Research Projects

Project Title Short Summary Lab Members




Na+ and K+ condensation around DNA

Chromatin & DNA Modeling

DNA associates with histon proteins in higher eukaryotic cells, compactifying million-fold. The resulting chromatin fibers are very dynamic, regulating gene transcription. Using all-atom and coarse-grained molecular dynamics simulations, we are developing new insights into the chromatin fiber structure and stability.  Learn more... Alex Savelyev




Rhodopsin Cascade  

Signal Transduction Processes

Using tools from diverse areas of physics and bioinformatics we are building nonequilibrium statistical mechanics of signal transduction networks. In particular, we are interested in spatio-temporal regulation of eukaryotic cell motility. Learn more... Natsuki Tanaka, Pavel Zhuravlev




Water in Protein Dynamics

Native Protein Dynamics

We are developing an integrated system of multi-scale computational techniques, from very coarse-grained to all-atom models, to describe the native dynamics of various enzymes and signaling proteins. In a related project, we are working on new free energy computational methods for proteins. Learn more...  Chris Materese, Sean Walder, Sangwook Wu, Pavel  Zhuravlev





Last updated: April 6, 2006