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I'm doing an undergrad research project that lies at the intersection of biology and nonequilibrium thermodynamics, but I'm starting to realize almost none of my equilibrium thermo/stat mech knowledge carries over.

What's a good book on this subject that covers both near-equilibrium (e.g. linear response) results, as well as more recent far-from-equilibrium (e.g. Jarzynski and Crooks equalities) results? Coverage of nonequilibrium steady states and simulation methods is a plus.

I'm going for a physical understanding, not complete mathematical rigor; I know real/complex analysis but not, say, probability theory or functional analysis.

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    $\begingroup$ I won't give any recommendations but I will give a warning. Non-equilibrium thermodynamics is, for the most part, an ad-hoc discipline. Whether any particular Ansatz works for a particular problem is only validated by the results of the specific experiment one is doing. My understanding is that many problems in biophysics (like protein or DNA/RNA folding/unfolding, optical tweezers etc.) are essentially random walks in a fixed low dimensional effective potential. This is a very special subset of much harder non-equilibrium problems which show phase transitions and dimensionality changes. $\endgroup$
    – CuriousOne
    Commented Jan 1, 2016 at 7:16

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You may want to check 'Elements of Non-Equilibrium Statistical Mechanics' by V. Balakrishnan. The book does not cover too large a ground but focuses on the basic probabilistic tools of the subject. It has plenty of appendixes to help the reader not get distracted by technical details. Its most appealing attribute is that it makes the reader feel that the subject follows logically from known basic physics instead of making a leap into the subject by starting from Onsager relations and the likes.

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I am sure there are more complete or simpler books on the topic, but I found very enlightening to read the first chapter of Puri's book on Kinetics of Phase Transitions. In particular, I think this is a book written by a researcher which works with phase transitions of mixtures, which can be particularly relevant for those studying non-equilibrium physics in biological systems. He works in India, but I found a version of the first chapter in this link from University of Kentucky: http://www.pa.uky.edu/~murthy/INES2011Kolkata/Lectures/Sanjay-Puri-Ch1.pdf. The book is aimed in researchers but I would say that the first lines might be useful for getting a general picture of the main universal steps involved in the non-equilibrium analysis of thermodynamic systems.

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Nonequilibrium Statistical Mechanics by Robert Zwanzig (of "Zwanzig equation" fame although that is not the topic of this book) has to be included in this list, as he is one of the pioneers of the field. The book is from 2004, so it's not an "old book".

It covers, Langevin equations, deriving several versions of the fluctuation dissipation Theorem, Fokker-Planck and Master equations, the protection operator formalism that he introduced for separating out slow deg. of freedom and much more.

Mentioning topics quickly becomes too much, so I'll just say that the book is very short (~220 pages of content) but covers a lot of ground quickly.

Which is also one of the downsides of the book, while the theory is developed from examples to more general ideas, not much time is spent on defining the mathematical objects we are dealing with, which was often confusing to me. It does not have exercises and is really aimed at a self sufficient reader.

This is in my opinion a hard book, but if you're a researcher it may be a great source, I am planning to revisit it some day with some functional analysis up my sleeve so I can follow everything, it gets very complex very fast so don't be fooled by the first few pages.

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