Computational biophysical modeling and simulation group in the Department of Chemistry at Temple University
Undergraduate Shahlo Solieva has been awarded a CARAS travel grant to attend the 64th Annual Meeting of the Biophysical Society in San Diego, CA. Shahlo presents her work, “Using Molecular Simulation to Understand the Role of Conserved Residues in an Extremophilic Beta-Galactosidase”, on February 18.
Congratulations Shahlo!
Congrats to Hongbin, Yunhui and Asghar on the publication our new paper on inferring conformational ensembles from MD and HDX, now out in the Journal of Chemical Theory and Computation! In this work, we used biased molecular dynamics (MD) simulations to construct a series of Markov Models which are then refined against hydrogen deuterium exchange (HDX) protection factor data using our Bayesian Inference of Conformational Populations (BICePs) algorithm. As part of this work, we also had to develop a new model to predict HDX protection factors from molecular simulation data. As an example, we apply this approach to modeling the partially disordered regions of apomyoglobin.
You can read the full paper here: https://pubs.acs.org/doi/10.1021/acs.jctc.9b01240
Hot off the press is our new paper on adaptive seeding in Journal of Chemical Physics. Congrats, Hongbin!
Hongbin Wan and Vincent A. Voelz. Adaptive Markov state model estimation using short reseeding trajectories. J. Chem. Phys. 152, 024103 (2020); https://doi.org/10.1063/1.5142457
ABSTRACT
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow time scales. A promising approach to enhanced sampling of MSMs is to use “adaptive” methods, in which new MD trajectories are “seeded” preferentially from previously identified states. Here, we investigate the performance of various MSM estimators applied to reseeding trajectory data, for both a simple 1D free energy landscape and mini-protein folding MSMs of WW domain and NTL9(1–39). Our results reveal the practical challenges of reseeding simulations and suggest a simple way to reweight seeding trajectory data to better estimate both thermodynamic and kinetic quantities.
Yunhui Ge has been selected to receive the 2019 Francis H. Case Fellowship Award for outstanding graduate research. The Case Fellowship was established several years ago as a memorial to Professor Francis Case, a truly distinguished member of the Department of Chemistry. It was designed to help outstanding graduate students as they pursue their dissertation research.
Congratulations Yunhui!
The Department of Chemistry has selected Rob Raddi to receive a Guy Allen Award for Outstanding Teaching for the 2019-2020 Academic Year.
Congratulations Rob!
We welcome three new graduate students to the lab: Paige Sheridan, Tim Marshall, and Steven Goold (co-advised with Ron Levy). Looking forward to all the great science ahead!
Jason Pattis has joined the Voelz lab as a new postdoc. Welcome Jason! Jason did his PhD work in Eric May’s group at the University of Connecticut. He’ll be working on new Markov State Model approaches for ligand binding.
Members of the Voelz lab met for a one-day Folding@home Consortium meeting at Washington University in St. Louis. The meeting focused on the science currently being performed on Folding@home, training new consortium members, and thinking ahead toward future technical capabilities, as well as user engagement and outreach.
Many thanks go to Joseph Coffland (Cauldron Development), Justin Porter (Bowman group) and Rafal Wiewiora (Chodera group) for giving insightful demos, and Greg Bowman for hosting such a productive event!
Temple’s College of Science and Technology (CST) recently announced their 2019 Distinguished Faculty Award recipients, and Prof. Voelz was among the recipients.
CST congratulates the 2019 Distinguished Faculty Award recipients:
Italia-Eire Foundation Distinguished Teacher of the Year (Funded by Joseph C. Allegra, BA ’70, Chem, CST Board of Visitors)
Amy Freestone
Associate Professor, Biology
William Caldwell Memorial Distinguished Teaching Award (Funded by Seda Tarzian, BA ’48, Bio, CST Board of Visitors)
Vincent Voelz
Associate Professor, Chemistry
Dean’s Distinguished Teaching Award (Funded by Barry Arkles, BA ’70, PhD ’76, Chem, CST Board of Visitors)
Meredith Hegg
Assistant Professor of Instruction, Mathematics
Dean’s Distinguished Teaching Award (Funded by Barry Arkles)
Athanasia Polychronopoulou
Assistant Professor of Instruction, CIS
Dean’s Distinguished Teaching Award (Funded by Barry Arkles)
Robert-André Rarig
Assistant Professor of Instruction, Chemistry
Dean’s Distinguished Excellence in Mentoring Award
Daniele Ramella
Assistant Professor of Instruction, Chemistry
Dean’s Distinguished Award for Excellence in Research
John Perdew
Laura H. Carnell Professor of Physics and Chemistry