We study the structure and dynamics of soft matter and biological materials.
We take a primarily deconstructionist approach to systematically investigate structure and molecular motions in complex systems at the nanometer length scale and sub-nanosecond time scale. This research is highly interdisciplinary, informing applied disciplines such as Chemical and Biomedical Engineering, as well as fundamental scientific fields such as physics, chemistry, biology, and biophsyics. We utilize approaches from experimental soft matter physics, molecular biology and microbiology.
A few of the topics that we are pursuing include: The Structure, Dynamics, and Phenomena of Biomolecular Hydration Water; Untangling the Nanoscopic Origins of Materials Properties in Low Entropy Liquids; and Insights and Applications from Lipid Phase Behavior.
Hydration water: water molecules at the interface
The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological/biophsyical study and for industrial formulations. We use direct physical measurements, like inelastic neutron scattering, in combination with molecular dynamics simulations to study the structure and motions of water at the molecular scale to learn about these changes in their molecular properties.
Perticaroli et al. JACS, 2017. Ishai et al. J. Phys. Chem. B. 2013. Nickels et al. Biophys. J. 2012.
Understanding the structure of biological membranes
The lipid raft hypothesis tells us that the lipids in the cell membrane are laterally organized to provide the resident membrane proteins an appropriate physical environment. The physical principles and biological mechanisms that control the size and composition of these lateral structure are the subject of substantial debate. We seek to leverage new methods to study the cell membrane at the molecular scale and to understand the many unexpected ways that it organizes itself.
Nickels et al. PLoS Bio. 2017, Nickels et al. J. Phys. Chem. Lett. 2017, Nickels et al. JACS. 2015.
Molecular origins of physical properties in liquids
In liquids, the ability of neighboring molecules to rearrange and jostle past each other is directly related to viscosity, the property which describes the propensity to flow. The presence of hydrogen bonds complicates the molecular scale picture of viscosity because hydrogen bonds are attractive, directional interactions which, in some cases, results in transient network structures. We use experimental and computational methods to investigate the hypothesis that the timescale of hydrogen bond network reorganization is the dominant dynamical timescale associated with viscosity. Evidence of this will inform our understanding of viscosity in these important liquids and in other low entropy systems.
Perticaroli et al Phys. Chem. Chem Phys. 2017
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Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. We advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model in Nickels et al. J. Phys. Chem. Lett. 2017. The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.
This link provides the files for the B. subtilis lipid extract model, please cite Nickels et al. J. Phys. Chem. Lett. 2017.