Selected Publications

See this work highlighted in the Biophysical Journal “New and Notables” Atomic-Scale Insights into Physical Mechanisms Driving Enzymes’ “Working Cycles” by Artem Efremov and Fazoil Ataullakhanov, and the UCSD In the News article It’s not “Intelligent Design” so how did molecular motors develop?.

Molecular motors are thought to generate force and directional motion via nonequilibrium switching between energy surfaces. Because all enzymes can undergo such switching, we hypothesized that the ability to generate rotary motion and torque is not unique to highly adapted biological motor proteins but is instead a common feature of enzymes. We used molecular dynamics simulations to compute energy surfaces for hundreds of torsions in three enzymes—adenosine kinase, protein kinase A, and HIV-1 protease—and used these energy surfaces within a kinetic model that accounts for intersurface switching and intrasurface probability flows. When substrate is out of equilibrium with product, we find computed torsion rotation rates up ∼140 cycles s−1, with stall torques up to ∼2 kcal mol−1 cycle−1, and power outputs up to ∼50 kcal mol−1 s−1. We argue that these enzymes are instances of a general phenomenon of directional probability flows on asymmetric energy surfaces for systems out of equilibrium. Thus, we conjecture that cyclic probability fluxes, corresponding to rotations of torsions and higher-order collective variables, exist in any chiral molecule driven between states in a nonequilibrium manner; we call this the “Asymmetry-Directionality” conjecture. This is expected to apply as well to synthetic chiral molecules switched in a nonequilibrium manner between energy surfaces by light, redox chemistry, or catalysis.
Biophysical Journal, 2018

Recent Publications

More Publications

(2018). Lipid membrane shape evolution and the actin cytoskeleton. Handbook of lipid membranes, molecular and materials aspects.

(2017). Overview of the SAMPL5 host-guest challenge: Are we doing better?, Overview of the SAMPL5 host–guest challenge: Are we doing better?. Journal of computer-aided molecular design, Journal of computer-aided molecular design.

DOI GitHub

(2016). Salmon-derived thrombin inhibits development of chronic pain through an endothelial barrier protective mechanism dependent on APC. Biomaterials.


(2015). Physical chemistry and membrane properties of two phosphatidylinositol bisphosphate isomers. Physical Chemistry Chemical Physics.


(2014). Counterion-mediated cluster formation by polyphosphoinositides. Chemistry and Physics of Lipids.


(2014). Counterion-mediated pattern formation in membranes containing anionic lipids. Advances in colloid and interface science.


(2014). Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids. Soft matter.



Force field development

A new approach to modern collaborative biomolecular force field development based on open source software, open science, and high-quality curated open datasets.

Improved binding free energy calculations

We are developing new methods and tools to calculate the binding free energy of host-guest and protein-ligand systems, with an eye towards drug discovery and supramolecular chemistry.

Optimization of molecular motors

We are interested in quantifying the performance of molecular motors and how to design motors on the nanoscale for specific properties: speed, torque, gearing, ability to perform work, or other tasks.


  • Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093