XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations

XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The equations are described in a high-level XML-based script, and the package generates low-level optionally parallelised C++ code for the efficient solution of those equations. It combines the advantages of high-level simulations, namely fast and low-error development, with the speed, portability and scalability of hand-written code. XMDS2 is a complete redesign of the XMDS package, and features support for a much wider problem space while also producing faster code.Comment: 9 pages, 5 figure

First-Principles Study of the Thermal Properties of Zr2C and Zr2CO

First-principles calculations of lattice thermal conductivities and thermodynamic properties of Zr2C and Zr2CO were performed using the quasi-harmonic approximation. Oxygen in the lattice gives Zr2CO higher bonding strength than Zr2C. Thus, the mechanical properties of Zr2C are enhanced when the vacancies in its crystal structure are filled with oxygen. Among the critical parameters that determine the lattice thermal conductivity, Zr2C has significantly higher Grüneisen parameters, thus Zr2C has lower lattice thermal conductivity than Zr2CO. In addition, Zr2CO has a higher heat capacity and thermal expansion coefficient than Zr2C at most temperatures. These results indicate that the addition of oxygen has increased the stiffness and thermal conductivity of zirconium carbide that contains a large fraction of carbon vacancies due to the filling of vacancies in the Zr2C lattice and the formation of Zr–O bonds

Calculation and Tabulation of Efficiencies for Tungsten Foil Positron Moderators

Monte Carlo radiation transport simulations were used to calculate the positron stopping profiles in tungsten positron moderator foils. Stopping profiles were numerically integrated with efficiency kernels derived from Green\u27s function solutions of the 3D diffusion equation to determine the moderation efficiency in both the backscattering and transmission geometries. Stopping profiles and efficiencies were calculated for positron energies from 10 keV to 10 MeV and incident angles from 0° to 75°. The resulting efficiencies agreed with other calculated and measured values in the literature, especially when similar values of the positron diffusion length and surface emission branching ratio were used. Large discrepancies with some of the values reported in the literature are mainly attributed to differences in foil manufacture and surface condition - factors which are known to greatly influence the diffusion length - as well as work function and branching ratios. This work provides tabulated efficiencies for tungsten foil moderators that can be interpolated and integrated with a positron flux having arbitrary energy and angular distributions

Reinforcement of the Plasmon–phonon Coupling in Α-Quartz Via Deposition of Gold Nanoparticles in Etched Ion Tracks

This study reports a large reinforcement of the plasmon–phonon coupling in alpha quartz achieved through the controlled deposition of gold nanoparticles into nano templates produced through chemical etching of ion tracks. Preferential agglomeration of nanoparticles within the etched ion tracks (nano wells) was observed in Scanning Electron Microscopy and Atomic Force Microscopy images. Raman characterization of quartz substrates with different nanoparticle concentrations revealed a relationship between the plasmon–phonon coupling intensity and nanoparticle concentration. Reinforcement of the plasmon–phonon coupling was observed as an increase in the Raman intensity with increasing concentration of deposited nanoparticles. The intensity initially increased linearly with nanoparticle concentration up to about 4 x 106 nps/µL where a saturation regime was identified. In the saturation regime, a roughly 200-fold increase in the scattering intensity was measured in the first micron of the specimen. At higher nanoparticle concentrations, the Raman intensity decreased exponentially following the Beer–Lambert Law. The reduction in the Raman intensity is attributed to increased laser absorption with increasing nanoparticle layer thickness. Comparatively weak reinforcement of Raman scattering was observed when nanoparticles were deposited on unirradiated and unetched samples, suggesting that the reinforcement of plasmon–phonon coupling may be favored by the anisotropic geometry of the nano wells. In particular, the etched tracks promote nanoparticles agglomeration likely promoting the formation of plasmon hotspots

Light Emission of Self-Trapped Excitons from Ion Tracks in Silica Glass: Interplay between Auger Recombination, Exciton Formation, Thermal Dissociation, and Hopping

The initial luminescence yield of amorphous silica under ion irradiation has been studied at temperatures between 30 and 100 K, using swift ions of different masses and energies (3 MeV H, 3.5 MeV He, 19 MeV Si and 19 MeV Cl). The intensity of the 2.1 eV emission band, ascribed to the intrinsic recombination of self-trapped excitons (STEs), has been found to vary systematically with ion mass, energy and irradiation temperature. A detailed model has been developed to quantitatively describe those variations in terms of the competition between non-radiative Auger recombination, STE formation, STE thermal dissociation, and subsequent STE hopping and capture at non-radiative sinks. The model, which uses a thermal spike approach to describe the effect of swift ion bombardment, is found to quantitatively predict the experimental data without adjustable parameters. It provides new insights into the interactions of carriers in an ion track and the behavior of the luminescence emissions during ion irradiation (ionoluminescence). The model is found to predict the correct temperature dependence of the yield if an activation energy for STE thermal migration of 0.12 eV is assumed, which is in good agreement with values previously reported

Defect Generation Mechanisms In Silica Under Intense Electronic Excitation By Ion Beams Below 100 K: Interplay Between Radiative Emissions

Ion-beam effects on bulk silica at low temperature have been studied with the aim of understanding the routes and mechanisms leading from the initial generation of free carriers and self-trapped excitons (STEs) to the production of two stable defect structures in irradiated silica, non-bridging oxygen hole centers (NBOHCs) and oxygen deficient centers (ODCs). Ion beam induced luminescence (ionoluminescence, IL) spectra were obtained using 3 MeV H, 3.5 MeV He, 19 MeV Si, and 19 MeV Cl ions and a range of cryogenic irradiation temperatures from 30 to 100 K. The kinetic behavior of three emission bands centered at 1.9 eV (assigned to NBOHCs), 2.1 eV (assigned to the intrinsic decay of STEs), and 2.7 eV (assigned to ODCs) reveal the physical origin of these emissions under intense electronic excitation. The creation of NBOHCs is governed by a purely electronic mechanism. The kinetics curve of the NBOHC band shows two main contributions: an instantaneous (beam-on) contribution, followed by a slower fluence- and temperature-dependent process correlated with the concentration of STEs. The beam-on contribution is proportional to deposited ionization energy. The growth of the ODC band is linear in fluence up to around 2 x 1012 cm−2. The growth rate is independent of temperature but proportional to the number of radiation-induced oxygen vacancies per ion, showing, unambiguously, that the 2.7 eV emission can be associated with ODCs created in an excited state

Transcriptome Sequencing Demonstrates that Human Papillomavirus Is Not Active in Cutaneous Squamous Cell Carcinoma

β-Human papillomavirus (β-HPV) DNA is present in some cutaneous squamous cell carcinomas (cuSCCs), but no mechanism of carcinogenesis has been determined. We used ultra-high-throughput sequencing of the cancer transcriptome to assess whether papillomavirus transcripts are present in these cancers. In all, 67 cuSCC samples were assayed for β-HPV DNA by PCR, and viral loads were measured with type-specific quantitative PCR. A total of 31 SCCs were selected for whole transcriptome sequencing. Transcriptome libraries were prepared in parallel from the HPV18-positive HeLa cervical cancer cell line and HPV16-positive primary cervical and periungual SCCs. Of the tumors, 30% (20/67) were positive for β-HPV DNA, but there was no difference in β-HPV viral load between tumor and normal tissue (P=0.310). Immunosuppression and age were significantly associated with higher viral load (P=0.016 for immunosuppression; P=0.0004 for age). Transcriptome sequencing failed to identify papillomavirus expression in any of the skin tumors. In contrast, HPV16 and HPV18 mRNA transcripts were readily identified in primary cervical and periungual cancers and HeLa cells. These data demonstrate that papillomavirus mRNA expression is not a factor in the maintenance of cuSCCs

Recent Advances on Carrier and Exciton Self-Trapping in Strontium Titanate: Understanding the Luminescence Emissions

An up-to-date review on recent results for self-trapping of free electrons and holes, as well as excitons, in strontium titanate (STO), which gives rise to small polarons and self-trapped excitons (STEs) is presented. Special attention is paid to the role of carrier and exciton self-trapping on the luminescence emissions under a variety of excitation sources with special emphasis on experiments with laser pulses and energetic ion-beams. In spite of the extensive research effort, a definitive identification of such localized states, as well as a suitable understanding of their operative light emission mechanisms, has remained lacking or controversial. However, promising advances have been recently achieved and are the objective of the present review. In particular, significant theoretical advances in the understanding of electron and hole self-trapping are discussed. Also, relevant experimental advances in the kinetics of light emission associated with electron-hole recombination have been obtained through time-resolved experiments using picosecond (ps) laser pulses. The luminescence emission mechanisms and the light decay processes from the self-trapped excitons are also reviewed. Recent results suggest that the blue emission at 2.8 eV, often associated with oxygen vacancies, is related to a transition from unbound conduction levels to the ground singlet state of the STE. The stabilization of small electron polarons by oxygen vacancies and its connection with luminescence emission are discussed in detail. Through ion-beam irradiation experiments, it has recently been established that the electrons associated with the vacancy constitute electron polaron states (Ti3+) trapped in the close vicinity of the empty oxygen sites. These experimental results have allowed for the optical identification of the oxygen vacancy center through a red luminescence emission centered at 2.0 eV. Ab-initio calculations have provided strong support for those experimental findings. Finally, the use of Cr-doped STO has offered a way to monitor the interplay between the chromium centers and oxygen vacancies as trapping sites for the electron and hole partners resulting from the electronic excitation

The Blue Emission at 2.8 EV in Strontium Titanate: Evidence for a Radiative Transition of Self-Trapped Excitons from Unbound States

The origin of the blue emission in SrTiO3 has been investigated as a function of irradiation fluence, electronic excitation density, and temperature using a range of ion energies and masses. The emission clearly does not show correlation with the concentration of vacancies generated by irradiation but is greatly enhanced under heavy-ion irradiation. The intensity ratio of the 2.8 and 2.5 eV bands is independent of fluence at all temperatures, but it increases with excitation rate. The 2.8 eV emission is proposed to correspond to a transition from conduction band states to the ground state level of the self-trapped exciton center

Real-Time Identification of Oxygen Vacancy Centers in LiNbO₃ and SrTiO₃ during Irradiation with High Energy Particles

Oxygen vacancies are known to play a central role in the optoelectronic properties of oxide perovskites. A detailed description of the exact mechanisms by which oxygen vacancies govern such properties, however, is still quite incomplete. The unambiguous identification of oxygen vacancies has been a subject of intense discussion. Interest in oxygen vacancies is not purely academic. Precise control of oxygen vacancies has potential technological benefits in optoelectronic devices. In this review paper, we focus our attention on the generation of oxygen vacancies by irradiation with high energy particles. Irradiation constitutes an efficient and reliable strategy to introduce, monitor, and characterize oxygen vacancies. Unfortunately, this technique has been underexploited despite its demonstrated advantages. This review revisits the main experimental results that have been obtained for oxygen vacancy centers (a) under high energy electron irradiation (100 keV-1 MeV) in LiNbO3, and (b) during irradiation with high-energy heavy (1-20 MeV) ions in SrTiO3. In both cases, the experiments have used real-time and in situ optical detection. Moreover, the present paper discusses the obtained results in relation to present knowledge from both the experimental and theoretical perspectives. Our view is that a consistent picture is now emerging on the structure and relevant optical features (absorption and emission spectra) of these centers. One key aspect of the topic pertains to the generation of self-trapped electrons as small polarons by irradiation of the crystal lattice and their stabilization by oxygen vacancies. What has been learned by observing the interplay between polarons and vacancies has inspired new models for color centers in dielectric crystals, models which represent an advancement from the early models of color centers in alkali halides and simple oxides. The topic discussed in this review is particularly useful to better understand the complex effects of different types of radiation on the defect structure of those materials, therefore providing relevant clues for nuclear engineering applications