Optimized Constant Pressure Stochastic Dynamics

A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward application of the standard Kramers-Moyal formalism. An integration scheme is developed which reduces to a time-reversible symplectic integrator in the limit of vanishing friction. This algorithm is hence expected to be quite stable for small friction, allowing for a large time step. We discuss the optimal choice of parameters, and present some numerical test results.Comment: 16 pages, 2 figures, submitted to J. Chem. Phy

Universality of the collapse transition of sticky polymers

The universality of the swelling of the radius of gyration of a homopolymer relative to its value in the $\theta$ state, independent of polymer-solvent chemistry, in the crossover regime between $\theta$ and athermal solvent conditions, is well known. Here we study, by Brownian dynamics, a polymer model where a subset of monomers is labelled as "stickers". The mutual interaction of the stickers is more attractive than those of the other ("backbone") monomers, and has the additional important characteristic of "functionality" $\varphi$, i.e., the maximum number of stickers that can locally bind to a given sticker. A saturated bond formed in this manner remains bound until it breaks due to thermal fluctuations, a requirement which can be viewed as an additional Boolean degree of freedom that describes the bonding. This, in turn, makes the question of the order of the collapse transition a non-trivial one. Nevertheless, for the parameters that we have studied (in particular, $\varphi=1$), we find a standard second-order $\theta$ collapse, using a renormalised solvent quality parameter that takes into account the increased average attraction due to the presence of stickers. We examine the swelling of the radius of gyration of such a sticky polymer relative to its value in the altered $\theta$ state, using a novel potential to model the various excluded volume interactions that occur between the monomers on the chain. We find that the swelling of such sticky polymers is identical to the universal swelling of homopolymers in the thermal crossover regime. Additionally, for our model, the Kuhn segment length under $\theta$ conditions is found to be the same for chains with and without stickers.Comment: 13 pages, 10 figures, supplementary material (see ancillary directory), to appear in Soft Matte

Shear thinning in dilute and semidilute solutions of polystyrene and DNA

The viscosity of dilute and semidilute unentangled DNA solutions, in steady simple shear flow, has been measured across a range of temperatures and concentrations. For polystyrene solutions, measurements of viscosity have been carried out in the semidilute unentangled regime, while results of prior experimental measurements in the dilute regime have been used for the purpose of data analysis, and for comparison with the behaviour of DNA solutions. Interpretation of the shear rate dependence of viscosity in terms of suitably defined non-dimensional variables, is shown to lead to master plots, independent of temperature and concentration, in each of the two concentration regimes. In the case of semidilute unentangled solutions, defining the Weissenberg number in terms of a concentration dependent large scale relaxation time is found not to lead to data collapse across different concentrations. On the other hand, the use of an alternative relaxation time, with the concentration dependence of a single correlation blob, suggests the existence of universal shear thinning behaviour at large shear rates.Comment: 24 pages, 13 figures, supplementary material (see ancillary directory), to appear in Journal of Rheolog

Equilibrium binding energies from fluctuation theorems and force spectroscopy simulations

Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead that is weakly bound to a cell and then removed by an optical tweezer. The external driving force arises from the combined optical tweezer and substrate potentials, and thermal fluctuations are taken into account by a Brownian force. The Jarzynski equality and Crooks' fluctuation theorem are applied to obtain the equilibrium free energy difference between the final and initial states. To this end, we sample non--equilibrium work trajectories for various tweezer pulling rates. We argue that this methodology should also be feasible experimentally for the envisioned system. Furthermore, we outline how the measurement of a whole free energy profile would allow the experimentalist to retrieve the unknown substrate potential by means of a suitable deconvolution. The influence of the pulling rate on the accuracy of the results is investigated, and umbrella sampling is used to obtain the equilibrium probability of particle escape for a variety of trap potentials.Comment: 21 pages, 11 figures, To appear in Soft Matte

On the size and shape of excluded volume polymers confined between parallel plates

A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between two parallel plates with varying plate separation. We show that the non-monotonic behavior of the overall size of the chain as a function of plate-separation, seen in computer simulations and reproduced by earlier theories, can already be predicted on the basis of scaling arguments. However, the behavior of the size in a plane parallel to the plates, a quantity observed in recent experiments, is predicted to be monotonic, in contrast to the experimental findings. We analyze this problem in depth with a mean-field approach that maps the confined polymer onto an anisotropic Gaussian chain, which allows the size of the polymer to be determined separately in the confined and unconfined directions. The theory allows the analytical construction of a smooth cross-over between the small plate-separation de Gennes regime and the large plate-separation Flory regime. The results show good agreement with Langevin dynamics simulations, and confirm the scaling predictions.Comment: 15 pages, 3 figure

Numerical simulations of compressible Rayleigh-Taylor turbulence in stratified fluids

We present results from numerical simulations of Rayleigh-Taylor turbulence, performed using a recently proposed lattice Boltzmann method able to describe consistently a thermal compressible flow subject to an external forcing. The method allowed us to study the system both in the nearly-Boussinesq and strongly compressible regimes. Moreover, we show that when the stratification is important, the presence of the adiabatic gradient causes the arrest of the mixing process.Comment: 15 pages, 11 figures. Proceedings of II Conference on Turbulent Mixing and Beyond (TMB-2009

Activity-induced clustering in model dumbbell swimmers:The role of hydrodynamic interactions

Using a fluid-particle dynamics approach, we numerically study the effects of hydrodynamic interactions on the collective dynamics of active suspensions within a simple model for bacterial motility: each microorganism is modeled as a stroke-averaged dumbbell swimmer with prescribed dipolar force pairs. Using both simulations and qualitative arguments, we show that, when the separation between swimmers is comparable to their size, the swimmers' motions are strongly affected by activity-induced hydrodynamic forces. To further understand these effects, we investigate semidilute suspensions of swimmers in the presence of thermal fluctuations. A direct comparison between simulations with and without hydrodynamic interactions shows these to enhance the dynamic clustering at a relatively small volume fraction; with our chosen model the key ingredient for this clustering behavior is hydrodynamic trapping of one swimmer by another, induced by the active forces. Furthermore, the density dependence of the motility (of both the translational and rotational motions) exhibits distinctly different behaviors with and without hydrodynamic interactions; we argue that this is linked to the clustering tendency. Our study illustrates the fact that hydrodynamic interactions not only affect kinetic pathways in active suspensions, but also cause major changes in their steady state properties.Comment: 18 pages, 14 figure