Generalized Energy-Conserving Dissipative Particle Dynamics with Reactions

• Published in: Journal of chemical theory and computation 2022-04, Vol.18 (4), p.2503-2512
• Main Authors: Lísal, Martin, Larentzos, James P, Avalos, Josep Bonet, Mackie, Allan D, Brennan, John K
• Format: Article
• Language: English
• Subjects: Algorithms; Equations of motion; Equations of state; Flexibility; Ideal gas; Mathematical models; Reaction kinetics; Reaction mechanisms; Reactivity; Temperature dependence
• ISSN: 1549-9618; 1549-9626
• DOI: 10.1021/acs.jctc.1c01294

We present an extension of the generalized energy-conserving dissipative particle dynamics method (J. Bonet Avalos, et al., , 24891-24911) to include chemical reactivity, denoted GenDPDE-RX. GenDPDE-RX provides a means of simulating chemical reactivity at the micro- and mesoscales, while exploiting the attributes of density- and temperature-dependent many-body force fields, which include improved transferability and scalability compared to two-body pairwise models. The GenDPDE-RX formulation considers intra-particle reactivity via a coarse-grain reactor construct. Extent-of-reaction variables assigned to each coarse-grain particle monitor the temporal evolution of the prescribed reaction mechanisms and kinetics assumed to occur within the particle. Descriptions of the algorithm, equations of motion, and numerical discretization are presented, followed by verification of the GenDPDE-RX method through comparison with reaction kinetics theoretical model predictions. Demonstrations of the GenDPDE-RX method are performed using constant-volume adiabatic heating simulations of three different reaction models, including both reversible and irreversible reactions, as well as multistep reaction mechanisms. The selection of the demonstrations is intended to illustrate the flexibility and generality of the method but is inspired by real material systems that span from fluids to solids. Many-body force fields using analytical forms of the ideal gas, Lennard-Jones, and exponential-6 equations of state are used for demonstration, although application to other forms of equation of states is possible. Finally, the flexibility of the GenDPDE-RX framework is addressed with a brief discussion of other possible adaptations and extensions of the method.