Solitons in a parametrically driven damped discrete nonlinear Schr\"odinger equation

We consider a parametrically driven damped discrete nonlinear Schr\"odinger (PDDNLS) equation. Analytical and numerical calculations are performed to determine the existence and stability of fundamental discrete bright solitons. We show that there are two types of onsite discrete soliton, namely onsite type I and II. We also show that there are four types of intersite discrete soliton, called intersite type I, II, III, and IV, where the last two types are essentially the same, due to symmetry. Onsite and intersite type I solitons, which can be unstable in the case of no dissipation, are found to be stabilized by the damping, whereas the other types are always unstable. Our further analysis demonstrates that saddle-node and pitchfork (symmetry-breaking) bifurcations can occur. More interestingly, the onsite type I, intersite type I, and intersite type III-IV admit Hopf bifurcations from which emerge periodic solitons (limit cycles). The continuation of the limit cycles as well as the stability of the periodic solitons are computed through the numerical continuation software Matcont. We observe subcritical Hopf bifurcations along the existence curve of the onsite type I and intersite type III-IV. Along the existence curve of the intersite type I we observe both supercritical and subcritical Hopf bifurcations.Comment: to appear in "Spontaneous Symmetry Breaking, Self-Trapping, and Josephson Oscillations in Nonlinear Systems", B.A. Malomed, ed. (Springer, Berlin, 2012

Molecular Dynamics-Based Strength Estimates of Beta-Solenoid Proteins

The use of beta-solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their mechanical strengths, we can efficiently design the proteins for specific functions. We present a study of the mechanical properties of seven beta-solenoid proteins using GROMACS molecular dynamics software to produce force/torque-displacement data, implement umbrella sampling of bending/twisting trajectories, produce Potentials of Mean Force (PMFs), extract effective spring constants, and calculate rigidities for two bending and two twisting directions for each protein. We examine the differences between computing the strength values from force/torque-displacement data alone and PMF data, and show how higher precision estimates can be obtained from the former. In addition to the analysis of the methods, we report estimates for the bend/twist persistence lengths for each protein, which range from 0.5-3.4 $\mu$m. We note that beta-solenoid proteins with internal disulfide bridges do not enjoy enhanced bending or twisting strength, and that the strongest correlate with bend/twist rigidity is the number of hydrogen bonds per turn. In addition, we compute estimates of the Young's modulus ($Y$) for each protein, which range from $Y$ = 3.5 to 7.2 GPa

Calculating the inherent visual structure of a landscape (inherent viewshed) using high-throughput computing

This paper describes a method of calculating the inherent visibility at all locations in a landscape (‘total viewshed’) by making use of redundant computer cycles. This approach uses a simplified viewshed program that is suitable for use within a distributed environment, in this case managed by the Condor system. Distributing the calculation in this way reduced the calculation time of our example from an estimated 34 days to slightly over 25 hours using a cluster of 43 workstations. Finally, we discuss the example ‘total viewshed’ raster for the Avebury region, and briefly highlight some of its implications

Discrete solitons in electromechanical resonators

We consider a parametrically driven Klein--Gordon system describing micro- and nano-devices, with integrated electrical and mechanical functionality. Using a multiscale expansion method we reduce the system to a discrete nonlinear Schrodinger equation. Analytical and numerical calculations are performed to determine the existence and stability of fundamental bright and dark discrete solitons admitted by the Klein--Gordon system through the discrete Schrodinger equation. We show that a parametric driving can not only destabilize onsite bright solitons, but also stabilize intersite bright discrete solitons and onsite and intersite dark solitons. Most importantly, we show that there is a range of values of the driving coefficient for which dark solitons are stable, for any value of the coupling constant, i.e. oscillatory instabilities are totally suppressed. Stability windows of all the fundamental solitons are presented and approximations to the onset of instability are derived using perturbation theory, with accompanying numerical results. Numerical integrations of the Klein--Gordon equation are performed, confirming the relevance of our analysis

Knowlesi malaria in Vietnam

The simian malaria parasite Plasmodium knowlesi is transmitted in the forests of Southeast Asia. Symptomatic zoonotic knowlesi malaria in humans is widespread in the region and is associated with a history of spending time in the jungle. However, there are many settings where knowlesi transmission to humans would be expected but is not found. A recent report on the Ra-glai population of southern central Vietnam is taken as an example to help explain why this may be so