Biophysics and Bioengineering

The biophysics group of Huey Huang works on a new class of peptide antibiotics that act on cell membranes rather than proteins. The group has invented new ways of studying supramolecular structures formed by peptides in membranes using optical, X-ray and neutron techniques. By such methods, they have identified two types of pores formed by antimicrobial peptides: a Barrel-Stave Model appropriate to alamethicin and a Toroidal (or Wormhole) Model appropriate to magainin

Barrel Stave pores (alamethicin)

Toroidal pores (maginin)

Anatoly Kolomeisky works in the areas of theoretical physical chemistry, theoretical biophysics and statistical mechanics. He is interested in biological transport problems which include 1) understanding of the mechanisms of transfer of chemical energy into mechanical motion by motor proteins moving in cells along rigid filaments and 2) modeling of the dynamic behavior of microtubules (biological filaments). He also works in the area of cooperative phenomena in non-equilibrium complex systems such as traffic problems, kinetics of biopolymerization, multi-particle biological transport and driven lattice gases. Other areas of interest are random walks, polymer dynamics, electrophoresis, thermodynamic properties of electrolytes and systems with long-range interactions, and hydrophobicity

The computational biophysics group of Jianpeng Ma is jointly appointed in the Verna and Marrs McLean Department of Biochemistry and Molecular Biology at Baylor College of Medicine and in the Department of Bioengineering at Rice University. The main focus of research is on computational study of structure-function relationship of proteins, especially on energetics and dynamics of large-scale conformational transitions. The primary tools employed are molecular dynamics simulation methods. Recent work conducted in the group on the huge ATP-driven molecular motors, the molecular chaperonin GroEL and the F1-ATP synthase, demonstrates that molecular dynamics simulation methods have come into an age that one can now use them to realistically study very large protein complexes.

Jason Hafner is interested in the application of nanostructures to molecular biophysics. His group employs carbon nanotubes as high-resolution probes for determining biomolecular structure and function by atomic force microscopy. In addition, nanotube growth and nucleation rates are being studied to elucidate the chemical kinetics of nanotube synthesis, which will allow the fabrication of probes with specific optical properties for near-field optical microscopy of biomolecules. Other research areas include the fabrication cell wall mimics for studying membrane protein dynamics by atomic force microscopy, and the use of nanoscale electrodes for studying ionic transport along protein fibrils.

Cecilia Clementi's research activity lays at interface of Physics, Chemistry and Biology. Her current research interests concern the theoretical and computational investigation of protein folding, protein interactions and functions. Her most recent research has focused on the definition and exploration of protein models with different levels of complexity aimed to study, and possibly predict, the folding mechanism of proteins. The modeling procedures rely mostly on the application of statistical mechanics techniques, to capture the important ingredients of the proteins systems. The kinetic and thermodynamics of the protein models is extensively studied through molecular dynamics simulations in order to compare with the experimental data. The models and theories developed so far have been successfully applied to a set of monomeric proteins. The study will be enlarged to include protein-protein interactions and assembling, in order to proceed toward an understanding of biological functions. Such studies can have important applications in pharmacology and medicine. Dr. Clementi has ongoing collaborations with the Department of Biochemistry and Cell Biology, and with the Department of Computer Science.

Configurational energy of different structures of Dihydrofolate Reductase (DHFR) protein

Using both Monte Carlo computer simulation and analytical field theory, Michael Deem develops techniques for the calculation of structural and transport properties of a variety of biological and inorganic materials. The field of materials science and chemistry has benefited tremendously from recent advances in synthesis, characterization, and processing. Novel microporous materials, including zeolites, clays, and porous carbons, are discovered and their properties examined at an increasing pace. Stochastic "diversity syntheses" are producing a tremendously increased number of solid-state, organic, and biological compounds, and associated selection schemes allow extraction of those compounds with the physical, chemical, or biological properties of interest. Simultaneously, among the most exciting developments in statistical mechanics over the past decade have been powerful methods for the computer simulation of materials. To date these methods have been developed and tested mainly on model systems. In many cases, however, formulations appear possible that allow investigation of novel materials of current interest. Moreover, new field-theoretic techniques in statistical mechanics allow computation of meso- and macroscopic material properties from such atomistic simulations.

Conservative (green) and non-conservative (yellow) mutations in the evolution of green fluorescent protein

The Deem group is interested in four main areas of research:

1. Bioinformatics.
2. Molecular evolution.
3. Zeolite structure and nucleation
4. Transport-limited chemical reactions

Both simulation and analytical statistical mechanics are used to attack these problems. Biased Monte Carlo and parallel tempering, in particular, are used to great advantage in determining equilibrium behaviors. Field theories are used to analyze the long-time dynamics of two-dimensional chemical reactions and to extend short-time computer simulations of transport. Combinatorial chemistry and protein molecular evolution are studied with a variety of random energy models.