I work at the crossover of biology, physics, chemistry and computer science, in the intramural research program of the National Institutes of Health (NIH).
Until Fall 2020, I worked in the Institute for Computational Molecular Science (ICMS) directed by Michael Klein
The sections below detail some of the research projects that I carried out in the past. They haven't been updated in a while! I will eventually add more recent info, also for the newer projects that I'm carrying out at NIH.
I use detailed models of atoms and molecules, non-equilibrium sampling methods, bioinformatics techniques and the largest supercomputers, seeking clear answers to complex problems: the self-assembly of biological matter, the flow of chemicals into the human body, and the replication of viruses and bacteria.
Structure of the lipid matrix of human stratum corneum; phase coexistence at low hydration and physiological pH; MD simulations (CHARMM36 force field) to interpret small angle X-ray and neutron scattering (SAXS and SANS) data; coarse-grained MD simulations to model the self-assembly of the lipid matrix.
Mapping the phase coexistence in lipid membranes with mixed composition and with embedded proteins; mechanism of membrane fusion in eukaryotes and viruses; development of coarse-grained models for biologically relevant molecules.
In the figure: hypothesized intermediate of virus-cell fusion (cross section of the two membranes).
Mechanism of proton conduction through the M2 viral channel; mapping drug-binding sites to guide the design of new inhibitors; predicting the fitness of viral mutations.
In the figure: density of water throughout M2's pore, seen from within the viral membrane.
Design of many-body variables and algorithms to follow or to bias complex phenomena.
Development of the collective variables module (colvars), a library for NAMD and LAMMPS obtained by combining a flexible C++ code to run metadynamics, and a re-implementation by Jérôme Hénin of the ABF method.
Many different algorithms are now supported in a unified flexible interface.
In the figure: tracking the configurations of a peptide dimer by using "tilt" and "spin" variables.
For 3+ year students of Biology and graduate students of the College of Science and Technology (CRN: 2926 and 2928, BIOL-3312 and BIOL-5312).
All course material (lecture slides, practice exams, exercises) is available for download through Blackboard.