Professor of Chemistry and Biochemistry & Molecular Biology
B.S. 1998, University of Science and Technology of China
Ph.D. 2002, University of California at Irvine
Our general interests are mainly in the development of advanced computational methods and their applications to the study of biomolecules and biomaterials. These methods include more accurate protein force fields at atomistic and coarse-grained levels, as well as various enhanced sampling and efficient GPU-enabled algorithms. A particular emphasis has been on understanding how intrinsical disorder of proteins mediates function and how such functional mechanisms may be altered in human diseases. Our research has been supported by NSF, NIH and various local and state funding agencies.
Research in the Chen lab currently focuses on five key areas:
- Development of advanced sampling techniques and accurate implicit solvent models, particularly multi-scale enhanced sampling (MSES) method and balanced implicit solvent force fields;
- Intrinsically disordered proteins: structure, function and disease;
- Multi-scale simulation of fibril growth and nucleation;
- Computational characterization and design of novel functional peptides; and
- Advanced software for molecular modeling of small angle scattering.
Learn more at http://people.chem.umass.edu/jchenlab/.
K. H. Lee and J. Chen (2017), "Re-balancing the GBMV implicit solvent protein force field for accurate simulation of protein conformational equilibra", J. of Comput. Chem. (in press).
K. H. Lee and J. Chen (2016), "Multiscale Enhanced Sampling of Intrinsically Disordered Protein Conformations" J. Comput. Chem. 37, 550-557.
Z. Jia, S. K. Whitaker, J. M. Tomich and J. Chen (2016), "Organization and structure of branched oligopeptide bilayers", Langmuir 32 (38), pp 9883–9891.
D. Ganguly and J. Chen (2015), "Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations" PLoS Comput. Biol. 11(4): e1004247.
W. Zhang and J. Chen (2014), "Accelerate sampling of atomistic energy landscapes using topology-based coarse-grained models" J. Chem. Theory Comput. 10, 918-923.
D. Ganguly, W. Zhang and J. Chen (2013), "Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins." PLoS Comput. Biol. 9(11): e1003363. doi:10.1371/journal.pcbi.1003363. http://dx.doi.org/10.1371/journal.pcbi.1003363
W. Zhang, D. Ganguly and J. Chen (2012). "Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins" PLoS Comput. Biol. 8(1): e1002353. doi:10.1371/journal.pcbi.1002353. http://dx.doi.org/10.1371/journal.pcbi.1002353
Y. Wang, J. C. Fisher, R. Matthew, L. Ou, S. Otieno, J. Sublett, L. Xiao, J. Chen, M. F. Roussel, and R. W. Kriwacki (2011). "Intrinsic Disorder Mediates the Diverse Cell Cycle Regulatory Functions of the Cyclin-dependent Kinase Inhibitor, p21Cip1", Nature Chem. Biol. 7, 214-221.