Time for an #introduction! I'm a PhD candidate in #computational #biophysics working on Markov analysis of molecular dynamics #simulations. I also work on weighted ensemble enhanced sampling, and am a core maintainer of the WESTPA project. I do a lot of work with #HPC and #supercomputing clusters as well.
I'm really passionate about bringing best practices from the software development world into computational research!
I love playing with software, and I like playing with #selfhosting a number of services on my #homelab servers, from . Current setup is a Thinkpad laptop that runs the essential services, and a Supermicro quad-socket server with 4x E7-4870s for the fun stuff.
Also really into DIY, including #3Dprinting, #smarthome stuff and #homeassistant -- I spent a couple months designing and building a smart thermostat with a wireless remote thermometer from scratch because my WFH desk was close to a window and got too cold.
#science #computationalchemistry #simulation #selfhost #DIY #linux #supercomputers #technology
@quasifrodo what does a Markov analysis of molecular dynamics simulations look like? I know what Markov chains are and how (some) molecular dynamics simulations work.
@gaymanifold Thanks for asking :D I do Markov state modeling where you take your simulation data, discretize it, and then construct a transition matrix. Very similar to Markov chains
Lots of room for flexibility in the discretization -- usually looks like some sort of featurization + dimensionality reduction, then clustering in that latent space.
Once you have the transition matrix, you can do things like estimate rate constants by computing fluxes into certain states, or estimate splitting probabilities/committors