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Education

AB, Harvard University (1999)
PhD, Stanford University (2005)
NIH Ruth L. Kirschstein-NRSA Fellow, Columbia University (2005-2008)

Awards

• AIChE Computational Molecular Science & Engineering Forum Impact Award (2020)
• NSF CAREER Award (2014)
• American Chemical Society COMP OpenEye Outstanding Junior Faculty Award (2012)
• Oak Ridge Associated Universities Ralph E. Powe, Jr. Faculty Enhancement Award (2009)
• University of Virginia FEST Distinguished Young Investigator Award (2009)
• National Institutes of Health Individual Postdoctoral Fellow, Ruth L. Kirschstein NRSA (2005-2008)
• Fannie and John Hertz Graduate Fellowship (1999-2004)

Selected Publications

• N. S. Abraham and M. R. Shirts, “Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules.” J. Chem. Theory Comput. 16(10), 6503-6512. (2020)

• B. J. Coscia and M. R. Shirts, “Capturing Subdiffusive Solute Dynamics and Predicting Selectivity in Nanoscale Pores with Time Series Modeling.” J. Chem. Theory Comput. 16(9), 5456-5473. (2020)

• E. C. Dybeck, D. P. McMahon, G. M. Day, and M. R. Shirts, “Exploring the Multi-minima Behavior of Small Molecule Crystal Polymorphs at Finite Temperature" Cryst. Growth Des 19(10), 5568–5580 (2019)

• R. A. Messerly, M. S. Barhaghi, J. J. Potoff, and M. R. Shirts "Histogram-free reweighting with grand canonical Monte Carlo: Post-simulation optimization of non-bonded potentials for phase equilibria." J. Chem. & Eng, Data, 64(9), 3701–3717, (2019)

• B. J. Coscia and M. R. Shirts, “Chemically Selective Transport in a Cross-Linked HII Phase Lyo- tropic Liquid Crystal Membrane” J. Phys. Chem. B. 123(29), 6314–6330, (2019)

• B. J. Coscia, J. Yelk, M. A. Glaser, D. L. Gin, X. Feng, and M. R. Shirts, “Understanding the Na- noscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes” J. Phys. Chem. B. 123(1), 289–309 (2019)

• D. L. Mobley, C. C. Bannan, A. Rizzi, C. I Bayly, J. D Chodera, V. T Lim, N. M. Lim, K. A Beau- champ, M. R. Shirts, M. K. Gilson, P. K Eastman, “Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0. 1”, J. Chem. Theory Comput., 14(11) 6076-6092 (2018)

• P. T. Merz and M. R. Shirts, “Testing for Physical Validity in Molecular Simulations”, PLoS ONE, 13(9), e0202764 (2018)

• N. P. Schieber, E. C. Dybeck, and M. R. Shirts, “Using reweighting and free energy surface interpola- tion to predict solid-solid phase diagrams,” J. Chem. Phys. 148(14), 144104 (2018)

Research Interests

Understanding and designing materials at the molecular scale:

We work with experimentalists to better understand the molecular details of protein purification materials, water filtration membranes, and nanotextured surfaces, and to suggest novel improvements. The wide physical and chemical diversity of biomolecular processes strongly suggests that the possibilities for novel function in human-engineered materials are far, far beyond our current capabilities. Designed materials can draw from a much larger range of chemical structure and functionality than exists biologically; if we can add significant chemical diversity to nature's already impressive toolkit, what else can be created? Computational approaches provide a vitally important tool to help explore this enormously large materials space.

Computed-aided drug design:

Drug resistance is one of the biggest challenges in the pharmacological treatment of infectious diseases, and current informatics based drug discovery methods are not well-suited to rapidly develop new drug variants that can successfully overcome resistance. Our research has demonstrated that statistical mechanical methods can predict ligand binding affinities to within 1 kcal/mol in simple atomistically detailed systems, a level that becomes useful for the pharmaceutical industry. However, significant effort is necessary to make such methods work in more typical drug systems and to make them scale efficiently enough to be useful in general practice.�� We work together with experimental researchers, software developers, and pharmaceutical companies to make computational drug design a reality, helping bring down the cost of developing cures to a host of diseases.

Improvements in molecular simulation and property prediction for engineering:

The two most pressing problems holding back improved atomic-level simulation of polymers, macromolecules, and other complicated dense fluids are the lack of sufficient sampling to accurately measure and observe molecular phenomena, and the choice of model parameters used to perform the simulations. It is currently only possible to simulate the equivalent of a few microseconds of all but the smallest biological systems, with some heroically expensive extensions to milliseconds with large supercomputers. Without sufficient conformational sampling, it is impossible even to verify if models are sufficiently faithful to experiment, let alone explore behavior of either long time scales or of larger molecular systems. Without good model parameters, atomistic predictions are unreliable and misleading, and developing new parameters is a labor-intensive process with significant guesswork. In the Shirts group, we research improved configurational sampling methods for macromolecules and more automated, statistically based methods for choosing molecular model parameters. These tools have the potential to assist researchers performing molecular simulation in all fields.