Research in the Dinner group centers on the statistical mechanics of systems far from equilibrium, particularly its application to understanding what is life.
Research Interests:
My group and I develop theoretical and computational approaches to understand the physical chemical basis of complex behavior in living systems. We are particularly interested in understanding how cells harness energy from their environments to organize their molecular interactions in space and time. To this end, we are working in close collaboration with experimental researchers to design and analyze quantitative measurements of living systems, and, in turn, implement predictive physical models. One feature of biological dynamics that makes this challenging is that they span a hierarchy of length and time scales ranging from Ångstroms and femtoseconds to millimeters and days.
In molecular simulations, bridging these gaps requires increasing the exploration of states that are visited relatively rarely (e.g., transition states) while still enabling recovery of unbiased statistical averages. We developed some of the most general and efficient methods available for accelerating the convergence of properties of microscopically irreversible models (nonequilibrium umbrella sampling and steered transition path sampling); we are now working with applied mathematicians to analyze these methods rigorously to improve and extend them. Additionally, we are exploring machine learning techniques to aid in interpreting simulations and connecting them with experimental observables.
Selected References
Tabei, SM Ali, Stanislav Burov, Hee Y. Kim, Andrey Kuznetsov, Toan Huynh, Justin Jureller, Louis H. Philipson, Aaron R. Dinner, and Norbert F. Scherer. "Intracellular transport of insulin granules is a subordinated random walk." Proceedings of the National Academy of Sciences 110, no. 13 (2013): 4911-4916.
Thiede, Erik H., Brian Van Koten, Jonathan Weare, and Aaron R. Dinner. "Eigenvector method for umbrella sampling enables error analysis." The Journal of Chemical Physics 145, no. 8 (2016): 084115.
Scholz, Monika, Stanislav Burov, Kimberly L. Weirich, Björn J. Scholz, SM Ali Tabei, Margaret L. Gardel, and Aaron R. Dinner. "Cycling state that can lead to glassy dynamics in intracellular transport." Physical Review X 6, no. 1 (2016): 011037.
Burov, Stanislav, Patrick Figliozzi, Binhua Lin, Stuart A. Rice, Norbert F. Scherer, and Aaron R. Dinner. "Single-pixel interior filling function approach for detecting and correcting errors in particle tracking." Proceedings of the National Academy of Sciences 114, no. 2 (2017): 221-226.
Banerjee, Shiladitya, Klevin Lo, Matthew K. Daddysman, Alan Selewa, Thomas Kuntz, Aaron R. Dinner, and Norbert F. Scherer. "Biphasic growth dynamics control cell division in Caulobacter crescentus." Nature Microbiology 2, no. 9 (2017): 17116.
Leypunskiy, Eugene, Jenny Lin, Haneul Yoo, UnJin Lee, Aaron R. Dinner, and Michael J. Rust. "The cyanobacterial circadian clock follows midday in vivo and in vitro." eLife 6 (2017): e23539.
Freedman, Simon L., Shiladitya Banerjee, Glen M. Hocky, and Aaron R. Dinner. "A versatile framework for simulating the dynamic mechanical structure of cytoskeletal networks." Biophysical Journal 113, no. 2 (2017): 448-460.
Stam, Samantha, Simon L. Freedman, Shiladitya Banerjee, Kimberly L. Weirich, Aaron R. Dinner, and Margaret L. Gardel. "Filament rigidity and connectivity tune the deformation modes of active biopolymer networks." Proceedings of the National Academy of Sciences (2017): E10037-E10045.
Dinner, Aaron R., Jonathan C. Mattingly, Jeremy O. B. Tempkin, Brian Van Koten, and Jonathan Weare. "Trajectory stratification of stochastic dynamics." SIAM Review, accepted (2018).