We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is robust against the details of the mesoscopic model owing to the conservation of linear momentum by the adaptive resolution forces. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under non-equilibrium conditions.
The GENERIC structure allows for a unified treatment of different discrete models of hydrodynamics. We first propose a finite volume Lagrangian discretization of the continuum equations of hydrodynamics through the Voronoi tessellation. We then show that a slight modification of these discrete equations has the GENERIC structure. The GENERIC structure ensures thermodynamic consistency and allows for the introduction of correct thermal noise. In this way, we obtain a consistent discrete model for Lagrangian fluctuating hydrodynamics. For completeness, we also present the GENERIC versions of the…
We highlight some recent developments that widen the scope and reach of mesoscopic thin-film (or long-wave) hydrodynamic models employed to describe the dynamics of thin films, drops and contact lines of simple and complex liquids on solid substrates. The basis of the discussed developments is the reformulation of various mesoscopic thin-film hydrodynamic models as gradient dynamics on underlying energy functionals. After briefly presenting the general approach, the following sections discuss how to improve these models by amending the energy functional and the mobility function, how to obtain…
A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle collisions which depend on the local velocities and densities. Momentum and energy are conserved locally, and entropically driven phase separation occurs for high collision rates. An explicit expression for the equation of state is derived, and the concentration dependence of the bulk free energy is shown to be the same as that of the Widom-Rowlinson model. Ana…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For numerical simulation to play a predictive and descriptive role, one must have theoretically sound methods that span orders of magnitude in physical scales, from the atomistic motions of particles inside the channels to the large-scale hydrodynamic gradients that drive transport. Here, we use constraint dynamics to derive a nonequilibrium molecular dynamics method …
Friction in liquids arises from conservative forces between molecules and atoms. Although the hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest in the non-Markovian dynamics of single molecules and solutes, the onset of friction from the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequency-resolved friction data from high-precision simulations of three prototypical liquids, including water. Combining with rigorous theoretical arguments, we show that friction in liquids emerges abruptly at a characteristic freq…
We present a mesoscopic lattice model for non-ideal fluid flows with directional interactions, mimicking the effects of hydrogen-bonds in water. The model supports a rich and complex structural dynamics of the orientational order parameter, and exhibits the formation of disordered domains whose size and shape depend on the relative strength of directional order and thermal diffusivity. By letting the directional forces carry an inverse density dependence, the model is able to display a correlation between ordered domains and low density regions, reflecting the idea of water as a denser liquid …
We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging Brownian quasiparticles arise naturally from its geometric definition and include both conservative repulsion and dissipative drag forces. The quasiparticles, which are composed of atomistic host solvent rather than being simply immersed in it, provide a link between the atomistic and DPD levels and a practical route to extract the DPD parameters as direct stat…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested o…
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle formation. The procedure hinges on the (expected) evolution of a few slow, coarse-grained mesoscopic observables of the MC simulation, and on (computational) time scale separation between these and the remaining "slaved", fast variables. Short bursts of appropriately initialized atomistic simulation are used to estimate the (coarse-grained, deterministic) local dynam…
Fluctuating hydrodynamics is used to describe the total energy fluctuations of a freely evolving gas of inelastic hard spheres near the threshold of the clustering instability. They are shown to be governed by vorticity fluctuations only, that also lead to a renormalization of the average total energy. The theory predicts a power-law divergent behavior of the scaled second moment of the fluctuations, and a scaling property of their probability distribution, both in agreement with simulations results. A more quantitative comparison between theory and simulation for the critical amplitudes and t…
We use a mesoscopic computer simulation method to study the interplay between hydrodynamic and Brownian fluctuations during steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.1 to 15. Even when the hydrodynamic interactions are an order of magnitude weaker than Brownian forces, they still induce backflow effects that dominate the reduction of the average sedimentation velocity with increasing particle packing fraction. Velocity fluctuations, on the other hand, begin to show nonequilibrium hydrodynamic character for Pe > 1
A novel approach to the dynamics of dilute solutions of polymer molecules under flow conditions is proposed by applying the rules of mesoscopic nonequilibrium thermodynamics (MNET). The probability density describing the state of the system is taken to be a function of the position and velocity of the molecules, and on a local vector parameter accounting for its deformation. This function obeys a generalized Fokker-Planck equation, obtained by calculating the entropy production of the system, and identifying the corresponding probability currents in terms of generalized forces. In simple form,…
We present a model based on the lattice Boltzmann equation that is suitable for the simulation of dynamic wetting. The model is capable of exhibiting fundamental interfacial phenomena such as weak adsorption of fluid on the solid substrate and the presence of a thin surface film within which a disjoining pressure acts. Dynamics in this surface film, tightly coupled with hydrodynamics in the fluid bulk, determine macroscopic properties of primary interest: the hydrodynamic slip; the equilibrium contact angle; and the static and dynamic hysteresis of the contact angles. The pseudo- potentials em…
Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an intermediate (mesoscopic) approach and show how to build a three dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also allows one to predict the thermodynamical a…
We derive the Hydrodynamics for a system of N active, spherical, underdamped particles, interacting through conservative forces. At the microscopic level, we represent the evolution of the particles in terms of the Kramers equation for the probability density distribution of their positions, velocities, and orientations, while at a mesoscopic level we switch to a coarse-grained description introducing an appropriate set of hydrodynamic fields given by the lower-order moments of the distribution. In addition to the usual density and polarization fields, the Hydrodynamics developed in this paper…
We present the results of mesoscopic dissipative particle dynamics (DPD) simulations of coupled electrohydrodynamic phenomena on the micro- and nanoscale. The effects of electroosmotic flow and slippage combined with polyelectrolyte electrophoresis are investigated in detail, taking full account of hydrodynamic and electrostatic interactions. Our numerical results are in excellent agreement with analytical calculations.
We present a mesoscopic hydrodynamic description of the dynamics of colloidal suspensions. We consider the system as a gas of Brownian particles suspended in a Newtonian heat bath subjected to stationary non-equilibrium conditions imposed by a velocity field. Using results already obtained in previous studies in the field by means of a generalized Fokker-Planck equation, we obtain a set of coupled differential equations for the local diffusion current and the evolution of the total stress tensor. We find that the dynamic shear viscosity of the system contains contributions arising from the fin…
A mesoscopic model for shear plasticity of amorphous materials in two dimensions is introduced, and studied through numerical simulations in order to elucidate the macroscopic (large scale) mechanical behavior. Plastic deformation is assumed to occur through a series of local reorganizations. Using a discretization of the mechanical fields on a discrete lattice, local reorganizations are modeled as local slip events. Local yield stresses are randomly distributed in space and invariant in time. Each plastic slip event induces a long-ranged elastic stress redistribution. Rate and thermal effects…
Chemically powered self-propelled colloids generate a motor force by converting locally a source of energy into directed motion, a process that has been explored both in experiments and in computational models. The use of active colloids as building blocks for nanotechnology opens the doors to interesting applications, provided we understand the behaviour of these elementary constituents. We build a consistent mesoscopic simulation model for self-propelled colloids of complex shape with the aim of resolving the coupling between their translational and rotational motion. Considering a passive L…
The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the polyelectrolyte and the fluid, a coarse-grained molecular dynamics model connected to a mesoscopic fluid described by the Lattice Boltzmann approach is used to investigate free-solution electrophoresis. Our study demonstrates the importance of hydrodynamic interactions for the electrophoretic motion of polyelectrolytes and quantifies the influence of surrounding io…
Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for both bulk hydrodynamics and interfacial fluctuations. Interfacial surface tension is modeled by imposing a pairwise force between SDPD particles. We show that the relationship between the model parameters and surface tension, previously derived under the assumption of zero thermal fluctuation, is accurate for fluid systems at low temperature but overestimates t…
The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance c…
We propose a model to understand periodic oscillations relevant to the origin of mesoscopic channels formed during a Langmuir-Blodgett deposition observed in recent experiments \{M. Gleiche, L.F. Chi, and H. Fuchs, Nature {\bf 403}, 173 (2000)\}. We numerically study one-dimensional flow of a van der Waals fluid near its discontinuous liquid-gas transition and find that steady-state flow becomes unstable in the vicinity of the phase transition. Instabilities leading to complex periodic density-oscillations are demonstrated at some suitably chosen sets of parameters.
We use a mesoscopic simulation technique to study the effect of short-ranged inter-particle attraction on the steady-state sedimentation of colloidal suspensions. Attractions increase the average sedimentation velocity $v_s$ compared to the pure hard-sphere case, and for strong enough attractions, a non-monotonic dependence on the packing fraction $ϕ$ with a maximum velocity at intermediate $ϕ$ is observed. Attractions also strongly enhance hydrodynamic velocity fluctuations, which show a pronounced maximum size as a function of $ϕ$. These results are linked to a complex interplay between hydr…
A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a BGK collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solvent-solvent and solvent-solute interactions are implemented using a pseudopotential model. The Nernst-Planck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the link-flux method. The colloids are resolved on the lattice and coupled to the hydrodynamics and electrokinetics thr…
Solid/liquid interfaces control various processes of technological relevance in the process industry and many fundamental physicochemical phenomena. This work examines the link between the atomistic description of mass transfer at solid/liquid interfaces out of equilibrium and the constitutive mass transfer equations typically used to model these processes at the mesoscale. In our analysis, we discuss the microscopic inconsistencies apparent in simplified models of mass transfer whenever non-idealities dominate the liquid phase in the proximity of solid/liquid interfaces. Using CμMD - a molecu…
A mesoscopic hydrodynamic model to simulate synthetic self-propelled Janus particles which is thermophoretically or diffusiophoretically driven is here developed. We first propose a model for a passive colloidal sphere which reproduces the correct rotational dynamics together with strong phoretic effect. This colloid solution model employs a multiparticle collision dynamics description of the solvent, and combines potential interactions with the solvent, with stick boundary conditions. Asymmetric and specific colloidal surface is introduced to produce the properties of self-phoretic Janus part…
Interfaces involving coexisting phases in condensed matter are essential in various examples of soft matter phenomena such as wetting, nucleation, morphology, phase separation kinetics, membranes, phase coexistence in nanomaterials, etc. Most analytical theories available use concepts derived from mean field theory which does not describe adequately these systems. Satisfactory numerical simulations for interfaces at atomistic to mesoscopic scales remains a challenge. In the present work, the interfacial tension between mixtures of organic solvents and water is obtained from mesoscopic computer…
We present simulations that reveal a surprisingly large effect of hydrodynamic coupling on the speed of thermal ratchet motors. The model that we use considers particles performing thermal ratchet motion in a hydrodynamic solvent. Using particle-based, mesoscopic simulations that maintain local momentum conservation, we analyze quantitatively how the coupling to the surrounding fluid affects ratchet motion. We find that coupling can increase the mean velocity of the moving particles by almost two orders of magnitude, precisely because ratchet motion has both a diffusive and a deterministic com…
Nanofluidics shows great promise for energy conversion and desalination applications. The performance of nanofluidic devices is controlled by liquid-solid friction, quantified by the Navier friction coefficient (FC). Despite decades of research, there is no well-established generic framework to determine the frequency dependent Navier FC from atomistic simulations. Here, we have derived analytical expressions to connect the Navier FC to the random force autocorrelation on the confining wall, from the observation that the random force autocorrelation can be related to the hydrodynamic boundary …
The spreading of polymer droplets is studied using molecular dynamics simulations. To study the dynamics of both the precursor foot and the bulk droplet, large drops of ~200,000 monomers are simulated using a bead-spring model for polymers of chain length 10, 20, and 40 monomers per chain. We compare spreading on flat and atomistic surfaces, chain length effects, and different applications of the Langevin and dissipative particle dynamics thermostats. We find diffusive behavior for the precursor foot and good agreement with the molecular kinetic model of droplet spreading using both flat and a…
An efficient simulation method is presented for Brownian fiber suspensions, which includes both uncrossability of the fibers and hydrodynamic interactions between the fibers mediated by a mesoscopic solvent. To conserve hydrodynamics, collisions between the fibers are treated such that momentum and energy are conserved locally. The choice of simulation parameters is rationalised on the basis of dimensionless numbers expressing the relative strength of different physical processes. The method is applied to suspensions of semiflexible fibers with a contour length equal to the persistence length,…
Multi-particle collision dynamics is an appealing numerical technique aiming at simulating fluids at the mesoscopic scale. It considers molecular details in a coarse-grained fashion and reproduces hydrodynamic phenomena. Here, the implementation of multi-particle collision dynamics for isotropic fluids is analysed under the so-called Andersen-thermostatted scheme, a particular algorithm for systems in the canonical ensemble. This method gives rise to hydrodynamic fluctuations that spontaneously relax towards equilibrium. This relaxation process can be described by a linearized theory and used …
A mesoscopic, mixed particle- and field-based Brownian dynamics methodology for the simulation of entangled polymer melts has been developed. Polymeric beads consist of several Kuhn segments, and their motion is dictated by the Helmholtz energy of the sample, which is a sum of the entropic elasticity of chain strands between beads, slip springs, and nonbonded interactions. The entanglement effect is introduced by the slip springs, which are springs connecting either nonsuccessive beads on the same chain or beads on different polymer chains. The terminal positions of slip springs are altered du…
A new method is presented for mesoscopic simulations of particle dispersions in liquid crystal solvents. It allows efficient first-principle simulations of the dispersions involving many particles with many-body interactions mediated by the solvents. Demonstrations have been performed for the aggregation of colloid dispersions in two-dimensional nematic and smectic-C* solvents neglecting hydrodynamic effects, which will be taken into account in the near future.
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that the use of periodic boundary conditions in the directions along the surfaces results in dramatic finite-size effects, in addition to that of the physically relevant confining length. As in the simulation of bulk fluids, these effects arise from spurious hydrodynamic interactions between periodic images and from the constraint of total momentum conservation.…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these coarse-grained models provide a reduced description of the molecular degrees of freedom and often remove entirely representation of the solvent degrees of freedom. In such implicit-solvent models the solvent contributions are treated through effective interaction terms within an effective potential for the free energy. For investigations of kinetics, Langevin dynamics…
