« Announcement: DIMACS/DyDAn Workshop on Computational Methods for Dynamic Interaction Networks | Main | Things to read while the simulator runs; part 5 »

July 05, 2007

Boulder School on Biophysics

Blogging this month will be light as I'm attending the Boulder School on Biophysics (ostensibly the Boulder School is about condensed matter, but the main topic changes each year and this year it's about squishy (soft) condensed matter). The talks so far remind me of how much easier good modeling is when you're constrained to 3 spatial dimensions and basically know what kind of forces you'll need to deal with in order to get relatively realistic behavior (at a variety of levels of realism). In the world of networks, we don't have these kinds of constraints and so coming up with reasonable mechanisms is significantly harder. As with biology, the data analysis for networks has advanced much more quickly than has the theory, precisely, I imagine, for this reason. Later in the school, there will be some presentations on micro-biological networks, which I'm looking forward to. These systems seem like more reasonable objects for good modeling than are things like the Internet, since we can actually do controlled experiments on many of them to see how well the theories hold up.

A few things I've learned so far.

Chromosomes seem to behave a lot like jointed chains wiggling around in solution, and yet they also tend to maintain their position inside the nucleus, suggesting some sort of tethering behavior -- a behavior that has been implicated as a mechanical gene-regulation mechanism. Similar tethering behavior seems to appear in prokaryotic cells as well. There's the suggestion that spatial location of genes has an important role in their expression levels and general regulation (a result known by experimental micro-biologists, but not well understood theoretically).

Histones (those bits of protein that DNA wraps itself around at regular intervals over the entire length of the chromosome) are also implicated in regulation, basically by making it more difficult to transcribe a gene when its start codon is in the middle of one of the turns around the histone; also, histones seem to have a preferred sequence of DNA for binding; the suggestion is that the copious amounts of repeated sequences in the genome may be related to binding these objects in a regular fashion.

Motor proteins are fascinating squishy things. Your muscles are composed of large quantities of myosin motor proteins that crawl along actin filaments by exerting a tiny force of a few tens of pico-newtons (it would take tens of billion of these to exert the equivalent force that the Earth exerts on an apple).

posted July 5, 2007 07:37 PM in Things that go squish | permalink