The dynamics of radio-frequency driven atmospheric pressure plasma jets

The complex dynamics of radio-frequency driven atmospheric pressure plasma jets is investigated using various optical diagnostic techniques and numerical simulations. Absolute number densities of ground state atomic oxygen radicals in the plasma effluent are measured by two-photon absorption laser induced fluorescence spectroscopy (TALIF). Spatial profiles are compared with (vacuum) ultra-violet radiation from excited states of atomic oxygen and molecular oxygen, respectively. The excitation and ionization dynamics in the plasma core are dominated by electron impact and observed by space and phase resolved optical emission spectroscopy (PROES). The electron dynamics is governed through the motion of the plasma boundary sheaths in front of the electrodes as illustrated in numerical simulations using a hybrid code based on fluid equations and kinetic treatment of electrons.

Inelastic quantum transport in nanostructures: The self-consistent Born approximation and correlated electron-ion dynamics

A dynamical method for inelastic transport simulations in nanostructures is compared to a steady-state method based on nonequilibrium Green's functions. A simplified form of the dynamical method produces, in the steady state in the weak-coupling limit, effective self-energies analogous to those in the Born approximation due to electron-phonon coupling. The two methods are then compared numerically on a resonant system consisting of a linear trimer weakly embedded between metal electrodes. This system exhibits an enhanced heating at high biases and long phonon equilibration times. Despite the differences in their formulation, the static and dynamical methods capture local current-induced heating and inelastic corrections to the current with good agreement over a wide range of conditions, except in the limit of very high vibrational excitations where differences begin to emerge.

The challenge of revealing and tailoring the dynamics of radio-frequency plasmas

The complex dynamics of ionization and excitation mechanisms in capacitively coupled radio-frequency plasmas is discussed for single- and dual-frequency operations in low-pressure and atmospheric pressure plasmas. Electrons are energized through the dynamics of electric fields in the vicinity of the plasma boundary sheaths. Distinctly different power dissipation mechanisms can either co-exist or initiate mode transitions exhibiting characteristic spatio-temporal ionization structures. Phase resolved optical emission spectroscopy, in combination with adequate modelling of the population dynamics of excited states, and numerical simulations reveal dissipation associated with sheath expansion, sheath collapse, transient electron avalanches and wave–particle interactions. In dual-frequency systems the relative phase between the two frequency components provides additional strategies to tailor the plasma dynamics.

A Geostatistical Investigation into Changing Permeability of Sandstones During Weathering Simulations

The ability to predict the behavior of masonry materials is crucial to conserve building stone. Natural stone, such as sandstone, is not immune from the processes of weathering in the built environment and suffers from decay by granular disintegration, contour scaling, and multiple flaking. Spatial variation of rock properties is a major contributing factor to inconsistent responses to weathering. This has implications for moisture movement and salt input and output and storage, and results in unpredictability in the decay dynamics of masonry materials. This article explores the use of variography and kriging to investigate the spatial interactions between the trigger factors of stone decay, in particular, permeability and its effect on salt penetration. Sandstone blocks were used to represent fresh building stones from a weathering perspective and gave baseline characteristics for the interpretation of subsequent deterioration and decay pathways. Simulated weathering trials involved preloading a sandstone block with salt and subjecting a separate block to 20 cycles of a weathering trial designed to simulate a temperate weathering regime. Geostatistical analysis indicated differences in the spatial variation of permeability of the fresh rock and that subjected to the weathering regimes. Spatial prediction and visualization showed differences in the spatial continuity of permeability in a horizontal and vertical direction through the preloaded block after salt weathering. Continual wetting with salt and alternate heating increased permeability in a vertical direction, enabling the ingress and movement of salt and moisture more effectively through the stone.

Dynamics of Gompertzian tumour growth under environmental fluctuations

We investigate the effect of correlated additive and multiplicative Gaussian white noise oil the Gompertzian growth of tumours. Our results are obtained by Solving numerically the time-dependent Fokker-Planck equation (FPE) associated with the stochastic dynamics. In Our numerical approach we have adopted B-spline functions as a truncated basis to expand the approximated eigenfunctions. The eigenfunctions and eigenvalues obtained using this method are used to derive approximate solutions of the dynamics under Study. We perform simulations to analyze various aspects, of the probability distribution. of the tumour cell populations in the transient- and steady-state regimes. More precisely, we are concerned mainly with the behaviour of the relaxation time (tau) to the steady-state distribution as a function of (i) of the correlation strength (lambda) between the additive noise and the multiplicative noise and (ii) as a function of the multiplicative noise intensity (D) and additive noise intensity (alpha). It is observed that both the correlation strength and the intensities of additive and multiplicative noise, affect the relaxation time.

Plasma surface dynamics and smoothing in the relativistic few-cycle regime

Efficient production of coherent harmonic radiation from solid targets relies critically on the formation of smooth, short density scalelength plasmas. Recent experimental results (Dromey et al 2009 Nat. Phys. 5 146) suggest, however, that the target roughness on the scale of the emitted harmonic wavelength does not result in diffuse reflection-in apparent contradiction to the Rayleigh criterion for coherent reflection. In this paper we show, for the first time, using analytic theory and 2D PIC simulations, that the interaction of relativistically strong laser pulses with corrugated target surfaces results in a highly effective smoothing of the interaction surface and consequently the generation of highly collimated and temporally confined XUV pulses from rough targets, in excellent agreement with experimental observations.

Dynamics of charge-displacement channeling in intense laser-plasma interactions

The dynamics of transient electric fields generated by the interaction of high intensity laser pulses with underdense plasmas has been studied experimentally with the proton projection imaging technique. The formation of a charged channel, the propagation of its front edge and the late electric field evolution have been characterized with high temporal and spatial resolution. Particle-in-cell simulations and an electrostatic, ponderomotive model reproduce the experimental features and trace them back to the ponderomotive expulsion of electrons and the subsequent ion acceleration.

Molecular dynamics studies of the STAT3 homodimer:DNA complex: relationships between STAT3 mutations and protein-DNA recognition.

Signal Transducers and Activators of Transcription (STAT) proteins are a group of latent cytoplasmic transcription factors involved in cytokine signaling. STAT3 is a member of the STAT family and is expressed at elevated levels in a large number of diverse human cancers and is now a validated target for anticancer drug discovery.. Understanding the dynamics of the STAT3 dimer interface, accounting for both protein-DNA and protein-protein interactions, with respect to the dynamics of the latent unphosphorylated STAT3 monomer, is important for designing potential small-molecule inhibitors of the activated dimer. Molecular dynamics (MD) simulations have been used to study the activated STAT3 homodimer:DNA complex and the latent unphosphorylated STAT3 monomer in an explicit water environment. Analysis of the data obtained from MD simulations over a 50 ns time frame has suggested how the transcription factor interacts with DNA, the nature of the conformational changes, and ways in which function may be affected. Examination of the dimer interface, focusing on the protein-DNA interactions, including involvement of water molecules, has revealed the key residues contributing to the recognition events involved in STAT3 protein-DNA interactions. This has shown that the majority of mutations in the DNA-binding domain are found at the protein-DNA interface. These mutations have been mapped in detail and related to specific protein-DNA contacts. Their structural stability is described, together with an analysis of the model as a starting-point for the discovery of novel small-molecule STAT3 inhibitors.

Dynamics of Self-Generated, Large Amplitude Magnetic Fields Following High-Intensity Laser Matter Interaction

The dynamics of magnetic fields with an amplitude of several tens of megagauss, generated at both sides of a solid target irradiated with a high-intensity (~1019W/cm2) picosecond laser pulse, has been spatially and temporally resolved using a proton imaging technique. The amplitude of the magnetic fields is sufficiently large to have a constraining effect on the radial expansion of the plasma sheath at the target surfaces. These results, supported by numerical simulations and simple analytical modeling, may have implications for ion acceleration driven by the plasma sheath at the rear side of the target as well as for the laboratory study of self-collimated high-energy plasma jets. © 2012 American Physical Society.

Three-Dimensional Dynamics of Breakout Afterburner Ion Acceleration Using High-Contrast Short-Pulse Laser and Nanoscale Targets

Breakout afterburner (BOA) laser-ion acceleration has been demonstrated for the first time in the laboratory. In the BOA, an initially solid-density target undergoes relativistically induced transparency, initiating a period of enhanced ion acceleration. First-ever kinetic simulations of the BOA in three dimensions show that the ion beam forms lobes in the direction orthogonal to laser polarization and propagation. Analytic theory presented for the electron dynamics in the laser ponderomotive field explains how azimuthal symmetry breaks even for a symmetric laser intensity profile; these results are consistent with recent experiments at the Trident laser facility. © 2011 American Physical Society.

Molecular dynamics simulation model for the quantitative assessment of tool wear during single point diamond turning of cubic silicon carbide

Silicon carbide (SiC) is a material of great technological interest for engineering applications concerning hostile environments where silicon-based components cannot work (beyond 623 K). Single point diamond turning (SPDT) has remained a superior and viable method to harness process efficiency and freeform shapes on this harder material. However, it is extremely difficult to machine this ceramic consistently in the ductile regime due to sudden and rapid tool wear. It thus becomes non trivial to develop an accurate understanding of tool wear mechanism during SPDT of SiC in order to identify measures to suppress wear to minimize operational cost.

In this paper, molecular dynamics (MD) simulation has been deployed with a realistic analytical bond order potential (ABOP) formalism based potential energy function to understand tool wear mechanism during single point diamond turning of SiC. The most significant result was obtained using the radial distribution function which suggests graphitization of diamond tool during the machining process. This phenomenon occurs due to the abrasive processes between these two ultra hard materials. The abrasive action results in locally high temperature which compounds with the massive cutting forces leading to sp3–sp2 order–disorder transition of diamond tool. This represents the root cause of tool wear during SPDT operation of cubic SiC. Further testing led to the development of a novel method for quantitative assessment of the progression of diamond tool wear from MD simulations.

Dynamics of dark hollow Gaussian laser pulses in relativistic plasma

Optical beams with null central intensity have potential applications in the field of atom optics. The spatial and temporal evolution of a central shadow dark hollow Gaussian (DHG) relativistic laser pulse propagating in a plasma is studied in this article for first principles. A nonlinear Schrodinger-type equation is obtained for the beam spot profile and then solved numerically to investigate the pulse propagation characteristics. As series of numerical simulations are employed to trace the profile of the focused and compressed DHG laser pulse as it propagates through the plasma. The theoretical and simulation results predict that higher-order DHG pulses show smaller divergence as they propagate and, thus, lead to enhanced energy transport. © 2013 American Physical Society.

Nanoindentation of polysilicon and single crystal silicon: Molecular dynamics simulation and experimental validation

This paper presents novel advances on the deformation behaviour of polycrystalline and single crystal silicon using molecular dynamics (MD) simulation and validation of the same via nanoindentation experiments. In order to unravel the mechanism of deformation, four simulations were performed: Indentation of polycrystalline silicon substrate with a (i) Berkovich pyramidal and a (ii) spherical (arc) indenter, and indentation of a single crystal silicon substrate with these two indenters. The simulation results reveal that high pressure phase transformation (HPPT) in silicon (Si-I to Si-II phase transformation) occurred in all cases, however, its extent and the manner in which it occurred differed significantly between polycrystalline silicon and single crystal silicon, and was the main driver of differences in nanoindentation deformation behaviour between the two types of silicon. An interesting observation was that in polycrystalline silicon, the HPPT was observed to occur preferentially along the grain boundaries than across the grain boundaries. An automated dislocation extraction algorithm (DXA) revealed no dislocations in the deformation zone, suggesting HPPT to be the primary mechanism in inducing plasticity in silicon.

Diamond machining of silicon: A review of advances in molecular dynamics simulation

Molecular dynamics (MD) simulation has enhanced our understanding about ductile-regime machining of brittle materials such as silicon and germanium. In particular, MD simulation has helped understand the occurrence of brittle–ductile transition due to the high-pressure phase transformation (HPPT), which induces Herzfeld–Mott transition. In this paper, relevant MD simulation studies in conjunction with experimental studies are reviewed with a focus on (i) the importance of machining variables: undeformed chip thickness, feed rate, depth of cut, geometry of the cutting tool in influencing the state of the deviatoric stresses to cause HPPT in silicon, (ii) the influence of material properties: role of fracture toughness and hardness, crystal structure and anisotropy of the material, and (iii) phenomenological understanding of the wear of diamond cutting tools, which are all non-trivial for cost-effective manufacturing of silicon. The ongoing developmental work on potential energy functions is reviewed to identify opportunities for overcoming the current limitations of MD simulations. Potential research areas relating to how MD simulation might help improve existing manufacturing technologies are identified which may be of particular interest to early stage researchers.

Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Modeling dynamical systems represents an important application class covering a wide range of disciplines including but not limited to biology, chemistry, finance, national security, and health care. Such applications typically involve large-scale, irregular graph processing, which makes them difficult to scale due to the evolutionary nature of their workload, irregular communication and load imbalance. EpiSimdemics is such an application simulating epidemic diffusion in extremely large and realistic social contact networks. It implements a graph-based system that captures dynamics among co-evolving entities. This paper presents an implementation of EpiSimdemics in Charm++ that enables future research by social, biological and computational scientists at unprecedented data and system scales. We present new methods for application-specific processing of graph data and demonstrate the effectiveness of these methods on a Cray XE6, specifically NCSA's Blue Waters system.