Physics and Astronomy Colloquia

*Fall Quarter Colloquia Start at 4:00 pm*

Title: The Mechanism of type IA Topoisomerases: From Structural to Single Molecule Studies

Speaker: Alfonso Mondragón, Northwestern University, Molecular Biosciences


Abstract: Topoisomerase I is an important E. coli enzyme that regulates the topology of DNA by removing negative supercoils and catenating/decatenating DNA molecules. Previously we solved the atomic structure of the domain responsible for the DNA strand passage reaction and proposed a mechanism of action for this type of enzymes that explains many of the most salient features of the reaction. To extend and complement our structural work, we used single molecule Magnetic Tweezers studies to reveal that the presence of pauses in between relaxation events is a major feature of the mechanism of topological transformations. In order to determine the origin of these pauses, we recently built a combined Magnetic Tweezers-Total Internal Reflection Fluorescence microscope which can simultaneously report on the topology of DNA and conformation changes of the protein. Using Protein Induced Fluorescent Enhancement we determined that topoisomerase I remains bound during relaxation pauses. Additionally, we observed short bursts of greater fluorescence enhancement correlated to relaxation events, indicating a conformational change in the protein that moves the fluorophore closer to the protein during the relaxation process. We observed more bursts than relaxation events, revealing that not every protein conformational change results in a relaxation event. We infer that the enzyme is constantly changing conformation and attempting to change the topology of DNA, but only succeeds in a fraction of the attempts. The mechanism can be described as a series of attempts to pass one DNA strand through a break in another strand, which generates the pauses, culminating in a successful relaxation event. The experiments demonstrate that conformational changes in a molecular motor can occur with more frequency than successful mechanical steps.

Host: Marko

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Keywords: Physics, Astronomy, colloquium


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Neelesh Patankar: TBA

October 7, 2016, 4:00 PM - 5:00 PM

Title: TBA

Speaker: Neelesh Patankar, Northwestern University, Mechanical Engineering


Abstract: TBA

Host: Garg/Dutta

Speaker Schedule

Keywords: Physics, Astronomy, colloquium


Title: Playing Newton: Learning equations of motion from data

Speaker: Ilya Nemenman, Emory University


Abstract: Arguably, the physics’ goal of understanding nature can be formulated as inferring mathematical laws that govern natural systems from experimental data. With the fast growth of power of modern computers and of artificial intelligence algorithms, there has been a recent surge in attempts to automate this goal and to design, to some extent, an “artificial scientist.” I will discuss this emerging field, but will focus primarily on our own approach to it. I will introduce an algorithm that we have recently developed, which allows one to infer the underlying dynamical equations behind a noisy time series, even if the dynamics are nonlinear, and only a few of the relevant variables are measured. I will illustrate the method on applications to toy problems, including inferring the iconic Newton’s law of universal gravitation. I will end with applications to biological systems: modeling calcium dynamics and insulin secretion in pancreatic beta cells, as well as modeling the landscape of possible behavioral states underlying reflexive escape from pain in a roundworm.

Host: Marko/Schwab

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Keywords: Physics, Astronomy, colloquium


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Paul J. Steinhardt: TBA

November 4, 2016, 4:00 PM - 5:00 PM

Title: TBA

Speaker: Paul J. Steinhardt, Princeton University


Abstract: TBA

Host: Mel Ulmer

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Keywords: Physics, Astronomy, colloquium


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Tommaso Dorigo: TBA

November 11, 2016, 4:00 PM - 5:00 PM

Title: TBA

Speaker: Tommaso Dorigo, CERN

Abstract: TBA

Host: Schmitt/Andre

Speaker Schedule

Keywords: Physics, Astronomy, colloquium


Title: Insights into the structure and dynamics of biomolecules in cellular environments from computer simulations

Speaker: Michael Feig, Michigan State University

Abstract: Biological macromolecules such as proteins and nucleic acids have become well-understood at the single molecule level but it is much less clear how the structure-dynamics-function paradigms established largely under dilute and homogeneous conditions hold up under realistic biological conditions where crowding, heterogeneity, and the presence of a diverse set of metabolites are important factors. Using computational approaches we are exploring model systems of dense crowded systems ranging from simple spherical crowder models to concentrated protein solutions and a comprehensive model of a bacterial cytoplasm with all of the key components present in full atomistic detail. Simulations of these systems show altered dynamic properties, suggest the possibility of protein native state destabilization due to protein-protein and protein-metabolite interactions, altered solvent and metabolite behavior, and non-specific interactions between functionally related enzymes as a result of crowding. Some of the work described involves very large scale computer simulations that were enabled by methodological advances that will also be briefly discussed.

Host: Marko

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Keywords: Physics, Astronomy, colloquium


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Abigail Vieregg: TBA

January 13, 2017, 4:00 PM - 5:00 PM

Title: TBA

Speaker: Abigail Vieregg, University of Chicago


Abstract: TBA

Host: Mel Ulmer

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Keywords: Physics, Astronomy, colloquium


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Joel Brock: TBA

January 20, 2017, 4:00 PM - 5:00 PM

Title: TBA

Speaker: Joel Brock, Cornell University 

Abstract: TBA

Host: Bedzyk

Speaker Schedule

Keywords: Physics, Astronomy, colloquium