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Postdoctoral Research Fellow, Dept. of Physics
Center for Network Dynamics
Northwestern University
10 | Experimental and theoretical tests of the foldon theory of protein folding
In the Bustamante lab, we use single molecule optical tweezing experiments and molecular dynamics simulations at multiple scales to test the foldon theory of protein folding. By pulling proteins apart and letting them refold, we learn that they leverage secondary structure to fold and unfold along only a handful of unique paths in a cascade like manner, leveraging one foldon as a template for the next to fold, and so on.
We use adaptive importance sampling to learn approximately counter-diabatic forces that make work measurements reversible even for short finite time protocols. With these forces, we estimate free energy differences of complex systems with significantly lower variance and fewer trajectories than by naive switching protocols.
A. Zhong* & B. Kuznets-Speck*, M.R. DeWeese, arXiv:2304.12287
08 | Inferring equilibrium rates with nonequilibrium protocols
We use statistics of the distribution of heat dissipation, conditioned on making a rare transition under applied force to estimate the rate of the transition when the system is unperturbed, at equilibrium.
07 | Variational path sampling (VPS) to control and learn the rates of rare events in noisy complex systems
VPS makes YOU the (puppet) master of your [nonequilibrium] potential
- Checkout our new theory and practical simulation framework to estimate the rate/mechanism of rare transitions in nonequilibrium many-body systems!
- We circumvent the problem of sampling rare events by making them typical-- learning and applying an optimal control force which mimics the force naturally felt along transition paths.
06 | Counter-diabatic control of biophysical processes
We developed a graph-theoretic formalism to control arbitrary biophysical systems out of equilibrium, and put concrete limits on what can be done to shape their function with partial control when some microscopic details of the underlying system remain unknown.
05 | Dissipation bounds transition rate amplification far from equilibrium
We uncover a universal tradeoff between speed and energetic resource consumption: the excess heat dissipated along a transition path sets a limit on the extent a transition rate can be accelerated
04 | Molding the (mal)function of von Willebrand factor
With coarse-grained MD simulations like the one in this clip, I'm studying how the protein that clots your blood and regenerates wounded tissue behaves and misbehaves in its nonequilibrium environment.
Here's a sneak peek from our manuscript exploring the trade-offs between speed, fidelity and energy consumption and selective pressure in Kinase-Phosphatase push-pull loops.
03 | The price of a bit: energetic costs and the evolution of cellular signaling
We recently published this awesome work, where we design non-equilibrium selection protocols to robustly steer the evolution of high-dimensional populations.
02 | Controlling the speed and trajectory of evolution in high-dimensional clonal populations
01 | Thermodynamic Properties of Molecular Communication
Here we take a duel view of Maxwell's Demon, showing that the Landauer bound falls out as the information capacity per unit energy cost to faithfully operate a communication channel comprised of low/high concentration reservoirs.
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