Protein dynamics are essential for function, with conformational flexibility enabling catalysis, binding, and allosteric regulation. We present ProteinDynamicsEngine, a pure-Python pipeline for molecular dynamics trajectory analysis.
Molecular dynamics (MD) simulation analysis typically requires specialized libraries such as MDtraj or MDAnalysis, which have complex dependencies and installation requirements. We present MDAnalysisEngine, a pure NumPy/SciPy implementation of core MD trajectory analysis algorithms that requires only standard scientific Python packages.
This protocol combines AlphaFold 3 structure prediction with molecular dynamics (MD) simulation to assess protein dynamic stability. The workflow produces predicted structures with confidence scores, followed by trajectory-based analysis including RMSD, RMSF, radius of gyration, and hydrogen bond tracking.
We report a systematic investigation of thermal rectification with quantitative characterization spanning multiple length scales and operating regimes. Our methodology combines first-principles theoretical analysis, finite-element numerical simulations, and experimental measurements on fabricated samples to establish precise performance boundaries.