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The book of Lectures in Theoretical Biophysics is organized into 18 chapters, which are: Introduction; Dynamics under the In uence of Stochastic Forces (Newton's Equation and Langevin's Equation, Stochastic Differential Equations, How to Describe Noise, Ito calculus, Fokker-Planck Equations, Stratonovich Calculus, Appendix: Normal Distribution Approximation:Stirling's Formula & Binomial Distribution); Einstein Diffusion Equation (Derivation and Boundary Conditions,Free Diffusion in One-dimensional Half-Space, Fluorescence Microphotolysis, Free Diffusion around a Spherical Object, Free Diffusion in a Finite Domain, Rotational Diffusion); Smoluchowski Diffusion Equation; Random Numbers ; Brownian Dynamics; The Brownian Dynamics Method Applied; Noise-Induced Limit Cycles; Adjoint Smoluchowski Equation Rates of Diffusion-Controlled Reactions (The Adjoint Smoluchowski Equation, Correlation Functions) ; Ohmic Resistance and Irreversible Work (Relative Difusion of two Free Particles, Diffusion-Controlled Reactions under Stationary Conditions); Smoluchowski Equation for Potentials: Extremum Principle and Spectral Expansion; The Brownian Oscillator; Fokker-Planck Equation in x and v for Harmonic Oscillator; Velocity Replacement Echoes; Rate Equations for Discrete Processes; Generalized Moment Expansion; Curve Crossing in a Protein: Coupling of the Elementary Quantum Process to Motions of the Protein (Introduction, The Generic Model: Two-State Quantum System Coupled to an Oscillator, Two-State System Coupled to a Classical Medium, Two State System Coupled to a Stochastic Medium, Two State System Coupled to a Single Quantum Mechanical Oscillator, Two State System Coupled to a Multi-Modal Bath of Quantum Mechanical Oscillators, From the Energy Gap Correlation Function
E[R(t)] to the Spectral Density J(w), Evaluating the Transfer Rate, Appendix: Numerical Evaluation of the Line Shape Function