arXiv subjects

Daan Frenkel

Publications and source records attributed to Daan Frenkel.

At least 109 records · Page 6Linked to original sources

arXiv2004

Length, Protein-Protein Interactions, and Complexity

The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein interactions has driven the selection of longer proteins, as longer proteins are more able to distinguish among a larger number of distinct interactions due to their greater average surface area. Annotated protein sequences available from the SWISS-PROT database were analyzed for thirteen eukaryotes, eight bacteria, and two archaea species. The number of subcellular locations to which each protein is associated is used as a measure of the number of interactions to which a protein participates. Two databases of yeast protein-protein interactions were used as another measure of the number of interactions to which each \emph{S. cerevisiae} protein participates. Protein length is shown to correlate with both number of subcellular locations to which a protein is associated and number of interactions as measured by yeast two-hybrid experiments. Protein length is also shown to correlate with the probability that the protein is encoded by an essential gene. Interestingly, average protein length and number of subcellular locations are not significantly different between all human proteins and protein targets of known, marketed drugs. Increased protein length appears to be a significant mechanism by which the increasing complexity of protein-protein interaction networks is accommodated within the natural evolution of species. Consideration of protein length may be a valuable tool in drug design, one that predicts different strategies for inhibiting interactions in aberrant and normal pathways.

q-bio.MN↗

arXiv2004

The steady-state of heterogeneous catalysis, studied by first-principles statistical mechanics

The turn-over frequency of the catalytic oxidation of CO at RuO2(110) was calculated as function of temperature and partial pressures using ab initio statistical mechanics. The underlying energetics of the gas-phase molecules, dissociation, adsorption, surface diffusion, surface chemical reactions, and desorption were obtained by all-electron density-functional theory. The resulting CO2 formation rate [in the full (T, p_CO, p_O2)-space], the movies displaying the atomic motion and reactions over times scales from picoseconds to seconds, and the statistical analyses provide insights into the concerted actions ruling heterogeneous catalysis and open thermodynamic systems in general.

cond-mat.mtrl-sci↗

arXiv2004

Modelling colloids with Baxter's adhesive hard sphere model

The structure of the Baxter adhesive hard sphere fluid is examined using computer simulation. The radial distribution function (which exhibits unusual discontinuities due to the particle adhesion) and static structure factor are calculated with high accuracy over a range of conditions and compared with the predictions of Percus--Yevick theory. We comment on rigidity in percolating clusters and discuss the role of the model in the context of experiments on colloidal systems with short-range attractive forces.

cond-mat.soft↗

arXiv2004

Homogeneous nucleation of colloidal melts under the influence of shearing fields

We study the effect of shear flow on homogeneous crystal nucleation, using Brownian Dynamics simulations in combination with an umbrella sampling like technique. The symmetry breaking due to shear results in anisotropic radial distribution functions. The homogeneous shear rate suppresses crystal nucleation and leads to an increase of the size of the critical nucleus. These observations can be described by a simple, phenomenological extension of classical nucleation theory. In addition, we find that nuclei have a preferential orientation with respect to the direction of shear. On average the longest dimension of a nucleus is along the vorticity direction, while the shortest dimension is preferably perpendicular to that and slightly tilted with respect to the gradient direction.

cond-mat.soft↗

arXiv2004

Crystal Nucleation of Colloidal Suspensions under Shear

We use Brownian Dynamics simulations in combination with the umbrella sampling technique to study the effect of shear flow on homogeneous crystal nucleation. We find that a homogeneous shear rate leads to a significant suppression of the crystal nucleation rate and to an increase of the size of the critical nucleus. A simple, phenomenological extension of classical nucleation theory accounts for these observations. The orientation of the crystal nucleus is tilted with respect to the shear direction.

cond-mat.soft↗

arXiv2004

Discrete solution of the electrokinetic equations

We present a robust scheme for solving the electrokinetic equations. This goal is achieved by combining the lattice-Boltzmann method (LB) with a discrete solution of the convection-diffusion equation for the different charged and neutral species that compose the fluid. The method is based on identifying the elementary fluxes between nodes, which ensures the absence of spurious fluxes in equilibrium. We show how the model is suitable to study electro-osmotic flows. As an illustration, we show that, by introducing appropriate dynamic rules in the presence of solid interfaces, we can compute the sedimentation velocity (and hence the sedimentation potential) of a charged sphere. Our approach does not assume linearization of the Poisson-Boltzmann equation and allows us for a wide variation of the Peclet number.

cond-mat.stat-mech↗

arXiv2004

Multiple stalk formation as a pathway of defect-induced membrane fusion

We propose that the first stage of membrane fusion need not be the formation of a single stalk. Instead, we consider a scenario for defect-induced membrane fusion that proceeds cooperatively via multiple stalk formation. The defects (stalks or pores) attract each other via membrane-mediated capillary interactions that result in a condensation transition of the defects. The resulting dense phase of stalks corresponds to the so-called fusion intermediate.

cond-mat.soft↗

arXiv2004

High pressure diamond-like liquid carbon

We report density-functional based molecular dynamics simulations, that show that, with increasing pressure, liquid carbon undergoes a gradual transformation from a liquid with local three-fold coordination to a 'diamond-like' liquid. We demonstrate that this unusual structural change is well reproduced by an empirical bond order potential with isotropic long range interactions, supplemented by torsional terms. In contrast, state-of-the-art short-range bond-order potentials do not reproduce this diamond structure. This suggests that a correct description of long-range interactions is crucial for a unified description of the solid and liquid phases of carbon.

cond-mat.other↗

arXiv2004

Melting of Polydisperse Hard Disks

The melting of a polydisperse hard disk system is investigated by Monte Carlo simulations in the semigrand canonical ensemble. This is done in the context of possible continuous melting by a dislocation unbinding mechanism, as an extension of the 2D hard disk melting problem. We find that while there is pronounced fractionation in polydispersity, the apparent density-polydispersity gap does not increase in width, contrary to 3D polydisperse hard spheres. The point where the Young's modulus is low enough for the dislocation unbinding to occur moves with the apparent melting point, but stays within the density gap, just like for the monodisperse hard disk system. Additionally, we find that throughout the accessible polydispersity range, the bound dislocation-pair concentration is high enough to affect the dislocation unbinding melting as predicted by Kosterlitz, Thouless, Halperin, Nelson and Young.

cond-mat.soft↗

arXiv2004

Phase Behavior and Selectivity of DNA-linked Nanoparticle Assemblies

We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles by dissolved DNA linker can be described by exploiting an analogy with quantum particles obeying fractional statistics. In accordance with experimental findings, we predict that the phase-separation temperature of the nano-colloids increases with the DNA coverage of the colloidal surface. Upon the addition of salt, the demixing temperature increases logarithmically with the salt concentration. Our analysis suggests an experimental strategy to map microscopic DNA sequences onto the macroscopic phase behavior of the DNA-nanoparticle solutions. Such an approach should enhance the efficiency of methods to detect (single) mutations in specific DNA sequences.

cond-mat.soft↗

arXiv2004

Large effect of polydispersity on defect concentrations in colloidal crystals

We compute the equilibrium concentration of stacking faults and point defects in polydisperse hard-sphere crystals. We find that, while the concentration of stacking faults remains similar to that of monodisperse hard sphere crystals, the concentration of vacancies decreases by about a factor two. Most strikingly, the concentration of interstitials in the maximally polydisperse crystal may be some six orders of magnitude larger than in a monodisperse crystal. We show that this dramatic increase in interstitial concentration is due to the increased probability of finding small particles and that the small-particle tail of the particle size distribution is crucial for the interstitial concentration in a colloidal crystal.

cond-mat.soft↗

arXiv2004

Cubatic phase for tetrapods

We investigate the phase behavior of tetrapods, hard non-convex bodies formed by 4 rods connected under tetrahedral angles. We predict that, depending on the relative lengths of the rods these particles can form a uniaxial nematic phase, and more surprisingly they can exhibit a cubatic phase, a special case of the biaxial nematic phase. These predictions may be experimentally testable, as experimental realizations of tetrapods have recently become available.

cond-mat.soft↗

arXiv2003

Large difference in the elastic properties of fcc and hcp hard-sphere crystals

We report a numerical calculation of the elastic constants of the fcc and hcp crystal phases of monodisperse hard-sphere colloids. Surprisingly, some of these elastic constants are very different (up to 20%), even though the free energy, pressure and bulk compressibility of the two crystal structures are very nearly equal. As a consequence, a moderate deformation of a hard-sphere crystal may make the hcp phase more stable than the fcc phase. This finding has implications for the design of patterned templates to grow colloidal hcp crystals. We also find that, below close packing, there is a small, but significant, difference between the distances between hexagonal layers (c/a ratios) of fcc and hcp crystals.

cond-mat.soft↗

arXiv2003

Lattice model study of the thermodynamic interplay of polymer crystallization and liquid-liquid demixing

We report Monte Carlo simulations of a lattice-polymer model that can account for both polymer crystallization and liquid-liquid demixing in solutions of semiflexible homopolymers. In our model, neighboring polymer segments can have isotropic interactions that affect demixing, and anisotropic interactions that are responsible for freezing. However, our simulations show that the isotropic interactions also have a noticeable effect on the freezing curve, as do the anisotropic interactions on demixing. As the relative strength of the isotropic interactions is reduced, the liquid-liquid demixing transition disappears below the freezing curve. A simple, extended Flory-Huggins theory accounts quite well for the phase behavior observed in the simulations.

cond-mat.soft↗

arXiv2003

Competition of percolation and phase separation in a fluid of adhesive hard spheres

Using a combination of Monte Carlo techniques, we locate the liquid--vapor critical point of adhesive hard spheres. We find that the critical point lies deep inside the gel region of the phase diagram. The (reduced) critical temperature and density are $τ_c=0.1133\pm0.0005$ and $ρ_c=0.508\pm0.01$. We compare these results with the available theoretical predictions. Using a finite-size scaling analysis, we verify that the critical behavior of the adhesive hard sphere model is consistent with that of the 3D Ising universality class.

cond-mat.stat-mech↗

arXiv2002

Free energy barrier for single-chain melting and crystallization

In this paper, we report dynamic Monte Carlo simulations of melting and crystallization in a single-chain system. Their free energy barriers are calculated by the umbrella sampling method and can be described well by a simple expression DeltaF = n Deltaf+sigma (N-n)^(2/3), where n is the amount of molten bonds, Deltaf is the free energy change of each molten bond from a crystalline state, N is the chain length, and sigma is the surface free energy of crystallite. We found that, together with the expression Delta F = n Delta f+ sigma (N-n)^(1/2) for molecular nucleation, the molecular-weight dependent properties of the free-energy barriers for polymer primary and secondary nucleation, in particular, the molecular segregation during crystal growth, can be reproduced. Then for the mechanism of polymer crystallization, we suggested a quantitative model of intramolecular nucleation, as a direct development from the previous qualitative description of molecular nucleation model.

cond-mat.soft↗

arXiv2002

Free-energy barrier to melting of single-chain polymer crystallite

We report Monte Carlo simulations of the melting of a single-polymer crystallite. We find that, unlike most atomic and molecular crystals, such crystallites can be heated appreciably above their melting temperature before they transform to the disordered "coil" state. The surface of the superheated crystallite is found to be disordered. The thickness of the disordered layer increases with superheating. However, the order-disorder transition is not gradual but sudden. Free-energy calculations reveal the presence of a large free-energy barrier to melting.

cond-mat.soft↗

arXiv2001

A Lattice-Boltzmann method for the simulation of transport phenomena in charged colloids

We present a new simulation scheme based on the Lattice-Boltzmann method to simulate the dynamics of charged colloids in an electrolyte. In our model we describe the electrostatics on the level of a Poisson-Boltzmann equation and the hydrodynamics of the fluid by the linearized Navier-Stokes equations. We verify our simulation scheme by means of a Chapman-Enskog expansion. Our method is applied to the calculation of the reduced sedimentation velocity U/U_0 for a cubic array of charged spheres in an electrolyte. We show that we recover the analytical solution first derived by Booth (F. Booth, J. Chem. Phys. 22, 1956 (1954)) for a weakly charged, isolated sphere in an unbounded electrolyte. The present method makes it possible to go beyond the Booth theory, and we discuss the dependence of the sedimentation velocity on the charge of the spheres. Finally we compare our results to experimental data.

cond-mat.dis-nn↗