We use a mesoscale simulation to measure the strength of the velocity flux needed to push a polymer into a narrow channel. We find excellent agreement with the prediction by T. Sakaue, E. Rapha€ el, P.G. de Gennes and F. Brochard-Wyart, Europhys. Lett., 2009, 72, 83, based on a de Gennes blob model of the polymer, that the critical velocity flux for translocation depends linearly on the temperature, but is independent of the length of the polymer chain or the width of the channel.

The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum solution for a Newtonian fluid and then compared to experimental values. The results show that the TIP4P/2005 model gives the best prediction of the viscosity for the complete range of temperatures for liquid water, and thus it is the preferred water model of these considered here for simulations where the magnitude of viscosity is crucial. On the other hand, with the TIP4P model, the viscosity is severely underpredicted, and overall the model performed worst, whereas the SPC/E and TIP4P/Ew models perform moderately.

In this paper, we demonstrate for the first time that insulative dielectrophoresis can induce size-dependent trajectories of DNA macromolecules. We experimentally use ͑48.5 kbp͒ and T4GT7 ͑165.6 kbp͒ DNA molecules flowing continuously around a sharp corner inside fluidic channels with a depth of 0.4 m. Numerical simulation of the electrokinetic force distribution inside the channels is in qualitative agreement with our experimentally observed trajectories. We discuss a possible physical mechanism for the DNA polarization and dielectrophoresis inside confining channels, based on the observed dielectrophoresis responses due to different DNA sizes and various electric fields applied between the inlet and the outlet. The proposed physical mechanism indicates that further extensive investigations, both theoretically and experimentally, would be very useful to better elucidate the forces involved at DNA dielectrophoresis. When applied for size-based sorting of DNA molecules, our sorting method offers two major advantages compared to earlier attempts with insulative dielectrophoresis: Its continuous operation allows for highthroughput analysis, and it only requires electric field strengths as low as ϳ10 V / cm.

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported. C 2015 AIP Publishing LLC. [http://dx

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One contribution of 13 to a Theme Issue 'Multi-scale systems in fluids and soft matter: approaches, numerics and applications' . Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-spacetime-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space-time, a novel hybrid atomistic-fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided.

Flow and noise solutions of the two Large Eddy Simulation (LES) approaches are evaluated for the jet flow conditions corresponding to a benchmark co-axial jet case from the EU CoJeN (Computation of Coaxial Jet Noise) experiment. The jet is heated and issues for a short-cowl axi-symmetric nozzle with a central body at a transonic speed. The first LES method is based on the Compact Accurately Boundary-Adjusting high-REsolution Technique (CABARET) scheme, for which implementation features include asynchronous time stepping at an optimal Courant-Friedrichs-Lewy (CFL) number, a wall model, and a synthetic turbulence inflow boundary condition. The CABARET LES is implemented on Graphics Processing Units (GPUs). The second LES approach is based on the hybrid 2 Reynolds Averaged Navier-Stokes (RANS)/ Implicit LES method that uses a mixture of high-order Roe and WENO scheme and a wall distance model of the Improved Delayed Detached Eddy Simulation (IDDES) type. The RANS/ILES method is run on an MPI cluster. Two grid generation approaches are considered: the unstructured grid using OpenFOAM utility "snappyHexMesh" (sHM) and the conventional structured multiblock body-fitted curvilinear grid. The LES flow solutions are compared with the experiment and also with solutions obtained from the standard axi-symmetric RANS method using the k- turbulence model. For noise predictions, The LES solutions are coupled with the penetrable surface formation of the Ffowcs Williams-Hawkings method. The results of noise predictions are compared with the experiment and the effect of different LES grids and acoustic integration surfaces is discussed.

Abstract. A multiscale Molecular Dynamics/Hydrodynamics implementation of the 2D Mercedes Benz (MB or BN2D) [1] water model is developed and investigated. The concept and the governing equations of multiscale coupling together with the results of the two-way coupling implementation are reported. The sensitivity of the multiscale model for obtaining macroscopic and microscopic parameters of the system, such as macroscopic density and velocity fluctuations, radial distribution and velocity autocorrelation functions of MB particles, is evaluated. Critical issues for extending the current model to large systems are discussed.