Research Mentors

Research Mentors in the Social Sciences and Humanities

Faculty mentors in the social sciences and humanities vary and are dependent upon faculty availability from year to year.  Applicants are encouraged to find faculty of interest and go to http://gradadmissions.uchicago.edu/academics_research/programs/, select a program, and then select the "Explore program faculty" link in the overview section.

Research Mentors in the Physical and Biological Sciences

The list of faculty below are small sample of research opportunities available in this program.  To find additional faculty, go to http://gradadmissions.uchicago.edu/academics_research/programs/, select a program, and then select the "Explore program faculty" link in the overview section.

Physical Sciences

Laurie Butler

l-butler@uchicago.edu

Research: http://chemistry.uchicago.edu/fac/butler.shtml

The area of spectroscopy and chemical reaction dynamics. Undergraduates work in collaboration with graduate students on state-of-the-art experiments and gain independence in data analysis and electronic structure calculations. Recent projects include probing the dynamics of bimolecular reactions by directly accessing the unstable radical intermediate along the reaction coordinate, investigating the stereoelectronic interactions important in the bond fission channels of organic radicals, and developing our predictive ability from first principle quantum mechanics for reaction rates and product branching. If you loved your undergraduate course in quantum mechanics and are interested in research at the interface of chemistry, mathematics, and physics, you'll enjoy working with us.

Aaron Dinner

dinner@uchicago.edu

How does the complex behavior that we associate with life come from elementary molecular interactions? We try to answer this question with computer simulations. Such models are useful because we can literally see how molecules move according to physical laws; they also enable us to independently change features that are normally coupled in experiments to probe their specific roles. The results can have important therapeutic applications. Students in our group are excited about combining chemistry, biology, mathematics, and computer science.

Research: http://chemistry.uchicago.edu/fac/dinner.shtml

Greg Engel

gsengel@uchicago.edu

Research: http://engelgroup.uchicago.edu/

Ultrafast photoenzyme dynamics

 

Dan Fabrycky

fabrycky@uchicago.edu 
http://astro.uchicago.edu/~fabrycky 
Extrasolar planets research. As of 2014, about 2000 planets are known to orbit around other stars in the Milky Way. Prof. Fabrycky studies the dynamical interactions of planets within these other planetary systems. Do they lie in the same plane, as do the planets of the Solar System? Do the eccentric shape of their orbits indicate a violent formation and early evolution? How do the dynamical interactions affect the possibility of life on the planetary surface? Do binary stars host planets with the same properties as single stars? Prof. Fabrycky has a variety of projects using state-of-the-art numerical simulations and analytic techniques.  As theory must be testable, the goal is always to explain the observational data or predict what new data should reveal.

Benson Farb

farb@math.uchicago.edu

Research: http://www.math.uchicago.edu/~farb/

My interests lie at the juncture of geometry, topology, group theory and dynamical systems. One common theme is how complicated objects are sometimes determined by very simple data. Here is a great example: Let M and N be two closed, locally symmetric (with no local torus factors), nonpositively curved manifolds of dimension at least 3. The Mostow Rigidity Theorem states that if M and N have isomorphic fundamental groups, then M must be isometric to N. In particular, invariants such as volume are actually topological invariants! Examples I study include discrete subgroups of Lie groups, 3-dimensional manifolds, groups acting on nonpositively curved singular spaces (e.g. trees, affine buildings, etc.), and groups of diffeomorphisms. I enjoy working in a number of different directions. These have included: geometric and combinatorial group theory; trying to understand the relationship between volume and degree (a topic combining differential geometry and ideas from dynamics); actions of infinite groups on manifolds; classifying manifolds with (sometimes hidden) symmetry. In the last few years, I have been focusing on studying mapping class groups and the moduli space of Riemann surfaces. Of special interest is the Torelli group, a classically studied but poorly understood group which is in many ways the mysterious part of the mapping class group. The interplay of combinatorial topology, 3-manifold theory, algebraic geometry and symplectic representation theory that one sees in this topic is especially fascinating.

Margaret Gardel

gardel@uchicago.edu

Research: http://squishycell.uchicago.edu/

Douglas MacAyeal (Glaciology/Geophysics/Earth Science/Climate Science)

contact: drm7@uchicago.edu

Research: http://geosci.uchicago.edu/research/glaciology_research.shtml

Internship announcement and suggested project topics: http://geosci.uchicago.edu/research/glaciology_summer_intern.shtml

I am a researcher who studies the Earth's glaciers and ice sheets to determine how they behave in the face of changing climate. Issues that motivate my research include human impacts associated with (1) sea-level rise that can occur when ice melts around the globe and also (2) glacier-fed water supplies that support agriculture and clean water needs in South America, Africa, and Asia. Summer interns working in the Glaciology/Geophysics/Earth and Climate Science group will collaborate with professors, postdoctoral scholars and graduate students (at an advanced level in PhD research) on a variety of scientific research topics and techniques. The research topics revolve around research that is designed to determine how the icy parts of the earth's environment (the ice sheets in Antarctica and Greenland, but also mountain glaciers in South America, Asia, and Africa) will change as a result of future climate warming. The techniques revolve around methods that either observe the behavior of these ice masses or that allow simulation of them on the computer using advanced numerical modeling techniques. Please refer to the internship announcement web page indicated immediately above for more specific ideas on intern projects and problems. Students who complete a successful internship with our group will walk away with experience in one or more of the fundamental modes of working that Earth Scientists need to have.

Benoit Roux

Research Interests:
We use theoretical and computational methods to advance our understanding of the structure, dynamics, and function of biological macromolecular systems at the atomic level. We are particularly interested in issues concerning the function of ion channels and other membrane transport proteins such as ion permeation, ion selectivity, and gating. Most of our work on ion channels is computational though we have recently started to add an experimental component to our research with electrophysiological measurements and protein crystallography. The computational approach called "molecular dynamics" (MD) is central to our work. It consists of constructing detailed atomic models of the macromolecular system and, having described the microscopic forces with a potential function, using Newton's classical equation, F=MA, to literally "simulate" the dynamical motions of all the atoms as a function of time. The calculated trajectory, though an approximation to the real world, provides detailed information about the time course of the atomic motions, which is nearly impossible to access experimentally. We use such all-atom MD simulations to rigorously compute conformational free energies, and binding free energies. In addition, other computational approaches, at different levels of complexity and sophistication, can be very useful. In particular, Poisson Boltzmann (PB) continuum electrostatic models, in which the influence of the solvent is incorporated implicitly, plays an increasingly important role in estimating the solvation free energy of macromolecular assemblies. We are also spending efforts in the development of new computational approaches (polarizable force field, solvent boundary potentials, efficient sampling methods) for studying biological macromolecular systems.

Lab Web Page:  http://thallium.bsd.uchicago.edu/RouxLab/

Email: roux@uchicago.edu

Greg Voth

gavoth@uchicago.edu

Research: The research in the Voth group involves theoretical and computer
simulation studies of biomolecular and liquid state phenomena, as well as
of novel materials. A primary goal of this effort is the development and
application of new computational methodologies to explain and predict the
behavior of complex systems. These methods are developed, for example, to
probe phenomena such as protein-protein self-assembly, membrane-protein
interactions, biomolecular and liquid state charge transport, complex
fluids, and nanoparticle self-assembly.

Center for Chemical Innovation (CCI)

This NSF Center for Chemical Innovation (CCI) project is focused on
developing a novel, systematic, and transformative scientific capability
for the scientific community. Our goal is to develop and apply new
theoretical and computational methods relating the molecular scale to
cellular processes. The project will combine conceptual advances in
statistical mechanics and condensed phase dynamics with computer
simulation methodology and cyberinfrastructure. For more information,
please visit: http://cmts.uchicago.edu/

Jonathan Weare

weare@math.uchicago.edu

Whether the goal is to find life on other planets, predict and  
understand climate change, or design new drugs, we are confronted with  
the need to simulate increasingly complex models. Unfortunately,  
achieving our simulation goals usually requires observing events that  
occur extremely infrequently or on very long time scales, and even  
today's increasingly powerful computers are not up to the task without  
the help of efficient numerical algorithms.  We develop and analyze  
new algorithms to tackle these challenges as well as work with  
specialists to apply the methods to real world problems.

Biological Sciences

Eric Beyer

ebeyer@peds.bsd.uchicago.edu

Research: My laboratory is investigating the process of intercellular communication; our specific goal is a molecular understanding of the structure and function of gap junctions. Gap junctions are the specialized plasma membrane structures that contain low resistance channels linking adjacent cells. In excitable tissues, they permit electrical coupling; in non-excitable tissues, they permit passage of small molecules involved in metabolic support, growth control, and embryogenesis. They may also facilitate drug metabolite delivery between cells. Gap junctions are encoded by a family of subunit proteins called connexins which are related in their transmembrane and extracellular regions, but which have unique cytoplasmic domains. Connexin-specific sequences confer different physiologic channel properties or regulation. Mutations of connexins have been associated with a number of diseases including non-syndromic deafness, Charcot-Marie-Tooth disease (neuropathy), cataracts, oculodentodigital dysplasia, and skin diseases. In vitro expression studies and transgenic mouse studies are being used to examine the consequences of disease-associated connexin mutations. The transfection of communication-deficient cells with connexin sequences (or expression of in vitro transcribed connexins in Xenopus oocytes) has demonstrated connexin-specific channel properties, permeabilities, and regulation. Site-directed mutagenesis is being used to identify sites within the connexins important in determining gating and permeability properties.

David Boone

dboone@medicine.bsd.uchicago.edu

Research: http://biomed.uchicago.edu/common/faculty/boone.html

Eugene Chang

echang@medicine.bsd.uchicago.edu

Research: Dr. Chang's laboratory investigations include the mechanisms of mucosal cytoprotection to inflammation and immune-associated injury that involves the study of inducible heat shock proteins. As the physiological expression of these proteins is maintained by the enteric flora and by bacteria-derived nutrient metabolites, many studies are focused on understanding the molecular signals and pathways that underlie microbial-host interaction. In this regard, the lab has identified several probiotic formulations that selectively induce intestinal epithelial heat shock proteins. The induction of Hsps results in increased resistance against many injurious agents and conditions, including bacterial cytotoxins, immune/inflammatory mediators, ionizing radiation, toxic injury, and bacterial (type III secretion apparatus) invasion.

Dr. Chang is also interested in Na absorptive mechanisms of the epithelial cell, which is focused on defining the role and regulatory mechanisms of Na-H exchange proteins in gut and renal cells. The four isoforms expressed by these epithelia have region- and cell-specific expression and differ in their physiological roles. His lab is currently studying how these isoforms reach different parts of the epithelial cell membrane and the cellular mechanisms involved in regulating their activities

Nathan Ellis

naellis@uchicago.edu

Research: Cells contain numerous DNA repair systems that maintain the integrity of the genome. When a component of one of these systems is mutated, either somatically or in the germline, cells accumulate mutations and susceptibility to cancer increases. Homologous recombination (HR) is an error-free pathway that can restart broken replication forks and repair DNA double-strand breaks. However, excessive recombination is dangerous because it can interfere with normal DNA replication and it can cause chromosome re-arrangements. Consequently, HR is carefully controlled so that it is called into play only when it is needed. There is one genetic disorder of the human-Bloom's syndrome (BS)-that features excessive HR. The gene mutated in BS is BLM. BLM is a DNA helicase of the RecQ family, and it plays a critical role in controlling excessive HR. We study the function of BLM in HR. BLM itself in regulated by a protein modification by peptides known as small ubiquitin-like modifiers (SUMOs). BLM contains four SUMO-acceptor sites. When one or more of these SUMO sites is mutated and the mutant protein is expressed in cells, it generates excessive replication-associated, double-strand breaks (DSBs). Predictably, the cells are hypersensitive to DNA damaging agents, epecially when the DNA damage is delivered to S phase cells. To our surprise, however, damage-induced HR is defective in cells that express SUMO-mutant BLM. We are now focusing on BLM interaction with proteins that mediate the HR process and characterizing SUMO's role in regulating those interactions. Our work in the function of BLM in HR has implications in the mechanisms by which cancers develop because DNA repair guards against the accumulation of somatic mutations and consequently impacts carcinogenesis. Germline genetic variation in DNA repair genes can compromise repair function and thereby cause increased susceptibility to a variety of cancers. We are characterizing the human genetic variation in key DNA repair genes and quantifying the effect of this variation in susceptibility to the development of colorectal cancer. As we identify risk-associated alleles, we study them functionally in cell-based systems.

Kathleen Millen

kmillen@bsd.uchicago.edu

Research: http://www.genes.uchicago.edu/millen.html

Glenn Randall

grandall@bsd.uchicago.edu

Research: http://microbiology.uchicago.edu/randall.htm
http://biomed.bsd.uchicago.edu/common/faculty/randall.html