Molecular dynamics simulations of isomerization kinetics in condensed fluids

Simulations of different reaction schemes for isomerization kinetics in a condensed fluid mixture between two species with small differences in the pair energies show that one of the species dominates at late reaction times. The isomerization is performed on the basis of the energy of the two states, either by choosing minimum energy or by use of Boltzmann weighted kinetics. Both kinetics are autocatalytic and establish domain decomposition with critical fluctuations, which ensure the symmetry break. The model(s) offers a possible explanation of the origin of biomolecular chirality.     

Rod-climbing effect in Newtonian fluids

When a rotating rod is brought into a polymer melt or concentrated polymer solution, the meniscus climbs the rod. This spectacular rod climbing is due to the normal stresses present in the polymer fluid and is thus a purely non-Newtonian effect. A similar rod climbing of an interface between two fluids has therefore been taken as a signature that one of the fluids exhibits normal stress effects. We show here, however, that the effect can occur with simple Newtonian fluids: it occurs when a Taylor-Couette instability happens in the less viscous of the two liquids but not in the more viscous one.     

Order and fluctuations in nonequilibrium molecular dynamics simulations of two-dimensional fluids

Finite systems of hard disks placed in a temperature gradient and in an external constant field have been studied, simulating a fluid heated from below. We used the methods of nonequilibrium molecular dynamics. The goal was to observe the onset of convection in the fluid. Systems of more than 5000 particles have been considered and the choice of parameters has been made in order to have a Rayleigh number larger than the critical one calculated from the hydrodynamic equations. The appearance of rolls and the large fluctuations in the velocity field are the main features of these simulations.     

3D vesicle dynamics simulations with a linearly triangulated surface

Simulations of biomembranes have gained an increasing interest in the past years. Specificities of these membranes propose new challenges for the numerics. In particular, vesicle dynamics are governed by bending forces as well as a surface incompressibility constraint. A method to compute the bending force density resultant onto piecewise linearly triangulated surface meshes is described. This method is coupled with a boundary element method solver for inner and outer fluids, to compute vesicle dynamics under external flows. The surface incompressibility constraint is satisfied by the construction of a projection operator.     

Undulatory swimming in viscoelastic fluids

The effects of fluid elasticity on the swimming behavior of the nematode Caenorhabditis elegans are experimentally investigated by tracking the nematode's motion and measuring the corresponding velocity fields. We find that fluid elasticity hinders self-propulsion. Compared to Newtonian solutions, fluid elasticity leads to up to 35% slower propulsion. Furthermore, self-propulsion decreases as elastic stresses grow in magnitude in the fluid. This decrease in self-propulsion in viscoelastic fluids is related to the stretching of flexible molecules near hyperbolic points in the flow.     

Impact of thermostat on interfacial thermal conductance prediction from non-equilibrium molecular dynamics simulations

The knowledge of interfacial thermal conductance (ITC) is key to understand thermal transport in nanostructures. The non-equilibrium molecular dynamics (NEMD) simulation is a useful tool to calculate the ITC. In this study, we investigate the impact of thermostat on the prediction of the ITC. The Langevin thermostat is found to result in larger ITC than the Nose-Hoover thermostat. In addition, the results from NEMD simulations with the Nose-Hoover thermostat exhibit strong size effect of thermal reservoirs. Detailed spectral heat flux decomposition and modal temperature calculation reveal that the acoustic phonons in hot and cold thermal reservoirs are of smaller temperature difference than optical phonons when using the Nose-Hoover thermostat, while phonons in the Langevin thermostat are of identical temperatures. Such a non-equilibrium state of phonons in the case of the Nose-Hoover thermostat reduces the heat flux of low-to-middle-frequency phonons. We also discuss how enlarging the reservoirs or adding an epitaxial rough wall to the reservoirs affects the predicted ITC, and find that these attempts could help to thermalize the phonons, but still underestimate the heat flux from low-frequency phonons.     

Terminal model of Newtonian dynamics

A new type of dissipation function which does not satisfy the Lipschitz condition at equilibrium states is proposed. Newtonian dynamics supplemented by this dissipation function becomes irreversible and has a well-organized probabilistic structure.     

Three-dimensional,fully adaptive simulations of phase-field fluid models

We present an efficient numerical methodology for the 3D computation of incompressible multi-phase flows described by conservative phase-field models. We focus here on the case of density matched fluids with different viscosity (Model H). The numerical method employs adaptive mesh refinements (AMR) in concert with an efficient semi-implicit time discretization strategy and a linear, multi-level multigrid to relax high order stability constraints and to capture the flow’s disparate scales at optimal cost. Only five linear solvers are needed per time-step. Moreover, all the adaptive methodology is constructed from scratch to allow a systematic investigation of the key aspects of AMR in a conservative, phase-field setting. We validate the method and demonstrate its capabilities and efficacy with important examples of drop deformation, Kelvin–Helmholtz instability, and flow-induced drop coalescence.     

Scale-bridging phase-field simulations of microstructure responses on nucleation in metals and colloids

In the present studies we investigate the connection between atomistic simulation methods, i.e. molecular dynamics (MD) and phase-field crystal (PFC), to the mesoscopic phase-field methods (PFM). While the first describes the evolution of a system on the basis of motion equations of particles the second uses a Cahn–Hilliard type equation to described an atomic density field and the third grounds on the evolution of continuous local order parameter field. The first aim is to point out the ability of the mesoscopic phase-field method to make predictions of growth velocity at the nanoscopic length scale. Therefore the isothermal growth of a spherical crystalline cluster embedded in a melt is considered. We also show simulation techniques that enable to computationally bridge from the atomistic up to the mesoscopic scale. We use a PFM to simulate symmetric thermal dendrites started at an early stage of solidification related to nucleation. These techniques allow to simulate three dimensional dendrites from the state of nuclei (≈50?Å) converted from MD up to a size of some μm where ternary side-arms start to grow.     

The problem of irreversibility in Newtonian dynamics

A new type of dissipation function which does not satisfy the Lipschitz condition at equilibrium states is proposed. It is shown that Newtonian dynamics supplemented by this dissipation function becomes irreversible, i.e., it is not invariant with respect to time inversion. Some effects associated with the approaching of equilibria in infinite time are eliminated. New meanings of chaos and turbulence are discussed.     

Coexistence and interfacial properties of triangle-well fluids

Coexistence and interfacial properties of triangle-well fluids are determined by combining the slab technique and the replica exchange algorithm for different interaction ranges (λ = 1.5, 1.75, 2.0, 2.5, and 3). This is implemented using both Monte Carlo and molecular dynamics methods. We make use of a recently proposed substitution of the hard-core repulsion by a linear function with a large negative slope. This makes possible to gain access through the virial route to thermodynamical properties and to employ widely spread packages such as Gromacs. Coexistence curves of these systems were calculated with both implementations and compared to those previously reported in the literature. A good agreement was found among them. Surface tension data obtained from Monte Carlo and molecular dynamics techniques also show a good agreement.     

Bubble oscillation and inertial cavitation in viscoelastic fluids

Non-linear acoustic oscillations of gas bubbles immersed in viscoelastic fluids are theoretically studied. The problem is formulated by considering a constitutive equation of differential type with an interpolated time derivative. With the aid of this rheological model, fluid elasticity, shear thinning viscosity and extensional viscosity effects may be taken into account. Bubble radius evolution in time is analyzed and it is found that the amplitude of the bubble oscillations grows drastically as the Deborah number (the ratio between the relaxation time of the fluid and the characteristic time of the flow) increases, so that, even for moderate values of the external pressure amplitude, the behavior may become chaotic. The quantitative influence of the rheological fluid properties on the pressure thresholds for inertial cavitation is investigated. Pressure thresholds values in terms of the Deborah number for systems of interest in ultrasonic biomedical applications, are provided. It is found that these critical pressure amplitudes are clearly reduced as the Deborah number is increased.     

Shear waves in viscoelastic wormlike micellar fluids

Low frequency (61 Hz) shear wave speeds have been measured in viscoelastic wormlike micellar (WM) fluids for a concentration range of 20/12-160/96 mM CTAB/NaSAL. The strain induced birefringence of the WM fluids was exploited to optically track the shear pulse using crossed polarizing filters and high speed video. It was found that shear speed increases roughly linearly with concentration at a rate of 3.5 mm s(-1) mM(-1) CTAB. Further, comparison with elastic and loss moduli obtained from rheology data show that shear wave propagation is dominated by the elastic modulus for this frequency range.     

Viscosity effects in foam drainage: Newtonian and non-newtonian foaming fluids

We have studied the drainage of foams made from Newtonian and non-Newtonian solutions of different viscosities. Forced-drainage experiments first show that the behavior of Newtonian solutions and of shear-thinning ones (foaming solutions containing either Carbopol or Xanthan) are identical, provided one considers the actual viscosity corresponding to the shear rate found inside the foam. Second, for these fluids, a drainage regime transition occurs as the bulk viscosity is increased, illustrating a coupling between surface and bulk flow in the channels between bubbles. The properties of this transition appear different from the ones observed in previous works in which the interfacial viscoelasticity was varied. Finally, we show that foams made of solutions containing long flexible PolyEthylene Oxide (PEO) molecules counter-intuitively drain faster than foams made with Newtonian solutions of the same viscosity. Complementary experiments made with fluids having all the same viscosity but different responses to elongational stresses (PEO-based Boger fluids) suggest an important role of the elastic properties of the PEO solutions on the faster drainage.     

X箍缩三维数值模拟

利用FOI-PERFECT程序对X箍缩进行了3D数值模拟研究,给出了X箍缩的物理图像和动力学过程,探讨了Z箍缩中出现磁重联的可能性,并指出如果双丝Z箍缩中能够出现磁重联,那么X箍缩是更有利于磁重联出现的位形,并且,X箍缩中出现多重X射线暴的一个可能原因是z轴上多个位置出现磁重联。     

X箍缩三维数值模拟

利用FOI-PERFECT程序对X箍缩进行了3D数值模拟研究,给出了X箍缩的物理图像和动力学过程,探讨了Z箍缩中出现磁重联的可能性,并指出如果双丝Z箍缩中能够出现磁重联,那么X箍缩是更有利于磁重联出现的位形,并且,X箍缩中出现多重X射线暴的一个可能原因是z轴上多个位置出现磁重联。     

Nonlinear oscillations of gas bubbles in viscoelastic fluids

Nonlinear oscillations of gas bubbles in viscoelastic fluids of a three-constant Oldroyd model are theoretically investigated. The equation of motion for a bubble in a viscoelastic fluid subject to a pulsating pressure, and the pressure equation at the bubble wall are obtained. By numerical calculations on these equations, the effects of relaxation time and retardation time on frequency response curves, and the relation between the maximum pressure at the bubble wall and the initial radius of the bubble are clarified.     

Non-hydrodynamic modes in viscoelastic behaviour of simple fluids

ABSTRACT

We discuss the role of non-hydrodynamic processes in viscoelastic transition in pure liquids. In particular, using both analytical results and molecular dynamics simulations, we clarify the effect of the shear stress relaxation on the transverse dynamics. We use as an example the Lennard-Jones fluids. We analyse the frequency dependence of the shear modulus and its connection to the non-hydrodynamic shear relaxation mode. The analysis of the relaxation times of the non-hydrodynamic modes in longitudinal and transverse dynamics makes evidence that the emergence of the non-hydrodynamic transverse excitations outside the propagation gap is not directly connected to the onset of the positive sound dispersion.     

Droplet detachment and satellite bead formation in viscoelastic fluids

The presence of a very small amount of high molecular weight polymer significantly delays the pinch-off singularity of a drop of water falling from a faucet and leads to the formation of a long-lived cylindrical filament. In this Letter, we present experiments, numerical simulations, and theory which examines the pinch-off process in the presence of polymers. The numerical simulations are found to be in good agreement with experiment. As a test case, we establish the conditions under which a small bead remains on the filament; we find that the presence of a bead is due to the asymmetry induced by the self-similar pinch off of the droplet.