The completion of the human genome project has introduced a new paradigm for the diagnosis and treatment of
diseases, i.e., through direct manipulation of our genes. A fundamental understanding of the
molecular mechanism behind gene regulation is required before one can begin to design molecules that can
recognize genes and alter their expression. Our research program aims to (a) fundamentally elucidate several
aspects of gene regulation ranging from chromatin structure regulation to protein-DNA recognition; (b) use such
insights to optimize the design of short peptides and siRNAs that can
bind to genes and mRNAs with maximum efficiency; and last but not least, (c) develop new, computationally
efficient multiscale simulation methods to allow the systematic study of such complex biological systems.
Below are listed five research topics that our group is currently focusing on.
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Elucidating the role of histone tail chemical modifications in chromatin structure and gene transcription regulation
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Mesoscopic modeling of RNA to elucidate the mechanism and kinetics of RNA tertiary folding
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Molecular modeling of silencing RNAs to improve their efficiency in gene silencing
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Optimizing amino-acid sequence of short peptides for the design of efficient DNA-recognizing &alpha-helical proteins
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Understanding and modeling the transport mechanism by which gene-regulatory proteins search for their target genes
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