The Dinner group seeks to develop a theoretical understanding of how complex biological behavior arises from molecular interactions. Because the defining properties of living systems (growth, movement, and directed response to environmental stimuli) rely on irreversible energy consumption and dissipation, much of our research centers on stochastic processes far from equilibrium. We quantitatively analyze experimental data on living systems, construct physical models to interpret the observed statistics, and implement algorithms for efficiently simulating the dynamics of such models.
Accelerating molecular simulations
We are developing, mathematically characterizing, and employing algorithms for enhancing the sampling of rare events and recovering their statistics.
Modeling living systems
We are building models to interpret dynamics observed in cells and exploring the behavior of these models both analytically and numerically.
I am a Professor of Chemistry and the Director of the James Franck Institute at the University of Chicago. I also hold appointments in the Institute for Biophysical Dynamics, the Computation Institute, and the Institute for Genomics and Systems Biology. My group’s most well known contributions are to machine learning methods for interpreting complex biomolecular simulations, sampling methods for systems far from equilibrium, and models of hematopoietic cell fate choice. Much of my current work is collaborative, and many of my students and postdoctoral scholars are jointly mentored by experimentalists and/or statisticians. My honors include a Searle Scholarship, NSF CAREER Award, Sloan Fellowship, and participation in the 2010 and 2014 Latke-Hamantash Debates.
Prior to joining the faculty at Chicago, I obtained my undergraduate (AB in Biochemical Sciences, 1994) and graduate (PhD in Biophysics, 1999) degrees at Harvard University, where I worked with Martin Karplus on Monte Carlo methods and their application to protein folding. Subsequently, I pursued postdoctoral studies at the University of Oxford (1999-2001), where I used hybrid quantum-mechanical/molecular-mechanical (QM/MM) methods to elucidate mechanisms of DNA repair, and the University of California, Berkeley (2001-2003), where I worked with David Chandler on transition path sampling and Arup Chakraborty on models of T lymphocyte signaling.professor | since 2003
My research interests broadly involve the applications of techniques from statistical mechanics and molecular modeling to better understand the mechanisms behind biological processes, particularly those involving interactions between macromolecules. Currently I am studying many aspects of the complex interactions occurring in the cell cytoskeleton.postdoctoral scholar | since 2014
I am interested in non-equilibrium statistical physics. I develop numerical methods to efficiently sample rare events. Another aspect of my research is designing models that help us better understand chemical reactions, information processing, biological processes and many other interesting phenomena far from thermal equilibrium.postdoctoral scholar | since 2016
I develop advanced algorithms for Bayesian Markov Chain Monte Carlo. I also work on using tools from molecular modeling to simulate catastrophic failure in the power grid.postdoctoral scholar | since 2014
Brian Van Koten
My research focuses on building a deep understanding of enhanced sampling algorithms using numerical analysis.postdoctoral scholar | since 2013
I study cytoskeletal networks using coarse-grained simulation to ultimately understand how mechanical interactions between individual proteins lead to cellular-scale effects, such as cell motility, division, and intracellular transport.graduate student | since 2014
I study the gene regulatory networks that govern cell fate commitment using genome-wide and single-cell measurements.graduate student | since 2013
I am studying the molecular mechanisms that govern the function of the KaiABC circadian oscillator through molecular dynamics simulations and biochemical experiments.graduate student | since 2016
I am interested in the role circadian clocks play in fluctuating light-dark conditions that have presumably provided selective pressure for the evolution of biological timekeeping. How precise is the adaptation of circadian clocks to 24-hr light-dark cycles? What is the range of light-dark frequencies in which biological clocks can correctly anticipate these environmental transitions? In what circumstances do circadian timekeepers enhance reproductive fitness -- and why?graduate student | since 2013
I am exploring the convergence of Jarzynski's equality for free energy estimates and how it can be accelerated with nonequilibrium umbrella sampling.graduate student | since 2016
Traditional enhanced sampling schemes are often limited to systems dominated by one or two important degrees of freedom. However, for many systems, such as disordered proteins, this is not the case. My research focuses on developing umbrella sampling algorithms for systems governed by many degrees of freedom.graduate student | since 2014
I study self-assembly processes in cells, specifically, those that occur during times of stress. Using both this and experimental approaches I hope to explain and predict the regulatory consequences of aggregation.graduate student | since 2014
I am developing statistical mechanical descriptions of nonequilibrium biomolecular processes. Specifically, I am using steered transition path sampling to study the mechanism of the dimer-to-monomer transition of insulin and simulating temperature-jump experiments for interpretation of infrared spectroscopy experiments on intrinsically disordered proteins.graduate student | since 2015
Eigenvector method for umbrella sampling enables error analysis
Erik Thiede, Brian Van Koten, Jonathan Weare, and Aaron R Dinner
Journal of Chemical Physics 145, 084115 (2016) Link
A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks
Simon L Freedman, Shiladitya Banerjee, Glen M Hocky, Aaron R Dinner
Biophysical Journal 113, 448-460 (2017) Link
The cyanobacterial circadian clock follows midday in vivo and in vitro
Eugene Leypunskiy, Jenny Lin, Haneul Yoo, UnJin Lee, Aaron R Dinner, Michael J Rust
eLife 6, e23539 (2017) Link
Biphasic growth dynamics control cell division in Caulobacter crescentus
Shiladitya Banerjee, Klevin Lo, Matthew K. Daddysman, Alan Selewa, Thomas Kuntz, Aaron R Dinner, Norbert F Scherer
Nature Microbiology 2, 17116 (2017) Link