TY - JOUR A1 - Delle Site, Luigi A1 - Krekeler, Christian A1 - Whittaker, John A1 - Agarwal, Animesh A1 - Klein, Rupert A1 - Höfling, Felix T1 - Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir JF - Advanced Theory and Simulations N2 - The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed. Y1 - 2019 U6 - https://doi.org/10.1002/adts.201900014 VL - 2 SP - 1900014 ER - TY - JOUR A1 - Dibak, Manuel A1 - Fröhner, Christoph A1 - Noé, Frank A1 - Höfling, Felix T1 - Diffusion-influenced reaction rates in the presence of pair interactions JF - The Journal of Chemical Physics N2 - The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi’s volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction–diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction–diffusion equation in the steady state and derive semi- analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions. Y1 - 2019 U6 - https://doi.org/10.1063/1.5124728 VL - 151 SP - 164105 ER -