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This textbook originated from the course "Simulation, Modeling, and Computations in Biophysics" that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).
Representation of molecular systems
Equilibrium statistical mechanics
Solvation free energy
Implicit solvent and continuum models
Binding equilibrium
Dynamics and time correlation functions
Effective dynamics of reduced models
Diffusion and time evolution of probability distribution
Transition rates
Dynamics of discrete state models
Stochastic simulations
Molecular machines