Cover; Biosimulation; Series; Title; Copyright; Contents; Preface; Extracts; 1: Introduction to simulation of biological systems; Overview; 1.1 Modeling approaches; 1.2 An introductory example: biochemistry of a home aquarium; 1.2.1 First model: a nonmechanistic analysis; 1.2.2 Nonmechanistic analysis with noise; 1.2.3 Mechanistic modeling; 1.3 Recapitulation and lessons learned; Problems; 2: Transport and reaction of solutes in biological systems; Overview; 2.1 Well-mixed systems: compartmental modeling; 2.2 Passive flow of water, solutes, and electrical current across membranes.2.2.1 Basic equations2.2.2 Example: volume changes in isolated glomeruli; 2.3 Simulating chemical reactions; 2.3.1 Example: synthesis of ethanol from xylose; 2.4 Distributed transport modeling; 2.4.1 Flowing systems: the advection equation; 2.4.2 Reaction-diffusion systems; 2.4.3 Advection-reaction-diffusion systems; 2.5 Recapitulation and lessons learned; Problems; 3: Physiologically based pharmacokinetic modeling; Overview; 3.1 Introduction to lumped compartmental PBPK modeling; 3.1.1 Basic equations; 3.1.2 Comparison of distributed and lumped transport models.3.1.3 Quasi-steady model reduction3.1.4 Lumped versus distributed transport modeling: a final word; 3.2 Overview of the mammalian circulatory system; 3.3 Whole-body PBPK simulation; 3.4 Example: uptake and delivery of matrine in rat; 3.4.1 A PBPK model for rat; 3.4.2 Model parameters; 3.4.3 Flow-limited transport; 3.4.4 Model validation and discrimination; 3.5 Recapitulation and lessons learned; Problems; 4: Cardiovascular systems simulation; Overview; 4.1 The Frank-Starling mechanism of heart; 4.2 An analysis of the physiological factors that control cardiac output.4.2.1 Guyton's model of the systemic circulation4.2.2 What the model tells us about the relationship between flow and right atrial pressure; 4.2.3 How the simple Guyton model is commonly misinterpreted; 4.3 Pulsatile mechanics of the circulatory system; 4.3.1 Time-varying elastance models of the heart; 4.3.2 Simulation of the aortic pressure waveform; 4.4 Dynamic changes in blood pressures and flows; 4.4.1 Baroreceptor control of systemic pressure; 4.5 Mechanisms of hypertension; 4.6 Recapitulation and lessons learned; Problems.5: Chemical reaction systems: thermodynamics and chemical equilibriumOverview; 5.1 Temperature, pressure, and entropy; 5.1.1 Microstates and macrostates; 5.1.2 Example: a simple two-state system; 5.1.3 Relationship between temperature and entropy; 5.1.4 Relationship between pressure and entropy; 5.2 Free energy under constant-temperature and constant-volume conditions; 5.3 Free energy under constant-temperature and constant-pressure conditions; 5.4 Thermodynamic ensembles, partition functions, and driving forces; 5.5 Chemical reactions, stoichiometry, and equilibrium constants; 5.6 Acids, bases, and buffers.