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A transport model is proposed for wax deposition onto a cold finger from flowing wax‐containing oils. The model solves transient energy and mass balances simultaneously for a reversible first‐order kinetic rate for precipitation of pseudo‐single‐component wax, and the effects of yield stress using a critical solid wax concentration to withstand flow‐induced stress at the deposit‐fluid interface. The model can predict the time evolution of the deposit thickness, and the spatial and temporal evolution of temperature and wax concentration as validated using cold finger experiments. It was found that for high wax content oils, deposit thickness growth is dominated by heat transfer. For low wax content oils that are unable to gel, the thickness growth is slow and accompanied by occasional sloughing. Regardless of the mechanism controlling the growth, mass transfer cannot be neglected as wax diffusion into the deposit continues to take place after the deposit has stopped growing. [ABSTRACT FROM AUTHOR]

We assess the accuracy and efficiency of two particle-based mesoscopic simulation methods, namely, Dissipative Particle Dynamics (DPD) and Stochastic Rotation Dynamics (SRD) for predicting a complex flow in a microfluidic geometry. Since both DPD and SRD use soft or weakly interacting particles to carry momentum, both methods contain unavoidable inertial effects and unphysically high fluid compressibility. To assess these effects, we compare the predictions of DPD and SRD for both an exact Stokes-flow solution and nearly exact solutions at finite Reynolds numbers from the finite element method for flow in a straight channel with periodic slip boundary conditions. This flow represents a periodic electro-osmotic flow, which is a complex flow with an analytical solution for zero Reynolds number. We find that SRD is roughly ten-fold faster than DPD in predicting the flow field, with better accuracy at low Reynolds numbers. However, SRD has more severe problems with compressibility effects than does DPD, which limits the Reynolds numbers attainable in SRD to around 25-50, while DPD can achieve Re higher than this before compressibility effects become too large. However, since the SRD method runs much faster than DPD does, we can afford to enlarge the number of grid cells in SRD to reduce the fluid compressibility at high Reynolds number. Our simulations provide a method to estimate the range of conditions for which SRD or DPD is preferable for mesoscopic simulations. [ABSTRACT FROM AUTHOR]

The authors propose a method to simulate the DNA motion in microchannels of complex geometry. It is based on stochastic rotation dynamics using a new scheme for the boundary condition. The method enables them to define a boundary wall of arbitrary shape and to describe a wall moving at an arbitrary velocity. As an application, they simulate the motion of DNA in Poiseuille flow between two parallel planes and show that DNA molecules tend to concentrate near the center of the channel in agreement with experimental results. [ABSTRACT FROM AUTHOR]

To understand the origin of transmembrane potentials, formation of transient pores, and the movement of anions and cations across lipid membranes, we have performed systematic atomistic molecular dynamics simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) lipids. A double bilayer setup was employed and different transmembrane potentials were generated by varying the anion (Cl-) and cation (Na+) concentrations in the two water compartments. A transmembrane potential of ∼350 mV was thereby generated per bilayer for a unit charge imbalance. For transmembrane potential differences of up to ∼1.4 V, the bilayers were stable, over the time scale of the simulations (10–50 ns). At larger imposed potential differences, one of the two bilayers breaks down through formation of a water pore, leading to both anion and cation translocations through the pore. The anions typically have a short residence time inside the pore, while the cations show a wider range of residence times depending on whether they bind to a lipid molecule or not. Over the time scale of the simulations, we do not observe the discharge of the entire potential difference, nor do we observe pore closing, although we observe that the size of the pore decreases as more ions translocate. We also observed a rare lipid flip-flop, in which a lipid molecule translocated from one bilayer leaflet to the opposite leaflet, assisted by the water pore. [ABSTRACT FROM AUTHOR]

A very stiff finitely extensible nonlinear elastic (FENE)-Fraenkel spring is proposed to replace the rigid rod in the bead-rod model. This allows the adoption of a fast predictor-corrector method so that large time steps can be taken in Brownian dynamics (BD) simulations without over- or understretching the stiff springs. In contrast to the simple bead-rod model, BD simulations with beads and FENE-Fraenkel (FF) springs yield a random-walk configuration at equilibrium. We compare the simulation results of the free-draining bead-FF-spring model with those for the bead-rod model in relaxation, start-up of uniaxial extensional, and simple shear flows, and find that both methods generate nearly identical results. The computational cost per time step for a free-draining BD simulation with the proposed bead-FF-spring model is about twice as high as the traditional bead-rod model with the midpoint algorithm of Liu [J. Chem. Phys. 90, 5826 (1989)]. Nevertheless, computations with the bead-FF-spring model are as efficient as those with the bead-rod model in extensional flow because the former allows larger time steps. Moreover, the Brownian contribution to the stress for the bead-FF-spring model is isotropic and therefore simplifies the calculation of the polymer stresses. In addition, hydrodynamic interaction can more easily be incorporated into the bead-FF-spring model than into the bead-rod model since the metric force arising from the non-Cartesian coordinates used in bead-rod simulations is absent from bead-spring simulations. Finally, with our newly developed bead-FF-spring model, existing computer codes for the bead-spring models can trivially be converted to ones for effective bead-rod simulations merely by replacing the usual FENE or Cohen spring law with a FENE-Fraenkel law, and this convertibility provides a very convenient way to perform multiscale BD simulations. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations are used for studying the multiple copies of unacetylated G5 and G7 and acetylated G5 dendrimers in dimyristoylphosphatidylcholine bilayers with explicit water using the coarse-grained model. The studies have shown that the effect on pore formation of the concentration and size of large nanoparticles is analyzed by coarse-grained MD simulations, provided that long-range electrostatic interactions are included.

A molecular dynamics simulations was performed for an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The observation revealed that the hydrophobic effect is the driving force for the SDS-PEO association while the interaction between the polymer oxygens and the micelle headgroups is weak.

The analysis uses the combination of the solid-state NMR experiments, as well as the molecular dynamics simulations to understand the mechanism, structure and topology of various cell-signaling peptides containing nuclear localization sequences (NLS) in the membrane bilayers. The results show that the decrease in the bilayer thickness highly increases the tilt of the helics, as the phase, order and structure of the lipid bilayers remain unchanged and the same.

A study performed 0.5-mus-long molecular dynamics (MD) simulations of third- generation (G3) and fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in dipalmitoylphosphatidylcholine (DPPC) bilayers with explicit water using the coarse-grained (CG) model, to understand the effect of dendrimer size, extent of terminal-acetylation, temperature, and salt concentration on dendrimer-lipid bilayer interactions. Results show that with inclusion of long-range electrostatic interactions into CG models, realistic MD simulation of membrane-disrupting effects of nanoparticles at the microsecond time scale is now possible.