Loomis Laboratory of Physics
1110 West Green Street
Urbana, IL 61801-3080
Interesting biological functions emerge from the detailed structure and dynamics of molecules. I use molecular dynamics simulations to distill quantitative micro-biological information from the trajectories of all-atom models of DNA–protein systems. Typically I use one of a variety of equilibrium and non-equilibrium enhanced-sampling techniques, including umbrella sampling and steered molecular dynamics. Once effective interactions have been extracted in this way, they can be used to explore biomolecular dynamics on timescales inaccessible to all-atom simulations. My work has focused on DNA–DNA and DNA–protein interactions, highlighting the importance of the physical properties of DNA in determining its behavior. Please see my curriculum vitae for more information about my skills, experience and the results of my work.
- MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems." Nucleic Acids Research (2020). "
- Single-molecule biophysics experiments in silico: Toward a physical model of a replisome." iScience 25:104264 (2022). "
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019). "
- A synthetic enzyme built from DNA flips 10⁷ lipids per second in biological membranes." Nature Communications 9:2426 (2018). "
- Optical voltage sensing using DNA origami." Nano Letters 18:1962-1971 (2018). "
- A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nat Commun 12:7138 (2021). "
- Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017). "
- De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016). "
- Close encounters with DNA." J Phys Condens Matter 26:413101 (2014). "
- A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment." Journal of Chemical Theory and Computation 10:2891-2896 (2014). "
- Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores." ACS Nano 7:6816-24 (2013). "
- Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012). "
- Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012). "
- End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). "
- DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010). "
- Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009). "