Harnessing Biological Complexity (eBook)

An Introduction to Computational Physiology

Taishin Nomura, Yoshiyuki Asai (Autoren)

eBook Download: PDF

2010 | 2011
X, 190 Seiten
Springer Tokyo (Verlag)
978-4-431-53880-6 (ISBN)

Infos

The challenge for the biosciences in the twenty-first century is to integrate genome sequencing information into a better understanding of biology, physiology, and human pathology. Such attempts at integration are moving the world toward a new generation of bioscience and bioengineering, where biological, physiological, and pathological information from humans and other living animals can be quantitatively described in silico across multiple scales of time and size and through diverse hierarchies of organization - from molecules to cells and organs, to individuals. To 'harness' such complexity, international communities of integrative bioscientists and bioengineers aim to establish frameworks and information infrastructures for describing biological structures and physiological functions on multiple scales of time and space. This textbook includes a public platform to describe physiological functions using mathematical equations and guides the reader to perform mathematical modeling and computer simulations, to combine existing models as well as to create new models. Accessible to biologists, physiologists, and students of the sciences, with illustrative details provided when necessary, this book seeks to achieve a systematic way of harnessing biological complexity. Sharing the databases among communities worldwide will help to find comprehensive answers to all the important questions.

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The challenge for the biosciences in the twenty-first century is to integrate genome sequencing information into a better understanding of biology, physiology, and human pathology. Such attempts at integration are moving the world toward a new generation of bioscience and bioengineering, where biological, physiological, and pathological information from humans and other living animals can be quantitatively described in silico across multiple scales of time and size and through diverse hierarchies of organization - from molecules to cells and organs, to individuals. To "e;harness"e; such complexity, international communities of integrative bioscientists and bioengineers aim to establish frameworks and information infrastructures for describing biological structures and physiological functions on multiple scales of time and space. This textbook includes a public platform to describe physiological functions using mathematical equations and guides the reader to perform mathematical modeling and computer simulations, to combine existing models as well as to create new models. Accessible to biologists, physiologists, and students of the sciences, with illustrative details provided when necessary, this book seeks to achieve a systematic way of harnessing biological complexity. Sharing the databases among communities worldwide will help to find comprehensive answers to all the important questions.

Inhalt

Harnessing Biological Complexity 1
Preface 4
Contents 7
1 Introduction 9
2 Modeling Cellular Dynamics 18
2.1 Ion Channels and Cellular Excitations 18
2.1.1 A Simple Open--Close Kinetics of a Channel Protein 20
2.2 First Encounter with Numerical Simulations of Ordinary Differential Equations 24
2.3 Gating of Ion Channels in the Hodgkin--Huxley Formulation 26
2.3.1 Electro-Chemical Potentials for Cell Membranes 32
2.3.2 Electric Circuit Model of Cell Membranes 36
2.4 Hodgkin--Huxley Formulation of Membrane Excitation 37
2.5 FitzHugh--Nagumo Model 45
2.5.1 More About Numerical Integrations of Ordinary Differential Equations 45
2.6 Examples from Cardiac Muscle Cell Models 49
2.7 Variety of Complex Dynamics of Ion Channels 68
2.8 Variety of Complex Dynamics of Cellular Excitations 76
2.9 Cellular Calcium Dynamics 80
2.10 Bridging Between Different Levels of Modeling:A Preliminary Example 83
3 Dynamics of Cellular Networks 89
3.1 Gap Junctions 89
3.2 Continuous Approximation and Reaction Diffusion Equations 91
3.2.1 Finite Difference Method for Reaction Diffusion Equations 93
3.2.2 Cable Equations and Compartment Models 93
3.2.3 Finite Element Method with Boundary Conditions for Active Transmission Lines 99
3.2.4 Excitation Conduction Through the Whole Heart 119
3.3 Synaptically Connected Neuronal Networks 121
3.3.1 Reciprocal Inhibition and Alternating Rhythms 127
4 Application of ISIDE to Create Models 131
4.1 Brief Introduction of ISML 131
4.2 Getting Started 132
4.3 Model Creations and Simulations on ISIDE 134
4.3.1 Hodgkin--Huxley Model 134
4.3.2 Modularity of a Model 136
4.3.3 Conductance Modules 138
4.3.4 Current Modules 142
4.3.5 Membrane Module 145
4.3.6 Add an External Stimulus Current Generator Model 145
4.3.7 Voltage Clamp Experiment 148
4.3.8 Replacement of Ionic Current Modules 149
4.4 Neural Network Model 152
4.4.1 Two-Coupled BVP Model 153
4.4.2 Three-Coupled FHN Model 161
4.4.3 Middle Scale Neuronal Network Model 168
4.5 Other Model Exchange Formats 186
4.5.1 From Cell to Intracellular Signaling 186
4.5.2 Yet Another Format 194
4.6 Integration of Morphological and Timeseries Data on an ISML Model 195
4.6.1 Visualization of ISML Models 196
4.6.2 PDEs Solved on Morphological Data 197
5 Key Concepts of insilicoML 201
5.1 Overview of Model Representation in ISML 201
5.2 Expressions Used in ISML 1.0 204
5.2.1 Modularity and Linkage Among Modules 204
5.2.2 Edge 206
5.2.3 Module 206
5.2.4 Port 207
5.2.5 Physical-Quantity 207
5.2.6 Capsulation 209
5.3 SBML--ISML Hybridization 209
5.4 Morphological Data and Mathematical Expressions 212
5.4.1 Morphology 213
5.4.2 Partial Differential Equation 216
5.5 Databasing, Tracking, and Relating Models 220
References 223
Index 226

Produkt-Details

• Erscheint lt. Verlag: 13.12.2010
• Reihe/Serie: A First Course in “In Silico Medicine”
• Reihe/Serie: A First Course in “In Silico Medicine”
• Mitarbeit: Herausgeber (Serie): Masao Tanaka
• Zusatzinfo: X, 190 p.
• Verlagsort: Tokyo
• Sprache: englisch
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Mathematik / Informatik ► Mathematik ► Angewandte Mathematik
• Themenwelt: Medizin / Pharmazie ► Physiotherapie / Ergotherapie ► Orthopädie
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Biochemie / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Chemie ► Organische Chemie
• Themenwelt: Technik ► Medizintechnik
• Schlagworte: biological complexity • Complexity • computational approaches to biological phenomena • integration of biological functions • model database • modeling and simulating biological dynamics • physiome, physiology, multi-physics • Simulation
• ISBN-10: 4-431-53880-1 / 4431538801
• ISBN-13: 978-4-431-53880-6 / 9784431538806