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).
General
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