Useful Books

The following books are those I think I should read or re-read and would like to recommend to new graduates interested in computational biophysics/biochemistry, especially molecular simulations.


  • Statistical Mechanics, by Donald A. McQuarrie.

  • Statistical Mechanics, Entropy, Order Parameters, and Complexity, by James P. Sethna. [PDF]

  • Statistical Mechanics, by R. K. Pathria & Paul D. Beale.

  • Nonequilibrium Statistical Mechanics, by Robert Zwanzig.

  • Theoretical Concepts in Physics: An Alternative View of Theoretical Reasoning in Physics, by Malcolm S. Longair.

  • 统计物理学 (in Chinese), by 苏汝铿.

  • 热力学与统计物理 (in Chinese), by 汪志诚.

  • 热力学与统计物理 (in Chinese), by 周子舫 & 曹烈兆.

  • Theory of Simple Liquids with Applications to Soft Matter, by Jean-Pierre Hansen and Ian R. McDonald.

  • Capillarity and Wetting Phenomena by Pierre-Gilles de Gennes et al.

  • Soft Mater Physics, by Maso Doi.


  • Molecular Driving Forces, by Ken A. Dill and Sarina Bromberg.

  • Statistical Physics of Biomolecules, by Daneil M. Zuckerman.

  • Protein Physics, by Alexei V. Finkelstein and Oleg B. Ptitsyn.

  • The Theory of Intermolecular Forces, by Anthony Stone.

  • Intermolecular and Surface Forces, by Jacob N. Israelachvili.


  • Polymer Physics, by Micheal Rubinstein and Ralph H. Colby.

  • Polymer Chemistry, by Paul C. Hiemenz and Timothy P. Lodge.

  • Scaling Concepts in Polymer Physics, by Pierre-Gilles de Gennes.


  • Physical Chemistry: Thermodynamic, Structure and Change, by Peter Atkins and Julio de Paula.

  • Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory, by Attila Szabo and Neil S. Ostlund.

  • Molecular Orbitals and Organic Chemical Reactions, by Ian Fleming.

MD & MC:

  • Computer Simulations of Liquids, by Michael P. Allen & Dominic J. Tildesley.

  • Understanding Molecular Simulation: From Algorithms to Applications, by Berend Smit and Daan Frenkel.

  • A Guide to Monte Carlo Simulations in Statistical Physics, by David P. Landau and Kurt Binder.

  • Free Energy Calculations: Theory and Applications in Chemistry and Biology, Editors: Ch. Chipot and A. Pohorille.

Markov State Models:

  • An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, Editors: Gregory R. Bowman, Vijay S. Pande and Frank Noé.


  • Molecular Biology of the Cell, by Alberts, Johnson, Lewis, Morgan Raff, Boberts and Walter.

  • Cell Biology by Pollard, Earnshaw, Lippincott-Schwartz and Johnson.

  • Pricinples of Biochemistry, by David L. Nelson and Michael M. Cox.

Computer Science:

  • Algorithms in C, by Robert Sedgewick.

  • Gaussian Processes for Machine Learning, by Carl Edward Rasmussen & Christopher K. I. Williams.

  • 统计学习方法 (in Chinese), by 李航.

  • 机器学习 (in Chinese), by 周志华.

  • C 语言点滴(in Chinese), by 赵岩.


[To be updated]