Self-propulsion through symmetry breaking

In addition to self-propulsion by phoretic mechanisms that arises from an asymmetric distribution of reactive species around a catalytic motor, spherical particles with a uniform distribution of catalytic activity may also propel themselves under suitable conditions. Reactive fluctuation-induced asymmetry can give rise to transient concentration gradients which may persist under certain conditions, giving rise to a bifurcation to self-propulsion. The nature of this phenomenon is analyzed in detail, and particle-level simulations are carried out to demonstrate its existence.Comment: 6 pages, 3 figures. Appeared in EPL (Europhysics Letters

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations

Pattern formation often occurs in spatially extended physical, biological and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular revealing for the Swift-Hohenberg equations a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of an weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.Comment: 9 pages, 10 figures, submitted to Chao

A Classical Density-Functional Theory for Describing Water Interfaces

We develop a classical density functional for water which combines the White Bear fundamental-measure theory (FMT) functional for the hard sphere fluid with attractive interactions based on the Statistical Associating Fluid Theory (SAFT-VR). This functional reproduces the properties of water at both long and short length scales over a wide range of temperatures, and is computationally efficient, comparable to the cost of FMT itself. We demonstrate our functional by applying it to systems composed of two hard rods, four hard rods arranged in a square and hard spheres in water

Spot deformation and replication in the two-dimensional Belousov-Zhabotinski reaction in water-in-oil microemulsion

In the limit of large diffusivity ratio, spot-like solutions in the two-dimensional Belousov-Zhabotinski reaction in water-in-oil microemulsion are studied. It is shown analytically that such spots undergo an instability as the diffusivity ratio is decreased. An instability threshold is derived. For spots of small radius, it is shown that this instability leads to a spot splitting into precisely two spots. For larger spots, it leads to deformation, fingering patterns and space-filling curves. Numerical simulations are shown to be in close agreement with the analytical predictions.Comment: To appear, PR

Molecular dynamics study of solvation effects on acid dissociation in aprotic media

Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders of magnitude which are in reasonable agreement with experimental results. Solvent separated ion pairs are found to exist in dimethylsulfoxide but not in acetonitrile. Dissociation mechanisms in small clusters are also investigated. Solvent separated ion pairs persist even in aggregates composed of rather few molecules, for instance, as few as thirty molecules. For smaller clusters or for large ion pair separations cluster finite-size effects come into play in a significant fashion.Comment: Plain LaTeX. To appear in JCP(March 15). Mpeg simulations available at http://www.chem.utoronto.ca/staff/REK/Videos/clusters/clusters.htm

Surface-hopping dynamics and decoherence with quantum equilibrium structure

In open quantum systems decoherence occurs through interaction of a quantum subsystem with its environment. The computation of expectation values requires a knowledge of the quantum dynamics of operators and sampling from initial states of the density matrix describing the subsystem and bath. We consider situations where the quantum evolution can be approximated by quantum-classical Liouville dynamics and examine the circumstances under which the evolution can be reduced to surface-hopping dynamics, where the evolution consists of trajectory segments evolving exclusively on single adiabatic surfaces, with probabilistic hops between these surfaces. The justification for the reduction depends on the validity of a Markovian approximation on a bath averaged memory kernel that accounts for quantum coherence in the system. We show that such a reduction is often possible when initial sampling is from either the quantum or classical bath initial distributions. If the average is taken only over the quantum dispersion that broadens the classical distribution, then such a reduction is not always possible.Comment: 11, pages, 8 figure

Sex Differences in Outcomes after Stroke in Patients with Diabetes in Ontario, Canada.

BACKGROUND: Outcomes after stroke in those with diabetes are not well characterized, especially by sex and age. We sought to calculate the sex- and age-specific risk of cardiovascular outcomes after ischemic stroke among those with diabetes. METHODS: Using population-based demographic and administrative health-care databases in Ontario, Canada, all patients with diabetes hospitalized with index ischemic stroke between April 1, 2002, and March 31, 2012, were followed for death, stroke, and myocardial infarction (MI). The Kaplan-Meier survival analysis and Fine-Gray competing risk models estimated hazards of outcomes by sex and age, unadjusted and adjusted for demographics and vascular risk factors. RESULTS: Among 25,495 diabetic patients with index ischemic stroke, the incidence of death was higher in women than in men (14.08 per 100 person-years [95% confidence interval [CI], 13.73-14.44] versus 11.89 [11.60-12.19]) but was lower after adjustment for age and other risk factors (adjusted hazard ratio [HR], .95 [.92-.99]). Recurrent stroke incidence was similar by sex, but men were more likely to be readmitted for MI (1.99 per 100 person-years [1.89-2.10] versus 1.58 [1.49-1.68] among females). In multivariable models, females had a lower risk of readmission for any event (HR, .96 [95% CI, .93-.99]). CONCLUSIONS: In this large, population-based, retrospective study among diabetic patients with index stroke, women had a higher unadjusted death rate but lower unadjusted incidence of MI. In adjusted models, females had a lower death rate compared with males, although the increased risk of MI among males persisted. These findings confirm and quantify sex differences in outcomes after stroke in patients with diabetes

Renormalized Equilibria of a Schloegl Model Lattice Gas

A lattice gas model for Schloegl's second chemical reaction is described and analyzed. Because the lattice gas does not obey a semi-detailed-balance condition, the equilibria are non-Gibbsian. In spite of this, a self-consistent set of equations for the exact homogeneous equilibria are described, using a generalized cluster-expansion scheme. These equations are solved in the two-particle BBGKY approximation, and the results are compared to numerical experiment. It is found that this approximation describes the equilibria far more accurately than the Boltzmann approximation. It is also found, however, that spurious solutions to the equilibrium equations appear which can only be removed by including effects due to three-particle correlations.Comment: 21 pages, REVTe

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics, which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.Comment: 15 pages in double column forma

Coarse-Grain Model for Lipid Bilayer Self-Assembly and Dynamics: Multiparticle Collision Description of the Solvent

A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for the solvent. Self-assembly of a membrane from a uniform mixture of lipids is observed. Simulations at different temperatures demonstrate that it reproduces the gel and liquid phases of lipid bilayers. Investigations of lipid diffusion in different phases reveals a crossover from subdiffusion to normal diffusion at long times. Macroscopic membrane properties, such as stretching and bending elastic moduli, are determined directly from the mesoscopic simulations. Velocity correlation functions for membrane flows are determined and analyzed