New article in Frontiers Journal on using machine learning to tune force field parameters for disordered protein systems

Congrats to Dr. Omar Demerdash on his first author paper to be published in the journal, Frontiers in Molecular Biosciences — Bimolecular modeling and simulations.

Our paper applies the ForceBalance approach (source code link: https://github.com/leeping/forcebalance), developed by Lee Ping Wang and colleagues, to refine force field parameters for intrinsically disordered protein (IDPs) ensembles.

The paper is a collaboration with the Center for Molecular Biophysics at Oak Ridge National Laboratory (Drs. Julie Mitchell, Jeremy Smith and Loukas Petridis).

This research was inspired by the fact that traditional experimental techniques such as NMR or X-ray crystallography find it challenging to resolve all of the structural diversity of IDPs.

Biophysical Journal cover!

Congrats to Dr. Blake A. Wilson @ Vanderbilt for making the cover of the Biophysical Journal! Working with Dr. Carlos Lopez, we utilized microsecond timescale simulations of cardiolipin membranes (at various concentrations) to understand the mechanisms of how it affects the membrane structure and dynamics. You can check out the cool image here: https://www.cell.com/biophysj/issue?pii=S0006-3495(18)X0017-4

Our article was also highlighted on the Biophysical Society Blog. Here is a link to the cover and its description on BPS Blog.

Code from the paper as part of the PyBILT toolkit is here: http://pybilt.readthedocs.io/en/latest.

Paper in Journal of Parallel and Distributed Computing (JPDC) is accepted!

Congrats to Michael T. Young (Todd) for getting his first author paper accepted to the Journal of Parallel & Distributed Computing (JPDC). The paper focuses on the use of HyperSpace, our distributed Bayesian hyper parameter optimization (HPO) approach for optimizing reinforcement learning algorithms. Joint work with M. T. Young, R. Kannan and J. D. Hinkle (all at Oak Ridge National Lab). The final copy of the paper will be available shortly!

Check out the code at: http://www.github.com/yngtodd/hyperspace for HyperSpace.

You can check out the repo: http://www.github.com/yngtodd/hyperpoints for the experiments run in our paper.

Hello from Argonne National Laboratory!

After nearly 8 years at Oak Ridge National Laboratory, TN, the Arvind Ramanathan Lab has moved to Argonne National Laboratory, IL. We are looking forward to expanding our research in the areas of computational biology through close knit interactions with both biologists and computer scientists. Using AI, we plan to advance our knowledge of how IDPs function.

We have various openings in the lab. If interested please leave me a message in the blog through contact page.

Thank you.