GPU Accelerated Particle Visualization with Splotch

Splotch is a rendering algorithm for exploration and visual discovery in particle-based datasets coming from astronomical observations or numerical simulations. The strengths of the approach are production of high quality imagery and support for very large-scale datasets through an effective mix of the OpenMP and MPI parallel programming paradigms. This article reports our experiences in re-designing Splotch for exploiting emerging HPC architectures nowadays increasingly populated with GPUs. A performance model is introduced for data transfers, computations and memory access, to guide our re-factoring of Splotch. A number of parallelization issues are discussed, in particular relating to race conditions and workload balancing, towards achieving optimal performances. Our implementation was accomplished by using the CUDA programming paradigm. Our strategy is founded on novel schemes achieving optimized data organisation and classification of particles. We deploy a reference simulation to present performance results on acceleration gains and scalability. We finally outline our vision for future work developments including possibilities for further optimisations and exploitation of emerging technologies.Comment: 25 pages, 9 figures. Astronomy and Computing (2014

Supercontinuum generation in media with sign-alternated dispersion

When an ultrafast optical pulse with high intensity is propagating through transparent material a supercontinuum can be coherently generated by self-phase modulation, which is essential to many photonic applications in fibers and integrated waveguides. However, the presence of dispersion causes stagnation of spectral broadening past a certain propagation length, requiring an increased input peak power for further broadening. We present a concept to drive supercontinuum generation with significantly lower input power by counteracting spectral stagnation via alternating the sign of group velocity dispersion along the propagation. We demonstrate the effect experimentally in dispersion alternating fiber in excellent agreement with modeling, revealing almost an order of magnitude reduced peak power compared to uniform dispersion. Calculations reveal a similar power reduction also with integrated optical waveguides, simultaneously with a significant increase of flat bandwidth, which is important for on-chip broadband photonics.Comment: Main text and supplementary informatio

Stochastic model for the 3D microstructure of pristine and cyclically aged cathodes in Li-ion batteries

It is well-known that the microstructure of electrodes in lithium-ion batteries strongly affects their performance. Vice versa, the microstructure can exhibit strong changes during the usage of the battery due to aging effects. For a better understanding of these effects, mathematical analysis and modeling has turned out to be of great help. In particular, stochastic 3D microstructure models have proven to be a powerful and very flexible tool to generate various kinds of particle-based structures. Recently, such models have been proposed for the microstructure of anodes in lithium-ion energy and power cells. In the present paper, we describe a stochastic modeling approach for the 3D microstructure of cathodes in a lithium-ion energy cell, which differs significantly from the one observed in anodes. The model for the cathode data enhances the ideas of the anode models, which have been developed so far. It is calibrated using 3D tomographic image data from pristine as well as two aged cathodes. A validation based on morphological image characteristics shows that the model is able to realistically describe both, the microstructure of pristine and aged cathodes. Thus, we conclude that the model is suitable to generate virtual, but realistic microstructures of lithium-ion cathodes

Ultrafast, low-power, all-optical switching via birefringent phase-matched transverse mode conversion in integrated waveguides

We demonstrate the potential of birefringence-based, all-optical, ultrafast conversion between the transverse modes in integrated optical waveguides by modelling the conversion process by numerically solving the multi-mode coupled nonlinear Schroedinger equations. The observed conversion is induced by a control beam and due to the Kerr effect, resulting in a transient index grating which coherently scatters probe light from one transverse waveguide mode into another. We introduce birefringent phase matching to enable efficient all-optically induced mode conversion at different wavelengths of the control and probe beam. It is shown that tailoring the waveguide geometry can be exploited to explicitly minimize intermodal group delay as well as to maximize the nonlinear coefficient, under the constraint of a phase matching condition. The waveguide geometries investigated here, allow for mode conversion with over two orders of magnitude reduced control pulse energy compared to previous schemes and thereby promise nonlinear mode switching exceeding efficiencies of 90% at switching energies below 1 nJ

Sequential interim analyses of survival data in DNA microarray experiments

<p>Abstract</p> <p>Background</p> <p>Discovery of biomarkers that are correlated with therapy response and thus with survival is an important goal of medical research on severe diseases, e.g. cancer. Frequently, microarray studies are performed to identify genes of which the expression levels in pretherapeutic tissue samples are correlated to survival times of patients. Typically, such a study can take several years until the full planned sample size is available.</p> <p>Therefore, interim analyses are desirable, offering the possibility of stopping the study earlier, or of performing additional laboratory experiments to validate the role of the detected genes. While many methods correcting the multiple testing bias introduced by interim analyses have been proposed for studies of one single feature, there are still open questions about interim analyses of multiple features, particularly of high-dimensional microarray data, where the number of features clearly exceeds the number of samples. Therefore, we examine false discovery rates and power rates in microarray experiments performed during interim analyses of survival studies. In addition, the early stopping based on interim results of such studies is evaluated. As stop criterion we employ the achieved average power rate, i.e. the proportion of detected true positives, for which a new estimator is derived and compared to existing estimators.</p> <p>Results</p> <p>In a simulation study, pre-specified levels of the false discovery rate are maintained in each interim analysis, where reduced levels as used in classical group sequential designs of one single feature are not necessary. Average power rates increase with each interim analysis, and many studies can be stopped prior to their planned end when a certain pre-specified power rate is achieved. The new estimator for the power rate slightly deviates from the true power rate but is comparable to other estimators.</p> <p>Conclusions</p> <p>Interim analyses of microarray experiments can provide evidence for early stopping of long-term survival studies. The developed simulation framework, which we also offer as a new R package 'SurvGenesInterim' available at <url>http://survgenesinter.R-Forge.R-Project.org</url>, can be used for sample size planning of the evaluated study design.</p