Toward Transferable Coarse-Grained Potentials for Poly-Aromatic Hydrocarbons: A Force Matching Approach

A Mori-Zwanzig Dissipative Particle Dynamics Approach for Anisotropic Coarse Grained Molecular Dynamics

Coarse grained (CG) molecular dynamics simulations are widely used to accelerate atomistic simulations but generally lack a formalism to preserve the dynamics of the system. For spherical particles, the Mori-Zwanzig approach, while computationally complex, has ameliorated this problem. Here we present an anisotropic dissipative particle dynamics (ADPD) model as an extension of this approach, which accounts for the anisotropy for both conservative and nonconservative interactions. For a simple anisotropic system we parametrize the coarse grained force field representing ellipsoidal CG particles from the full-atomistic simulation. To represent the anisotropy of the system, both the conservative and dissipative terms are approximated using the Gay-Berne (GB) functional forms via a force-matching approach. We compare our model with other CG models and demonstrate that it yields better results in both static and dynamical properties. The inclusion of the anisotropic nonconservative force preserves the microscopic dynamical details, and hence the dynamical properties, such as diffusivity, can be better reproduced by the aspherical model. By generalizing the isotropic DPD model, this framework is effective and promising for the development of the CG model for polymers, macromolecules, and biological systems.

Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles

We derive a systematic and general method for parametrizing coarse-grained molecular models consisting of anisotropic particles from fine-grained (e.g. all-atom) models for condensed-phase molecular dynamics simulations. The method, which we call anisotropic force-matching coarse-graining (AFM-CG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarse-grained and fine-grained phase-space distributions to derive equations for the coarse-grained forces, torques, masses, and moments of inertia in terms of properties of a condensed-phase fine-grained system. We verify the accuracy and efficiency of the method by coarse-graining liquid-state systems of two different anisotropic organic molecules, benzene and perylene, and show that the parametrized coarse-grained models more accurately describe properties of these systems than previous anisotropic coarse-grained models parametrized using other methods that do not account for finite-temperature and many-body effects on the condensed-phase coarse-grained interactions. The AFM-CG method will be useful for developing accurate and efficient dynamical simulation models of condensed-phase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids.

Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations

Fully atomistic simulations of models of asphaltenes in simple solvents have allowed the study of trends in aggregation phenomena to understand the underlying role played by molecular structure. The detail included at this scale of molecular modeling is, however, at odds with the required spatial and temporal resolution needed to fully understand asphaltene aggregation. The computational cost required to explore the relevant scales can be reduced by employing coarse-grained (CG) models, which consist of lumping a few atoms into a single segment that is characterized by effective interactions. In this work, CG force fields developed via the statistical associating fluid theory (SAFT-γ) [ Müller , E. A. ; Jackson , G. Annu. Rev. Chem. Biomol. Eng. 5 , 2014 , 405 - 427 ] equation of state (EoS) provide a reliable pathway to link the molecular description with macroscopic thermophysical data. A recent modification of the SAFT-VR EoS [ Müller , E. A. ; Mejía , A. Langmuir 33 , 2017 , 11518 - 11529 ], which allows for the parameterization of homonuclear rings, is selected as the starting point to develop CG models for polycyclic aromatic hydrocarbons. The new aromatic-core models, along with others published for simpler organic molecules, are adopted for the construction of asphaltene models by combining different chemical moieties in a group-contribution fashion. We apply the procedure to two previously reported asphaltene models and perform molecular dynamics simulations to validate the coarse-grained representation against benchmark systems of 27 asphaltenes in a pure solvent (toluene or heptane) described in a fully atomistic fashion. An excellent match between both levels of description is observed for the cluster size, radii of gyration, and relative-shape-anisotropy-factor distributions. We exploit the advantages of the CG representation by simulating systems containing up to 2000 asphaltene molecules in an explicit solvent investigating the effect of asphaltene concentration, solvent composition, and temperature on aggregation. By studying large systems facilitated by the use of CG models, we observe stable continuous distributions of molecular aggregates at conditions away from the two-phase precipitation point. As a further example application, a widely accepted interpretation of cluster-size distributions in asphaltenic systems is challenged by performing system-size tests, reversibility checks, and a time-dependence analysis. The proposed coarse-graining procedure is seen to be general and predictive and, hence, can be applied to other asphaltenic molecular structures.