| |
Description: Designed for biology, physics, and medical students, Introductory Biophysics: Perspectives on the Living State, provides a comprehensive overview of the complex subject of biological physics. The accompanying CD-ROM, which contains MATLAB® examples and the fully functional student version of QuickField™ 5.7, allows the student to perform biophysical simulations and modify the textbook example files.
The text includes many computer models and simulations of biophysical phenomena such as thermodynamics, astrobiology, the response of living cells to external fields, chaos in population dynamics, numerical models of evolution, electrical circuit models of cell suspensions, gap junctions, and neuronal action potentials. Using this text students will be able to perform biophysical simulations within hours.
Key Features:
• Designed to prepare students for practical applications of physics that they will encounter in the fields of biology and medicine.
• Using MATLAB and Quickfield, computer models allow for hands-on investigation of problems relevant to biophysics, such as modeling biophysical processes and dynamics
• Includes cutting-edge material in complexity, space biology, and astrobiology
• Includes a CD-ROM with biophysical lab simulations, example files, 4-color figures from the text, articles from experts in the field, and the fully functional student version of QuickField 5.7
MATLAB examples on the CD-ROM and in the text include:
• The Hodgkin Huxley equations
• The FitzHugh-Nagumo model of action potentials
• Fractal structures in biology
• Chaos in population dynamics
• The cellular automaton model - the game of life
• Pattern formation in reaction-diffusion systems
QuickField tutorials and examples on the CD-ROM include:
• Calculation of currents in biological tissue
• Cells under electrical stimulation
• Induced membrane potentials
• Heat transfer and analysis of stress in biomaterialsContents: Chapter 1: Building Blocks and Structure • Atoms and Ions • Subatomic Particles • Atomic Constituents of Life Ions • Molecules Essential for Life • Water • Proteins • Lipids • Carbohydrates • Cholesterol • Nucleic Acid • What Is Life? • Requirements for Life • Domains of Life • Characteristics of Living Cells • Structure of Living Cells • Boundary of Life
Chapter 2: Living State Interactions • Forces and Molecular Bonds • Ionic Bonds • Covalent Bonds • Hydrogen Bonds • Van der Waal Forces • Electric and Thermal Interactions • Electric Dipoles • Polarization and Induced Dipoles • Casimir Interactions • Domains of Physics in Biology • Exercises
Chapter 3: Heat Transfer in Biomaterials • Heat Transfer Mechanisms • Conduction • Convection • Radiation • The Heat Equation • Transient Heat Flow • Steady State Heat Flow • Joule Heating of Tissue • Exercises
Chapter 4: Living State Thermodynamics • Thermodynamic Equilibrium • First Law of Thermodynamics and Conservation of Energy • Entropy and the Second Law of Thermodynamics • Does Life Violate the Second Law? • Measures of Entropy? • Free Expansion of a Gas • Physics of Many Particle Systems • How Boltzmann Factors in Biology • Canonical Partition Function • Average Energy • Entropy and Free Energy • Heat Capacity • Two-State Systems • Continuous Energy Distribution • Composite Systems • DNA Stretching • Casimir Contribution to the Free Energy • Lipid Bilayer Tubes • Rouleax • Protein Folding and Unfolding • Protein Unfolding • Levinthal’s Paradox • Energy Landscape • Folding on a Lattice • Monte Carlo Methods • Folding @ home • Exercises
Chapter 5: Open Systems and Chemical Thermodynamics • Enthalpy, Gibbs Free Energy, and Chemical Potential • Chemical Reactions • First-Order Reactions • Second-Order Reactions • Activation Energy and Rate Constants • Detailed Balance • Nitrogen Fixation • Enzymatic Reactions • ATP Hydrolysis and Synthesis • Entropy of Mixing • The Grand Canonical Ensemble • Hemoglobin • Exercises
Chapter 6: Diffusion and Transport • Maxwell-Boltzmann Statistics • Brownian Motion • Fick’s Laws of Diffusion • Fick’s First Law • Fick’s Second Law • Quantum Diffusion • Time-Independent Concentrations • Fick’s Law for Growing Bacterial Cultures • Sedimentation of Cell Cultures • Diffusion in a Centrifuge • Diffusion in an Electric Field • Lateral Diffusion in Membranes • Navier-Stokes Equation • Reynolds Number • Low Reynolds Number Transport • Purcell’s “Life at Low Reynolds Number” • Coasting Distance of a Bacterium • Active and Passive Membrane Transport • Exercises
Chapter 7: Fluids • Laminar and Turbulent Fluid Flow • Bernoulli’s Equation • Equation of Continuity • Venturi Effect • Fluid Dynamics of Circulatory Systems • Viscous Flow • Vessel Constriction and Aneurysm • Variation of Blood Pressure with Depth • Microgravity Effects • Capillary Action • Exercises
Chapter 8: Bioenergetics and Molecular Motors • Kinesins, Dyneins, and Microtubule Dynamics • Brownian Motors • Feynman Ratchet • Kinesin Brownian Dynamics • Myosin Brownian Dynamics • ATP Synthesis in Mitochondria • Electron Transport Chain • ATP Synthase • Torque Generation in ATP Synthase • Photosynthesis in Chloroplasts • Photosystem II • Photosystem I • Light Absorption in Biomolecules • Vibrational Spectra of Biomolecules • Square Well Potential • Harmonic Oscillator Potential • Exercises
Chapter 9: Passive Electrical Properties of Living Cells • Poisson-Boltzmann Equation • One-One Valent Electrolytes • Low Field Limit • Spherical Solution • Intrinsic Membrane Potentials • Induced Membrane Potentials • Plasma Membrane • Liposome in a Static Electric Field • Spherical Cell in an Alternating Electric Field • Inertial Effects in Field-Induced Counterion Motion • Induced Potentials in Organelle Membranes • Mitochondrion in an Alternating Electric Field • Bioimpedance • Time Harmonic Current Flow • Dielectric Spectroscopy • Deybe Relaxation Model • Cole Equation • Maxwell-Wagner Effect • Skin Impedance • Electrode Polarization • Bioimpedance Simulator • Nonlinear Effects • Exercises
Chapter 10: Nerve Conduction • Nerve Impulses • Neurotransmitters and Synapses • Passive Transport in Dendrites • Active Transport and the Hodgkin-Huxley Equations • Simulation of Action Potential • Excitation Threshold • Neuronal Refactoriness • Repetitive Spiking • FitzHugh-Nagumo Model • Action Potentials in the Earthworm Nerve Fiber • Exercises
Chapter 11: Mechanical Properties of Biomaterials • Elastic Moduli • Young’s Modulus • Shear Modulus • Poisson’s Ratio • Electric Stresses in Biological Membranes • Mechanical Effects of Microgravity During Spaceflight • Exercises
Chapter 12: Biomagnetism • Biomagnetic Field Sources • Current Dipole Model • Vector Potential Formulation • Nerve impulses • Magnetotactic Bacteria • SQUID Magnetometry • Josephson Effect • Flux-Locked Loop • Intrinsic Noise Factors Extrinsic Noise Factors • Digital Filters • Magnetocardiography • Fetal Magnetocardiography • Magnetoencephalography • Exercises
Chapter 13: Nonlinearity and Chaos in Biological Systems • Chaotic Dynamics • Characteristics of Chaotic Dynamics • Sensitive Dependence on Initial Conditions • Phase Space • Phase Space Reconstruction • Poincare Sections • Lyapunov Exponents • Power Spectra • Population Growth in a Limited Environment • Predator-Prey Models of Population Dynamics • Discrete Logistic Equation • Period-Doubling Route to Chaos • Bifurcation Diagrams • Lyapunov Exponent of the Logistic Equation • Shannon Entropy • Chaos in the Heart • Reaction Diffusion Equations • Action Potentials • Fertilization Calcium Waves • Pattern Formation • Dynamics of the Driven Hodgkin-Huxley System • Models of DNA Motility • Exercises
Chapter 14: Fractals and Complexity in the Life Sciences • Fractal Geometry • Computing Fractal Dimension • Fractal Structures in Biology • Fractal Ferns • Diffusion-Limited Aggregation • Power Laws in Biology • Self-Organized Criticality • BTW Sandpile Model • Extinction in the Bak-Sneppen Model • Power Law Behavior in Chemical Reactions • The Game of Life • SOC in the Game of Life • Exercises
Chapter 15: Life and the Universe • Astrobiology • Extremophiles • Primordial Soup, Interstellar Gas, and Dust • The Miller Experiment • Chemistry of the Interstellar Medium • Searches for Life in the Solar System • Mars • Europa • Lake Vostok • Search for Life Outside the Solar System • Extrasolar Planets • SET! Initiatives • Anticoded Signals • Frequency Domain Searches • Radio Interferometry • The Drake Equation • Implications for Life in the Multiverse Picture • The Multiverse • The Anthropic Principle • Multiverse Cosmological Models • Exercises
Appendix 1: Mathematical Formulas • Appendix 2: Overview of MATLAB@ • Appendix 3: Derivation of the Heat Equation • Appendix 4: Derivation of Shannon’s Entropy Formula • Appendix 5: Thermodynamic Identities • Appendix 6: Kramers-Kronig Transformations • Appendix 7: Solution to the One-Dimensional Schrodinger Equation • Appendix 8: Biophysical Applications of QuickField™ • Appendix 9: Biological Material Properties • Appendix 10: Solutions of the Linearized Poisson-Boltzmann Equation • References and Further Reading • IndexISBN - 9789380853222
|
| |
Pages : 376
|