Hydrodynamic Interactions in Protein Folding

We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also study HIV-1 protease and show that HI make the flap closing dynamics faster. The HI are found to affect time correlation functions in the vicinity of the native state even though they have no impact on same time characteristics of the structure fluctuations around the native state

Direct contact and authoritarianism as moderators between extended contact and reduced prejudice: Lower threat and greater trust as mediators

Using a representative sample of Dutch adults (N = 1238), we investigated the moderating influence of direct contact and authoritarianism on the potential of extended contact to reduce prejudice. As expected, direct contact and authoritarianism moderated the effect of extended contact on prejudice. Moreover, the third-order moderation effect was also significant, revealing that extended contact has the strongest effect among high authoritarians with low levels of direct contact. We identified trust and perceived threat as the mediating processes underlying these moderation effects. The present study thus attests to the theoretical and practical relevance of reducing prejudice via extended contact. The discussion focuses on the role of extended contact in relation to direct contact and authoritarianism as well as on the importance of trust in intergroup contexts

Concentration Dependen Sedimentation of Collidal Rods

In the first part of this paper, an approximate theory is developed for the leading order concentration dependence of the sedimentation coefficient for rod-like colloids/polymers/macromolecules. To first order in volume fraction $\phi$ of rods, the sedimentation coefficient is written as $1+\alpha \phi$. For large aspect ratio L/D (L is the rod length, D it's thickness) $\alpha$ is found to very like $\propto (\frac{L}{D})^2/\log (\frac{L}{D})$. This theoretical prediction is compared to experimental results. In the second part, experiments on {\it fd}-virus are described, both in the isotropic and nematic phase. First order in concentration results for this very long and thin (semi-flexible) rod are in agreement with the above theoretical prediction. Sedimentation profiles for the nematic phase show two sedimentation fronts. This result indicates that the nematic phase becomes unstable with the respect to isotropic phase during sedimentation.Comment: Submitted to J. Chem. Phys. See related webpage http://www.elsie.brandeis.ed

Crystallization Kinetics of Colloidal Spheres under Stationary Shear Flow

A systematic experimental study of dispersions of charged colloidal spheres is presented on the effect of steady shear flow on nucleation and crystal-growth rates. In addition, the non-equilibrium phase diagram as far as the melting line is concerned is measured. Shear flow is found to strongly affect induction times, crystal growth rates and the location of the melting line. The main findings are that (i) the crystal growth rate for a given concentration exhibits a maximum as a function of the shear rate, (ii) contrary to the monotonous increase of the growth rate with increasing concentration in the absence of flow, a maximum of the crystal growth rate as a function of concentration is observed for sheared systems, and (iii) the induction time for a given concentration exhibits a maximum as a function of the shear rate. These findings will be partly explained on a qualitative level.Comment: 17 pages, 10 figures, accepted in Langmui

Aggregation of self-propelled colloidal rods near confining walls

Non-equilibrium collective behavior of self-propelled colloidal rods in a confining channel is studied using Brownian dynamics simulations and dynamical density functional theory. We observe an aggregation process in which rods self-organize into transiently jammed clusters at the channel walls. In the early stage of the process, fast-growing hedgehog-like clusters are formed which are largely immobile. At later stages, most of these clusters dissolve and mobilize into nematized aggregates sliding past the walls.Comment: 5 pages, 4 figure

Translational and rotational friction on a colloidal rod near a wall

We present particulate simulation results for translational and rotational friction components of a shish-kebab model of a colloidal rod with aspect ratio (length over diameter) $L/D = 10$ in the presence of a planar hard wall. Hydrodynamic interactions between rod and wall cause an overall enhancement of the friction tensor components. We find that the friction enhancements to reasonable approximation scale inversely linear with the closest distance $d$ between the rod surface and the wall, for $d$ in the range between $D/8$ and $L$. The dependence of the wall-induced friction on the angle $\theta$ between the long axis of the rod and the normal to the wall is studied and fitted with simple polynomials in $\cos \theta$.Comment: 8 pages, 8 figure

Kinetic pathways of the Nematic-Isotropic phase transition as studied by confocal microscopy on rod-like viruses

We investigate the kinetics of phase separation for a mixture of rodlike viruses (fd) and polymer (dextran), which effectively constitutes a system of attractive rods. This dispersion is quenched from a flow-induced fully nematic state into the region where the nematic and the isotropic phase coexist. We show experimental evidence that the kinetic pathway depends on the overall concentration. When the quench is made at high concentrations, the system is meta-stable and we observe typical nucleation-and-growth. For quenches at low concentration the system is unstable and the system undergoes a spinodal decomposition. At intermediate concentrations we see the transition between both demixing processes, where we locate the spinodal point.Comment: 11 pages, 6 figures, accepted in J. Phys.: Condens. Matter as symposium paper for the 6th Liquid Matter Conference in Utrech

Colloidal glass transition: Beyond mode-coupling theory

A new theory for dynamics of concentrated colloidal suspensions and the colloidal glass transition is proposed. The starting point is the memory function representation of the density correlation function. The memory function can be expressed in terms of a time-dependent pair-density correlation function. An exact, formal equation of motion for this function is derived and a factorization approximation is applied to its evolution operator. In this way a closed set of equations for the density correlation function and the memory function is obtained. The theory predicts an ergodicity breaking transition similar to that predicted by the mode-coupling theory, but at a higher density.Comment: to be published in PR

The probability distribution of a trapped Brownian particle in plane shear flows

We investigate the statistical properties of an over-damped Brownian particle that is trapped by a harmonic potential and simultaneously exposed to a linear shear flow or to a plane Poiseuille flow. Its probability distribution is determined via the corresponding Smoluchowski equation, which is solved analytically for a linear shear flow. In the case of a plane Poiseuille flow, analytical approximations for the distribution are obtained by a perturbation analysis and they are substantiated by numerical results. There is a good agreement between the two approaches for a wide range of parameters.Comment: 5 pages, 4 figur

Note: Scale-free center-of-mass displacement correlations in polymer films without topological constraints and momentum conservation

We present here computational work on the center-of-mass displacements in thin polymer films of finite width without topological constraints and without momentum conservation obtained using a well-known lattice Monte Carlo algorithm with chain lengths ranging up to N=8192. Computing directly the center-of-mass displacement correlation function C_N(t) allows to make manifest the existence of scale-free colored forces acting on a reference chain. As suggested by the scaling arguments put forward in a recent work on three-dimensional melts, we obtain a negative algebraic decay C_N(t) \sim -1/(Nt) for times t << T_N with T_N being the chain relaxation time. This implies a logarithmic correction to the related center-of-mass mean square-displacement h_N(t) as has been checked directly