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publications
Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling
Published in Journal of Chemical Theory and Computation, 2020
G-quadruplexes (GQs) are nucleic acid structures critical for gene regulation and genomic stability, making them promising drug targets for diseases like leukemia and gastrointestinal stromal tumors. Using molecular dynamics simulations with nonpolarizable and polarizable force fields, we highlighted the importance of ion interactions, base substitutions, and structural dynamics in GQ stability, providing insights to guide the development of GQ-targeting therapeutics and importance of polarizability in modelling these structures.
Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling
Published in Journal of Chemical Theory and Computation, 2020
G-quadruplexes (GQs) are nucleic acid structures critical for gene regulation and genomic stability, making them promising drug targets for diseases like leukemia and gastrointestinal stromal tumors. Using molecular dynamics simulations with nonpolarizable and polarizable force fields, we highlighted the importance of ion interactions, base substitutions, and structural dynamics in GQ stability, providing insights to guide the development of GQ-targeting therapeutics and importance of polarizability in modelling these structures.
Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity
Published in The Journal of Physical Chemistry B, 2024
Striga Hermothica is a parasitic plant which costs agriculture billions of dollars per year. It perceives host plants via ShHTL7, an enzyme which binds to plant hormones named strigolactones. Using umbrella sampling, we explain the structural cause of the heightened sensitivity over ShHTL6 and host plant protein OsD3.
Two for the Price of One: Integrating Larnge Language Models to Learn Biophysical Interactions
Published in arXiv Preprint, 2025
In this paper, we review methods for combining molecular representations in drug design and proposes that merging internal layers of domain-specific biological language models can improve both efficiency and accuracy in modeling molecular interactions, offering a compact yet effective alternative to standard approaches.
Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple mutant
Published in Biophysical Journal, 2025
This study uses molecular dynamics simulations to show how specific mutations in the Arabidopsis KAI2 receptor enhance strigolactone sensitivity by stabilizing ligand binding, enlarging the binding pocket, and increasing binding rates—offering insight into engineering crop receptors to better detect and resist the parasitic weed Striga hermonthica.
talks
Dynamics of the 1:2:1 and 1:6:1 C-Myc G-Quadruplexes with the Drude Polarizable Force Field
Published:
Predicting the Substrate Specificity and Regioselectivity of Halogenases Using Deep Learning
Published:
teaching
BIOP 401: Introduction to Biophysics
Undergraduate/Graduate course, University of Illinois Urbana-Champaign, School of Molecular & Cellular Biology, 2023
Teaching Assistant. (Graded assignments and created slides for/taught weekly recitation sections)