Electrons and Excitations
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Taylor & Francis Ltd Proteins Energy Heat and Signal Flow 01 Computation in Chemistry
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Taylor & Francis Ltd Textbook of Ion Channels Volume I
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£87.39
Taylor & Francis Ltd Textbook of Ion Channels Volume II
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Taylor & Francis Ltd Textbook of Ion Channels Volume III
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Taylor & Francis Ltd Imaging from Cells to Animals In Vivo
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£43.69
Taylor & Francis Ltd RNA the Epicenter of Genetic Information
Book SynopsisThe origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information.Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers. The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license.Trade Review“Thrilling and provocative ... There is a need for such a book... There’s nothing quite like this out there.An epic tale of biology’s central molecule, RNA.DNA does only one thing, store information. RNA has a thrilling plethora of functions, including telling DNA what to do. This book takes the reader on an odyssey through the wonders of RNA and its central role in biology.DNA science dominated the second half of the 20th Century, but it’s clear that the 21st Century belongs to RNA. This long-overdue book reveals the diverse wonders of RNA in a series of thrilling and provocative stories.”Tom Cech, Nobel laureate, University of Colorado Boulder_____________________________________“The book is truly monumental and will be treasured by RNA scientists and others, as well. It beautifully captures the excitement and wonder that I have been lucky to experience working in the RNA field since the early 1960s.”Joan Steitz, Yale University_____________________________________“This book is really disruptive and presents a coherent view of our understanding of biology in terms of the genetic molecules, the nucleic acids, DNA and RNA. It covers an immense territory of molecular biology and its history of discoveries, all presented with a clear-cut intellectual thread.... It is very timely by its breadth and emphasis on the role of RNA in biology. It makes a strong case for RNA and its late acceptance... the fight uphill, like that of Sisyphus, was tough and demanded a lot of perseverance. It is really rather complete.”Eric Westhof, University of Strasbourg_____________________________________“The book is unique. It provides the long-overdue correction of the still widespread static views on evolution, development and genome organization and function. It has the potential to induce radical changes in widely held views and attitudes.”Peter Vogt, Scripps Research Institute, La Jolla_____________________________________"History is the key to our modern understanding of RNA. This magnum opus describes how science, scientific thought and landmark discoveries revealed the central role of RNA in molecular biology and evolution. The authors are not only modern pioneers of RNA science, but also the best histo-RNA-ians of our time.”John Rinn, University of Colorado, Boulder_____________________________________"RNA, the Epicenter of Genetic Information is much more than what its title might suggest. This epic book by Mattick and Amaral superbly reflects the continuing excitement about RNA research. It is not only a description of our current understanding of the role of RNA in cell and developmental biology but is also a useful history of molecular biology. Each of the eighteen chapters is a brilliantly written semi-autonomous essay on a particular segment of the RNA odyssey. I wholeheartedly recommend this book to anybody interested in the biology of RNA, in evolution, and in the organization and function of complex genomes." Witold Filipowicz, Friedrich Miescher Institute for Biomedical Research, Basel_____________________________________"Those who might think that this book is only for the scientists, think again. It is not. It will appeal in equal measure to the thinking generalist and culturally curious interested in the thrilling history of molecular biology, the wonders of the long-overlooked central molecule RNA and its pivotal role in human development and evolution.An epic, provocative, and highly original book that highlights the way science is so often sidetracked by preconceptions and hubris, and explores the struggle to understand all that junk DNA we were told we had. The junk is not junk! The answers are all there. A story and a journey not to be missed!"Gabriel Farago (USA TODAY Bestselling author of the Jack Rogan Mysteries Series) Table of ContentsPreface, Chapter 1. Overview, Chapter 2. The genetic material?, Chapter 3. Halcyon days, Chapter 4. Worlds apart, Chapter 5. Strange genomes, strange genetics, Chapter 6. The Age of Aquarius, Chapter 7. All that junk, Chapter 8. The expanding repertoire of RNA, Chapter 9. Glimpses of a modern RNA world, Chapter 10. Genome sequences and transposable elements, Chapter 11. The human genome, Chapter 12. Small RNAs with mighty functions, Chapter 13. Large RNAs with many functions, Chapter 14. The epigenome, Chapter 15. The programming of development, Chapter 16. RNA and repeats rule, Chapter 17. Plasticity, Chapter 18. Beyond the jungle of dogmas, References
£41.99
Taylor & Francis Ltd Molecular Modeling at the Atomic Scale
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Taylor & Francis Ltd Introduction to Molecular Biophysics
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Taylor & Francis Ltd Ventilation of Normobaric and Hyperbaric Objects
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Taylor & Francis Ltd Metabolism and Medicine
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Taylor & Francis Ltd Metabolism and Medicine
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Taylor & Francis Ltd Science of Diving Concepts and Applications
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Taylor & Francis Ltd Nonequilibrium Statistical Mechanics
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Taylor & Francis Ltd An Introduction to Computational Systems Biology
Book SynopsisThis book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networksa 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 featuringTrade ReviewThis is a very comprehensive read that provides a solid base in computational biology. The book is structured in 4 parts and 14 chapters which cover all the way from the more basic concepts to advanced material, including the state-of-the-art methodologies in synthetic and systems biology. This is a bedside book for those researchers embarking to do investigation in computational biology and a great office companion for anyone working on systems and synthetic biology. -- Rodrigo Ledesma Amaro, Lecturer, Imperial College London This is a fantastic book. It offers an elegant introduction to both classical and modern concepts in computational biology. To the uninitiated, it is a terrific first read, bringing alive the glory of the past and the promise of the future. To the interested, it handholds and offers a springboard to dive deep. To the practitioner, it serves as a valuable resource bringing together in a panoramic view many diverse streams that adorn the landscape. -- Narendra M. Dixit, Professor, Indian Institute of Science This is a very comprehensive read that provides a solid base in computational biology. The book is structured in 4 parts and 14 chapters which cover all the way from the more basic concepts to advanced material, including the state-of-the-art methodologies in synthetic and systems biology. This is a bedside book for those researchers embarking to do investigation in computational biology and a great office companion for anyone working on systems and synthetic biology. -- Rodrigo Ledesma Amaro, Lecturer, Imperial College London This is a fantastic book. It offers an elegant introduction to both classical and modern concepts in computational biology. To the uninitiated, it is a terrific first read, bringing alive the glory of the past and the promise of the future. To the interested, it handholds and offers a springboard to dive deep. To the practitioner, it serves as a valuable resource bringing together in a panoramic view many diverse streams that adorn the landscape. -- Narendra M. Dixit, Professor, Indian Institute of Science Table of ContentsPreface Introduction to modelling 1.1 WHAT IS MODELLING? 1.1.1 What are models? 1.2 WHYBUILD MODELS? 1.2.1 Why model biological systems? 1.2.2 Why systems biology? 1.3 CHALLENGES IN MODELLING BIOLOGICAL SYSTEMS 1.4 THE PRACTICE OF MODELLING 1.4.1 Scope of the model1.4.2 Making assumptions 1.4.3 Modelling paradigms 1.4.4 Building the model 1.4.5 Model analysis, debugging and (in)validation 1.4.6 Simulating the model 1.5 EXAMPLES OF MODELS 1.5.1 Lotka–Volterra predator–prey model 1.5.2 SIR model: a classic example 1.6 TROUBLESHOOTING 1.6.1 Clarity of scope and objectives 1.6.2 The breakdown of assumptions 1.6.3 Ismy model fit for purpose? 1.6.4 Handling uncertainties EXERCISES REFERENCES FURTHER READING Introduction to graph theory 2.1 BASICS 2.1.1 History of graph theory 2.1.2 Examples of graphs 2.2 WHYGRAPHS? 2.3 TYPES OF GRAPHS 2.3.1 Simple vs. non-simple graphs 2.3.2 Directed vs. undirected graphs 2.3.3 Weighted vs. unweighted graphs 2.3.4 Other graph types 2.3.5 Hypergraphs 2.4 COMPUTATIONAL REPRESENTATIONS OF GRAPHS 2.4.1 Data structures 2.4.2 Adjacency matrix 2.4.3 The laplacian matrix 2.5 GRAPH REPRESENTATIONS OF BIOLOGICAL NETWORKS 2.5.1 Networks of protein interactions and functional associations2.5.2 Signalling networks 2.5.3 Protein structure networks 2.5.4 Gene regulatory networks 2.5.5 Metabolic networks 2.6 COMMONCHALLENGES&TROUBLESHOOTING 2.6.1 Choosing a representation 2.6.2 Loading and creating graphs 2.7 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Structure of networks 3.1 NETWORK PARAMETERS 3.1.1 Fundamental parameters 3.1.2 Measures of centrality 3.1.3 Mixing patterns: assortativity 3.2 CANONICAL NETWORK MODELS 3.2.1 Erdos–Rényi (ER) network model 3.2.2 Small-world networks 3.2.3 Scale-free networks 3.2.4 Other models of network generation 3.3 COMMUNITY DETECTION 3.3.1 Modularity maximisation 3.3.2 Similarity-based clustering 3.3.3 Girvan–Newman algorithm 3.3.4 Other methods 3.3.5 Community detection in biological networks 3.4 NETWORKMOTIFS 3.4.1 Randomising networks 3.5 PERTURBATIONS TO NETWORKS 3.5.1 Quantifying e□fects of perturbation 3.5.2 Network structure and attack strategies 3.6 TROUBLESHOOTING 3.6.1 Is your network really scale-free? 3.7 SOFTWARE TOOLS EXERCISES REFERENCESFURTHER READING Applications of network biology 4.1 THE CENTRALITY–LETHALITY HYPOTHESIS 4.1.1 Predicting essential genes fromnetworks 4.2 NETWORKS AND MODULES IN DISEASE 4.2.1 Disease networks 4.2.2 Identification of disease modules 4.2.3 Edgetic perturbation models 4.3 DIFFERENTIAL NETWORK ANALYSIS 4.4 DISEASE SPREADING ON NETWORKS 4.4.1 Percolation-based models 4.4.2 Agent-based simulations 4.5 MOLECULAR GRAPHS AND THEIR APPLICATIONS 4.5.1 Retrosynthesis 4.6 PROTEIN STRUCTURE, ENERGY & CONFORMATIONAL NETWORKS4.6.1 Protein folding pathways 4.7 LINK PREDICTION EXERCISES REFERENCES FURTHER READING Introduction to dynamic modelling5.1 CONSTRUCTING DYNAMIC MODELS 5.1.1 Modelling a generic biochemical system 5.2 MASS-ACTION KINETIC MODELS 5.3 MODELLING ENZYME KINETICS 5.3.1 The Michaelis–Menten model 5.3.2 Extending the Michaelis–Menten model 5.3.3 Limitations of Michaelis–Menten models 5.3.4 Co-operativity: Hill kinetics 5.3.5 An illustrative example: a three-node oscillator 5.4 GENERALISED RATE EQUATIONS 5.4.1 Biochemical systems theory 5.5 SOLVING ODES 5.6 TROUBLESHOOTING 5.6.1 Handing sti□f equations 5.6.2 Handling uncertainty 5.7 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Parameter estimation 6.1 DATA-DRIVEN MECHANISTIC MODELLING: AN OVERVIEW 6.1.1 Pre-processing the data 6.1.2 Model identification 6.2 SETTING UP AN OPTIMISATION PROBLEM 6.2.1 Linear regression 6.2.2 Least squares 6.2.3 Maximumlikelihood estimation 6.3 ALGORITHMS FOR OPTIMISATION 6.3.1 Desiderata 6.3.2 Gradient-based methods 6.3.3 Direct search methods 6.3.4 Evolutionary algorithms 6.4 POST-REGRESSION DIAGNOSTICS 6.4.1 Model selection 6.4.2 Sensitivity and robustness of biological models 6.5 TROUBLESHOOTING 6.5.1 Regularisation 6.5.2 Sloppiness 6.5.3 Choosing a search algorithm 6.5.4 Model reduction 6.5.5 The curse of dimensionality 6.6 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Discrete dynamic models: Boolean networks 7.1 INTRODUCTION 7.2 BOOLEAN NETWORKS: TRANSFER FUNCTIONS 7.2.1 Characterising Boolean network dynamics 7.2.2 Synchronous vs. asynchronous updates 7.3 OTHER PARADIGMS 7.3.1 Probabilistic Boolean networks 7.3.2 Logical interaction hypergraphs 7.3.3 Generalised logical networks 7.3.4 Petri nets 7.4 APPLICATIONS 7.5 TROUBLESHOOTING 7.6 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Introduction to constraint-based modelling 8.1 WHAT ARE CONSTRAINTS? 8.1.1 Types of constraints 8.1.2 Mathematical representation of constraints 8.1.3 Why are constraints useful? 8.2 THE STOICHIOMETRICMATRIX 8.3 STEADY-STATEMASSBALANCE:FLUXBALANCEANALYSIS (FBA)8.4 THE OBJECTIVE FUNCTION 8.4.1 The biomass objective function 8.5 OPTIMISATION TO COMPUTE FLUX DISTRIBUTION 8.6 AN ILLUSTRATION 8.7 FLUX VARIABILITY ANALYSIS (FVA) 8.8 UNDERSTANDING FBA 8.8.1 Blocked reactions and dead-end metabolites 8.8.2 Gaps in metabolic networks 8.8.3 Multiple solutions8.8.4 Loops 8.8.5 Parsimonious FBA (pFBA) 8.8.6 ATP maintenance fluxes 8.9 TROUBLESHOOTING 8.9.1 Zero growth rate 8.9.2 Objective values vs. flux values 8.10 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Extending constraint-based approaches 9.1 MINIMISATION OF METABOLIC ADJUSTMENT (MOMA) 9.1.1 Fitting experimentally measured fluxes 9.2 REGULATORY ON-OFF MINIMISATION (ROOM) 9.2.1 ROOMvs.MoMA 9.3 BI-LEVEL OPTIMISATIONS 9.3.1 OptKnock9.4 INTEGRATING REGULATORY INFORMATION 9.4.1 Embedding regulatory logic: regulatory FBA (rFBA) 9.4.2 Informing metabolic models with omic data 9.4.3 Tissue-specific models 9.5 COMPARTMENTALISED MODELS 9.6 DYNAMIC FLUX BALANCE ANALYSIS (dFBA) 9.7 13C-MFA 9.8 ELEMENTARY FLUX MODES AND EXTREME PATHWAYS 9.8.1 Computing EFMs and EPs 9.8.2 Applications EXERCISES REFERENCES FURTHER READING Perturbations to metabolic networks10.1 KNOCK-OUTS 10.1.1 Gene deletions vs. reaction deletions 10.2 SYNTHETIC LETHALS 10.2.1 Exhaustive enumeration 10.2.2 Bi-level optimisation 10.2.3 Fast-SL: massively pruning the search space 10.3 OVER-EXPRESSION 10.3.1 Flux Scanning based on Enforced Objective Flux (FSEOF) 10.4 OTHER PERTURBATIONS 10.5 EVALUATING AND RANKING PERTURBATIONS 10.6 APPLICATIONS OF CONSTRAINT-BASED MODELS 10.6.1 Metabolic engineering 10.6.2 Drug target identification 10.7 LIMITATIONS OF CONSTRAINT-BASED APPROACHES 10.7.1 Scope of genome-scale metabolic models 10.7.2 Incorrect predictions 10.8 TROUBLESHOOTING10.8.1 Interpreting gene deletion simulations 10.9 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Modelling cellular interactions 11.1 MICROBIAL COMMUNITIES 11.1.1 Network-based approaches 11.1.2 Population-based and agent-based approaches 11.1.3 Constraint-based approaches 11.2 HOST–PATHOGEN INTERACTIONS (HPIs) 11.2.1 Network models 11.2.2 Dynamic models 11.2.3 Constraint-based models 11.3 SUMMARY11.4 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Designing biological circuits 12.1 WHAT IS SYNTHETIC BIOLOGY? 12.2 FROMLEGO BRICKS TO BIOBRICKS 12.3 CLASSIC CIRCUIT DESIGN EXPERIMENTS 12.3.1 Designing an oscillator: the repressilator 12.3.2 Toggle switch 12.4 DESIGNING MODULES 12.4.1 Exploring the design space 12.4.2 Systems-theoretic approaches 12.4.3 Automating circuit design 12.5 DESIGN PRINCIPLES OF BIOLOGICAL NETWORKS 12.5.1 Redundancy 12.5.2 Modularity 12.5.3 Exaptation 12.5.4 Robustness 12.6 COMPUTING WITH CELLS 12.6.1 Adleman’s classic experiment 12.6.2 Examples of circuits that can compute 12.6.3 DNA data storage 12.7 CHALLENGES 12.8 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Robustness and evolvability of biological systems 13.1 ROBUSTNESS IN BIOLOGICAL SYSTEMS 13.1.1 Key mechanisms 13.1.2 Hierarchies and protocols 13.1.3 Organising principles 13.2 GENOTYPE SPACES AND GENOTYPE NETWORKS 13.2.1 Genotype spaces 13.2.2 Genotype–phenotype mapping 13.3 QUANTIFYING ROBUSTNESS AND EVOLVABILITY 13.4 SOFTWARE TOOLS EXERCISES REFERENCES FURTHER READING Epilogue: The Road Ahead Index 325
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