The flow behavior of lipid bilayer membranes is characterized by a surface viscosity for in-plane shear deformations, and an intermonolayer friction coefficient for slip between the two leaflets of ...the bilayer. Both properties have been studied for a variety of coarse-grained double-tailed model lipids, using equilibrium and nonequilibrium molecular dynamics simulations. For lipids with two identical tails, the surface shear viscosity rises rapidly with tail length, while the intermonolayer friction coefficient is less sensitive to the tail length. Interdigitation of lipid tails across the bilayer midsurface, as observed for lipids with two distinct tails, strongly enhances the intermonolayer friction coefficient, but hardly affects the surface shear viscosity. The simulation results are compared against the available experimental data.
In this paper, a previous coarse-grain model J. T. Padding and W. J. Briels, J. Chem. Phys. 117, 925 (2002) to simulate melts of linear polymers has been adapted to simulate polymers with more ...complex hierarchies. Bond crossings between highly coarse-grained soft particles are prevented by applying an entanglement algorithm. We first test our method on a virtual branch point inside a linear chain to make sure it works effectively when linking two linear arms. Next, we apply our method to study the diffusive and rheological behaviors of a melt of three-armed stars. We find that the diffusive behavior of the three-armed star is very close to that of a linear polymer with the same molecular weight, while its rheological properties are close to those of a linear chain with molecular mass equal to that of the longest linear sub-chain in the star.
Atomistic molecular dynamics simulations of a lipid bilayer were performed to calculate the free energy of a trans-membrane pore as a function of its radius. The free energy was calculated as a ...function of a reaction coordinate using a potential of mean constraint force. The pore radius was then calculated from the reaction coordinate using Monte Carlo particle insertions. The main characteristics of the free energy that comes out of the simulations are a quadratic shape for a radius less than about 0.3 nm, a linear shape for larger radii than this, and a rather abrupt change without local minima or maxima between the two regions. In the outer region, a line tension can be calculated, which is consistent with the experimentally measured values. Further, this line tension can be rationalized and understood in terms of the energetic cost for deforming a part of the lipid bilayer into a hydrophilic pore. The region with small radii can be described and understood in terms of statistical mechanics of density fluctuations. In the region of crossover between a quadratic and linear free energy there was some hysteresis associated with filling and evacuation of the pore with water. The metastable prepore state hypothesized to interpret the experiments was not observed in this region.
The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a ...flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.
We study liquid migration in partly saturated shear bands of granular media where liquid is transported away from the shear-band centre. Earlier studies show that the liquid migration can be modelled ...as a diffusive process with a shear-rate-dependent diffusion coefficient. Here, we apply this model in a two-dimensional Cartesian split-bottom shear cell with one wide, steady shear band. Initially, a high liquid concentration peak develops at the edges of the shear band, which propagates away from the shear band, splitting the shear cell into a liquid-depleted shear-band region and an outer region not yet affected by the liquid migration. Assuming the liquid transport in the vertical direction is negligible, we simplify the liquid migration model to a one-dimensional form evolving over time. By coordinate transformation, an analytically solvable drift-diffusion model is obtained for liquid migration from the simplified model. From here, we obtain analytical solutions for the liquid concentration as a function of space and time. The significance of the mechanisms is studied in terms of the local Péclet number. While drift enhances drying of the shear band and accumulates the liquid in the peak, diffusion shifts the liquid further away from the shear band. To validate the model, we predict numerically the trajectory of the liquid concentration peak from the continuum model and compare with discrete particle method (DPM) simulations. Our continuum model results give a perfect qualitative and an approximate quantitative agreement with the overall results predicted from the DPM model.
We simulate the linear and nonlinear rheology of two different viscoelastic polymer solutions, a polyisobutylene solution in pristane and an aqueous solution of hydroxypropylcellulose, using a highly ...coarse-grained approach known as Responsive Particle Dynamics (RaPiD) model. In RaPiD, each polymer has originally been depicted as a spherical particle with the effects of the eliminated degrees of freedom accounted for by an appropriate free energy and transient pairwise forces. Motivated by the inability of this spherical particle representation to entirely capture the nonlinear rheology of both fluids, we extended the RaPiD model by introducing a deformable particle capable of elongation. A Finite-Extensible Non-Linear Elastic potential provides a free energy penalty for particle elongation. Upon disentangling, this deformability allows more time for particles to re-entangle with neighbouring particles. We show this process to be integral towards recovering the experimental nonlinear rheology, obtaining excellent agreement. We show that the nonlinear rheology is crucially dependent upon the maximum elongation and less so on the elasticity of the particles. In addition, the description of the linear rheology has been retained in the process.
We investigate the shear-induced structure formation of colloidal particles dissolved in non-Newtonian fluids by means of computer simulations. The two investigated visco-elastic fluids are a ...semi-dilute polymer solution and a worm-like micellar solution. Both shear-thinning fluids contain long flexible chains whose entanglements appear and disappear continually as a result of Brownian motion and the applied shear flow. To reach sufficiently large time and length scales in three-dimensional simulations with up to 96 spherical colloids, we employ the responsive particle dynamics simulation method of modeling each chain as a single soft Brownian particle with slowly evolving inter-particle degrees of freedom accounting for the entanglements. Parameters in the model are chosen such that the simulated rheological properties of the fluids, i.e., the storage and loss moduli and the shear viscosities, are in reasonable agreement with experimental values. Spherical colloids dispersed in both quiescent fluids mix homogeneously. Under shear flow, however, the colloids in the micellar solution align to form strings in the flow direction, whereas the colloids in the polymer solution remain randomly distributed. These observations agree with recent experimental studies of colloids in the bulk of these two liquids.
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