Early stages of clathrin aggregation at a membrane in coarse-grained simulations.

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 ß 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.

Modifying self-assembly and species separation in three-dimensional systems of shape-anisotropic particles.

The behaviors of large, dynamic assemblies of macroscopic particles are of direct relevance to geophysical and industrial processes and may also be used as easily studied analogs to micro- or nano-scale systems, or model systems for microbiological, zoological, and even anthropological phenomena. We study vibrated mixtures of elongated particles, demonstrating that the inclusion of differing particle "species" may profoundly alter a system's dynamics and physical structure in various diverse manners. The phase behavior observed suggests that our system, despite its athermal nature, obeys a minimum free energy principle analogous to that observed for thermodynamic systems. We demonstrate that systems of exclusively spherical objects, which form the basis of numerous theoretical frameworks in many scientific disciplines, represent only a narrow region of a wide, multidimensional phase space. Thus, our results raise significant questions as to whether such models can accurately describe the behaviors of systems outside this highly specialized case.

Coarse grain forces in star polymer melts.

An analysis is presented of forces acting on the centers of mass of three-armed star polymers in the molten state. The arms consist of 35 Kremer-Grest beads, which is slightly larger than needed for one entanglement mass. For a given configuration of the centers of mass, instantaneous forces fluctuate wildly around averages which are two orders of magnitude smaller than their root mean square deviations. Average forces are well described by an implicit many-body potential, while pair models fail completely. The fluctuating forces are modelled by means of dynamical variables quantifying the degree of mixing of the various polymer pairs. All functions and parameters in a coarse grain model based on these concepts are obtained from the underlying small scale simulation. The coarse model reproduces both the diffusion coefficient and the shear relaxation modulus. Ways to improve the model suggest themselves on the basis of our findings.

Mesoscale modeling of shear-thinning polymer solutions.

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.

Coarse-grained simulations of moderately entangled star polyethylene melts.

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.

Inducement by directional fields of rotational and translational phase ordering in polymer liquid-crystals.

The effects of aligning fields on models of polymer liquid crystals were simulated using the dissipative particle dynamics method. Exposing a liquid crystal of rod-like particles to a directional field causes a stabilization of the phases with orientational order, shifts the isotropic-nematic and nematic-smectic-A phase transitions to higher temperatures, makes the transitions continuous beyond a critical field strength, and induces weak para-nematic alignment in the zero-field isotropic phase. The interplay of liquid-crystalline ordering, microphase separation, and an alignment field endows the diblock and triblock copolymers studied here with rich phase behavior. The simulations suggest that field-induced orientational ordering can give rise to positional ordering. Reversely, positional ordering resulting from rod-coil demixing may be accompanied by orientational ordering, which is enhanced by external fields. For highly asymmetric rod-coil copolymers, the microphase separation pattern formed by the rigid segments can be altered by an aligning field.

The origin of flow-induced alignment of spherical colloids in shear-thinning viscoelastic fluids.

We have studied the poorly understood process of flow-induced structure formation by colloids suspended in shear-thinning fluids. These viscoelastic fluids contain long flexible chains whose entanglements appear and disappear continuously as a result of brownian motion and the applied shear flow. Responsive particle dynamics simulates each chain as a single smooth brownian particle, with slowly evolving inter-particle degrees of freedom accounting for the entanglements. The colloids mixed homogeneously in all simulated quiescent dispersions and they remain dispersed under slow shear flow. Beyond a critical shear rate, which varies depending on the fluid, the colloids aggregate and form flow-aligned strings in the bulk of the fluid. In this work we explore the physical origins of this hitherto unexplained ordering phenomena, both by systematically varying the parameters of the simulated fluids and by analyzing the flow-induced effective colloidal interactions. We also present an expression for the critical shear rate of the studied fluids.

Alignment of particles in sheared viscoelastic fluids.

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.

Microphase separation and liquid-crystalline ordering of rod-coil copolymers.

Microphase separation and liquid-crystalline ordering in diblock and triblock rod-coil copolymers (with rod-to-coil fraction f=0.5) were investigated using the dissipative particle dynamics method. When the isotropic disordered phases of these systems were cooled down below their order-disorder transition temperatures T(ODT), lamellar structures were observed. For rod-coil diblock copolymers, the lamellar layers were obtained below T=2.0. This temperature was found to be higher than the T(ODT) for normal coil-coil diblock copolymers. Significant ordering of the rods was observed only below T=0.9 which is the isotropic-nematic transition temperature for rodlike fluids. For the triblock rod-coil copolymers, both microphase separation and rod ordering occurred at T=0.9. Normal coil-coil triblock copolymers were found to undergo microphase separation at T=0.8, which is about half the T(ODT) of the normal diblock copolymers. Investigations of the mean square displacement and the parallel and the perpendicular components of the spatial distribution function revealed that at low temperatures, the rod-coil diblock copolymers exhibit smectic-A and crystalline phases, while the triblock copolymers show smectic-C and crystalline phases. No nematic phases were observed at the density and interaction parameters used in this study.

Low-dose IL-2 therapy reduces HCV RNA and HBV DNA: case report.

BACKGROUND: Patients with concomitant hepatitis C (HCV) and B (HBV) infection are difficult to treat due to lack of medicines that control these viral infections and the high risk of hepatocellular carcinoma. Currently, there are insufficient data regarding the therapeutic effect of interleukin-2 (IL-2) during chronic viral infection, but this cytokine has shown antineoplastic activity and may have also an antiviral effect. CASE REPORT: We present the case of a 44-year-old patient with hemophilia A, HBV and HCV related compensated liver cirrhosis (Child-Pugh A) with several zones in the liver, highly suspicious for hepatocellular carcinoma. The patient was treated with low-dose intermittent subcutaneous IL-2 immunotherapy, followed by standard therapy with pegasys and copegus. During 23 months' follow-up, no tumour progression occurred, and the patient remained in Child-Pugh A stage. The initial HCV and HBV loads were significant (538,207 IU/ml) and minimal (825 copies/ml), respectively. The patient was treated with intermittent subcutaneously applied low-dose IL-2 cycles for ten months. HBV DNA and HCV RNA were undetectable 3 months after the last IL-2 cycle. After cessation of IL-2 therapy, the patient received standard antiviral treatment with pegasys and copegus. Nine months later, a slight reactivation of viruses was observed: HBV DNA was 18,600 copies/ml and HCV RNA was 58 IU/ml. Twenty-three months after the last IL-2 treatment (at the time of writing), the patient is alive and in a good clinical condition. CONCLUSION: The decrease of HBV and HCV nucleic acids during immunotherapy with IL-2 predicts a possible new therapeutic option for these chronic viral infections.

Spinodal decomposition of asymmetric binary fluids in a micro-Couette geometry simulated with molecular dynamics.

The spinodal decomposition of quenched polymer/solvent and liquid-crystal/solvent mixtures in a miniature Taylor-Couette cell has been simulated by molecular dynamics. Three stacking motifs, each reflecting the geometry and symmetry of the cell, are most abundant among the fully phase separated stationary states. At zero or low angular velocity of the inner cylindrical drum, the two segregated domains have a clear preference for the stacking with the lowest free energy and hence the smallest total interfacial tension. For high shear rates, the steady state appears to be determined by a minimum dissipation mechanism, i.e., the mixtures are likely to evolve into the stacking demanding the least mechanical power by the rotating wall. The partial slip at the polymer-solvent interfaces then gives rise to a new pattern: A stack of three concentric cylindrical shells with the viscous polymer layer sandwiched between two solvent layers. Neither of these mechanisms can explain all simulation results, as the separating mixture easily becomes kinetically trapped in a long-lived suboptimal configuration. The phase separation process is observed to proceed faster under shear than in a quiescent mixture.

Finite system size effects in the interfacial dynamics of binary liquid films.

We study the relaxation dynamics of capillary waves in the interface between two confined liquid layers by means of molecular dynamics simulations. We measure the autocorrelations of the interfacial Fourier modes and find that the finite thickness of the liquid layers leads to a marked increase of the relaxation times as compared to the case of fluid layers of infinite depth. The simulation results are in good agreement with a theoretical first-order perturbation derivation, which starts from the overdamped Stokes' equation. The theory also takes into account an interfacial friction, but the difference with no-slip interfacial conditions is small. When the walls are sheared, it is found that the relaxation times of modes perpendicular to the flow are unaffected. Modes along the flow direction are relatively unaffected as long as the equilibrium relaxation time is sufficiently short compared to the rate of deformation. We discuss the consequences for experiments on thin layers and on ultralow surface tension fluids, as well as computer simulations.

Molecular dynamics simulation of phase separating binary liquids in cylindrical Couette flow.

We use molecular dynamics simulations to study phase separation of a 50:50 (by volume) fluid mixture in a confined and curved (Taylor-Couette) geometry, consisting of two concentric cylinders. The inner cylinder may be rotated to achieve a shear flow. In nonsheared systems we observe that, for all cases under consideration, the final equilibrium state has a stacked structure. Depending on the lowest free energy in the geometry the stack may be either flat, with its normal in the z direction, or curved, with its normal in the r or theta direction. In sheared systems we make several observations. First, when starting from a prearranged stacked structure, we find that sheared gradient and vorticity stacks retain their character for the durations of the simulation, even when another configuration is preferred (as found when starting from a randomly mixed configuration). This slow transition to another configuration is attributed to a large free energy barrier between the two states. In case of stacks with a normal in the gradient direction, we find interesting interfacial waves moving with a prescribed angular velocity in the flow direction. Because such a wave is not observed in simulations with a flat geometry at similar shear rates, the curvature of the wall is an essential ingredient of this phenomenon. Second, when starting from a randomly mixed configuration, stacks are also observed, with an orientation that depends on the applied shear rate. Such transitions to other orientations are similar to observations in microphase separated diblock copolymer melts. At higher shear rates complex patterns emerge, accompanied by deviations from a homogeneous flow profile. The transition from steady stacks to complex patterns takes place around a shear rate 1/tau(dv), where tau(dv) is the crossover time from diffusive to viscous dominated growth of phase-separated domains, as measured in equilibrium simulations.

Domain formation and growth in spinodal decomposition of a binary fluid by molecular dynamics simulations.

The two initial stages of spinodal decomposition of a symmetric binary Lennard-Jones fluid have been simulated by molecular dynamics simulations, using a hydrodynamics-conserving thermostat. By analyzing the growth of the average domain size R(t) with time, a satisfactory agreement is found with the R(t) proportional t1/3 Lifshitz-Slyozov growth law for the early diffusion-driven stage of domain formation in a quenched homogeneous mixture. In the subsequent stage of viscous-dominated growth, the mean domain size appears to follow the linear growth law predicted by Siggia.

Intermonolayer friction and surface shear viscosity of lipid bilayer membranes.

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.

Simulations of the dynamics of thermal undulations in lipid bilayers in the tensionless state and under stress.

The relaxation processes of height undulations and density fluctuations in a membrane have been studied by molecular dynamics simulations of a coarse grained amphiphilic bilayer model. We observe a double exponential decay in their time correlations, with relaxation rates in good quantitative agreement with the theory by Seifert and Langer [Europhys. Lett. 23, 71 (1993)]. Intermonolayer friction due to slippage between the two monolayers is shown to be the dominant dissipative mechanism at the high wave numbers, q>10 mum(-1), typically encountered in computer simulations. We briefly discuss the ramifications of the slow undulatory relaxation process for the calculation of bending rigidities from the static undulation structure factors. The relaxation rates are sensitive to the surface tension, and at high elongations an oscillatory contribution is observed in the time correlation of the undulations.

Treatment of ocular squamous cell carcinomas in cattle with interleukin-2.

In total, 174 bovine ocular squamous cell carcinomas of varying sizes (20 to 2800 mm(2) in area) were treated daily with peritumoural injections of solvent, or solvent containing 5000 U, 20,000 U, 200,000 U, 500,000 U, 1 million U or 2 million U interleukin-2 (IL-2) for 10 days. The tumours were measured and clinically staged before treatment and at one, three, four, nine and 20 months after treatment. After 20 months, 14 per cent of the tumours treated with the solvent had regressed completely, a significantly smaller proportion than the 55 per cent treated with 5000 U IL-2, 52 per cent treated with 20,000 U IL-2, 58 per cent treated with 200,000 U IL-2, 50 per cent treated with 500,000 U IL-2, 69 per cent of tumours treated with 1 million U IL-2, 52 per cent treated with 2 million U IL-2. The tumours on the third eyelid and limbus were the most responsive.

Periodic orientational motions of rigid liquid-crystalline polymers in shear flow.

The collective periodic motions of liquid-crystalline polymers in a nematic phase in shear flow have, for the first time, been simulated at the particle level by Brownian dynamics simulations. A wide range of parameter space has been scanned by varying the aspect ratio L/D between 10 and 60 at three different scaled volume fractions Lphi/D and an extensive series of shear rates. The influence of the start configuration of the box on the final motion has also been studied. Depending on these parameters, the motion of the director is either characterized as tumbling, kayaking, log-rolling, wagging, or flow-aligning. The periods of kayaking and wagging motions are given by T=4.2(Lphi/D)gamma(-1) for high aspect ratios. Our simulation results are in agreement with theoretical predictions and recent shear experiments on fd viruses in solution. These calculations of elongated rigid rods have become feasible with a newly developed event-driven Brownian dynamics algorithm.

Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations.

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.