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Appointments:
Assistant Professor
Department of Chemistry
Institute for Genomics and
Systems Biology
Institute for Biophysical Dynamics
James Franck Institute
Committee on Immunology
Committee on Biophysics
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Education:
Ph.D., Harvard University, 1999
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Contact:
Phone: (773) 702-2330
Fax:
(773) 834-5250
E-Mail:
dinner@uchicago.edu
Address:
The University of Chicago
GCIS E139E
929 East 57th Street
Chicago, Illinois 60637
Lab: GCIS E126, E135
Lab
Website
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Related Research Interests:
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Aaron Dinner, Ph.D.
Molecular Mechanisms of Cellular Dynamics through the
Development and Application of Theoretical Approaches
Research Summary
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The Dinner group develops theoretical models for
relating cellular behavior to molecular properties.
We have studied aspects of signaling, gene regulation, and
rearrangement in lymphocytes as well as the specification of other
hematopoietic lineages. Recently, we have been particularly
focused on how antigen receptor specificities impact the dynamics of
the humoral immune response. Please see the group webpage or the Chemistry webpage
for details about our broader research program. |
Selected Papers
Ma, A. & Dinner, A. R. (2005) An automatic method for identifying reaction coordinates in complex systems. J. Phys. Chem. B, 109, 6769-6779.
Warmflash, A., Weigert, M. & Dinner, A. R. (2005) Control of genotypic allelic inclusion through TCR surface expression. J. Immunol. 175, 6412-6419.
Hu, J., Ma, A. & Dinner, A. R. (2006) Monte Carlo simulations of biomolecules: The MC module in CHARMM. J. Comp. Chem. 27, 203-216.
Nag, A. & Dinner, A. R. (2006) Enhancement of diffusion-controlled reaction rates by surface-induced orientational restriction. Biophys. J. 90, 896-902.
Ma, A., Nag, A. & Dinner, A. R. (2006) Dynamic coupling between coordinates in a model for biomolecular isomerization. J. Chem. Phys. 124, 144911.
Hou, P., Araujo, E., Massenburg, D., Veselits, M., Doyle, C., Dinner, A. R. & Clark, M. R. (2006) B cell antigen receptor signaling and internalization are mutually exclusive events. PLoS Biol. 4, 1147-1158.
Laslo, P., Spooner, C. J., Warmflash, A., Lancki, D. W., Lee, H.-J., Sciammas, R., Gantner, B. N., Dinner, A. R., & Singh, H. (2006) Multilineage transcriptional priming and stabilization of alternate hematopoietic cell fates. Cell, 126, 755-766.
Warmflash, A. & Dinner, A. R. (2006) A model for TCR gene segment use. J. Immunol. 177, 3857-3864.
Hu, J., Ma, A. & Dinner, A. R. (2006) Bias annealing: a method for obtaining transition paths de novo. J. Chem. Phys., 125, 114101.
Nag, A., Zhao, T. & Dinner, A. R. (2007) Effects of non-productive binding on the kinetics of enzymatic reactions with patterned substrates. J. Chem. Phys. 126, 035103.
Stewman, S. F. & Dinner, A. R. (2007) A lattice model for self-assembly with application to the formation of cytoskeletal-like structures. Phys. Rev. E, 76 016103.
Warmflash, A., Bhimalapuram, P. & Dinner, A. R. (2007) Umbrella sampling for non-equilibrium processes. J. Chem. Phys. 127, 154112.
Zhao, T. & Dinner, A. R. (2008) Apparent directional scanning for DNA repair. Biophys. J. 94, 47-52.
Li, Y., Zhao, T., Bhimalapuram, P. & Dinner, A. R. (2008) How the nature of an observation affects single-trajectory entropies. J. Chem. Phys. 128, 074102.
Hu, J., Ma, A. & Dinner, A. R. (2008) A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc. Natl. Acad. Sci. USA, 105, 4615-4620.
Chen H, Hu J, Chen PR, Lan L, Li Z, Hicks LM, Dinner AR, He C. (2008) The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A. 105:13586-91
Warmflash A, Adamson DN, Dinner AR. (2008). How noise statistics impact models of enzyme cycles. J Chem Phys. Jun 14;128(22):225101.
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Faculty and Research
Programs
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