Advances and challenges in computational research of micro and nano flows

This paper presents an overview of past and current research in computational modelling of micro- and nanofluidic systems with particular focus on recent advances in multiscale modelling. Different mesoscale and hybrid molecular-continuum methods are presented. The contributions of these methods to a broad range of applications, as well as the physical and computational modelling challenges associated with the development of these methods, are also discussed

Progress in particle-based multiscale and hybrid methods for flow applications

This work focuses on the review of particle-based multiscale and hybrid methods that have surfaced in the field of fluid mechanics over the last 20 years. We consider five established particle methods: molecular dynamics, direct simulation Monte Carlo, lattice Boltzmann method, dissipative particle dynamics and smoothed-particle hydrodynamics. A general description is given on each particle method in conjunction with multiscale and hybrid applications. An analysis on the length scale separation revealed that current multiscale methods only bridge across scales which are of the order of O(102)−O(103) and that further work on complex geometries and parallel code optimisation is needed to increase the separation. Similarities between methods are highlighted and combinations discussed. Advantages, disadvantages and applications of each particle method have been tabulated as a reference

Low Mach Number Fluctuating Hydrodynamics for Electrolytes

We formulate and study computationally the low Mach number fluctuating hydrodynamic equations for electrolyte solutions. We are interested in studying transport in mixtures of charged species at the mesoscale, down to scales below the Debye length, where thermal fluctuations have a significant impact on the dynamics. Continuing our previous work on fluctuating hydrodynamics of multicomponent mixtures of incompressible isothermal miscible liquids (A. Donev, et al., Physics of Fluids, 27, 3, 2015), we now include the effect of charged species using a quasielectrostatic approximation. Localized charges create an electric field, which in turn provides additional forcing in the mass and momentum equations. Our low Mach number formulation eliminates sound waves from the fully compressible formulation and leads to a more computationally efficient quasi-incompressible formulation. We demonstrate our ability to model saltwater (NaCl) solutions in both equilibrium and nonequilibrium settings. We show that our algorithm is second-order in the deterministic setting, and for length scales much greater than the Debye length gives results consistent with an electroneutral/ambipolar approximation. In the stochastic setting, our model captures the predicted dynamics of equilibrium and nonequilibrium fluctuations. We also identify and model an instability that appears when diffusive mixing occurs in the presence of an applied electric field.Comment: 37 pages, 5 figure

Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface, with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at different temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuum-based analytical solutions. Subsequently, we simulate shear flows over polydimethylsiloxane (PDMS)-grafted surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a "universal" power law exists for the sliplength, in agreement with published results. Having validated the MD-DPD coupling method, we simulate time-dependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.Comment: 11 pages, 12 figure

Multi-Particle Collision Dynamics -- a Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids

In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD). The method consists of alternating streaming and collision steps in an ensemble of point particles. The multi-particle collisions are performed by grouping particles in collision cells, and mass, momentum, and energy are locally conserved. This simulation technique captures both full hydrodynamic interactions and thermal fluctuations. The first part of the review begins with a description of several widely used MPC algorithms and then discusses important features of the original SRD algorithm and frequently used variations. Two complementary approaches for deriving the hydrodynamic equations and evaluating the transport coefficients are reviewed. It is then shown how MPC algorithms can be generalized to model non-ideal fluids, and binary mixtures with a consolute point. The importance of angular-momentum conservation for systems like phase-separated liquids with different viscosities is discussed. The second part of the review describes a number of recent applications of MPC algorithms to study colloid and polymer dynamics, the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of viscoelastic fluids

JDFTx: software for joint density-functional theory

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs. This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.Comment: 9 pages, 3 figures, 2 code listing