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If you want a textbook, I would recommend one of two books:

Biological Physics by Philip Nelson is a pretty good starting point. The author tried to write a book that is both as accessible as possible and introduces only the most important topics. He covers a lot of interesting, but important material like random walks and molecular machines assuming that the reader does not have a very strong background in either biology or physics. The advantage to this is that he covers only the most important ideas, and in a way that someone with only introductory physics and calculus can understand. The downside is that some of the results are not general, focussing on one dimension instead of three for example, and for the experienced his introductions can be a little redundant. Nelson tries to get around this by having an optional “Track 2” that goes into greater detail and looks are tough problems and original papers.

Physical Biology of the Cell by Rob Phillips is also very good. This book is much longer than the Nelson book and goes into greater detail on a lot of the material. Where Nelson was trying to include only the most important topics, Phillips tries to include everything. The upside is that this book covers more examples and often includes more general results, but it makes for a long read at over a thousand pages. A fairly strong background in some higher level physics, like knowing how to set up and use a partition function, makes reading this book much easier.

I personally like the Phillips book more than the Nelson book, but it depends on where you are at in your major. If you have just taken introductory physics, the Nelson book might be better, if you have taken some higher level courses (especially thermodynamics/statistical mechanics) the Phillips book would be better. Either way I recommend checking them out from the library before you buy them.

Edit: How could I forget this little gem: Can a Biologist Fix a Radio? by Lazebnik. If you want a nice introduction into the philosophy of biophysics, I strongly recommend this well written article.

Let me recommend An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon. This book is extremely well-written and approaches cellular systems from the perspective of an engineer or physicist. It will help to orient you to the "big picture" of how cells work without swamping you in molecular details. Systems biology is a hot, emerging field at the intersection of molecular biology, biophysics, and computational biology. Feel free to PM me if you're interested in the field and want a few suggestions about which are the top labs.

I would recommend getting more information about the molecular details elsewhere. I haven't read Alberts, but it seems like a classic text (I often see it on bookshelves). I read Watson's Molecular Biology of the Gene, and thought it was quite good.

For a biochemical perspective, I recommend Stryer's Biochemistry, which covers many common biological molecules. It is a very readable classic and serves as a good reference text. It should give you an idea of how the molecular machines operate on a chemical level.

You can probably find these in your school's library.

Edit: Just realized this post is 3 months old (hah). Hope this helps nevertheless.

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!

I've read a couple books in the past and think [this one by Andrew Leach] (https://www.amazon.com/dp/0582382106/ref=pd_lpo_sbs_dp_ss_1?pf_rd_p=1944687722&pf_rd_s=lpo-top-stripe-1&pf_rd_t=201&pf_rd_i=0122673514&pf_rd_m=ATVPDKIKX0DER&pf_rd_r=RBQQJGVYTNCM7XBM7SF3) is the best one, for use as a good intro and also as a reference. It's actually a surprisingly engrossing read.

I highly recommend Molecular Biology of the Cell. This is a graduate level cell/molecular bio book and goes into pretty good detail on a ton of topics. I know a ton a people with a Physics background who used this book to get a knowledge basis in bio (myself included).

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.

My favorite undergrad course that I ever took was biophysics (under the physics dept). The course used this textbook: http://www.amazon.com/Physical-Biology-Cell-Rob-Phillips/dp/0815344503/ref=dp_ob_title_bk. I highly recommend it for a first look at biophysics.

http://www.amazon.com/Molecular-Driving-Forces-Statistical-Thermodynamics/dp/0815320515

this book was great when I took statistical thermodynamics which deals with everything you discussed.

McQuarrie's Stat. Mech. text would likely serve you well...

http://www.amazon.com/Channels-Excitable-Membranes-Third-Edition/dp/0878933212