Mesoscale simulations of polymer dynamics in microchannel flows

The non-equilibrium structural and dynamical properties of flexible polymers confined in a square microchannel and exposed to a Poiseuille flow are investigated by mesoscale simulations. The chain length and the flow strength are systematically varied. Two transport regimes are identified, corresponding to weak and strong confinement. For strong confinement, the transport properties are independent of polymer length. The analysis of the long-time tumbling dynamics of short polymers yields non-periodic motion with a sublinear dependence on the flow strength. We find distinct differences for conformational as well as dynamical properties from results obtained for simple shear flow

Dynamics of short polymer chains in solution

We present numerical and analytical results describing the effect of hydrodynamic interactions on the dynamics of a short polymer chain in solution. A molecular dynamics algorithm for the polymer is coupled to a direct simulation Monte Carlo algorithm for the solvent. We give an explicit expression for the velocity autocorrelation function of the centre of mass of the polymer which agrees well with numerical results if Brownian dynamics, hydrodynamic correlations and sound wave scattering are included

Dynamics and Scaling of 2D Polymers in a Dilute Solution

The breakdown of dynamical scaling for a dilute polymer solution in 2D has been suggested by Shannon and Choy [Phys. Rev. Lett. {\bf 79}, 1455 (1997)]. However, we show here both numerically and analytically that dynamical scaling holds when the finite-size dependence of the relevant dynamical quantities is properly taken into account. We carry out large-scale simulations in 2D for a polymer chain in a good solvent with full hydrodynamic interactions to verify dynamical scaling. This is achieved by novel mesoscopic simulation techniques

Synchnonization, zero-resistance states and rotating Wigner crystal

We show that rotational angles of electrons moving in two dimensions (2D) in a perpendicular magnetic field can be synchronized by an external microwave field which frequency is close to the Larmor frequency. The synchronization eliminates collisions between electrons and thus creates a regime with zero diffusion corresponding to the zero-resistance states observed in experiments with high mobility 2D electron gas (2DEG). For long range Coulomb interactions electrons form a rotating hexagonal Wigner crystal. Possible relevance of this effect for planetary rings is discussed.Comment: 4 pages, 4 fig

Two-Dimensional Fluctuating Vesicles in Linear Shear Flow

The stochastic motion of a two-dimensional vesicle in linear shear flow is studied at finite temperature. In the limit of small deformations from a circle, Langevin-type equations of motion are derived, which are highly nonlinear due to the constraint of constant perimeter length. These equations are solved in the low temperature limit and using a mean field approach, in which the length constraint is satisfied only on average. The constraint imposes non-trivial correlations between the lowest deformation modes at low temperature. We also simulate a vesicle in a hydrodynamic solvent by using the multi-particle collision dynamics technique, both in the quasi-circular regime and for larger deformations, and compare the stationary deformation correlation functions and the time autocorrelation functions with theoretical predictions. Good agreement between theory and simulations is obtained.Comment: 13 pages, 7 figure

A Numerical Model for Brownian Particles Fluctuating in Incompressible Fluids

We present a numerical method that consistently implements thermal fluctuations and hydrodynamic interactions to the motion of Brownian particles dispersed in incompressible host fluids. In this method, the thermal fluctuations are introduced as random forces acting on the Brownian particles. The hydrodynamic interactions are introduced by directly resolving the fluid motions with the particle motion as a boundary condition to be satisfied. The validity of the method has been examined carefully by comparing the present numerical results with the fluctuation-dissipation theorem whose analytical form is known for dispersions of a single spherical particle. Simulations are then performed for more complicated systems, such as a dispersion composed of many spherical particles and a single polymeric chain in a solvent.Comment: 6 pages, 8 figure

Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length-scales

We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The importance of carefully tuning the simulation parameters to correctly resolve the multiple time and length-scales of this problem is emphasized. We systematically analyze how our coarse-graining scheme resolves dimensionless hydrodynamic numbers such as the Reynolds number, the Schmidt number, the Mach number, the Knudsen number, and the Peclet number. The many Brownian and hydrodynamic time-scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant physical processes. We also show how to control a number of numerical artifacts, such as finite size effects and solvent induced attractive depletion interactions. When all these considerations are properly taken into account, the measured colloidal velocity auto-correlation functions and related self diffusion and friction coefficients compare quantitatively with theoretical calculations. By contrast, these calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity auto-correlation function in the colloidal regime, strongly underestimating it at short times and strongly overestimating it at long times. Finally, we discuss in detail how to map the parameters of our method onto physical systems, and from this extract more general lessons that may be relevant for other coarse-graining schemes such as Lattice Boltzmann or Dissipative Particle Dynamics.Comment: 31 pages, 14 figure

Semiflexible polymer conformation, distribution and migration in microcapillary flows

The flow behavior of a semiflexible polymer in microchannels is studied using Multiparticle Collision Dynamics (MPC), a particle-based hydrodynamic simulation technique. Conformations, distributions, and radial cross-streamline migration are investigated for various bending rigidities, with persistence lengths Lp in the range 0.5 < Lp/Lr < 30. The flow behavior is governed by the competition between a hydrodynamic lift force and steric wall-repulsion, which lead to migration away from the wall, and a locally varying flow-induced orientation, which drives polymer away from the channel center and towards the wall. The different dependencies of these effects on the polymer bending rigidity and the flow velocity results in a complex dynamical behavior. However, a generic effect is the appearance of a maximum in the monomer and the center-of-mass distributions, which occurs in the channel center for small flow velocities, but moves off-center at higher velocities.Comment: in press at J. Phys. Condens. Matte

Biscale Chaos in Propagating Fronts

The propagating chemical fronts found in cubic autocatalytic reaction-diffusion processes are studied. Simulations of the reaction-diffusion equation near to and far from the onset of the front instability are performed and the structure and dynamics of chemical fronts are studied. Qualitatively different front dynamics are observed in these two regimes. Close to onset the front dynamics can be characterized by a single length scale and described by the Kuramoto-Sivashinsky equation. Far from onset the front dynamics exhibits two characteristic lengths and cannot be modeled by this amplitude equation. An amplitude equation is proposed for this biscale chaos. The reduction of the cubic autocatalysis reaction-diffusion equation to the Kuramoto-Sivashinsky equation is explicitly carried out. The critical diffusion ratio delta, where the planar front loses its stability to transverse perturbations, is determined and found to be delta=2.300.Comment: Typeset using RevTeX, fig.1 and fig.4 are not available, mpeg simulations are at http://www.chem.utoronto.ca/staff/REK/Videos/front/front.htm

Interplay of buried histidine protonation and protein stability in prion misfolding

Misofolding of mammalian prion proteins (PrP) is believed to be the cause of a group of rare and fatal neurodegenerative diseases. Despite intense scrutiny however, the mechanism of the misfolding reaction remains unclear. We perform nuclear Magnetic Resonance and thermodynamic stability measurements on the C-terminal domains (residues 90–231) of two PrP variants exhibiting different pH-induced susceptibilities to aggregation: the susceptible hamster prion (GHaPrP) and its less susceptible rabbit homolog (RaPrP). The pKa of histidines in these domains are determined from titration experiments, and proton-exchange rates are measured at pH 5 and pH 7. A single buried highly conserved histidine, H187/H186 in GHaPrP/RaPrP, exhibited a markedly down shifted pKa ~5 for both proteins. However, noticeably larger pH-induced shifts in exchange rates occur for GHaPrP versus RaPrP. Analysis of the data indicates that protonation of the buried histidine destabilizes both PrP variants, but produces a more drastic effect in the less stable GHaPrP. This interpretation is supported by urea denaturation experiments performed on both PrP variants at neutral and low pH, and correlates with the difference in disease susceptibility of the two species, as expected from the documented linkage between destabilization of the folded state and formation of misfolded and aggregated species