DynaLab

DynaLab is a coarse-grained molecular dynamics platform for protein mechanobiology - basically, it lets you watch how a protein folds, flexes, and unfolds when you pull on it. By representing each residue with just three or four beads instead of every atom, it reaches the microsecond-to-millisecond timescales where real conformational changes happen, timescales that conventional all-atom simulation usually can’t touch without a huge cluster. The engine traces its lineage to Upside2 from the Sosnick lab at UChicago (co-authored by John Jumper, who went on to co-create AlphaFold), and I extended it with constant-tension and velocity-clamp pulling, replica-exchange sampling, and a full analysis suite that turns raw trajectories into folding thermodynamics, mechanical stability, and contact maps. The technical core is a differentiable, composable force field expressed as a computation graph, so new energy terms and restraints can be added without ever recompiling the engine, and the whole thing runs from a guided browser app so the science stays in focus instead of the tooling.