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

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

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

Synchronisation in Coupled Sine Circle Maps

We study the spatially synchronized and temporally periodic solutions of a 1-d lattice of coupled sine circle maps. We carry out an analytic stability analysis of this spatially synchronized and temporally periodic case and obtain the stability matrix in a neat block diagonal form. We find spatially synchronized behaviour over a substantial range of parameter space. We have also extended the analysis to higher spatial periods with similar results. Numerical simulations for various temporal periods of the synchronized solution, reveal that the entire structure of the Arnold tongues and the devil's staircase seen in the case of the single circle map can also be observed for the synchronized coupled sine circle map lattice. Our formalism should be useful in the study of spatially periodic behaviour in other coupled map lattices.Comment: uuencoded, 1 rextex file 14 pages, 3 postscript 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

Resonant forcing of select degrees of freedom of multidimensional chaotic map dynamics

We study resonances of multidimensional chaotic map dynamics. We use the calculus of variations to determine the additive forcing function that induces the largest response, that is, the greatest deviation from the unperturbed dynamics. We include the additional constraint that only select degrees of freedom be forced, corresponding to a very general class of problems in which not all of the degrees of freedom in an experimental system are accessible to forcing. We find that certain Lagrange multipliers take on a fundamental physical role as the efficiency of the forcing function and the effective forcing experienced by the degrees of freedom which are not forced directly. Furthermore, we find that the product of the displacement of nearby trajectories and the effective total forcing function is a conserved quantity. We demonstrate the efficacy of this methodology with several examples.Comment: 11 pages, 3 figure

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu

The branch processes of vortex filaments and Hopf Invariant Constraint on Scroll Wave

In this paper, by making use of Duan's topological current theory, the evolution of the vortex filaments in excitable media is discussed in detail. The vortex filaments are found generating or annihilating at the limit points and encountering, splitting, or merging at the bifurcation points of a complex function $Z(\vec{x},t)$. It is also shown that the Hopf invariant of knotted scroll wave filaments is preserved in the branch processes (splitting, merging, or encountering) during the evolution of these knotted scroll wave filaments. Furthermore, it also revealed that the "exclusion principle" in some chemical media is just the special case of the Hopf invariant constraint, and during the branch processes the "exclusion principle" is also protected by topology.Comment: 9 pages, 5 figure

Generalized Boltzmann Equation for Lattice Gas Automata

In this paper, for the first time a theory is formulated that predicts velocity and spatial correlations between occupation numbers that occur in lattice gas automata violating semi-detailed balance. Starting from a coupled BBGKY hierarchy for the $n$-particle distribution functions, cluster expansion techniques are used to derive approximate kinetic equations. In zeroth approximation the standard nonlinear Boltzmann equation is obtained; the next approximation yields the ring kinetic equation, similar to that for hard sphere systems, describing the time evolution of pair correlations. As a quantitative test we calculate equal time correlation functions in equilibrium for two models that violate semi-detailed balance. One is a model of interacting random walkers on a line, the other one is a two-dimensional fluid type model on a triangular lattice. The numerical predictions agree very well with computer simulations.Comment: 31 pages LaTeX, 12 uuencoded tar-compressed Encapsulated PostScript figures (`psfig' macro), hardcopies available on request, 78kb + 52k

MolProbity: all-atom structure validation for macromolecular crystallography

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction