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Quantum-mechanically-driven charge polarization and charge transfer areubiquitous in biomolecular systems, controlling reaction rates, allostericinteractions, ligand-protein binding, membrane transport, anddynamically-driven structural transformations. Molecular dynamics (MD)simulations of these processes require quantum mechanical (QM) information inorder to accurately describe their reactive dynamics. However, currenttechniques -- empirical force fields, subsystem approaches, ab initio MD, andmachine learning -- vary in their ability to achieve a consistent chemicaldescription across multiple atom types, and at scale. Here we present aphysics-based, atomistic force field, the ensemble DFT charge-transferembedded-atom method, in which QM forces are described at a uniform level oftheory across all atoms, avoiding the need for explicit solution of theSchr\"{o}dinger equation or large, precomputed training datasets. Couplingbetween the electronic and atomistic length scales is effected through anensemble density functional theory formulation of the embedded atom methodoriginally developed for elemental materials. Charge transfer is expressed interms of ensembles of ionic states basis densities of individual atoms, andcharge polarization, in terms of atomic excited state basis densities. Thisprovides a highly compact yet general representation of the force field,encompassing both local and system-wide effects. Charge rearrangement isrealized through the evolution of ensemble weights, adjusted at each dynamicaltimestep via chemical potential equalization.

Embedding quantum statistical excitations in a classical force field