New Type of Work Unit and New Team Members for FightAIDS@Home - Phase 2

New Work Units

For the past year and a half, the research team at Temple University has worked closely with the World Community Grid software developers (particularly Keith Uplinger and Jonathan Armstrong) to create and implement a simulation scheme that more closely mimics the simulations run on non-grid computing resources. This new sampling protocol is called asynchronous replica exchange.

How Asynchronous Replica Exchange Works

Previous Process: Multiple copies of a protein-ligand complex (the structure consisting of a drug candidate compound docked with a protein receptor) were sent out to many volunteers and are simulated with no interaction with one another. The collective information from all those simulations are combined during analysis at the very end.

New Process: Asynchronous replica exchange allows information from the different copies to be shared and exchanged among all copies dynamically after the simulations. This process yields the correct equilibrium statistical physics needed for our analysis.

Asynchronous replica exchange drastically increases the efficiency of the computations. This means that, in addition to being more valuable in terms of analysis, the number of batches running simultaneously can be increased and each batch will have shorter total simulation times.

We first protoyped this new technique on our own BOINC-powered grid at Temple University. Over the past year and a half, the World Community Grid software developers have worked with us to test, refine, and now to implement the same technique on the World Community Grid platform. This effort is the largest replica exchange simulations (by two orders of magnitude) ever performed.

For more information about this work, see these two articles:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.23996/abstract

http://www.sciencedirect.com/science/article/pii/S0010465515002556

New Team Members

We’re excited to welcome four new members of the Levy Group as research team members for the FightAIDS@Home project.

• Bin Zhang is an associate research professor from Ron Levy's Group at Temple University. He holds a Ph.D degree in physics from the University of Pittsburgh. Bin joined Dr. Levy's group in 2013. His research focuses on developing advanced sampling and reweighting algorithms in biophysics and computer simulations.

• Dr. Di Cui is a computational chemist with an interest in biomolecular modeling. Currently, he is an assistant research professor in the Department of Chemistry, Center for Biophysics and Computational Biology, Temple University. His research has been focused on understanding the mechanisms and estimation the binding affinity of small-molecule ligands to protein active sites using molecular dynamic simulations. His current work involves the application of molecular modeling techniques to analyze the binding affinities to the target proteins, with the goal to design new ligand molecules that could serve as leads and optimized compounds for drug discovery.

• Avik Biswas is currently a Ph.D (Physics) student in the Ron Levy group at Temple University, Philadelphia. Prior to joining the Levy group in 2016, Avik completed his Integrated BS-MS from the Indian Institute of Science Education and Research (Bhopal, India) where his research involved using molecular dynamics and ab initio methods (Density Functional Theory) to understand the mechanics of rolling graphene. Currently, his research is focused on using Potts Hamiltonian models of protein evolutionary fitness to study the inter-relations between protein sequence, structure, and fitness, with a particular interest in the evolution of drug resistance in HIV.

• Shima Arasteh is a Ph.D student from Ron Levy's group at Temple University. She holds a bachelor's degree in physics and a master's degree in biophysics from the University of Tehran. Before joining Dr. Levy's group in 2015, her research focused on the functions and stability of membrane ion channels. Currently, she is studying the conformational transitions of protein kinases, and developing advanced algorithms to measure the free energy changes of these transitions.

Thank you to everyone who is supporting FightAIDS@Home. We couldn’t do it without your donated computing power.