Margaret Shun Cheung
Assistant Professor of Physics
629C SRI
University of Houston
Houston, TX, 77204
Tel: 713-743-8358
Fax: 713-743-3589
email: mscheung_at_uh.edu
NSM website


Fall08 PHYS1301 Introductory General Physics I

Research Interests:
Theoretical Biological Physics, Nanobiophysics, and Soft Condensed Matter

Research projects in my group focus on the development of models and physico-chemical principles for macromolecular dynamics at various stress conditions. A complete understanding of the physics behind a collective behavior of biomacromolecules in response to incoming signals or changes in environments will in turn shed lights on better designs of probes to manipulate living matter in cell-like conditions. To tackle macromolecular dynamics that spans multiple orders of magnitudes in space and time, we develop and apply state-of-the-art multi-scale molecular simulation approaches that integrate high-performance computing to investigate the relationship of structure-function-environment in biomolecules that dictate biological functions.

Projects in my group strongly tie to interdisciplinary research activities in the city of Houston that is a nationally recognized hub of medical centers, petroleum industries, and material sciences. We work on various issues in biological physics, nanobiology, and soft condensed matter.

  • Protein dynamics in vivo

  • Biopolymer dynamics in nano-sized confinement

  • Simulation of surfactant self-assembly


  • Protein dynamics in vivo:

    How the crowded environment inside cells affects the structures of proteins with aspherical shapes is a vital question because many proteins and protein-protein complexes in vivo adopt anisotropic shapes. Here we address this question by combining computational and experimental studies of a football-shaped protein (i.e., Borrelia burgdorferi VlsE) in crowded, cell-like conditions. The results show that macromolecular crowding affects protein-folding dynamics as well as overall protein shape. In crowded milieus, distinct conformational changes in VlsE are accompanied by secondary structure alterations that lead to exposure of a hidden antigenic region. Our work demonstrates the malleability of "native" proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo.


    To investigate the consequences of macromolecular crowding on the behavior of a globular protein, we performed a combined experimental and computational study on the 148-residue, single-domain protein, Desulfovibrio desulfuricans apo-flavodoxin. In vitro thermal unfolding experiments, as well as assessment of native and denatured structures, were probed using far-UV circular dichroism (CD) in the presence of various amounts of Ficoll 70, an inert spherical crowding agent. Ficoll 70 has a concentration-dependent effect on the thermal stability of apo-flavodoxin. As judged by CD, addition of Ficoll 70 causes an increase in the amount of secondary structure in the native-state ensemble but only minor effects on the denatured state. Theoretical calculations, based on an off-lattice model for an apoflavodoxin protein and hard-sphere particles for Ficoll 70, are in good agreement with the in vitro data. The simulations demonstrate that, in the presence of 25 % volume occupancy of spheres, native flavodoxin is thermally stabilized and the free energy landscape shifts to favor more compact structures in both native and denatured states. It is revealed that the native-state compaction originates in stronger interactions between the helices and the central beta-sheet, as well as by less fraying in the terminal helices. This is the first study to demonstrate that macromolecular crowding has structural effects on the folded ensemble of polypeptides.


  • Biopolymer dynamics in nano-sized confinement:

    The behavior of biopolymers in nano-sized confinement is investigated using coarse-grained models and molecular simulations. We address the effects of geometry of a confinement and the wall-protein interactions on protein folding dynamics. By measuring folding rates and dissecting structural properties of the transition states in nano-sized spheres and ellipsoids, we are able to justify the best form of a confinement in which the rates of folding kinetics are most enhanced. This knowledge in identifying optimal conditions for reactions will have a broad impact in nanotechnology and pharmaceutical sciences.


  • Simulation of surfactant self-assembly:

    An understanding of how hydrocarbons and surfactants interact in wet and porous media is essential to improve petroleum production rates. We investigate hydrophobic interactions in hydrocarbons and surfactants at multiple scales ranging from a nano-sized pore in an aquifer to a meter-sized reservoir. Specifically, this project will examine principles of how surfactants transfer hydrocarbons from solid surfaces to solutions as a function of the pore size and material composition using molecular simulations. Because these dynamics occur at multiple length and time scales all-atomistic models are not viable for simulations of a large complex system that involves hydrocarbons, surfactants, and water molecules. To circumvent these difficulties, we develop and apply multi-grained molecular simulations to investigate dynamics of hydrocarbons and surfactants in bedrocks.