Department of Applied Physics

Description

Biophysics

My group is using small angle x-ray scattering to measure structure-function relationships for small functional RNA molecules such as ribo-switches. This work is being done in collaboration with Dan Herschlag and Rhiju Das of the Biochemistry dept. We are also actively working on modeling pf RA structure and thermodynamics.

Lasers and Accelerators

I am collaborating with John Spence of Arizona state Univ on measurement of correlated scattering using the x-ray laser LCLS to capture enzyme function on micro-second to millisecond time scales. Other people involved include Vijay Pande of Chemistry, Dan Herschlag of biochemistry, and Jerry Hastings and Sébastien Boutet of SLAC.

Nanoscience and Quantum Engineering

My group is working as part of a consortium with Sarah Heilshorn (MSE) Nick Melosh (MSE) and Andy Spakowitz (Chem Eng) on self-assembly of nano structures from the natural protein clathrin to act as templates for metallization. These could potentially be of interest as experimental battery electrodes or for other applications.

Condensed Matter Physics

I am working on the overlap between statistical mechanics and biomolecular kinetics in terms of analytic solutions of the Fokker Planck equation for simplifies models of molecular motion. This work is being done in collaboration with Joel Franklin of Reed College and Marc Delarue of Inst. Pasteur.

Courses Taught

• Introductory Biophysics
• Methods in Computational Biology
• Numerical Methods for Physicists and Engineers

Selected Publications

• Reconstruction Of Low-Resolution Three-Dimensional Density Maps From One-Dimensional Small-Angle X-Ray Solution Scattering Data For Biomolecules
• Simulation Of Protein Folding By Reaction Path Annealing
• Closing The Folding Chamber Of The Eukaryotic Chaperonin Requires The Transition State Of Atp Hydrolysis
• A Comparative Study Of Motor-Protein Motions By Using A Simple Elastic-Network Model
• Random-Coil Behavior And The Dimensions Of Chemically Unfolded Proteins (Vol 101, Pg 12491, 2004)
• Protein Misfolding And Amyloid Formation For The Peptide Gnnqqny From Yeast Prion Protein Sup35: Simulation By Reaction Path Annealing
• Evaluation Of Ion Binding To Dna Duplexes Using A Size-Modified Poisson-Boltzmann Theory
• Low-Resolution Models For Nucleic Acids From Small-Angle X-Ray Scattering With Applications To Electrostatic Modeling
• Minactionpath: Maximum Likelihood Trajectory For Large-Scale Structural Transitions In A Coarse-Grained Locally Harmonic Energy Landscape
• The Complete Vs Ribozyme In Solution Studied By Small-Angle X-Ray Scattering
• The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure
• Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble