Center for Computing Research (CCR)

Center for Computing Research

Joshua Rackers (Josh)

Joshua Rackers (Josh)
Computational Multiscale
Email: jracker@sandia.gov
Phone: 505/284-2187

Mailing address:
Sandia National Laboratories
P.O. Box 5800, MS 1322
Albuquerque, NM
87185-1320

I am interested in predicting how molecules move and interact at the atomic scale. In particular, I research methods for producing quantum-accurate potential energy surfaces for biological molecules. The tools I build for this purpose draw on the fields of chemical physics, quantum chemistry, statistical physics, and machine learning.

Primary Areas of Research:

1. Simulating ion channels with the HIPPO (Hydrogen-like Intermolecular Polarizable POtential) and AMOEBA (Atomic Multipoles Optimized Energetics for Biomolecular Applications) polarizable force fields. Ion channels are proteins that are essential to life. They selectively permit ions to be shuttled across a cell membrane, allowing our hearts to beat and neurons to fire. However, the mechanism of this selectivity is still unknown. Polarizable force field simulations of ion channels may unlock the mystery of ion channel selectivity.

2. Massively parallel polarizable force field simulations on GPUs (Graphical Processing Units) with LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) and OpenMM. Polarizable force fields like AMOEBA and HIPPO are currently unable to access today's tremendously powerful supercomputing resources. Interfacing LAMMPS to OpenMM will solve this problem.

3. Using machine learning to predict electron densities. The electron density is the single most important property of a molecule. By combining what we know about the physics of atomic interactions with innovative machine learning techniques, we may be able to obtain the electron density directly. This would not only bypass computationally expensive ab initio calculations, but enable large-scale, quantum-accurate simulations of biomolecular systems.

Education/Background

2006-2010: B.S. The Ohio State University (Physics and Political Science)

2010-2013: Teach for America, Baltimore, MD

2011-2012: Ms.Ed. Johns Hopkins University (Urban Education)

2013-2019: Ph.D. Washington University in St. Louis (Biophysics)

2019-current: Truman Fellow, Sandia National Laboratories