- Biomedical Sciences Graduate Program | Kateri H. DuBay

Kateri H. DuBay

Education

  • BS, Georgetown University
  • Mphil, University of Cambridge
  • PhD, University of California, Berkeley

Primary Appointment

  • Assistant Professor, Chemistry

Contact

Research Interest(s)

The design of self-assembling nanomaterials

Research Description

The design of self-assembling nanomaterials stands as one of the great challenges in modern molecular science. The DuBay group employs theoretical and computational tools to address this challenge through investigations that lie at the intersection of soft condensed matter physics, polymer chemistry, biophysics, and nanomaterials.

At these very small length-scale, the effects of thermal fluctuations, entropy, energy, and kinetics are often comparable in magnitude, rendering materials highly sensitive to perturbations such as chemical doping and environmental changes. While a wide variety of useful structures can be made via self-assembly within a static environment by precisely tuning the interactions between assembling components, environmental controls give us the means to advance beyond the limitations of such endeavors. Biological systems provide a host of examples, demonstrating the remarkable complexity and high responsivity of materials formed via environmentally-directed assembly. Specifically our group looks at assembly within environments that vary either in space, such as in the presence of a chemical gradient, or in time, such as in response to biological signaling.

Given the physical length-scales of the systems we study and the time-scale over which they evolve, we design theoretical models to capture the essential physics of the studied phenomenon. Such schematic models leave out unnecessary details in order to isolate the factors of interest and enable us to probe more directly the fundamental questions surrounding the emergence of order and responsivity within the studied nanoassemblies.

An improved understanding of the rules governing assembly in these environments will yield novel insights into the formation of functional biomaterials as well as information useful for improving light harvesting, drug-delivery, environmental-sensing, and material fabrication; countless technological innovations await the ability to rationally design artificially-ordered and environmentally-responsive nanomaterials.

UNLEASH:

Because work in this lab is computational, beginner's level programming experience is required. Please indicate experience in the application.

Selected Publications

  • DuBay K, Bowman G, Geissler P. Fluctuations within folded proteins: implications for thermodynamic and allosteric regulation. Accounts of chemical research. 2015;48(4): 1098-105. PMID: 25688669
  • Weisman A, DuBay K, Willets K, Friesner R. A first-principles polarized Raman method for determining whether a uniform region of a sample is crystalline or isotropic. The Journal of chemical physics. 2014;141(22): 224702. PMID: 25494765
  • Dell E, Capozzi B, DuBay K, Berkelbach T, Moreno J, Reichman D, Venkataraman L, Campos L. Impact of molecular symmetry on single-molecule conductance. Journal of the American Chemical Society. 2013;135(32): 11724-7. PMID: 23905714
  • Heckel J, Weisman A, Schneebeli S, Hall M, Sherry L, Stranahan S, DuBay K, Friesner R, Willets K. Polarized Raman spectroscopy of oligothiophene crystals to determine unit cell orientation. The journal of physical chemistry. A. 2012;116(25): 6804-16. PMID: 22571336
  • Bounos G, Ghosh S, Lee A, Plunkett K, DuBay K, Bolinger J, Zhang R, Friesner R, Nuckolls C, Reichman D, Barbara P. Controlling chain conformation in conjugated polymers using defect inclusion strategies. Journal of the American Chemical Society. 2011;133(26): 10155-60. PMID: 21612291
  • Dubay K, Bothma J, Geissler P. Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone. PLoS computational biology. 2011;7(9): e1002168. PMID: 21980271 | PMCID: PMC3182858
  • DuBay K, Geissler P. Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions. Journal of molecular biology. 2009;391(2): 484-97. PMID: 19481551
  • Pawar A, Dubay K, Zurdo J, Chiti F, Vendruscolo M, Dobson C. Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. Journal of molecular biology. 2005;350(2): 379-92. PMID: 15925383
  • DuBay K, Pawar A, Chiti F, Zurdo J, Dobson C, Vendruscolo M. Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. Journal of molecular biology. 2004;341(5): 1317-26. PMID: 15302561
  • Leed A, DuBay K, Ursos L, Sears D, De Dios A, Roepe P. Solution structures of antimalarial drug-heme complexes. Biochemistry. 2002;41(32): 10245-55. PMID: 12162739
  • Ursos L, DuBay K, Roepe P. Antimalarial drugs influence the pH dependent solubility of heme via apparent nucleation phenomena. Molecular and biochemical parasitology. 2001;112(1): 11-7. PMID: 11166382
  • DuBay K, Hall M, Hughes T, Wu C, Reichman D, Friesner R. Accurate Force Field Development for Modeling Conjugated Polymers. Journal of Chemical Theory and Computation. 8 4556−4569.
  • Traub M, DuBay K, Ingle S, Zhu X, Plunkett K, Reichman D, Vanden Bout D. Chromophore-Controlled Self-Assembly of Highly Ordered Polymer Nanostructures Journal of Physical Chemistry Letters. 4(15): 2520-2524.