Research
$ ./mechanistic-biophysics --integrate force-field AI
[ FORCE FIELD / MD ] [ AI / ML ]
U(r) = U_bonded + U_nonbonded [o_o]
F = -grad U /|_|\
\ /
+-------------+--------------+
v
[ PROTEIN ENSEMBLES ]
v
[ INTERACTIONS -> FUNCTION -> DISEASE ]
[ PROTEIN INTERACTION MODES ]
CONFORMATIONAL ENSEMBLE
states: ~\/\~ ~~\_/~ ~/\/~~
|
+-------+-------+
↓ ↓ ↓
SPECIFIC DYNAMIC CONDENSATE
~\/\~ ~\/\~ ( ~\/\~ ~~ )
|| . . . ( ~~ ~\_/~ )
[====] ~~\_/~ ( ~/\/~~ ~~ )status: resolving molecular mechanisms across biological scales
Disease-Relevant Biophysics
Mechanistic studies linking protein dynamics, molecular interactions, and biomolecular organization to disease and regulation.
01NeurodegenerationProtein structure, interactions, and condensate organization3 papers
JACSToward Accurate Simulation of Coupling between Protein Secondary Structure and Phase SeparationJournal of the American Chemical Society, 2024↗ BSTBackbone Interactions and Secondary Structures in Phase Separation of Disordered ProteinsBiochemical Society Transactions, 2024↗ JACSA Glimpse into the Initial Microsecond of Biomolecular CondensationJournal of the American Chemical Society, 2026↗
02Cancerp53 regulation and disease-associated protein mechanisms2 papers
03Post-Translational ModificationPhosphorylation-dependent regulation of protein ensembles1 paper
04ImmunologyBacterial immune evasion and viral protease dynamics2 papers
Protein Dynamics & Interactions
How conformational ensembles and molecular interactions regulate recognition, catalysis, phase behavior, and biological function.
01Phase SeparationStructure, molecular grammar, and condensate dynamics3 papers
JACSToward Accurate Simulation of Coupling between Protein Secondary Structure and Phase SeparationJournal of the American Chemical Society, 2024↗ BSTBackbone Interactions and Secondary Structures in Phase Separation of Disordered ProteinsBiochemical Society Transactions, 2024↗ JACSA Glimpse into the Initial Microsecond of Biomolecular CondensationJournal of the American Chemical Society, 2026↗
02p53Dynamic interactions and phosphorylation-regulated ensembles2 papers
03Viral & Pathogen-Associated ProteinsEnzyme inhibition and conformational dynamics2 papers
Multiscale Molecular Modeling
Physics-based and data-informed methods for accurate, efficient simulation of folded, disordered, and assembling biomolecular systems.
01Atomistic Model DevelopmentProtein-water balance and transferable interactions1 paper
02Enhanced SamplingReplica exchange, multiscale acceleration, and complex conformational dynamics3 papers
BPJTracking Flaviviral Protease Conformational Dynamics by Tuning Single-Molecule Nanopore TweezersBiophysical Journal, 2025↗ JCTCRe-balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein ConformationsJournal of Chemical Theory and Computation, 2023↗ MOFF2MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate SimulationsbioRxiv, 2026↗
03Coarse-Grained Model DevelopmentTransferable force fields for dynamic protein systems2 papers
04Theory & Off-Lattice ModelingValency, molecular organization, and phase behavior1 paper
MD + ML
Interpretable and physics-aware learning approaches for biomolecular sequence, molecular interactions, conformational ensembles, and function.