Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications

Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir

In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this Letter, we show a novel approach where the latest version of the adaptive resolution scheme (AdResS), with noninteracting tracers as particles' reservoir, is combined with a fluctuating hydrodynamics (FHD) solver. The resulting algorithm, supported by a solid mathematical model, allows for a physically consistent exchange of matter and energy between the particle domain and its fluctuating continuum reservoir. Numerical tests are performed to show the validity of the algorithm. Differently from previous algorithms of the same kind, the current approach allows for simulations where, in addition to density fluctuations, also thermal fluctuations can be accounted for, thus large complex molecular systems, as, for example, hydrated biological membranes in a thermal field, can now be efficiently treated.

Modeling electrokinetic flows with the discrete ion stochastic continuum overdamped solvent algorithm

In this article we develop an algorithm for the efficient simulation of electrolytes in the presence of physical boundaries. In previous work the discrete ion stochastic continuum overdamped solvent (DISCOS) algorithm was derived for triply periodic domains, and was validated through ion-ion pair correlation functions and Debye-Hückel-Onsager theory for conductivity, including the Wien effect for strong electric fields. In extending this approach to include an accurate treatment of physical boundaries we must address several important issues. First, the modifications to the spreading and interpolation operators necessary to incorporate interactions of the ions with the boundary are described. Next we discuss the modifications to the electrostatic solver to handle the influence of charges near either a fixed potential or dielectric boundary. An additional short-ranged potential is also introduced to represent interaction of the ions with a solid wall. Finally, the dry diffusion term is modified to account for the reduced mobility of ions near a boundary, which introduces an additional stochastic drift correction. Several validation tests are presented confirming the correct equilibrium distribution of ions in a channel. Additionally, the methodology is demonstrated using electro-osmosis and induced-charge electro-osmosis, with comparison made to theory and other numerical methods. Notably, the DISCOS approach achieves greater accuracy than a continuum electrostatic simulation method. We also examine the effect of under-resolving hydrodynamic effects using a "dry diffusion" approach, and find that considerable computational speedup can be achieved with a negligible impact on accuracy.

Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir

We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point-particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space-dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms' delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive.

Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique

We use the adaptive resolution simulation (AdResS) technique to estimate the region in space where water-mediated effects in molecule-molecule interactions are relevant. AdResS is employed to identify the region around the solute (solvation shell) where the atomistic details of the hydrogen bonding network are relevant while outside water plays the role of a thermodynamic bath that can be described at simplified macroscopic level. The consequence is that for the interaction of two solutes the intermolecular distance at which water mediated effects start to be relevant is represented by the sum of the radii of the two respective solvation shells identified via AdResS. The hypothesis formulated above will be proven by calculating the solute-solute potential of mean force for different solutes. As test molecules we use amino acids derived from fragments of the FCHo2-F-BAR domain protein; this choice stems from the fact that the current results, beside proving the technical capability of AdResS in this context, may provide data for future actual coarse-grained models.

From adaptive resolution to molecular dynamics of open systems

ABSTRACT

We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.

Theory and simulation of open systems out of equilibrium

We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations.