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.
Recent Publications
Rui Zhang, Steven A. Redford, Paul V. Ruijgrok, Nitin Kumar, Ali Mozaffari, Sasha Zemsky, Aaron R. Dinner, Vincenzo Vitelli, Zev Bryant, Margaret L. Gardel, and Juan J. de Pablo. "Spatiotemporal control of liquid crystal structure and dynamics through activity patterning." Nature Materials 20, (2021): 875–882.
John Strahan, Adam Antoszewski, Chatipat Lorpaiboon, Bodhi P. Vani, Jonathan Weare, and Aaron R. Dinner. "Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein." Journal of Chemical Theory and Computation 17, no. 5 (2021): 2948-2963.
Shiladitya Banerjee, Klevin Lo, Nikola Ojkic, Roisin Stephens, Norbert F. Scherer, and Aaron R. Dinner. "Mechanical feedback promotes bacterial adaptation to antibiotics." Nature Physics 17, (2021): 403–409.
Danielle R. Scheff, Steven A. Redford, Chatipat Lorpaiboon, Sayantan Majumdar, Aaron R. Dinner, and Margaret L. Gardel. "Actin filament alignment causes mechanical hysteresis in cross-linked networks." Soft Matter 17, (2021): 5499-5507.
Robert J. Webber , Erik H. Thiede, Douglas Dow, Aaron R. Dinner, and Jonathan Weare. "Error Bounds for Dynamical Spectral Estimation." SIAM Journal on Mathematics of Data Science 3(1), (2021): 225–252.
Paraskevi Gkeka, Gabriel Stoltz, Amir Barati Farimani, Zineb Belkacemi, Michele Ceriotti, John D. Chodera, Aaron R. Dinner, Andrew L. Ferguson, Jean-Bernard Maillet, Hervé Minoux, Christine Peter, Fabio Pietrucci, Ana Silveira, Alexandre Tkatchenko, Zofia Trstanova, Rafal Wiewiora, and Tony Lelièvre. "Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems." Journal of Chemical Theory and Computation 16 (8), (2020): 4757-4775.
Adam Antoszewski, Chi-Jui Feng, Bodhi P. Vani, Erik H. Thiede, Lu Hong, Jonathan Weare, Andrei Tokmakoff, and Aaron R. Dinner. "Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding." The Journal of Physical Chemistry B 124 (27), (2020): 5571-5587.
Lu Hong, Danylo O Lavrentovich, Archana Chavan, Eugene Leypunskiy, Eileen Li, Charles Matthews, Andy LiWang, Michael J Rust, and Aaron R Dinner. "Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock." Molecular Systems Biology 16:e9355 (2020).
Xiang Gao, Yuanwen Jiang, Yiliang Lin, Kyoung-Ho Kim, Yin Fang, Jaeseok Yi, Lingyuan Meng, Hoo-Cheol Lee, Zhiyue Lu, Owen Leddy, Rui Zhang, Qing Tu, Wei Feng, Vishnu Nair, Philip J. Griffin, Fengyuan Shi, Gajendra S. Shekhawat, Aaron R. Dinner, Hong-Gyu Park, and Bozhi Tian. "Structured silicon for revealing transient and integrated signal transductions in microbial systems." Science Advances 6, 7 (2020).
Monika Scholz, Kimberly L. Weirich, Margaret L. Gardel, and Aaron R. Dinner. "Tuning molecular motor transport through cytoskeletal filament network organization." Soft Matter 16, (2020): 2135-2140.