(6cx) Diffusion in Biophysics, from Protons to Cargo: A Model System Approach
AIChE Annual Meeting
2019
2019 AIChE Annual Meeting
Meet the Faculty and Post-Doc Candidates Poster Session -- Sponsored by the Education Division
Meet the Faculty and Post-Doc Candidates Poster Session
Sunday, November 10, 2019 - 1:00pm to 3:00pm
Research Interests:
Biological systems rely on diffusion for mass transport in a wide variety of contexts and across a range of scales, from ion transport in membrane ion channels to RNA transport across the nuclear membrane. Using molecular dynamics (MD) simulation techniques, including heavily coarse-grained model system approaches, atomistic classical MD, and ab initio MD, I will study the diversity with which biology harnesses diffusion to diverse ends. As MD simulation techniques have matured and computer power increased, MD simulations have been applied to study larger and larger biological systems on longer and longer timescales. This usually involves coarse-grained approaches, which are often non-transferable, not straightforward to parameterize, and not uniquely defined. Instead, I will exploit the inherent strengths of MD by using model system, or "top down," approaches. This still allows for the prediction of qualitative trends, permitting close collaboration with experiment. Simultaneously, this approach yields more intuitive descriptions of complex biological processes by allowing the systematic simplification of the processes being studied, until only the relevant features remain.
Successful Proposals: 2014 NSF Graduate Research Fellowship, XSEDE Allocation TG-CHE140096, 2015 and 2016 University of Colorado Research Computing General Allocations, 2015 University of Colorado UGGS Travel Grant, 2016 University of Colorado Graduate School Travel Grant
Postdoctoral Work:
The effects of off-diagonal fluctuations on charge transport in organic semiconductors.
Under supervision of James L. Skinner, Pritzker School of Molecular Engineering, University of Chicago
PhD Dissertation: “Molecular Dynamics in Mesoscopic Equilibrium and Nonequilibrium Systems with Applications in Sustainabilityâ€
Under supervision of Joel D. Eaves, Department of Chemistry and Biochemistry, University of Colorado
Research Experience:
My academic career has focused on the applications of molecular dynamics to a wide array of problems in condensed phase physics and chemistry. My experience spans across physical length scales, and my work has often unified the disparate descriptions of these different scales in a variety of ways: I developed a molecular dynamics approach for nonequilibrium simulation that bridges the gap between continuum hydrodynamics and atomistic mechanics. On the other side of the spectrum, I have discovered and explained correspondences between the quantum mechanical descriptions of IR spectroscopy and classical rotational mechanics. I am currently working on extending this approach to study optical spectroscopy and charge transport in organic semiconductors. Techniques like these, which allow direct comparison between simulation and experiment, are critical because they foster collaboration with experiment. Through these collaborations, I have been exposed to the fascinating and important applications of these approaches to the realm of biophysics.
Teaching Interests:
I enjoy teaching and I look forward to the opportunity to pursue it further. My teaching experience includes TAing undergraduate laboratory courses and guest-lecturing graduate courses in the Chemistry Department at the University of Colorado. I have also spent significant time tutoring high school and college students, as well as mentoring graduate students. I plan to pursue problem-based learning, which I think could make many undergraduate and graduate courses more effective. For example, the Ising/lattice gas model could be a recurring example in a thermodynamics course, which provides a backdrop for many important core concepts, from heat capacity to phase transitions to Monte Carlo simulation.
Future Direction:
As faculty I will apply my background in a range of MD approaches to study the wide array of diffusive processes in biology. For example, the nuclear membrane protects and encloses the cell nucleus, but must permit selective transport. This is accomplished through nuclear pores, which permit specific cargo to pass when accompanied by specific chaperones. A variety of mechanisms for the selectivity and transport of these cargoes have been suggested, some of which involve a binding-diffusion process that explains the selectivity of the pores. If understood, this mechanism could be leveraged for a variety of applications, from water purification to blood diagnostics. I will use top-down coarse-grained model systems to study the efficiency and selectivity of transport as a function of the cargo-pore binding strength.
The binding-diffusion mechanism for cargo transport in the nuclear pore has surprising similarities with the diffusion mechanism of the excess proton in water, several orders of magnitude smaller in scale. Here, the critical step in diffusion is thought to involve the breakage of a hydrogen bond in the second hydration shell of the hydronium ion, just like the cargo diffusion depends on the breakage of one of its bonds with the pore medium. In biological contexts, however, proton transport often occurs in the proximity of large biomolecules, which interact with the surrounding water to varying degrees. While significant work has been done to characterize the static behavior of excess protons at water interfaces, surprisingly little has focused on the dynamic proton transport process. I will use a variety of MD approaches to study this transport process. I will again leverage the top-down model system approach, by modeling the biologically relevant interfaces as non-hydrogen-bonding solutes. By varying the size of these solutes and water-solute interaction strength, I will systematically study the effect of interface curvature and chemistry on proton transport.
I value close collaboration with experiment, and in both contexts above, my experience connecting MD simulation with experimental observables like IR and optical spectroscopy will be crucial. I am also interested in applying this general approach, using simple model systems to understand the qualitative trends in important biological systems, to a wide variety of other systems. Applications in chemical separations and battery technology are especially interesting to me.
Selected Publications:
*These authors contributed equally
*Strong. S. E., *Hestand, N. J., Kananenka, A. K., Zanni, M. T., Skinner, J. L. IR spectroscopy can reveal the mechanism of K+ transport in ion channels. 2019 In Progress.
*Hestand, N. J., *Strong, S. E., Shi, L. & Skinner, J. L. Mid-IR spectroscopy of supercritical water: From dilute gas to dense fluid. 2019 J. Chem. Phys. 150.
Strong, S. E., Shi, L. & Skinner, J. L. Percolation in supercritical water: Do the Widom and percolation lines coincide? 2019 J. Chem. Phys. 149.
Strong, S. E. & Eaves, J. D. Linear response theory for water transport through dry nanopores. 2017 J. Phys. Chem. A 121.
Strong, S. E. & Eaves, J. D. The dynamics of water in porous two-dimensional crystals. 2017 J. Phys. Chem. B 121.
Strong, S. E. & Eaves, J. D. Atomistic hydrodynamics and the dynamical hydrophobic effect in porous graphene. 2016 J. Phys. Chem. Lett. 7.