Software
Biomolecular Condensate Nucleation MC | GitHub | Publication
Fortran/MPI Monte Carlo framework for nucleation free-energy calculations of biomolecular condensates in the grand canonical ensemble. Implements aggregation-volume-bias (AVBMC) and configurational-bias (CBMC) Monte Carlo with long-chain insertion and deletion moves, umbrella sampling with WHAM, and distance- and energy-based cluster criteria, supporting residue-level condensate force fields (Mpipi and HPS force field variants)
FALK22 Analysis | GitHub | Publication
Python pipeline for proteome-scale sequence analysis of phase-separation propensity: UniProt retrieval, calculation of 22 physicochemical sequence features (net charge, disorder, κ, SCD), UMAP projection, HDBSCAN clustering, and mutual-information feature attribution.
DDFT for Biomolecular Condensates | GitHub | Publication
Dynamical density functional theory solver for the time evolution of concentration profiles in biomolecular condensates, implemented with FiPy and parameterized from coarse-grained OpenMM simulations.
DeepDrive-MD | GitHub | Publication
Weighted ensemble extension of Deep Drive MD adaptive sampling workflow, coupling molecular dynamics to a convolutional variational autoencoder that identifies outlier conformations to steer sampling.
Force field parameters
Modified Martini 3 interaction parameters for biomolecular condensate formation, with GROMACS topologies and equilibrated inputs spanning protein–water interaction scalings (1.00–1.03) at 0 and 100 mM salt | GitHub | Publication
Coarse-grained solvent parameters, simulation inputs and plotting data reproducing the coarse-grained molecular liquids for mesoscale simulations | GitHub | Publication
Reproducibility Data
Simulation inputs and PLUMED scripts reproducing multiple-medoid OPES simulations of the SARS-CoV-2 frameshifting stimulatory element from two starting motifs. | GitHub | Publication
Simulation inputs and PLUMED scripts reproducing OPES free-energy surfaces of an H-type RNA pseudoknot across two orthogonal collective-variable sets (Q_stem, N_HB) over 300–480 K | GitHub | Publication