Biophysics Books
John Wiley & Sons Inc Physical Chemistry of Polyelectrolyte Solutions
Book SynopsisThe Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This volume explores topics from Thermodynamic Properties of Polyelectrolyte Solutions to ion-binding of polyelectrolytes. The book features: The only series of volumes available that presents the cutting edge of research in chemical physics Contributions from experts in this field of research Representative cross-section of research that questions established thinking on chemical solutions An editorial framework that makes the book an excellent supplement to an advanced graduate class in physical chemistry or chemical physics Table of ContentsPreface to the Series vii Preface ix Introductory Remarks 1 Thermodynamic Properties of Polyelectrolyte Solutions 21 Ionization Equilibrium and Potentiometric Titration of Weak Polyelectrolytes 67 Molecular Conformation of Linear Polyelectrolytes 115 Radius of Gyration and Intrinsic Viscosity of Linear Polyelectrolytes 153 Transport Phenomena of Linear Polyelectrolytes 193 Ion-Binding 241 Author Index 277 Subject Index 281
£160.50
John Wiley & Sons Inc Applied Biophysics for Drug Discovery
Book SynopsisApplied Biophysics for Drug Discovery is a guide to new techniques and approaches to identifying and characterizing small molecules in early drug discovery.Table of ContentsList of Contributors xiii 1 Introduction 1Donald Huddler References 3 2 Thermodynamics in Drug Discovery 7Ronan O’Brien, Natalia Markova, and Geoffrey A. Holdgate 2.1 Introduction 7 2.2 Methods for Measuring Thermodynamics of Biomolecular Interactions 8 2.2.1 Direct Method: Isothermal Titration Calorimetry 8 2.2.2 Indirect Methods: van’t Hoff Analysis 8 2.2.2.1 Enthalpy Measurement Using van’t Hoff Analysis 8 2.3 Thermodynamic‐Driven Lead Optimization 9 2.3.1 The Thermodynamic Rules of Thumb 9 2.3.2 Enthalpy–Entropy Compensation 10 2.3.3 Enthalpy–Entropy Transduction 13 2.3.4 The Role of Water 14 2.4 Enthalpy as a Probe for Binding 15 2.4.1 Thermodynamics in Fragment‐Based Drug Design (FBDD) 15 2.4.2 Experimental Considerations and Limitations When Working with Fragments 16 2.4.3 Enthalpic Screening 17 2.5 Enthalpy as a Tool for Studying Complex Interactions 17 2.5.1 Identifying and Handling Complexity 17 2.6 Current and Future Prospects for Thermodynamics in Decision‐Making Processes 24 References 25 3 Tailoring Hit Identification and Qualification Methods for Targeting Protein–Protein Interactions 29Björn Walse, Andrew P. Turnbull, and Susan M. Boyd 3.1 Introduction 29 3.2 Structural Characteristics of PPI Interfaces 29 3.3 Screening Library Properties 31 3.3.1 Standard/Targeted Libraries/DOS 31 3.3.2 Fragment Libraries 33 3.3.3 Macrocyclic and Constrained Peptides 33 3.3.4 DNA‐Encoded Libraries 34 3.4 Hit‐Finding Strategies 34 3.4.1 Small‐Molecule Approaches 36 3.4.2 Peptide‐Based Approaches 38 3.4.3 In Silico Approaches 39 3.5 Druggability Assessment 39 3.5.1 Small Molecule: Ligand‐Based Approaches 41 3.5.2 Small Molecule: Protein Structure‐Based Approaches 41 3.6 Allosteric Inhibition of PPIs 42 3.7 Stabilization of PPIs 43 3.8 Case Studies 43 3.8.1 Primary Peptide Epitopes 43 3.8.1.1 Bromodomains 44 3.8.2 Secondary Structure Epitopes 46 3.8.2.1 Bcl‐2 46 3.8.2.2 p53/MDM2 47 3.8.3 Tertiary Structure Epitopes 47 3.8.3.1 CD80–CD28 48 3.8.3.2 IL‐17A 48 3.9 Summary 49 References 50 4 Hydrogen–Deuterium Exchange Mass Spectrometry in Drug Discovery - Theory, Practice and Future 61Thorleif Lavold, Roman Zubarev, and Juan Astorga‐Wells 4.1 General Principles 61 4.2 Parameters Affecting Deuterium Incorporation 63 4.2.1 Primary Sequence 63 4.2.2 Intramolecular Hydrogen Bonding 63 4.2.3 Solvent Accessibility 63 4.2.4 pH Value 63 4.3 Utilization of HDX MS 64 4.3.1 Binding Site and Structural Changes Characterization upon Ligand Binding 64 4.3.1.1 Protein Stability - Biosimilar Characterization 64 4.4 Practical Aspects of HDX MS 65 4.4.1 Labeling 66 4.4.1.1 Deuterium Oxide and Protein Concentration 66 4.4.1.2 Ligand/Protein Ratio 66 4.4.1.3 Incubation–Labeling Time 66 4.4.1.4 Careful Preparation of the Control Sample 66 4.4.2 Sample Analysis 66 4.4.3 Data Analysis 67 4.5 Advantages of HDX MS 67 4.6 Perspectives and Future Application of HDX MS 68 References 69 5 Microscale Thermophoresis in Drug Discovery 73Tanja Bartoschik, Melanie Maschberger, Alessandra Feoli, Timon André, Philipp Baaske, Stefan Duhr, and Dennis Breitsprecher 5.1 Microscale Thermophoresis 73 5.1.1 Theoretical Background 74 5.1.2 Added Values for Small‐Molecule Interaction Studies 76 5.1.2.1 Size‐Change Independent Binding Signals 76 5.1.2.2 Difficult Targets and Assay Conditions 78 5.1.2.3 Detection of Aggregation and Other Secondary Effects 80 5.1.2.4 Quantification of Thermodynamic Parameters by MST 80 5.2 MST‐Based Lead Discovery 82 5.2.1 Single‐Point Screening 82 5.2.2 Secondary Affinity‐Based Fragment Screening by MST 85 5.2.3 Hit Identification and Affinity Determination of Small‐Molecule Binders to p38 Alpha Kinase 87 References 87 6 SPR Screening: Applying the New Generation of SPR Hardware 93Kartik Narayan and Steven S. Carroll 6.1 Platforms for Screening 93 6.2 SensiQ Pioneer as a “OneStep” Solution for Hit Identification 95 6.3 Deprioritization of False Positives Arising from Compound Aggregation 99 6.4 Concluding Remarks 103 References 104 7 Weak Affinity Chromatography (WAC) 107Sten Ohlson and Minh‐Dao Duong‐Thi 7.1 Introduction 107 7.2 Theory of WAC 109 7.3 Virtual WAC 110 7.4 Equipment and Procedure 111 7.5 Validation of WAC 113 7.6 Applications 114 7.6.1 Inhibitors for Cholera Toxin 115 7.6.2 Drug/Hormone: Protein Binding 115 7.6.3 Analysis of Stereoisomers 119 7.6.4 Carbohydrate Analysis with Antibodies and Lectins 120 7.6.5 Fragment Screening 121 7.6.6 Membrane Proteins 122 7.7 Conclusions and Future Perspectives 124 Acknowledgments 125 References 125 8 1D NMR Methods for Hit Identification 131Mary J. Harner, Guille Metzler, Caroline A. Fanslau, Luciano Mueller, and William J. Metzler 8.1 Introduction 131 8.2 NMR Methods for Quality Control 131 8.2.1 Compound DMSO Stock Concentration Determination 132 8.2.2 Compound Solubility Measurements in Aqueous Buffer 134 8.2.3 Compound Structural Integrity 136 8.2.4 Protein Reagent Characterization 136 8.3 NMR Binding Assays 136 8.3.1 Saturation Transfer Difference Assay 138 8.3.2 T2 Relaxation Assay 140 8.3.3 WaterLOGSY Assay 141 8.3.4 19F Displacement Assay 142 8.4 Multiplexing 143 8.5 Specificity 144 8.6 Automation 146 8.7 Practical Considerations for NMR Binding Assays 146 8.7.1 Compound Libraries 146 8.7.2 Tube Selection and Filling 147 8.7.3 Buffers 148 8.7.4 Targets 149 8.7.5 Experiment Selection 150 8.8 Conclusions 151 References 151 9 Protein‐Based NMR Methods Applied to Drug Discovery 153Alessio Bortoluzzi and Alessio Ciulli 9.1 Introduction 153 9.2 Chemical Shift Perturbation 154 9.2.1 Using Chemical Shift Perturbation to Study a Binding Event Between a Protein and a Ligand 154 9.2.2 Tackling the High Molecular Weight Limit by Reducing Transverse Relaxation and by Selective Labeling Patterns 156 9.2.3 CSP as Tool for Screening Campaigns 157 9.2.4 Structure–Activity Relationship by NMR 160 9.3 Methods for Obtaining Structural Information on Protein–Ligand Complex 160 9.3.1 SOS‐NMR 161 9.3.2 NOE‐Matching 162 9.3.3 Paramagnetic NMR Spectroscopy 162 9.4 Recent and Innovative Examples of Protein‐Observed NMR Techniques Applied Drug Discovery 163 9.4.1 An NMR‐Based Conformational Assay to Aid the Drug Discovery Process 163 9.4.2 In‐Cell NMR Techniques Applied to Drug Discovery 165 9.4.3 Time‐Resolved NMR Spectroscopy as a Tool for Studying Inhibitors of Posttranslational Modification Enzymes 166 9.4.4 Protein‐Observed 19F NMR Spectroscopy 168 9.5 Conclusions and Future Perspectives 170 References 170 10 Applications of Ligand and Protein‐Observed NMR in Ligand Discovery 175Isabelle Krimm 10.1 Introduction 175 10.2 Ligand‐Observed NMR Experiments Based on the Overhauser Effect 176 10.2.1 Transferred NOE, ILOE, and INPHARMA Experiments 176 10.2.1.1 Principle of the Transferred 2D 1H‐1H NOESY Experiment 176 10.2.1.2 Fragment‐Based Screening Using 2D Tr‐NOESY Experiment 178 10.2.1.3 Elucidation of the Active Conformation of the Ligand Using 2D 1H‐1H NOESY Experiment 178 10.2.1.4 Design of Protein Inhibitors Using Interligand NOEs 178 10.2.1.5 Identification of the Ligand Binding Site and Binding Mode Using INPHARMA 178 10.2.1.6 Design of Protein Inhibitors Using INPHARMA with Protein–Peptide Complexes 179 10.2.1.7 Experimental Conditions of the 2D 1H‐1H NOESY Experiment 179 10.2.2 Saturation Transfer Difference Experiment 180 10.2.2.1 Principle of the STD Experiment 180 10.2.2.2 Detection of Interactions and Library Screening by STD 180 10.2.2.3 Epitope Mapping by STD 181 10.2.2.4 Affinity Measurement by STD 181 10.2.2.5 Quantitative STD Using CORCEMA 183 10.2.2.6 Experimental Conditions 183 10.2.3 WaterLOGSY Experiment 184 10.2.3.1 Principle of the WaterLOGSY Experiment 184 10.2.3.2 Screening and Affinity Measurement by WaterLOGSY 184 10.2.3.3 Epitope Mapping and Water Accessibility in Protein–Ligand Complexes by WaterLOGSY 184 10.2.3.4 Experimental Conditions 185 10.3 Protein‐Observed NMR Experiments: Chemical Shift Perturbations 185 10.3.1 Principle 185 10.3.2 Affinity Measurement Using CSPs 186 10.3.3 Localization of Binding Sites Using CSPs 186 10.3.3.1 Chemical Shift Mapping 186 10.3.3.2 J‐Surface Modeling 187 10.3.4 Comparison of CSPs from Analogous Ligands 187 10.3.5 Back‐Calculation of Ligand‐Induced CSPs for Ligand Docking 187 10.3.5.1 CSP‐Based Post‐Docking Filter 189 10.3.5.2 CSP‐Guided Docking 189 10.4 Conclusion 189 Acknowledgments 191 References 191 11 Using Biophysical Methods to Optimize Compound Residence Time 197Geoffrey A. Holdgate, Philip Rawlins, Michal Bista, and Christopher J. Stubbs 11.1 Introduction 197 11.2 Biophysical Methods for Measuring Ligand Binding Kinetics 197 11.3 Measuring Structure–Kinetic Relationships: Some Example Case Studies 200 11.4 Effects of Conformational Dynamics on Binding Kinetics 201 11.5 Kinetic Selectivity 204 11.6 Mechanism of Binding and Kinetics 207 11.7 Optimizing Residence Time 207 11.8 Role of BK in Improving Efficacy 209 11.9 Effect of Pharmacokinetics and Pharmacodynamics 210 11.10 Summary 212 References 213 12 Applying Biophysical and Biochemical Methods to the Discovery of Allosteric Modulators of the AAA ATPase p97 217Stacie L. Bulfer and Michelle R. Arkin 12.1 p97 and Proteostasis Regulation 217 12.2 Structure and Dynamics of p97 218 12.3 Drug Discovery Efforts against p97 222 12.4 Uncompetitive Inhibitors of p97 Discovered by High‐Throughput Screening 223 12.4.1 Biochemical MOA Studies 223 12.4.2 Surface Plasmon Resonance 225 12.4.3 Nuclear Magnetic Resonance 226 12.4.4 Cryo‐EM Defines the Binding Site for an Uncompetitive Inhibitor of p97 228 12.4.5 Effect of Inhibitors on p97 PPI and MSP1 Disease Mutations 231 12.5 Fragment‐ Based Ligand Screening 231 12.5.1 Targeting the ND1 Domains 232 12.5.2 Targeting the N‐Domain 233 12.6 Conclusions 234 References 234 13 Driving Drug Discovery with Biophysical Information: Application to Staphylococcus aureus Dihydrofolate Reductase (DHFR) 241Parag Sahasrabudhe, Veerabahu Shanmugasundaram, Mark Flanagan, Kris A. Borzilleri, Holly Heaslet, Anil Rane, Alex McColl, Tim Subashi, George Karam, Ron Sarver, Melissa Harris, Boris A.Chrunyk, Chakrapani Subramanyam, Thomas V. Magee, Kelly Fahnoe, Brian Lacey, Henry Putz, J. Richard Miller, Jaehyun Cho, Arthur Palmer III, and Jane M. Withka 13.1 Introduction 241 13.2 Results and Discussion 245 13.2.1 Protein Dynamics of SA WT and S1 Mutant DHFR in Apo and Bound States 245 13.2.2 Protein Backbone 15N, 13C, and 1H NMR Resonance Assignments 246 13.2.3 Protein Residues Show Severe Line Broadening due to Conformational Exchange 246 13.2.4 R2 Relaxation Dispersion NMR Experiments 248 13.2.5 Kinetic Profiling of DHFR Inhibitors 251 13.2.6 Characterization of SA WT and S1 Mutant DHFR–TMP Interactions in Solution 253 13.2.7 Prospective Biophysics Library Design 254 13.3 Conclusion 258 References 259 14 Assembly of Fragment Screening Libraries: Property and Diversity Analysis 263Bradley C. Doak, Craig J. Morton, Jamie S. Simpson, and Martin J. Scanlon 14.1 Introduction 263 14.2 Physicochemical Properties of Fragments 265 14.3 Molecular Diversity and Its Assessment 268 14.4 Experimental Evaluation of Fragments 274 14.5 Assembling Libraries for Screening 275 14.6 Concluding Remarks 279 References 280 Index 285
£121.46
John Wiley & Sons Inc Introductory Bioelectronics
Book SynopsisBioelectronics is a rich field of research involving the application of electronics engineering principles to biology, medicine, and the health sciences. With its interdisciplinary nature, bioelectronics spans state-of-the-art research at the interface between the life sciences, engineering and physical sciences.Table of ContentsAbout the Authors xiii Foreword xv Preface xvii Acknowledgements xix 1 Basic Chemical and Biochemical Concepts 1 1.1 Chapter Overview 1 1.2 Energy and Chemical Reactions 1 1.3 Water and Hydrogen Bonds 15 1.4 Acids, Bases and pH 18 1.5 Summary of Key Concepts 25 2 Cells and their Basic Building Blocks 29 2.1 Chapter Overview 29 2.2 Lipids and Biomembranes 29 2.3 Carbohydrates and Sugars 32 2.4 Amino Acids, Polypeptides and Proteins 34 2.5 Nucleotides, Nucleic Acids, DNA, RNA and Genes 43 2.6 Cells and Pathogenic Bioparticles 51 2.7 Summary of Key Concepts 70 3 Basic Biophysical Concepts and Methods 73 3.1 Chapter Overview 73 3.2 Electrostatic Interactions 74 3.3 Hydrophobic and Hydration Forces 90 3.4 Osmolarity, Tonicity and Osmotic Pressure 91 3.5 Transport of Ions and Molecules across Cell Membranes 94 3.6 Electrochemical Gradients and Ion Distributions Across Membranes 99 3.7 Osmotic Properties of Cells 103 3.8 Probing the Electrical Properties of Cells 105 3.9 Membrane Equilibrium Potentials 111 3.10 Nernst Potential and Nernst Equation 112 3.11 The Equilibrium (Resting) Membrane Potential 114 3.12 Membrane Action Potential 116 3.13 Channel Conductance 120 3.14 The Voltage Clamp 121 3.15 Patch-Clamp Recording 122 3.16 Electrokinetic Effects 124 4 Spectroscopic Techniques 147 4.1 Chapter Overview 147 4.2 Introduction 148 4.3 Classes of Spectroscopy 151 4.4 The Beer-Lambert Law 165 4.5 Impedance Spectroscopy 170 5 Electrochemical Principles and Electrode Reactions 177 5.1 Chapter Overview 177 5.2 Introduction 178 5.3 Electrochemical Cells and Electrode Reactions 180 5.4 Electrical Control of Electron Transfer Reactions 194 5.5 Reference Electrodes 203 5.6 Electrochemical Impedance Spectroscopy (EIS) 208 6 Biosensors 215 6.1 Chapter Overview 215 6.2 Introduction 215 6.3 Immobilisation of the Biosensing Agent 217 6.4 Biosensor Parameters 218 6.5 Amperometric Biosensors 228 6.6 Potentiometric Biosensors 233 6.7 Conductometric and Impedimetric Biosensors 237 6.8 Sensors Based on Antibody–Antigen Interaction 240 6.9 Photometric Biosensors 242 6.10 Biomimetic Sensors 245 6.11 Glucose Sensors 247 6.12 Biocompatibility of Implantable Sensors 252 7 Basic Sensor Instrumentation and Electrochemical Sensor Interfaces 259 7.1 Chapter Overview 259 7.2 Transducer Basics 260 7.3 Sensor Amplification 262 7.4 The Operational Amplifier 264 7.5 Limitations of Operational Amplifiers 269 7.6 Instrumentation for Electrochemical Sensors 271 7.7 Impedance Based Biosensors 278 7.8 FET Based Biosensors 284 8 Instrumentation for Other Sensor Technologies 297 8.1 Chapter Overview 297 8.2 Temperature Sensors and Instrumentation 298 8.3 Mechanical Sensor Interfaces 304 8.4 Optical Biosensor Technology 325 8.5 Transducer Technology for Neuroscience and Medicine 335 9 Microfluidics: Basic Physics and Concepts 343 9.1 Chapter Overview 343 9.2 Liquids and Gases 343 9.3 Fluids Treated as a Continuum 346 9.4 Basic Fluidics 354 9.5 Fluid Dynamics 356 9.6 Navier-Stokes Equations 365 9.7 Continuum versus Molecular Model 369 9.8 Diffusion 378 9.9 Surface Tension 383 10 Microfluidics: Dimensional Analysis and Scaling 391 10.1 Chapter Overview 391 10.2 Dimensional Analysis 391 10.3 Dimensionless Parameters 400 10.4 Applying Nondimensional Parameters to Practical Flow Problems 411 10.5 Characteristic Time Scales 412 10.6 Applying Micro- and Nano-Physics to the Design of Microdevices 413 Problems 415 References 416 Appendix A: SI Prefixes 417 Appendix B: Values of Fundamental Physical Constants 419 Appendix C: Model Answers for Self-study Problems 421 Index 435
£64.55
Springer Nature Switzerland AG Pathomechanics of Common Foot Disorders
Book SynopsisThis new book consolidates the current knowledge of lower extremity biomechanics and pathomechanics and makes this information relevant to the study of common foot and ankle pathologies. The content is presented in a language and format that allows the clinician to review current evidence explaining the etiology of these disorders in order to formulate effective treatment interventions. In order to understand pathomechanics, the clinician must also become versed in the normal, healthy biomechanics of the lower extremity. A review of gait, muscle function and forces acting on the lower extremities during physical activity will be the focus of the first part of this book. The second part of the book will study the common, challenging pathologies treated on a daily basis by foot and ankle clinicians: hallux abducto valgus, hallux rigidus, metatarsalgia, digital deformities, adult acquired flatfoot, and plantar heel pain. These chapters discuss all the relevant factors contributing to these conditions, evaluating and exposing myths and misconceptions about the pathomechanics and treatments of these conditions. For each disorder, a comprehensive review of published research provides a foundation for an updated, valid description of etiology and risk factors. Providing a fresh approach to lower extremity pathomechanics and management strategies, Pathomechanics of Common Foot Disorders is a valuable resource for podiatrists and orthopedic foot and ankle surgeons at all levels. Table of ContentsPreface Chapter 1: Comparative Anatomy and Introduction to the Twisted Plate Mechanism Chapter 2: Human Walking: The Gait Cycle Chapter 3: Motion of the Foot: Joints, Muscles and Sensorimotor Control Chapter 4: Disorders of the First Ray: Part 1: Hallux Abductovalgus Deformity Chapter 5: Disorders of the First Ray: Part 2: Hypermobility, Functional Hallux Limitus and Hallux Rigidus Chapter 6: Metatarsalgia and Digital Deformities Chapter 7: Adult Acquired Flatfoot Chapter 8: Plantar Heel Pain
£113.99
Springer Nature Switzerland AG Mechanics of Biological Systems and Materials &
Book SynopsisMechanics of Biological Systems & Micro-and Nanomechanics, Volume 5 of the Proceedings of the 2020 SEM Annual Conference & Exposition on Experimental and Applied Mechanics, the fifth volume of seven from the Conference, brings together contributions to important areas of research and engineering. The collection presents early findings and case studies on a wide range of topics, including:Cell Mechanics & Traumatic Brain InjuryMicromechanical TestingAdhesion and FractureMEMS Devices and TechnologyNano-scale Deformation Mechanisms1D & 2D MaterialsTribology & WearResearch and Applications in ProgressTable of ContentsChapter 1. Determination of Texture Properties of White Long Turnip Flesh.- Chapter 2. Impact Testing of a Commercial Poly-Lactic Acid.- Chapter 3. Underwater Explosion Gas Bubble Collapse in the Vicinity of a Rigid Boundary.- Chapter 4. Optimization for Improved Energy Absorption and the Effect of Density Gradation in Cellular Materials.- Chapter 5. Quantifying Ultrasonic Deformation of Cell Membranes with Ultra-High Speed Imaging.- Chapter 6. A Mathematical Model of Nitric Oxide Mechanotransduction in Brain.- Chapter 7. Evaluating the Application 0f DIC on Heartbeat Detection by Using a Self-Developed Artery Vessel Simulator.- Chapter 8. Measuring Strain Distribution of Knee Cartilage Using Digital Volume Correlation.- Chapter 9. Characterization of Shear Band Nucleation and Propagation in Bulk Metallic Glasses.- Chapter 10. Suppression of Parkisonian Hand Tremors.- Chapter 11. Biomechanical Testing of Human Red Blood Cells Under Controlled Oxygen Tension.- Chapter 12. High Speed Holographic Shape and Vibration Measurement of the Semi-transparent Tympanic Membrane.- Chapter 13. Adhesion Index- A Novel Bio-compatibility Assessment Standard for Medical Devices.- Chapter 14. Evaluate the Fidelity of Synthetic Tissues Used in Escharotomy Simulators.- Chapter 15. Bacterial Cell Wall Glycopolymers Affect Polymer Chain Alignment and Mechanics of Streptococcus mutans.- Chapter 16. Characterization of Reversible Tablet Sliding In Nacre From Haliotis Rufescens (Red Abalone).- Chapter 17. Failure of Three-Tab Shingle System Subjected to Wind Gusts up to 150 MPH – A DIC Based Study.- Chapter 18. Design and Rapid Prototyping of Fiber Optic-Based Micro-Force Sensors by Two-Photon Polymerization.- Chapter 19. Experimental study of shear and tensile properties of LIGA Ni-Fe and Ni-Co alloys at quasi-static and intermediate strain rates.
£161.99
Springer Nature Switzerland AG Wavelets in Neuroscience
Book SynopsisThis book illustrates how modern mathematical wavelet transform techniques offer fresh insights into the complex behavior of neural systems at different levels: from the microscopic dynamics of individual cells to the macroscopic behavior of large neural networks. It also demonstrates how and where wavelet-based mathematical tools can provide an advantage over classical approaches used in neuroscience. The authors well describe single neuron and populational neural recordings.This 2nd edition discusses novel areas and significant advances resulting from experimental techniques and computational approaches developed since 2015, and includes three new topics:• Detection of fEPSPs in multielectrode LFPs recordings.• Analysis of Visual Sensory Processing in the Brain and BCI for Human Attention Control;• Analysis and Real-time Classification of Motor-related EEG Patterns;The book is a valuable resource for neurophysiologists and physicists familiar with nonlinear dynamical systems and data processing, as well as for graduate students specializing in these and related areas.Table of ContentsMathematical Methods of Signal Processing in Neuroscience.- Brief Tour of Wavelet Theory.- Analysis of Single Neuron Recordings.- Classification of Neuronal Spikes from Extracellular Recordings.- Analysis of Gamma-Waves in Multielectrode LFP Recordings.- Wavelet Approach to the Study of Rhythmic Neuronal Activity.- Wavelet-based Approach to Epilepsy.- Analysis of Visual Sensory Processing in the Brain and Brain-Computer Interfaces for Human Attention Control.- Analysis and Real-Time Classification of Motor-related EEG and MEG Patterns.- Conclusion.
£132.99
Springer Nature Switzerland AG IoT System Design: Project Based Approach
Book SynopsisThis book presents a step by step design approach to develop and implement an IoT system starting from sensor, interfacing to embedded processor, wireless communication, uploading measured data to cloud including data visualization along with machine learnings and artificial intelligence. The book will be extremely useful towards a hands-on approach of designing and fabricating an IoT system especially for upper undergraduate, master and PhD students, researchers, engineers and practitioners.Table of ContentsIoT System Design– The Big Picture.- Design Considerations for IoT node.- Programming Arduino for IoT System.- Bluetooth based IoT System.- Cloud Computing for IoT Systems.- Simulation based Projects on IoT Systems.
£113.99
Springer International Publishing AG Optical Whispering Gallery Modes for Biosensing:
Book SynopsisThis interdisciplinary book covers the fundamentals of optical whispering gallery mode (WGM) microcavities, light–matter interaction, and biomolecular structure with a focus on applications in biosensing. Novel biosensors based on the hybridization of WGM microcavities and localized surface plasmon resonances (LSPRs) in metal nanoparticles have emerged as the most sensitive microsystem biodetection technology that boasts single molecule detection capability without the need for amplification and labeling of the analyte. The book provides an ample survey of the physical mechanisms of WGMs and LSPRs for detecting affinity, concentration, size, shape and orientation of biomarkers, while informing the reader about different classes of biomolecules, their optical properties and their importance in label-free clinical diagnostics.This expanded and updated second edition features a new chapter that introduces the reader to advanced in vivo biosensing techniques using WGM microcavities, looking at photothermal sensing, methods for trapping neutral atoms around WGM microcavities, and practical aspects of optoplasmonic sensing. The second Edition now provides a comprehensive introduction to the use of WGM microcavities in physical sensing which includes measurements with frequency combs, macro and micro (one atom) lasers, gyroscopes, optomechanical and parity-time-symmetric sensor devices.Chapter-end problems round out this comprehensive and fundamental textbook, inspiring a host of up-and-coming physicists, bioengineers, and medical professionals to make their own breakthroughs in this blossoming new field. This textbook can be used for both introductory and advanced courses about the modern optics of optical microcavities.Table of ContentsSensing with Light.- Surface Plasmon Resonance.- Whispering Gallery Modes in Optical Microcavities.- Applications of WGM Microcavities in Physics.- Single Molecule Sensing.- Fundamentals of Quantum Optics.- Molecular cavity QED.
£42.74
Springer International Publishing AG Sensors and Microsystems: Proceedings of AISEM
Book SynopsisThis book showcases the state of the art in the field of sensors and microsystems, revealing the impressive potential of novel methodologies and technologies. It covers a broad range of aspects, including: bio-, physical and chemical sensors, actuators, micro- and nano-structured materials, mechanisms of interaction and signal transduction, polymers and biomaterials, sensor electronics and instrumentation, analytical microsystems, recognition systems and signal analysis and sensor networks as well as manufacturing technologies, environmental, food, energy and biomedical applications. The contents reflect the outcomes of the activities of AISEM (Italian Association of Sensors and Microsystems) in 2021. Co-Edited by B. Andò, F. Baldini, G. Betta, D. Compagnone, S. Conoci, E. Comini, V. Ferrari, E. La Salandra, L. Lorenzelli, A.G. Mignani, G. Marrazza, G. Neri, P. Siciliano.
£189.99
Springer Vieweg Vaskuläre Biomechanik
Book Synopsis1 Modellierung in der Biomechanik 1.- 1.1 Die verschiedenen Perspektiven 2.- 1.1.1 Der technische Ansatz 2.- 1.1.2 Der klinische Ansatz 2.- 1.1.3 Die präklinischen Ansätze 2.- 1.2 Chancen und Herausforderungen 2.- 1.3 Statistische Analyse 3.- 1.3.1 Wahrscheinlichkeitsverteilungen 4.- 1.3. 2 Hypothesentests 7.- 1.3.3 Korrelation zwischen Variablen 9.- 1.3.4 Regressionsmodellierung 10.- 1.3.5 Mittelwertdifferenztest 13.- 1.3.6 Studiendesign 14.- 1.4 Modelldefinition 16.- 1.5 Modellentwicklung und -prüfung 17.- 1.5.1 Sensitivitätsanalyse 17.- 1.5.3 Validierung 21.- 1.6 Fallstudie: Biomechanische Bruchrisikobewertung (BRRA) 21.- 1.6.1 Unzulänglichkeiten der derzeitigen AAA-Risikobewertung 21.- 1.6.2 Beabsichtigte Modellanwendung (IMA) 21.- 1.6.3 Versagenshypothese 22.- 1.6.4 Arbeitsablauf und Diagnoseinformationen 22.- 1.6.5 Wichtige Modellierungsannahmen 23.- 1.6.6 Klinische Validierung 24.- 1.7 Zusammenfassung und Schlussfolgerung 25.- Anhang: Biomechanik-Modellierung 27.- A.1 Definitionen und Terminologie in der Statistik 27.- 2 Das Kreislaufsystem 29.- 2.1 Physiologie 29.- 2.1.1 Gefäßsystem 29.- 2.1.2 Schlüsselkonzepte 31.- 2.1.3 Zellen im Gefäßsystem 32.- 2.1.4 Makrozirkulation 33.- 2.1.5 Lymphsystem 37.- 2.1.6 Mikrozirkulation 38.- 2.1.7 Hämodynamische Regulation 41.- 2.2 Mechanische Systemeigenschaften 42.- 2.2.1 Gefäßdruck 43. - 2.2.2 Gefäßfluss 44.- 2.2.3 Gefäßwiderstand 45.- 2.2.4 Transkapillarer Transport 45.- 2.3 Modellierung der Makrozirkulation 45.- 2.3.1 Windkessel (WK)-Modelle 46.- 2.3.2 Modellierung von Gefäßnetzwerken 57.- 2.4 Modellierung der Mikrozirkulation 63.- 2.4.1 Transkapillare Konzentrationsdifferenz 63.- 2.4.2 Filtration 65.- 2.5 Zusammenfassung und Fazit 70.- Anhang: Mathematische Vorüberlegungen 72.- A.1 Komplexe Zahlen 72.- A.2 Fourierreihen-Approximation 72.- Anhang: Grundelemente der Schaltung 73.- B.1 Widerstandselement 73.- B.2 Kondensatorelement 73.- B.3 Induktorelement 74.- Anhang: Transportmechanismen 74.- C.1 Diffusion 74.- C.2Advektion 75.- Anhang: Osmose 75.- D.1 Osmotischer Druck 75.- D.2 Transport durch semipermeable Membranen 76.- 3 Kontinuumsmechanik 77.- 3.1 Kinematik 78.- 3.1.1 Deformationsgradient 78.- 3.1.2 Multiplikative Zerlegung 79.- 3.1.3 Polare Zerlegung 79.- 3.1.4 Deformation des Linienelements 79.- 3.1.5 Deformation des Volumenelements 80.- 3.1.6 Deformation des Flächenelements 80.- 3.1. 7 Begriff der Dehnung 81.- 3.2 Begriff der Spannung 85.- 3.2.1 Cauchy-Spannungstheorem 86.- 3.2.2 Hauptspannungen 87.- 3.2.3 Isochore und Volumenspannung 89.- 3.2.4 Oktaederspannung und von-Mises-Spannung 89.- 3.2.5 Cauchy-Spannung in gedrehten Koordinaten 91.- 3.2.6 Erste Piola-Kirchhoff-Spannung 91.- 3.2.7 Zweite Piola-Kirchhoff-Spannung 92.- 3.2. 8 Auswirkung der Inkompressibilität des Materials auf den Spannungszustand 93.- 3.3. Materialzeitableitungen 94.- 3.3.1 Kinematische Variablen 94.- 3.3.2 Spannungsraten 95.- 3.3.3 Potenzkonjugierte Spannungs- und Dehnungsraten 96.- 3.4 Konstitutive Modellierung 97.- 3.4.1 Einige mechanische Eigenschaften von Materialien 97.- 3.4.2 Linear elastisches Material 100.- 3.4. 3 Hyperelastizität 102.- 3.4.4 Viskoelastizität 105.- 3.5 Gesetzmäßigkeiten 113.- 3.5.1 Massenbilanz 114.- 3.5.2 Bilanz des linearen Impulses 116.- 3.5.3 Maxwell-Transport und Lokalisierung 118.- 3.5.4 Thermodynamische Prinzipien 119.- 3.6 Allgemeine Prinzipien 125.- 3.6.1 Freikörper-Diagramm 125.- 3.6.2 Anfängliches Randwertproblem 126.- 3.6.3 Prinzip der virtuell.- 3.7 Schädigung und Versagen 129.- 3.7.1 Physikalische Konsequenzen 129.- 3.7.2 Dehnungslokalisierung 130.- 3.7.3 Lineare Bruchmechanik 132.- 3.7.4 J.- Integral 133.- 3.7.5 Kohäsionszonenmodellierung 133.- 3.8 Mehrphasige Kontinuumstheorien 134.- 3.8.1 Mischungstheorie 134.- 3.8.2 Poroelastizitätstheorie 134.- 3.9 Zusammenfassung und Fazit 135.- Anhang: Mathematische Präliminarien 136.- A.1 Laplace- und Fourier-Transformationen 136.- A.2 Matrixalgebra 136.- A.2.1 Spur einer Matrix 137.- A.2.2 Identitätsmatrix 137.- A.2.3 Determinante einer Matrix 137.- A.2.4 Inverse und orthogonale Matrix 138.- A.2.5 Lineare Vektortransformation 138.- A.2.6 Eigenwertproblem 138.- A.2.7 Beziehung zwischen der Spur und den Eigenwerten 139.- A.2 .8 Cayley-Hamilton-Theorem 139.- A.3 Vektoralgebra 140.- A.3.1 Grundlegende Vektoroperationen 140.- A.3.2 Koordinatentransformation 142.- A.4 Tensoralgebra 144.- A.4.1 Sphärischer Tensor 144.- A.4 .2 Tensoroperationen 145.- A.4.3 Invarianten von Tensoren zweiter Ordnung 145.- A.5 Vektor- und Tensorrechnung 146.- A.5.1 Lokale Änderungen von Feldvariablen 146.- A.5.2 Divergenzsatz 147.- Anhang: Einige nützliche Laplace- und Fourier-Transformationen 148.- B.1 Laplace-Transformationen 148.- B.2 Fourier-Transformationen 150.- Anhang: Einige nützliche Tensorrelationen 151.- 4 Leitende Gefäße 153.- 4.1 Histologie und Morphologie der Gefäßwand 154.- 4.1.1 Geschichteter Aufbau der Gefäßwand 154.- 4.1.2 Unterschiede zwischen Arterien und Venen 155.- 4.1. 3 Extrazelluläre Matrix (ECM) 156.- 4.1.4 Zellen 157.- 4.2 Mechanische Eigenschaften und experimentelle Beobachtungen 158.- 4.2.1 Aorta 160.- 4.2.2 Karotisarterie 161.- 4.2.3 Koronararterie 162.- 4.2.4 Iliaca 163.- 4.3 Gefäßerkrankungen 163.- 4.3.1 Diagnostische Untersuchungen 164.- 4.3.2 Atherosklerose 165.- 4.3.3 Biomechanische Faktoren bei Atherosklerose 167.- 4.3.4 Karotiserkrankung 169.- 4.3.5 Koronare Herzkrankheit 171.- 4.3.6 Aneurysmaerkrankung 172.- 4.4 Gefäßadaptation 174.- 4.5 Konstitutive Beschreibungen 175.- 4.5.1 Kapazität eines Gefäßsegmentes 176.- 4.5.2 Hyperelastizität für inkompressible Festkörper 177.- 4.5.3 Rein phänomenologische Beschreibungen 178.- 4.5.4 Histomechanische Beschreibungen 183.- 4.5.5 Allgemeine Theorie des faserigen Bindegewebes 185.- 4.5.6 Eigenspannung und Last.-freie Konfiguration 188.- 4.5.7 Viskoelastische Beschreibungen 189.- 4.5.8 Schädigungs- und Versagensbeschreibungen 191.- 4.5.9 Nicht-passive Gefäßwandeigenschaften 194.- 4.6 Identifikation von konstitutiven Parametern 194.- 4.6.1 Analytische Gefäßwandmodelle 197.- 4.6.2 Optimierungsproblem 199.- 4.7 Fallbeispiel:Wandspannungsanalyse der normalen und aneurysmatischen.- infrarenalen Aorta 205.- 4.7.1 Der Analysetyp 205.- 4.7.2 Einstellen der Randbedingungen - Dirichlet-Rand 205.- 4.7.3 Einstellen der Belastungsbedingungen - Neuman-Rand 205.- 4.7.4 Einstellen der Gefäßwandeigenschaften 206.- 4.7.5 Einstellen der Ausgabeoptionen 206.- 4.8 Zusammenfassung und Fazit 206.- Anhang:Protokoll der experimentellen Gefäßwandprüfung 208.- A.1 Gewebeentnahme und Probenvorbereitung 208.- A.2 Prüfprotokolldefinition und Datenaufzeichnung 208.- A.3 Erfasst.- x INHALT.- 5 Blutfluss 211.- 5.1 Zusammensetzung des Blutes 211.- 5.1.1 Erythrozyten (oder rote Blutkörperchen) 212.- 5.1.2 Leukozyten (oder weiße Blutkörperchen) 212.- 5.1.3 Thrombozyten (oder Blutplättchen) 213.- 5.1.4 Plasma 213.- 5.2 Kräfte, die auf Blutteilchen wirken 214.- 5.2.1 Luftwiderstand 214.- 5.2.2 Schwerkraft und Trägheitskräfte 214. - 5.2.3 Kräfte,die mit dem Flüssigkeitsdruck zusammenhängen 214.- 5.2.4 Kräfte, die mit der Flüssigkeitsgeschwindigkeit und der Schubspannung zusammenhängen 215.- 5.2.5 Kräfte, die durch Kollisionen entstehen 216.- 5.2.6 Chemische und elektrische Kräfte 216.- 5.2.7 Segregation von Blutpartikeln 218.- 5.3 Modellierung der Blutrheologie 218.- 5. 3.1 Änderung der Blutmikrostruktur mit der Scherrate 218.- 5.3.2 Modellierung verallgemeinerter Newtonscher Flüssigkeiten 219.- 5.3.3 Einphasen-Viskositätsmodelle für Blut 220.- 5.3.4 Zusammensetzungsbasierte Viskositätsmodelle für Blut 221.- 5.4 Blutschädigung 224.- 5.5 Beschreibung inkompressibler Strömungen 224. - 5.5.1 Energieerhaltung 224.- 5.5.2 Lineare Impulserhaltung 226.- 5.6 Blutströmungsphänomene 232.- 5.6.1 Laminare und turbulente Strömung 232.- 5.6.2 Grenzschichtströmung 233.- 5.6.3 Blutströmung durch kreisförmige Rohre 233.- 5.6.4 Mehrdimensionale Strömungsphänomene 234.- 5.7 Fallbeispiel:Wandschubspannungsanalyse der normalen und.- aneurysmatischen infrarenalen Aorta 236.- 5.7.1 Einstellen des Analysetyps 236.- 5.7.2 Einstellen der Randbedingungen -Dirichlet-Rand 236.- 5.7.3 Einstellen der Belastungsbedingungen -Neuman-Rand 237.- 5.7.4 Einstellen der rheologischen Eigenschaften des Blutes 237.- 5.7.5 Einstellen der Ausgabeoptionen 237.- 5.8 Zusammenfassung und Fazit 238.- Anhang:Mathematische Präliminarien 239.- 6 Die Gefäßwand, eine aktive Einheit 241.- 6.1 Vasoreaktivität 242.- 6.1.1 Struktur der kontraktilen SMC 242.- 6.1.2 Kontraktionsregulation der SMC 243.- 6.2 Arteriogenese 243.- 6.3 Angiogenese 244.- 6.4 Schädigung, Heilung und Versagen 244.- 6.5 Modellierungsrahmen 244.- 6.5.1 Offene Systemgesetze 245.- 6.5.2 Kinematik-basierte Wachstumsbeschreibung 246.- 6.5.3 Tensoriale Verteilung des Volumenwachstums 248.- 6.5.4 Homöostatisches Wachstum 249.- 6.5.5 Auf Umsatz basierende Wachstumsbeschreibung 252.- 6.5.6 Andere Formulierungen 256.- 6.5.7 Anwendungen von Wachstumsbeschreibungen 257.- 6.6 Fazit und Diskussion 258.- 6.7 Anwendungen 259.- 6.7.1 Zugversuch an der passiven und aktiven Gefäßwand 259.- 6.7.2 Biaxial belastetes Gefäßwandstück 260.- 6.7.3 Ringversuch an Gefäßsegmenten 262.- Referenzen 265.- Problemlösungen 287.- Index 373.
£52.24
Springer MacroMolecular Crowding
Book SynopsisChapter 1: A brief historico-philosophical overview of macromolecular crowding: Making “physiological conditions” more physiological.- Chapter 2: Effects of molecular crowding on the structural, dynamic, and functional properties of biological macromolecules: A general overview.- Chapter 3: (Macro)molecular crowding effects beyond volume exclusion.- Chapter 4: Role of aqueous media in macromolecular crowding.- Chapter 5: Effects of macromolecular crowding on the structure and dynamics of biological membranes.- Chapter 6: Effects of molecular crowding on the structure, folding, and stability of DNA.- Chapter 7: Effects of molecular crowding on the structure, folding, stability, and catalysis of RNA.- Chapter 8: Understanding the effect of macromolecular crowding on protein misfolding and aggregation.- Chapter 9: The role of macromolecular crowding in cytoskeletal organization.- Chapter 10: Macromolecular crowding in cytoplasm and cellular organelles.- Chapter 11: Macromolecular crowding in mitochondria.- Chapter 12: Molecular crowing in nuclear pore.- Chapter 13: Catalytic Droplets: Enzyme Containing Microcompartments.- Chapter 14: Macromolecular crowding in cell stress and death.- Chapter 15: Heterogeneity of molecular crowding and liquid-liquid phase separation.- Chapter 16: Reshuffling overcrowded milieu: Stress-induced reorganization of the eukaryotic membrane-less organelles.- Chapter 17: Crowding in Anhydrobiosis.- Chapter 18: Crowding and in-cell crystallization.- Chapter 19: Macromolecular crowding for reparative medicine and drug discovery applications.- Chapter 20: Simulating crowding in vitro: Not an elusive goal any longer.- Chapter 21: Molecular Crowding by Computational Approaches.- Chapter 22: Modeling Facilitated Diffusion of Proteins in Crowded Environment.- Chapter 23: The Hidden Influences of Macromolecular Crowding: A New Frontier in Cellular Biology and Medicine.
£134.99
De Gruyter Biomedical Methods
Book SynopsisThis book presents a comprehensive description of the basic concepts of soft matter mechanics and of the nano- and microscale biomedical methods that allow characterizing the mechanical properties of cells and tissues.
£68.85
De Gruyter Biomechanics of Dance: Applications of Classical
Book SynopsisThis book provides a detailed analysis of human movement, building from simple physical models to more complex analyses and biomechanical models, including forces internal to the body. The book integrates principles of Physics with the functioning of the nervous and musculoskeletal systems to understand how movement in general, and dance movements specifically, can be executed to enhance performance and reduce injury risk.
£69.75
De Gruyter Biomedical Applications
Book SynopsisThis book is dedicated to the discussion of several biomedical applications of the mechanical phenotyping of cells and tissues to specific disease models. The topical chapters on mechanics in disease are preceded by chapters describing cell and tissue structure and their relationship with the biomechanical properties, as well as by the description of dedicated sample preparation methods for the nano- and microscale mechanical measurements.
£77.85
Springer International Publishing AG Intermediate Physics for Medicine and Biology
Book SynopsisThis classic text has been used in over 20 countries by advanced undergraduate and beginning graduate students in biophysics, physiology, medical physics, neuroscience, and biomedical engineering. It bridges the gap between an introductory physics course and the application of physics to the life and biomedical sciences. Extensively revised and updated, the fifth edition incorporates new developments at the interface between physics and biomedicine. New coverage includes cyclotrons, photodynamic therapy, color vision, x-ray crystallography, the electron microscope, cochlear implants, deep brain stimulation, nanomedicine, and other topics highlighted in the National Research Council report BIO2010. As with the previous edition, the first half of the text is primarily biological physics, emphasizing the use of ideas from physics to understand biology and physiology, and the second half is primarily medical physics, describing the use of physics in medicine for diagnosis (mainly imaging) and therapy. Prior courses in physics and in calculus are assumed. Intermediate Physics for Medicine and Biology is also ideal for self study and as a reference for workers in medical and biological research. Over 850 problems test and enhance the student's understanding and provide additional biological examples. A solutions manual is available to instructors. Each chapter has an extensive list of references.Table of ContentsMechanics.- Exponential Growth and Decay.- Systems of Many Particles.- Transport in an Infinite Medium.- Transport Through Neutral Membranes.- Impulses in Nerve and Muscle Cells.- The Exterior Potential and the Electrocardiogram.- Biomagnetism.- Electricity and Magnetism at the Cellular Level.- Feedback and Control.- The Method of Least Squares and Signal Analysis.- Images.- Sound and Ultrasound.- Atoms and Light.- Interaction of Photons and Charged Particles with Matter.- Medical Use of X Rays.- Nuclear Physics and Nuclear Medicine.- Magnetic Resonance Imaging.- Appendices.- Plane and Solid Angles.- Vectors: Displacement, Velocity and Acceleration.- Properties of Exponents and Logarithms.- Taylor’s Series.- Some Integrals of Sines and Cosines.- Linear Differential Equations with Constant Coefficients.- Mean and Standard Deviation.- Binomial Probability Distribution.- Gaussian Probability Distribution.- Poisson Distribution.- Integrals Involving exp(-ax^2).- Spherical and Cylindrical Coordinates.- Joint Probability Distributions.- Partial Derivatives.- Fundamental Constants and Conversion Factors.
£85.49
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?
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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.
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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.
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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
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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
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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
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Taylor & Francis Ltd Molecular Modeling at the Atomic Scale
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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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Taylor & Francis Ltd Computational Biology
a huge range and FREE tracked UK delivery on ALL orders.
£42.74
Taylor & Francis Ltd Fields Forces and Flows in Biological Systems
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£58.89
Taylor & Francis Ltd Stem Cell Labeling for Delivery and Tracking Using Noninvasive Imaging
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£45.59
Taylor & Francis Ltd Handbook of Tissue Optical Clearing
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£237.50
Taylor & Francis Ltd Exploring Life Phenomena with Statistical
Book SynopsisIn a living body, a variety of molecules are working in a concerted manner to maintain its life, and to carry forward the genetic information from generation to generation. A key word to understand such processes is water, which plays an essential role in life phenomena. This book sheds light on life phenomena, which are woven by biomolecules as warp and water as weft, by means of statistical mechanics of molecular liquids, the RISM and 3D-RISM theories, both in equilibrium and non-equilibrium. A considerable number of pages are devoted to basics of mathematics and physics, so that students who have not majored in physics may be able to study the book by themselves. The book will also be helpful to those scientists seeking better tools for the computer-aided-drug-discovery. Explains basics of the statistical mechanics of molecular liquids, or RISM and 3D-RISM theories, and its application to water. Provides outline of the generalTable of ContentsGeneral Introduction. Fundamentals: Basic Concepts Related to Statistical Mechanics. Statistical Mechanics of Liquid and Solutions. Dynamics of Liquids and Solutions. Theory of Biomolecular Solvation and Molecular Recognition. Structural Fluctuation and Dynamics of Protein in Aqueous Solutions. Applications of the Theories to In-silico Drug Discovery. References. Epilogue.
£156.75
