Optimisation of a Brownian dynamics algorithm for semidilute polymer solutions

Simulating the static and dynamic properties of semidilute polymer solutions with Brownian dynamics (BD) requires the computation of a large system of polymer chains coupled to one another through excluded-volume and hydrodynamic interactions. In the presence of periodic boundary conditions, long-ranged hydrodynamic interactions are frequently summed with the Ewald summation technique. By performing detailed simulations that shed light on the influence of several tuning parameters involved both in the Ewald summation method, and in the efficient treatment of Brownian forces, we develop a BD algorithm in which the computational cost scales as O(N^{1.8}), where N is the number of monomers in the simulation box. We show that Beenakker's original implementation of the Ewald sum, which is only valid for systems without bead overlap, can be modified so that \theta-solutions can be simulated by switching off excluded-volume interactions. A comparison of the predictions of the radius of gyration, the end-to-end vector, and the self-diffusion coefficient by BD, at a range of concentrations, with the hybrid Lattice Boltzmann/Molecular Dynamics (LB/MD) method shows excellent agreement between the two methods. In contrast to the situation for dilute solutions, the LB/MD method is shown to be significantly more computationally efficient than the current implementation of BD for simulating semidilute solutions. We argue however that further optimisations should be possible.Comment: 17 pages, 8 figures, revised version to appear in Physical Review E (2012

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

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

Brownian dynamics simulations of planar mixed flows of polymer solutions at finite concentrations

Periodic boundary conditions for planar mixed flows are implemented in the context of a multi-chain Brownian dynamics simulation algorithm. The effect of shear rate $\dot{\gamma}$, and extension rate $\dot{\epsilon}$, on the size of polymer chains, \left, and on the polymer contribution to viscosity, $\eta$, is examined for solutions of FENE dumbbells at finite concentrations, with excluded volume interactions between the beads taken into account. The influence of the mixedness parameter, $\chi$, and flow strength, $\dot{\Gamma}$, on \left and $\eta$, is also examined, where $\chi \rightarrow 0$ corresponds to pure shear flow, and $\chi \rightarrow 1$ corresponds to pure extensional flow. It is shown that there exists a critical value, $\chi_\text{c}$, such that the flow is shear dominated for $\chi < \chi_\text{c}$, and extension dominated for $\chi > \chi_\text{c}$.Comment: 18 pages, 12 figures, to appear in Chemical Engineering Scienc

Compositional changes on GaN surfaces under low-energy ion bombardment studied by synchrotron-based spectroscopies

We have investigated compositional changes on GaNsurfaces under Ar-ion bombardment using synchrotron-based high-resolution x-rayphotoemission (PES) and near-edge x-ray absorption fine structure(NEXAFS)spectroscopy. The low-energy ion bombardment of GaN produces a Ga-rich surface layer which transforms into a metallic Ga layer at higher bombarding energies. At the same time, the photoemissionspectra around N 1s core levels reveal the presence of both uncoordinated nitrogen and nitrogen interstitials, which we have analyzed in more details by x-rayabsorption measurements at N K edge. We have demonstrated that PES and NEXAFS provide a powerful combination for studying the compositional changes on GaNsurfaces. A mechanism for the relocation and loss of nitrogen during ion bombardment in agreement with some recent experimental and theoretical studies of defect formation in GaN has been proposed.P.N.K.D. is grateful for the financial support of the Australian Research Council

Rouse Chains with Excluded Volume Interactions: Linear Viscoelasticity

Linear viscoelastic properties for a dilute polymer solution are predicted by modeling the solution as a suspension of non-interacting bead-spring chains. The present model, unlike the Rouse model, can describe the solution's rheological behavior even when the solvent quality is good, since excluded volume effects are explicitly taken into account through a narrow Gaussian repulsive potential between pairs of beads in a bead-spring chain. The use of the narrow Gaussian potential, which tends to the more commonly used delta-function repulsive potential in the limit of a width parameter "d" going to zero, enables the performance of Brownian dynamics simulations. The simulations results, which describe the exact behavior of the model, indicate that for chains of arbitrary but finite length, a delta-function potential leads to equilibrium and zero shear rate properties which are identical to the predictions of the Rouse model. On the other hand, a non-zero value of "d" gives rise to a prediction of swelling at equilibrium, and an increase in zero shear rate properties relative to their Rouse model values. The use of a delta-function potential appears to be justified in the limit of infinite chain length. The exact simulation results are compared with those obtained with an approximate solution which is based on the assumption that the non-equilibrium configurational distribution function is Gaussian. The Gaussian approximation is shown to be exact to first order in the strength of excluded volume interaction, and is found to be accurate above a threshold value of "d", for given values of chain length and strength of excluded volume interaction.Comment: Revised version. Long chain limit analysis has been deleted. An improved and corrected examination of the long chain limit will appear as a separate posting. 32 pages, 9 postscript figures, LaTe

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

The common and uncommon cestodal infestation encountered in routine histopathological practice from a semi-urban population in south India and their public health importance.

Parasites are encountered uncommonly in routine histopathologic practice. Among them, cestodes form a major bulk. Cysticercosis heads the list forming the bulk of cases followed by Hydatidosis and Sparganosis. Microscopic identification of inflammation with surrounding reactions along with other morphological features forms the mainstay of diagnosis of parasitic diseases on histopathology. Identification of the parasites on histopathological examination would reduce the cost-diagnosis ratio avoiding expensive serological investigation

MHD Mixed Convective Flow of Viscoelastic and Viscous Fluids in a Vertical Porous Channel

In this paper, we analyze the problem of steady, mixed convective, laminar flow of two incompressible, electrically conducting and heat absorbing immiscible fluids in a vertical porous channel filled with viscoelastic fluid in one region and viscous fluid in the other region. A uniform magnetic field is applied in the transverse direction, the fluids rise in the channel driven by thermal buoyancy forces associated with thermal radiation. The equations are modeled using the fully developed flow conditions. An exact solution is obtained for the velocity, temperature, skin friction and Nusselt number distributions. The physical interpretation to these expressions is examined through graphs and table for the shear stress and rate of heat transfer coefficients at the channel walls

Universal scaling and characterisation of gelation in associative polymer solutions

A Brownian dynamics algorithm is used to describe the static behaviour of associative polymer solutions. Predictions for the fractions of stickers bound by intra-chain and inter-chain association, as a function of system parameters, such as the number of stickers, the number of monomers between stickers, the solvent quality, and concentration are obtained. A systematic comparison with the scaling relations predicted by the mean-field theory of Dobrynin (Macromolecules, 37, 3881, 2004) is carried out. Different regimes of scaling behaviour are identified depending on the monomer concentration, the density of stickers on a chain, and the solvent quality for backbone monomers. Simulation results validate the predictions of the mean-field theory across a wide range of parameter values in all the scaling regimes. The value of the des Cloizeaux exponent proposed by Dobrynin for sticky polymer solutions, is shown to lead to a collapse of simulation data for all the scaling relations considered here. Three different signatures for the characterisation of gelation are identified, with each leading to a different value of the concentration at the sol-gel transition. The modified Flory-Stockmayer expression is found to be validated by simulations for all three gelation signatures. Simulation results confirm the prediction of scaling theory for the gelation line that separates sol and gel phases, when the modified Flory-Stockmayer expression is used. Phase separation is found to occur with increasing concentration for systems in which the backbone monomers are under theta-solvent conditions, and is shown to coincide with a breakdown in the predictions of scaling theory.Comment: 34 pages, 22 figures, includes Supplemental Material, accepted versio