Force Field Refinements Towards Super-Accuracy Molecular Dynamics Simulation
- Molecular Dynamics Simulations of DNA-DNA and DNA-Protein Interactions. Current Opinion in Structural Biology, In press, 2020
- Improved Parameterization of Protein–DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA. Journal of Chemical Theory and Computation, In press, 2020
- New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Physical Chemistry Chemical Physics, 20:8432–8449, 2018
- Improved parameterization of amine–carboxyate and amine–phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields. Journal of Chemical Theory and Computation, 12:430–443, 2016
- Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields. Biopolymers, 105:752–763, 2016
- Improved parametrization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems. The Journal of Physical Chemistry Letters, 3:45–50, 2012
Protein folding & drug docking
Self-assembly in Living Cells
Epigenetics is the study on how cells with identical genomic DNA differentiate into various cell types (e.g., brain, heart, cancer etc.). Recently, epigenetics has been expanding from the conventional information-centric view (e.g., the human genome project) to the structure-centric view (e.g., the 4D nucleome project). This updated view indicates that the self-assembled structure of the gene-carrying chromosomes and the nuclear envelop provide a way to regulate gene activities. We aim to answer the unresolved question in epigenetics: What are the physical driving forces between epigenetic building blocks (nucleosome and lamin complexes for chromosome and nuclear envelop, respectively)? How do those forces control the self-assembled structure of chromosomes inside a nucleus? To answer those questions, we will develop a physics-based model of chromosome that describes the forces between nucleosomes in a physically correct way. Then, we will develop a physical model of nuclear envelop that correctly describe the interaction between lamin and nucleosome complexes. Finally, we will build the standard model of a whole nucleus that has never been built yet.
- Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation” Nature Communications, 7:11045, 2016
- Effect of cytosine modifications on DNA flexibility and nucleosome mechanical stability” Nature Communications, 7:10813, 2016
- The structure and intermolecular forces of DNA condensates” Nucleic Acids Research, 44:2036–2046, 2016
- In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.” Proceedings of the National Academy of Sciences, 110:20099–20104, 2013.
- Molecular dynamics of membrane-spanning DNA channels: Conductance mechanism, electro-osmotic transport and mechanical gating” The Journal of Physical Chemistry Letters, 6:4680–4687, 2015