MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

Effect of Pressure on Boron Diffusion in Silicon

We are studying the effect of pressure on boron diffusion in silicon in order to better understand the nature of the point defects responsible for diffusion. Si homoepitaxial layers delta-doped with boron were grown using molecular beam epitaxy. Diffusion anneals were performed in a high temperature diamond anvil cell using fluid argon as a pressure medium. Diffusivities were deduced from B concentration-depth profiles measured with using secondary ion mass spectrometry. Preliminary results indicate that pressure enhances B diffusion in Si at 850 ˚C, characterized by an average activation volume of -0.125±0.02 times the atomic volume, and thus appear consistent with an interstitial-based diffusion mechanism. Results are compared with previous hydrostatic-pressure studies, with results in biaxially strained films, and with atomistic calculations of activation volumes for self diffusion.Engineering and Applied Science

Localization Enhanced Mobile Networks

The interest in mobile ad-hoc networks (MANETs) and often more precisely vehicular ad-hoc networks (VANETs) is steadily growing with many new applications, and even anticipated support in the emerging 5G networks. Particularly in outdoor scenarios, there are different mechanisms to make the mobile nodes aware of their geographical location at all times. The location information can be utilized at different layers of the protocol stack to enhance communication services in the network. Specifically, geographical routing can facilitate route management with smaller overhead than the traditional proactive and reactive routing protocols. In order to achieve similar advantages for radio resource management (RRM) and multiple access protocols, the concept of virtual cells is devised to exploit fully distributed knowledge of node locations. The virtual cells define clusters of MANET nodes assuming a predefined set of geographically distributed anchor points. It enables fast response of the network to changes in the nodes spatial configuration. More importantly, the notion of geographical location can be generalized to other shared contexts which can be learned or otherwise acquired by the network nodes. The strategy of enhancing communication services by shared contexts is likely to be one of the key features in the beyond-5G networks

Activation Volume for Arsenic Diffusion in Germanium

We have measured the effect of pressure on As diffusion in Ge. Diffusion anneals on ion-implanted samples were carried out in a high-temperature diamond anvil cell using fluid argon as a clean, hydrostatic pressure medium. At 575 °C over the pressure range 0.1–4 GPa, pressure slightly enhances the diffusivity, characterized by an activation volume of –1.7 ± 1.4 cm3/mole or –0.12 ± 0.10 times the atomic volume. The results call into question the prevailing view that diffusion of groups III, IV, and V elements are mediated entirely by vacancies. If diffusion of As is mediated entirely by vacancies then either the vacancy formation volume must be unexpectedly low or the energy of vacancy migration must be unexpectedly high.Engineering and Applied Science

How Do Violent News Stories Affect Viewers?

Television news broadcasts have been airing since the mid-1930s, and has since then, implemented itself into viewer’s everyday lives. In the 1980s, Cable News Network, or CNN, introduced the 24-hour news cycle. Because of this, there was a sharp increase of violent news being reported. In this study, the researchers chose to study both the emotional and physical reactions to the violent news media. Specifically, the researchers explored the possibility that too much violence could affect their mental and physical health. Participants from this study hailed from a faith-based institution of higher learning in an urban area of the Midwestern United States. The study found that there is a relationship between the violence in news media and mental and physical effects of the body