|PhD||University of California, San Diego||San Diego, Calif.||Physics|
We are studying the statistical thermodynamics and kinetics and computer modeling of biomolecules and polymers, particularly RNA and protein folding.
Biological molecules are large organic molecules composed of hundreds or thousands of atoms bound together by covalent bonds into a chain-like structure. One of the best known challenges in biology is to understand how biomolecules fold properly into compact structures to perform biological functions and how they mis-fold to cause disease. A fundamental problem we are pursuing is the study of the physical principles that govern folding-unfolding of bio-molecules. Based on the physical principles, we develop statistical mechanical theories and computational models to accurately predict the sequence-structure and structure-activity relationships for biomolecules. This involves biology, physics, computer science and, of course, mathematics.
Jose Almeida Cruz, Marc-Frederick Blanchet, Michal Boniecki, Janusz M. Bujnick, Shi-Jie Chen, Song Cao, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Samuel Coulbourn Flores, Lili Huang, Christopher A. Lavender, Veronique Lisi, Francois Major, Katarzyna Mikolajczak, Dinshaw J. Patel, Anna Philips, Tomasz Puton, John Santalucia, Fredrick Sijenyi, Thomas Hermann, Kristian Rother, Magdalena Rother, Alexander Serganov, Marcin Skorupski, Tomasz Soltysinski, Parin Sripakdeevong, Irina Tuszynska, Kevin M. Weeks, Christina Waldsich, Michael Wildauer, Neocles B. Leontis, and Eric Westhof. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA. 18 (4) doi: 10.1261/rna.031054.111 (2012).
Tian K, He Z, Wang Y, Chen SJ, Gu LQ. Designing a Polycationic Probe for Simultaneous Enrichment and Detection of MicroRNAs in a Nanopore. ACS Nano. 2013 Apr 10. [Epub ahead of print]
Liu L, Chen SJ. Coarse-grained prediction of RNA loop structures. PLoS One. 2012;7(11):e48460. doi: 10.1371/journal.pone.0048460. Epub 2012 Nov 8.
He Z, Chen SJ. Predicting ion-nucleic acid interactions by energy landscape-guided sampling. J Chem Theory Comput. 2012 Jun 12;8(6):2095-2101. Epub 2012 Apr 30.
Tan ZJ, Chen SJ. Ion-mediated RNA structural collapse: effect of spatial confinement. Biophys J. 2012 Aug 22;103(4):827-36. doi: 10.1016/j.bpj.2012.06.048.