Dissipative Particle Dynamics with energy conservation

Dissipative particle dynamics (DPD) does not conserve energy and this precludes its use in the study of thermal processes in complex fluids. We present here a generalization of DPD that incorporates an internal energy and a temperature variable for each particle. The dissipation induced by the dissipative forces between particles is invested in raising the internal energy of the particles. Thermal conduction occurs by means of (inverse) temperature differences. The model can be viewed as a simplified solver of the fluctuating hydrodynamic equations and opens up the possibility of studying thermal processes in complex fluids with a mesoscopic simulation technique.Comment: 5 page

Spinodal decomposition of off-critical quenches with a viscous phase using dissipative particle dynamics in two and three spatial dimensions

We investigate the domain growth and phase separation of hydrodynamically-correct binary immiscible fluids of differing viscosity as a function of minority phase concentration in both two and three spatial dimensions using dissipative particle dynamics. We also examine the behavior of equal-viscosity fluids and compare our results to similar lattice-gas simulations in two dimensions.Comment: 34 pages (11 figures); accepted for publication in Phys. Rev.

Fluctuating hydrodynamic modelling of fluids at the nanoscale

A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the hydrodynamics of nanoscale molecular assemblies are lacking, at least in part because of the stochastic character of the underlying fluctuating hydrodynamic equations. Here we derive a finite volume discretization of the compressible isothermal fluctuating hydrodynamic equations over a regular grid in the Eulerian reference system. We apply it to fluids such as argon at arbitrary densities and water under ambient conditions. To that end, molecular dynamics simulations are used to derive the required fluid properties. The equilibrium state of the model is shown to be thermodynamically consistent and correctly reproduces linear hydrodynamics including relaxation of sound and shear modes. We also consider non-equilibrium states involving diffusion and convection in cavities with no-slip boundary conditions

Lattice-Gas Simulations of Minority-Phase Domain Growth in Binary Immiscible and Ternary Amphiphilic Fluid

We investigate the growth kinetics of binary immiscible fluids and emulsions in two dimensions using a hydrodynamic lattice-gas model. We perform off-critical quenches in the binary fluid case and find that the domain size within the minority phase grows algebraically with time in accordance with theoretical predictions. In the late time regime we find a growth exponent n = 0.45 over a wide range of concentrations, in good agreement with other simluations. In the early time regime we find no universal growth exponent but a strong dependence on the concentration of the minority phase. In the ternary amphiphilic fluid case the kinetics of self assembly of the droplet phase are studied for the first time. At low surfactant concentrations, we find that, after an early algebraic growth, a nucleation regime dominates the late-time kinetics, which is enhanced by an increasing concentration of surfactant. With a further increase in the concentration of surfactant, we see a crossover to logarithmically slow growth, and finally saturation of the oil droplets, which we fit phenomenologically to a stretched exponential function. Finally, the transition between the droplet and the sponge phase is studied.Comment: 22 pages, 13 figures, submitted to PR

Proteomic profiling reveals the transglutaminase-2 externalization pathway in kidneys after unilateral ureteric obstruction

Increased export of transglutaminase-2 (TG2) by tubular epithelial cells (TECs) into the surrounding interstitium modifies the extracellular homeostatic balance, leading to fibrotic membrane expansion. Although silencing of extracellular TG2 ameliorates progressive kidney scarring in animal models of CKD, the pathway through which TG2 is secreted from TECs and contributes to disease progression has not been elucidated. In this study, we developed a global proteomic approach to identify binding partners of TG2 responsible for TG2 externalization in kidneys subjected to unilateral ureteric obstruction (UUO) using TG2 knockout kidneys as negative controls. We report a robust and unbiased analysis of the membrane interactome of TG2 in fibrotic kidneys relative to the entire proteome after UUO, detected by SWATH mass spectrometry. The data have been deposited to the ProteomeXchange with identifier PXD008173. Clusters of exosomal proteins in the TG2 interactome supported the hypothesis that TG2 is secreted by extracellular membrane vesicles during fibrosis progression. In established TEC lines, we found TG2 in vesicles of both endosomal (exosomes) and plasma membrane origin (microvesicles/ectosomes), and TGF-β1 stimulated TG2 secretion. Knockout of syndecan-4 (SDC4) greatly impaired TG2 exosomal secretion. TG2 coprecipitated with SDC4 from exosome lysate but not ectosome lysate. Ex vivo, EGFP-tagged TG2 accumulated in globular elements (blebs) protruding/retracting from the plasma membrane of primary cortical TECs, and SDC4 knockout impaired bleb formation, affecting TG2 release. Through this combined in vivo and in vitro approach, we have dissected the pathway through which TG2 is secreted from TECs in CKD

Fluctuating lattice Boltzmann

The lattice Boltzmann algorithm efficiently simulates the Navier Stokes equation of isothermal fluid flow, but ignores thermal fluctuations of the fluid, important in mesoscopic flows. We show how to adapt the algorithm to include noise, satisfying a fluctuation-dissipation theorem (FDT) directly at lattice level: this gives correct fluctuations for mass and momentum densities, and for stresses, at all wavevectors $k$. Unlike previous work, which recovers FDT only as $k\to 0$, our algorithm offers full statistical mechanical consistency in mesoscale simulations of, e.g., fluctuating colloidal hydrodynamics.Comment: 7 pages, 3 figures, to appear in Europhysics Letter

Lattice-gas simulations of Domain Growth, Saturation and Self-Assembly in Immiscible Fluids and Microemulsions

We investigate the dynamical behavior of both binary fluid and ternary microemulsion systems in two dimensions using a recently introduced hydrodynamic lattice-gas model of microemulsions. We find that the presence of amphiphile in our simulations reduces the usual oil-water interfacial tension in accord with experiment and consequently affects the non-equilibrium growth of oil and water domains. As the density of surfactant is increased we observe a crossover from the usual two-dimensional binary fluid scaling laws to a growth that is {\it slow}, and we find that this slow growth can be characterized by a logarithmic time scale. With sufficient surfactant in the system we observe that the domains cease to grow beyond a certain point and we find that this final characteristic domain size is inversely proportional to the interfacial surfactant concentration in the system.Comment: 28 pages, latex, embedded .eps figures, one figure is in colour, all in one uuencoded gzip compressed tar file, submitted to Physical Review

Three dimensional hysdrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media

We report the results of a study of multiphase flow in porous media. A Darcy's law for steady multiphase flow was investigated for both binary and ternary amphiphilic flow. Linear flux-forcing relationships satisfying Onsager reciprocity were shown to be a good approximation of the simulation data. The dependence of the relative permeability coefficients on water saturation was investigated and showed good qualitative agreement with experimental data. Non-steady state invasion flows were investigated, with particular interest in the asymptotic residual oil saturation. The addition of surfactant to the invasive fluid was shown to significantly reduce the residual oil saturation.Comment: To appear in Phys. Rev.

Thermodynamically admissible form for discrete hydrodynamics

We construct a discrete model of fluid particles according to the GENERIC formalism. The model has the form of Smoothed Particle Hydrodynamics including correct thermal fluctuations. A slight variation of the model reproduces the Dissipative Particle Dynamics model with any desired thermodynamic behavior. The resulting algorithm has the following properties: mass, momentum and energy are conserved, entropy is a non-decreasing function of time and the thermal fluctuations produce the correct Einstein distribution function at equilibrium.Comment: 4 page

Static and Dynamic Properties of Dissipative Particle Dynamics

The algorithm for the DPD fluid, the dynamics of which is conceptually a combination of molecular dynamics, Brownian dynamics and lattice gas automata, is designed for simulating rheological properties of complex fluids on hydrodynamic time scales. This paper calculates the equilibrium and transport properties (viscosity, self-diffusion) of the thermostated DPD fluid explicitly in terms of the system parameters. It is demonstrated that temperature gradients cannot exist, and that there is therefore no heat conductivity. Starting from the N-particle Fokker-Planck, or Kramers' equation, we prove an H-theorem for the free energy, obtain hydrodynamic equations, and derive a non-linear kinetic equation (the Fokker-Planck-Boltzmann equation) for the single particle distribution function. This kinetic equation is solved by the Chapman-Enskog method. The analytic results are compared with numerical simulations.Comment: 22 pages, LaTeX, 3 Postscript figure