Research interestsWe work on problems in quantitative biology, non-equilibrium dynamics, and theoretical computer science.
A frequent theme in our work is how the collective dynamics of physical and biological systems can generalize past experiences (i.e., learn) and create internal models of the external world. This ability is critical to understanding biology in changing environments and to engineer neuro-inspired functions in matter. Current work includes: 1. Decoding information in time-varying signals using non-equilibrium dynamics (in circadian clocks with the Rust lab, in gene regulation with the Tay lab, in neural networks) 2. Exploiting transients in learning and evolution by time-varying environments (in immunology with the Wang lab, in neural networks) 3. Learning behaviors from examples in mechanical systems. Openings: If you are interested in working on such themes as a postdoc, graduate student or undergrad, contact amurugan@uchicago.edu. Funding: Our work is primarily supported by the NSF and the Simons Foundation Investigator award. Lab members have been supported by the James S. McDonnell Foundation and the NSF. |
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Some recent publications (List + summaries here) |
News
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Temporal pattern recognition through analog molecular computation
with: J O'Brien arXiv (Oct 2018) Popular summary Non-equilibrium statistical mechanics of continuous attractors with: W. Zhong, Z. Lu, D.J. Schwab arXiv (Sep 2018) Information content of downwelling skylight for non-imaging visual systems with: R. Thiermann, A. Sweeney bioRxiv (Sep 2018) Biophysical clocks face a trade-off between internal and external noise resistance with: W. Pittayakanchit*, Z. Lu*, J. Chew, M. Rust eLife 2018;7:e37624 High Protein Copy Number Is Required to Suppress Stochasticity in the Cyanobacterial Circadian Clock with: J. Chew, E. Leypunskiy, J. Lin, M. Rust Nature Communications 9:3004 (2018) Shaping dynamical pathways in mechanical systems with: M. Stern, V. Jayaram Nature Communications 9:4303 (2018) The difficulty of folding self-folding origami with: M. Stern, M. Pinson Physical Review X, arXiv link (2017) Self-folding origami at any energy scale with: M. Pinson*, M. Stern*, A Ferrero, T.Witten, E. Chen Nature Communications 8:15477 (2017) Associative pattern recognition through macro-molecular self-assembly with: W. Zhong, D.J. Schwab Journal of Statistical Physics, Volume 167, Issue 3–4, May 2017 Topologically protected modes in non-equilibrium stochastic systems with: S. Vaikuntanathan Nature Communications (Jan 2017) The Information Capacity of Specific Interactions with: M. Huntley, M. Brenner Proceedings of the National Academy of Sciences (May 2016) Receptor arrays optimized for natural odor statistics, with: D. Zwicker, M. Brenner Proceedings of the National Academy of Sciences (Apr 2016) Biological implications of dynamical phases in non-equilibrium reaction networks, with: S. Vaikuntanathan invited contribution, Journal of Statistical Physics (2016, 162 (5)) Undesired usage and the robust self-assembly of heterogeneous structures, with: J. Zou, and M. Brenner Nature Communications 6, 6203 (Jan 2015) Multifarious Assembly Mixtures: Systems Allowing Retrieval of Diverse Stored Structures, with: Z. Zeravcic, S. Leibler and M. Brenner Proceedings of the National Academy of Sciences 112(1) 54-59 (Dec 2014) |
10/09/2018: Jackson presents work on temporal pattern recognition using molecules at DNA24 (Jinan, China). Arvind gives plenary talk on computing using transients. 09/05/2018: Ex-UChicago undergrad Ryan Thiermann's preprint on the color of twilight is out on the bioRxiv. 07/09/2018: Menachem Stern gives invited talk on learning in mechanics at SIAM. 06/26/2018: Group presents work at Q-Bio 2018. 06/23/2018: Wee's and Zhiyue's paper on clocks accepted at eLife. Related experiments from the Rust lab accepted at Nature Communications. 04/04/2018: Kabir Husain joins the group. 11/20/2017: Menachem's paper on NP-hardness and folding accepted at PRX. 7/24/2017: Talk on Wee's circadian work + poster on Jackson's work at QBio 2017 Summer schools 2017: Wee and Jackson attend the Cargese biophysics school, Jackson goes to UIUC's biophysics school, Menachem at the Boulder summer school. 4/24/2017: Lenka Zdeborova (CEA/Saclay) visits. 3/24/2017: Menachem's origami paper accepted at Nature Communications. 3/16/2017: Weishun's paper on pattern recognition published in J. Stat. Phys. 3/6/2017: Menachem, Weishun present work at APS March meeting. 1/11/2017: Weishun's poster (with David Schwab, NU) accepted at COSYNE'17. 9/15/2016: Alan Selewa joins. 6/14/2016: Alexandra Carruthers arrives. 5/28/2016 : Weerapat Pittayakanchit arrives. 5/26/2016 : Weishun Zhong arrives. 5/19/2016 : Workshop on Aging and Failure in biology @ Harvard 4/14/2016 : FNANO 16 (Foundations of Nanoscience), Snowbird, UT 3/15/2016 : UIUC Condensed Matter Symposium. 2/19/2016 : Ryan Thiermann joins. 2/16/2016: Menachem Stern joins. ~ 2/9/2016 : Sheets 2016 workshop at KITP, Santa Barbara. |