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The Dinner Group

Current Group Members

Principal Investigator

Secretary

Postdoctoral Scholars

Graduate Students

Undergraduate Students

Dinner Group Alumni

Contact Information

All offices are in the
Gordon Center for Integrative Science (GCIS)
929 East 57th Street
Chicago, Illinois 60637
Lab Phone: 773-702-7232

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Principal Investigator

Aaron Dinner
Office: GCIS E139E
Phone: 773-702-2330
Fax: 773-702-4180
E-mail:







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Secretary

Zena Anderson
Office: GCIS E145
Phone: 773-702-7180
E-mail:


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Postdoctoral Scholars

Shiladitya Banerjee
Postdoctoral scholar with the group since 2013
Office: GCIS E208
E-mail:
Education
2013: Ph.D. in Physics (Advisor: Christina Marchetti), Syracuse University
2008: Bsc., Chennai Mathematical Institute.
Research

My research focuses on developing theoretical models for understanding collective behavior in active matter systems. Of particular interest is the actomyosin cytoskeleton, which is the site for mechanical force generation in living cells. To investigate the origin of these cellular forces, I'm currently developing microscopic models for motor-filament interactions in the cytoskeletal gel. A key challenge is to delineate the cellular mechanical response by modeling its inherent stochasticity and non-thermal activity. The goal is to qualitatively and quantitatively capture the emergent spatiotemporal patterns and nonequilibrium dynamics observed in vitro and in vivo experiments. To this end, I'm working closely with the experimental groups of Margaret Gardel and Norbert Scherer. A successful microscopic description can throw significant light on how to control cellular dynamics by specific design of biochemical components.

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Stas Burov
Postdoctoral scholar with the group since 2011
Office: GCIS E135
E-mail:
Education
2010: Ph.D. in Physics (Advisor: Eli Barka), Bar-Ilan University
2002: M.A., Bar-Ilan University
2001: B.A., Bar-Ilan University
Research

Using stochastic theory to interpret imaging data.


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Srividya Iyer-Biswas
Postdoctoral scholar with the group since 2011
Office: GCIS E135
E-mail:
Education
2009: Ph.D. in Physics, Ohio State University
Research

I work on understanding the physical principles governing stochastic single cell behavior, evidenced in three different contexts: cell-to-cell variability in copy numbers, the timing of key events, and the spatial locations of key geometrical features. Theoretically, I develop non-traditional analytical approaches for doing this, from a top-down perspective, that do not make ad hoc assumptions, such as, the noise must be delta-correlated white noise, that the networks must be quasi-linear, the system must be in steady state, etc. Experimentally, I have helped develop a unique combination of technologies that allows observing single cells grow and divide for >100 generations, under invariant environmental conditions, with enough precision to elucidate the scaling laws governing fluctuations in growth and division at the single-cell level. I am also interested in the overarching systems design question of how cells must compute and optimize the energetic costs of efficient information transduction. Please see my personal website at http://home.uchicago.edu/~iyerbiswas/.


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Seyit Kale
Postdoctoral scholar with the group since 2012
Office: GCIS E126
E-mail:
Education
2012: Ph.D. in Biohysics and Structural Biology (Advisor: Judith Herzfeld), Brandeis University
Research

My research focuses on enhanced sampling methods for studying rare events in chemistry. Typical timescales we can access with molecular calculations are orders of magnitude smaller than those associated with most biological phenomena. Demand for more accurate, higher levels of theory exacerbates this gap. To circumvent this issue, we develop novel computational methods that enforce a more homogeneous statistical sampling than suggested by natural thermodynamic distribution. In collaboration with Prof. Jonathan Weare, I work on new approaches for how we can accelerate reaction path search and optimization problems typically encountered in chemistry and biochemistry.


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S. M. Ali Tabei
Postdoctoral scholar with the group since 2008
Office: GCIS E126
E-mail:
Education
2008: Ph.D. in Physics (Advisor: Michel Gingras), University of Waterloo
2001: M.S., Sharif University of Technology
1999: B.S., Sharif University of Technology
Research

The general scope of my research is to develop theoretical models and stochastic analysis to understand the mechanisms of strongly coupled nonlinear biological systems that are not in equilibrium. I am inspired by how spatial and temporal fluctuations lead to precise emergent properties in living systems. I have theoretically investigated a number of synergistic topics in the context of oscillatory synchronization, intracellular transport, adaptive immunity and spatial pattern formation.

1) Entrainment of stochastic oscillators: I am interested in the analogy between dynamical phase transitions in classical nonequilibrium systems and quantum phase transitions. By borrowing phenomena from quantum systems and using the theory of large deviation functions, I show that how the entrainment of a stochastic oscillator to an external driving force can be described as a phase transition. The results provide a platform to study synchronization among biological oscillators.

2) Intracellular Transport: I am collaborating with the laboratories of Profs. Norbert Scherer and Louis Philipson at the University of Chicago on a microscopy project. We employed a variety of statistical analyses as well as simple numerical simulations to show that insulin secretory granules have dynamics like a subordinated random walk, and this explains their remarkable transport properties. Our work opens a new avenue to understanding how diverse pools of insulin granules can arise. The theoretical platform we developed in this project enables the use of a wider range of experimental data and the extraction of more information from biological time series.

3) HIV Infection and Adaptive Immune Response: I collaborated on a biomedically relevant project with Prof. Martin Wiegert. I developed a mathematical and computational framework to explain why passive administration of anti-HIV broadly neutralizing antibodies do not modulate viral load in vivo in contrast to previous in vitro studies. We quantitatively investigated a factor that could limit the impact of cross-reactive broadly neutralizing antibodies on the viral load in vivo. The study is motivated by the observation that HIV broadly neutralizing antibodies bind to a variety of self-epitopes. I have also studied the dynamics of adaptive immune system via agent based modeling.

4) Spatial Pattern Formation: In collaboration with the laboratories of Profs. Ilaria Rebay and Richard Carthew, I have modeled cell-fate decisions to show that the competition of spatial and temporal interactions in cellular signaling brings about the emergence of spatial patterns of gene expression in the development of the Drosophila melanogaster eye.


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Graduate Students

Herman Gudjonson
Graduate Student with the group since 2013
Office: GCIS E126
E-mail:
Education
2012: A.B., Harvard University
Research

Regulatory networks in NKT cell development.


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Alan Hutchison
Graduate Student with the group since 2012
Office: GCIS E126
E-mail:
Education
2010: B.S., Yale University
Research

Assembly of regulatory networks.


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Monika Kauer
Graduate Student with the group since 2013
Office: GCIS E135
E-mail:
Education
2012: Dipl.Phys, TU Dresden
2010: B.Sc. in Physics, University of Wurzburg
Research

Stochastic processes.


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Eugene Leypunskiy
Graduate Student with the group since 2013
Office: KCBD
E-mail:
Education
2011: B.A., Princeton University
Research

Fitness in circadian systems.


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Kayoko Beth Shimmyo
Graduate Student with the group since 2011
Office: GCIS E135
E-mail:
Education
2010: B.A., Brown University
Research

Phase behavior of binary nanoparticle mixtures.


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Jeremy Tempkin
Graduate Student with the group since 2013
Office: GCIS E126
E-mail:
Education
2012: B.A., University
Research

Multiscale methods.


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Undergraduate Students

Jennifer Momkus
Undergraduate Student with the group since 2012
Office: GCIS E126
E-mail:
Research

Anomalous dynamics in intracellular transport.


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