The Flexible Rare Event Sampling Harness System (FRESHS)

We present the software package FRESHS (http://www.freshs.org) for parallel simulation of rare events using sampling techniques from the ‘splitting’ family of methods. Initially, Forward Flux Sampling (FFS) and Stochastic Process Rare Event Sampling (SPRES) have been implemented. These two methods together make rare event sampling available for both quasi-static and full non-equilibrium regimes. Our framework provides a plugin system for software implementing the underlying physics of the system of interest. At present, example plugins exist for our framework to steer the popular MD packages GROMACS, LAMMPS and ESPResSo, but due to the simple interface of our plugin system, it is also easy to attach other simulation software or self-written code. Use of our framework does not require recompilation of the simulation program. The modular structure allows the flexible implementation of further sampling methods or physics engines and creates a basis for objective comparison of different sampling algorithms.     

Herpes simplex virus-2 transmission probability estimates based on quantity of viral shedding

Herpes simplex virus (HSV)-2 is periodically shed in the human genital tract, most often asymptomatically, and most sexual transmissions occur during asymptomatic shedding. It would be helpful to identify a genital viral load threshold necessary for transmission, as clinical interventions that maintain viral quantity below this level would be of high utility. However, because viral expansion, decay and re-expansion kinetics are extremely rapid during shedding episodes, it is impossible to directly measure genital viral load at the time of sexual activity. We developed a mathematical model based on reproducing shedding patterns in transmitting partners, and median number of sex acts prior to transmission in discordant couples, to estimate infectivity of single viral particles in the negative partner''s genital tract. We then inferred probability estimates for transmission at different levels of genital tract viral load in the transmitting partner. We predict that transmission is unlikely at viral loads less than 10⁴ HSV DNA copies. Moreover, most transmissions occur during prolonged episodes with high viral copy numbers. Many shedding episodes that result in transmission do not reach the threshold of clinical detection, because the ulcer remains very small, highlighting one reason why HSV-2 spreads so effectively within populations.     

Crystallization kinetics of Sn40Se60 thin films for phase change memory applications

The crystallization kinetics of Sn₄₀Se₆₀ thin films has been successfully investigated using sheet resistance versus temperature measurements. Thermal evaporation was used to deposit the films on ordinary glass substrates. The crystallization temperature for Sn₄₀Se₆₀ thin film was found to be 156.6 ± 0.3 ℃. In the as-deposited state, the sheet resistance was found to be 195 MΩ, this value declined to 1560 Ω/口 upon annealing. The value of activation energy obtained from the Kissinger plot was 0.62 ± 0.07 eV. From the results obtained, Sn₄₀Se₆₀ is a promising alloy for PCM application because of its high electrical contrast, high crystallization temperature, and relatively high activation energy.     

Wind characteristics and energy potential assessment in Akure,South West Nigeria: econometrics and policy implications

This paper analysed 11 years of daily mean wind-speed data, measured at Akure, Ondo State, Nigeria, using Weibull and Rayleigh distribution functions. While both distributions showed good agreements in extreme-value estimation patterns, investigation of their wind-speed characteristics modelling criteria, using goodness-of-fit statistics, revealed that the wind data followed the Weibull more than Rayleigh. Monthly wind-speed of Akure city ranged from 1.41 to 4.24 m/s by the Weibull fittings and from 1.40 to 4.16 m/s by the Rayleigh fittings. Overall results, of 2.71 m/s (Weibull) or 2.70 m/s (Rayleigh) mean wind-speed and 18.51 W/m² (Weibull) or 22.26 W/m² (Rayleigh) mean power density, indicated Akure a low wind-speed site, requiring low wind-speed turbine for generating wind energy. Econometric analyses of power output simulations using such turbine system resulted in affordable wind energy cost. These bear policy implications for sustainable wind energy usage in this and similar regions of the world.