Reddit reviews Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Edition

Dill and Bromberg's Molecular Driving Forces is a good intro book that basically builds up from rudimentary math/chem/physics to a basic understanding of rates, diffusion and random walk processes, folding mechanisms, and stat mech. This would be very helpful for you, as Dill is known for his work on energy landscapes of protein folding and conformation.

A good introductory text on the statistical mechanics of biopolymers (including a number of models of DNA) is Ken Dill's Molecular Driving Forces. Much of it is undergraduate level, and it will necessarily include simple models that are primarily pedagogical, but they are nonetheless incredibly useful tools for connecting to the literature in a deeper way. For example, two state models can deliver some surprising results despite how simple they are -- such models show up in the literature in the form of elastic network models (ENMs), where two well-defined configurations are used to construct harmonic approximations to the state space. These can then be used to model transitions between states across the potential surface. ENMs aren't as relevant to DNA, as far as I know (I work on a membrane transporter at the moment), but is representative of the simpler tools used in the field.

Additionally, Rob Phillips has some very useful texts (that emphasize an intuition of the length- and time-scales involved): Physical Biology of the Cell and Cell Biology by the Numbers.

Hope that helps!

Ken Dill has the easiest to follow stat mech book I have encountered. McQuarrie has lots of good problems to work through. David Chandler is the shortest, and simultaneously most brilliant and difficult work on the subject I have read. His brief review of thermodynamics in the first couple chapters is fantastic if you only have a day or two to get back on the horse.