Statistical Biophysics Blog
by dmz
3M ago
So you know about molecular biophysics and want to think about cells. How should you get started? Let’s take the first few steps. We’ll start with some concepts that should be familiar: coordinates and equilibrium vs. nonequilibrium behavior. We can frame our discussion by comparing something familiar, a protein, to a cell. Conceptual hierarchy of ..read more
Statistical Biophysics Blog
by dmz
1y ago
When we want to estimate parameters from data (e.g., from binding, kinetics, or electrophysiology experiments), there are two tasks: (i) estimate the most likely values, and (ii) equally importantly, estimate the uncertainty in those values. After all, if the uncertainty is huge, it’s hard to say we really know the parameters. We also need to ..read more
Statistical Biophysics Blog
by dmz
2y ago
I think of knowledge like a house: it’s assembled from bricks that separately don’t do much. On its own, each brick is more prone to weathering. Likewise, each of our calculation bricks is easy to forget. We must learn to put these in context. We must always seek the connections to build a stronger house ..read more
Statistical Biophysics Blog
by dmz
2y ago
Three states – now that is exciting! And I’m not kidding. You are poised to understand critical timescales in non-equilibrium statistical mechanics. We have been studying the linear three-state system. Let’s quickly go over the answers from last time. Write down the ODEs for this system. These are a straightforward generalization of the two-state case ..read more
Statistical Biophysics Blog
by dmz
2y ago
I think self-confidence is an essential ingredient of doing well in science, but it’s not discussed enough. I have thought about confidence a lot because I don’t always have it. I’m over 50 years old and have published plenty of papers, but often enough I doubt myself. I have this intermittent, but deep-seated worry that ..read more
Statistical Biophysics Blog
by dmz
2y ago
Markov state models (MSMs) are very popular and have a rigorous basis in principle, but applying them in practice must be done with great caution. There is no guarantee the results will be reliable for complex systems of typical interest unless there is an enormous amount of data and significant expertise and validation goes into ..read more
Statistical Biophysics Blog
by dmz
2y ago
Count me among the weak of science. Here I am again, feeling defensive, irate at reviewer critiques of our recent sub-Nobel prize work. Only in this case, the reviews are in my mind, yet to arrive. In fact, we haven’t even drafted the paper yet! But I can foresee what will happen. After all, if ..read more
Statistical Biophysics Blog
by dmz
2y ago
Many scientists say they dislike writing, but I want to persuade you not to be one of them. Writing not only is the way to convince folks how important your work is, but it can be a key part of doing good science in the first place. Your work must be explainable in a concise ..read more
Statistical Biophysics Blog
by dmz
2y ago
Did you know that you can significantly change women’s performance on a challenging math test simply by providing a different explanation of the purpose of the test up front? And the same for Black students? Did you know there are ways to give advice and feedback that are demonstrated to improve performance in groups that ..read more
Statistical Biophysics Blog
by dmz
2y ago
The key lesson of all these exercises is that you can push yourself to be better and more confident in theory by tackling simple, paradigmatic problems in an incremental way. You must put pencil to paper! You must do it regularly. But once you do, the benefits come quickly. Each mini-realization builds into knowledge. Each ..read more

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