Yong Duan

Associate Professor

Office: 4335 GBSF
Telephone: (530) 754 7632
Email: duan@ucdavis.edu Lab: Duan Lab

Personal Education
Ph.D., Physics, University of Pittsburgh, 1996
M.S., Physics (NMR), Wuhan Institute of Physics and Mathematics, Academia Sinica, P.R. China
B.S., Physics, Wuhan University, China

Research Interests:
Our main research interests are development and application of computational methods to study the structure and dynamics of bio-molecular systems. We focus on protein folding and aggregation and protein structure prediction, simulation method development, structure and dynamics of G-protein coupled receptors, DNA-protein interactions, and computer aided drug design.

Proteins need to “fold” to their native productive states to become biologically active. A number of proteins can also misfold and have been linked to a number of human diseases, including cystic fibrosis, Alzheimer’s disease and other amyloidoses, and prion spongiform encephalopathies such as Creutzfeldt-Jacob disease. An understanding of the mechanism differentiating productive protein folding from misfolding and aggregation is critical to preventing misfolding and misassembly of proteins and would enable us to predict protein structures more accurately and to design new proteins. We are conducting simulation studies to elucidate the process of protein folding and aggregation.

G-protein coupled receptors (GPCR) are membrane proteins that can be activated/deactivated by external stimuli and initiate signal transduction. GPCR have been the premier targets of drug development effort and about 50% of the existing drugs on the market are designed to interact with GPCRs. GPCRs are believed to share a common 7 transmembrane architecture with relatively flexible extra-cellular and cytoplasmic domains. Therefore, computational modeling can play important role to provide detailed and accurate information on the structure and dynamics of GPCRs.

The interactions between proteins and DNA play a central role in molecular biology and genomics. These interactions include both sequence-specific and sequence-non-specific types. In the sequence-specific interactions, proteins recognize a specific DNA sequence (e.g., restriction enzymes and transcription factors). In the non-specific type, proteins interact with DNA regardless of the sequence. These interactions are crucial for gene expression, gene activation/repression. Thus, understanding these interactions is considered a key step toward functional interpretation of genetic sequences in the post-genomic era.

Atul N. Parikh

Professor

Office: 3007 Engineering III

Telephone: (530) 754-7055
Email: anparikh@ucdavis.edu
Lab: Parikh Lab

Personal Education

1994 Ph.D. Polymer Science, The Pennsylvania State University Materials Science
1987 B.S.  Chemical Engineering, University of Bombay

Research Interests:

Self-Assembled Systems

• •molecular monolayers
• •phospholipid bilayers
• •surfactant-templated silica mesophases
• •Colloidal crystals

Physical Processes and Phenomena

• •self-assembly mechanisms
• •templating effects
• •phase stability and dynamics
• •phase transitions
• •dimensional confinement effects
• •structure-dynamics-function relations

David Rocke

Distinguished Professor

Office: Med Sci 1C, Room 146
Telephone: (530) 752-6999
Email: dmrocke@ucdavis.edu

Personal Education

Ph.D., University of Illinois, Chicago (Mathematics)
Supplemental Coursework, University of Chicago (Statistics)
M.A., University of Illinois, Chicago (Mathematics)
A.B., Shimer College (Mathematics and Physics)

Research Interests

•Statistical analysis of gene expression, proteomics, and metabolomics data
•Radiation biology: effects of low and moderate dose radiation on human skin
•Biomedical statistics
•Wound healing
•Formal models in international relations

Eduardo A. Silva

Assistant Professor

Email: esilva@ucdavis.edu
Lab: Silva Lab

Personal Education
Ph.D. Engineering Sciences: Bioengineering, University of Porto, Portugal (2008)

Research Interests

Our research focuses on the field of translation stem cell bioengineering. Our research aim is to develop new material platforms that enable one to control stem/progenitor cell trafficking in the body.