SaM would like to acknowledge and congratulate our poster session winners from our recent Advancing Research through Computing symposium! Two winners were selected from more than 20 submissions. Each winner received a $500 travel stipend. More information about each winner below.
Bio: I received my B.S. in Chemistry from West Virginia University, where I did undergraduate research in the organic synthesis lab of Dr. Xiaodong Shi. Currently, I am working on my Ph.D. at the University of Pittsburgh in the theoretical chemistry lab of Dr. Kenneth Jordan. My areas of study are vibrational spectroscopy of gas-phase molecular clusters and application of quantum chemistry methods to quantum Drude oscillators. Finally, I am starting a project on the correlation-bound superatom anionic states of spherical fullerenes on a Cu(111) surface.
Poster Title: Exploring H3O+ hydration in the gas-phase through infrared spectroscopy
Poster Abstract: The origins of the red-shift in the vibrational signatures of H3O+ in gas-phase H+(H2O)n clusters are presented. Using symmetry-adapted perturbation theory and second-order vibrational perturbation theory, we deduce that the observed red-shift originates from a field-effect due to the first two hydration shells, as well as coupling between the three stretching modes of the H3O+ ion.
Bio: I went to undergrad at Reed College in Portland, Oregon, where I studied physics and liberal arts. After undergrad, I spent three years studying theoretical physics at the University of Washington in Seattle, before leaving to work as a chef. I started my current PhD work in computational biology four years ago, and since then have been working with Dan Zuckerman and a host of collaborators. Our work has focused on the difficulty of understanding complex biological models when stochasticity (randomness) plays an essential role in the process. Using Weighted Ensemble sampling, we are able to drastically reduce the amount of computation needed to study these systems, which makes using detailed models of biological processes much more practical.
More details about Rory’s research are available here.
Poster Title: Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories
Poster Abstract: The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to spatially resolved cell-scale simulations. The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample regions. The method can also generate unbiased estimates of non-equilibrium and equilibrium observables, sometimes with significantly less aggregate computing time than would be possible using standard parallelization. Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular species. We study a series of models exhibiting spatial, temporal and biochemical complexity and show that although WE has important limitations, it can achieve performance significantly exceeding standard parallel simulation — by orders of magnitude for some observables.