Implementation and evaluation of the Level Set method: towards efficient and accurate simulation of wet etching for microengineering applications

The use of atomistic methods, such as the Continuous Cellular Automaton (CCA), is currently regarded as a computationally efficient and experimentally accurate approach for the simulation of anisotropic etching of various substrates in the manufacture of Micro-electro-mechanical Systems (MEMS). However, when the features of the chemical process are modified, a time-consuming calibration process needs to be used to transform the new macroscopic etch rates into a corresponding set of atomistic rates. Furthermore, changing the substrate requires a labor-intensive effort to reclassify most atomistic neighborhoods. In this context, the Level Set (LS) method provides an alternative approach where the macroscopic forces affecting the front evolution are directly applied at the discrete level, thus avoiding the need for reclassification and/or calibration. Correspondingly, we present a fully-operational Sparse Field Method (SFM) implementation of the LS approach, discussing in detail the algorithm and providing a thorough characterization of the computational cost and simulation accuracy, including a comparison to the performance by the most recent CCA model. We conclude that the SFM implementation achieves similar accuracy as the CCA method with less fluctuations in the etch front and requiring roughly 4 times less memory. Although SFM can be up to 2 times slower than CCA for the simulation of anisotropic etchants, it can also be up to 10 times faster than CCA for isotropic etchants. In addition, we present a parallel, GPU-based implementation (gSFM) and compare it to an optimized, multicore CPU version (cSFM), demonstrating that the SFM algorithm can be successfully parallelized and the simulation times consequently reduced, while keeping the accuracy of the simulations. Although modern multicore CPUs provide an acceptable option, the massively parallel architecture of modern GPUs is more suitable, as reflected by computational times for gSFM up to 7.4 times faster than for cSFM. (c) 2013 Elsevier B.V. All rights reserved.We thank the anonymous reviewers for their valuable comments and suggestions. This work has been supported by the Spanish FPI-MICINN BES-2011-045940 grant and the Ramon y Cajal Fellowship Program by the Spanish Ministry of Science and Innovation. Also, we acknowledge support by the JAE-Doc grant from the Junta para la Ampliacion de Estudios program co-funded by FSE and the Professor Partnership Program by NVIDIA Corporation.Montoliu Álvaro, C.; Ferrando Jódar, N.; Gosalvez, MÁ.; Cerdá Boluda, J.; Colom Palero, RJ. (2013). Implementation and evaluation of the Level Set method: towards efficient and accurate simulation of wet etching for microengineering applications. Computer Physics Communications. 184(10):2299-2309. https://doi.org/10.1016/j.cpc.2013.05.016S229923091841

Stallion sperm quality after combined ejaculate fractionation and colloidal centrifugation

This study investigated the possible additive benefit of ejaculate fractionation and colloidal centrifugation on stallion sperm quality. Using an open-end artificial vagina, the sperm-rich fraction (FRAC-1) was separated from the rest of the ejaculate (FRAC-2) and a third sperm sample representing the combined ejaculate was reconstituted post-ejaculation (RAW). Each semen sample was processed for colloidal centrifugation. The percentage of abnormal spermatozoa was 17.8 ± 7.0% in RAW and 14.6 ± 9.5% in FRAC-1 but decreased to 11.4 ± 4.7% and 9.6 ± 6.9% respectively, after colloidal centrifugation. A sperm DNA fragmentation index of 10.9 ± 5.1% was observed in RAW and 7.5 ± 2.4% in FRAC-1 semen collected with the AV but this decreased to 7.8 ± 2.8% and 5.2 ± 2.3% after colloidal centrifugation. The rate of increase in sperm DNA fragmentation during the first 6 h of incubation at 37 ºC was 1.8 ± 0.9% per hour in RAW semen and 2.0 ± 2.0% per hour in FRAC-1 but this significantly decreased to 1.3 ± 1.4% and 0.9 ± 0.8% respectively after colloidal centrifugation. While stallion seminal characteristics can be improved using colloidal centrifugation, further enhancement is possible if the ejaculate is initially fractionatedThis research was supported by the Spanish Ministry of Economy and Competitiveness, MINECO (BFU-2013-44290-R

Surface damage in TEM thick α-Fe samples by implantation with 150 keV Fe ions

We have performed molecular dynamics simulations of implantation of 150 keV Fe ions in pure bcc Fe. The thickness of the simulation box is of the same order of those used in in situ TEM analysis of irradiated materials. We assess the effect of the implantation angle and the presence of front and back surfaces. The number and type of defects, ion range, cluster distribution and primary damage morphology are studied. Results indicate that, for the very thin samples used in in situ TEM irradiation experiments the presence of surfaces affect dramatically the damage produced. At this particular energy, the ion has sufficient energy to damage both the top and the back surfaces and still leave the sample through the bottom. This provides new insights on the study of radiation damage using TEM in situ.This work was supported by the European Fusion Development Agreement (EFDA), the VII EC framework through the GETMAT and MATISSE projects, and the Generalitat Valenciana PROMETEO2012/011

Molecular dynamics simulations of irradiation of α-Fe thin films with energetic Fe ions under channeling conditions

Using molecular dynamics simulations with recent interatomic potentials developed for Fe, we have studied the defects in thin films of pure bcc Fe induced by the displacement cascade produced by Fe atoms of 50, 100, and 150 keV impinging under a channeling incident angle of 6° to a [001] direction. The thin films have a thickness between 40 and 100 nm, to reproduce the thickness of the samples used in transmission electron microscope in-situ measurements during irradiation. In the simulations we focus mostly on the effect of channeling and free surfaces on damage production. The results are compared to bulk cascades. The comparison shows that the primary damage in thin films of pure Fe is quite different from that originated in the volume of the material. The presence of near surfaces can lead to a variety of events that do not occur in bulk collisional cascades, such as the production of craters and the glide of self-interstitial defects to the surface. Additionally, in the range of energies and the incident angle used, channeling is a predominant effect that significantly reduces damage compared to bulk cascades.This work was supported by the FPVII projects FEMaS, GETMAT and PERFECT and by the MAT-IREMEV program of EFDA. We acknowledge the support of the European Commission, the European Atomic Energy Community (Euratom), the European Fusion Development Agreement (EFDA) and the Forschungszentrum Jülich GmbH, jointly funding the Project HPC for Fusion (HPC-FF), Contract number FU07-CT-2007-00055

Koilocytes are enriched for alkaline-labile sites

This study investigated possible variations in the chromatin structure of koilocytes resulting from human papillomavirus (HPV) infection. Alkaline-labile sites (ALS) were detected with the DNA breakage detection–fluorescence in situ hybridization (DBD-FISH) technique using a whole human genome DNA probe obtained from individuals without koilocytosis. The variable levels of ALS present were measured quantitatively using image analysis after whole-genome DNA hybridization. A significant increase in the number of ALS was observed in koilocytes compared with normal cells. We demonstrated that the presence of ALS could be an indicator of chromatin change in koilocytes caused by HPV infection

Transport of cattle in Spain. Technical, administrative and welfare aspects according to the destination.

To obtain a thorough description of how are cattle transported in Spain with respect to the journey destination a survey was performed in 2004 and 2005. Information was obtained by means of a 119-parameters questionnaire, and 44 transport operators representative of the sector (27 slaughterhouses, 10 traders, and 7 cattle markets) were interviewed. Over 80% of journeys transported growing-finishing/finished animals, and about 3% of journeys transported both growing-finishing/finished and reproductive animals. With respect to farm transports, slaughter transports loaded in fewer farms (1.2 vs. 1.4 farms; pPara conocer en detalle como se transporta el ganado vacuno en España según el destino del viaje, entre los años 2004 y 2005 se entrevistaron 44 operadores representativos del sector (27 mataderos, 10 comerciantes y 7 mercados) mediante cuestionarios que recogían información relativa a 119 parámetros. Más del 80% de los viajes fueron de animales cebados/para cebo, y algo más de un 3% de los viajes transportaban animales cebados/para cebo y reproductores. Los transportes a matadero cargaron en un menor número de explotaciones (1,2 vs. 1,4 granjas;

Sex chromosome and autosome divergence in Podisma (Orthoptera) in western Europe

International audienc

Rapid and accurate detection of escherichia coli and klebsiella pneumoniae strains susceptible/resistant to cotrimoxazole through evaluation of cell elongation

Trimethoprim-sulfamethoxazole is a well-known antibiotic that inhibits folic acid synthesis, a topic of renewed interest. Since resistant strains are increasingly more common, an early and accurate discrimination of susceptibility may assure confident therapy. Two morphological assays were performed in Escherichia coli (n = 50; 27 non-susceptible) and Klebsiella pneumoniae (n = 52; 18 non-susceptible). First, the strains were incubated with the CLSI breakpoint of cotrimoxazole for 150 min, which induced cell lengthening in the susceptible strains. Second, the bacteria were incubated with mitomycin C (MMC) (0.5 mg/L) for 120 min to induce a SOS-linked cell enlargement higher than that obtained by cotrimoxazole alone. When cotrimoxazole was added 30 min before MMC, the inhibition of folic acid synthesis in the susceptible strain resulted in the suppression of MMC-induced extra elongation. In the non-susceptible strains, folic acid synthesis continued despite the antibiotic, so that the MMC-induced extra cell lengthening could not be impeded. Whereas the first assay resulted in five false negatives and four false positives of resistance, the results of the second assay matched those of the conventional antibiogram. This simple morphological procedure is performed in 2 h and 45 min and may allow a rapid selection of useful and relatively inexpensive therapy, thereby preserving the newer broad-spectrum antibiotics

Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces

Presently, dynamic surface-based models are required to contain increasingly larger numbers of points and to propagate them over longer time periods. For large numbers of surface points, the octree data structure can be used as a balance between low memory occupation and relatively rapid access to the stored data. For evolution rules that depend on neighborhood states, extended simulation periods can be obtained by using simplified atomistic propagation models, such as the Cellular Automata (CA). This method, however, has an intrinsic parallel updating nature and the corresponding simulations are highly inefficient when performed on classical Central Processing Units (CPUs), which are designed for the sequential execution of tasks. In this paper, a series of guidelines is presented for the efficient adaptation of octree-based, CA simulations of complex, evolving surfaces into massively parallel computing hardware. A Graphics Processing Unit (GPU) is used as a cost-efficient example of the parallel architectures. For the actual simulations, we consider the surface propagation during anisotropic wet chemical etching of silicon as a computationally challenging process with a wide-spread use in microengineering applications. A continuous CA model that is intrinsically parallel in nature is used for the time evolution. Our study strongly indicates that parallel computations of dynamically evolving surfaces simulated using CA methods are significantly benefited by the incorporation of octrees as support data structures, substantially decreasing the overall computational time and memory usage. © 2010 Elsevier B.V. All rights reserved.We thank the anonymous reviewers for their valuable comments and suggestions. This work has been supported by Programa de Becas de Excelencia de la Universidad Politecnica de Valencia (PAID-09-09), MEXT Grant in Aid Research (Kakenhi: Silicon etching (A) 19201026), and the Global COE program of Japan (GCOE, Wakate JSPS Young Scientist Fund).Ferrando Jódar, N.; Gosalvez, M.; Cerdá Boluda, J.; Gadea Gironés, R.; Sato, K. (2011). Octree-based, GPU implementation of a continuous cellular automaton for the simulation of complex, evolving surfaces. Computer Physics Communications. 182(3):628-640. https://doi.org/10.1016/j.cpc.2010.11.004S628640182

Optimismo y ejecución en el deporte en situaciones adversas. Replicando a Seligman 1990

Optimism is considered a relevant parameter in sport performance and this study aims to analyse its effects in adverse circumstances. In this study, 66 swimmers (boys and girls) with an average age of 13.66 completed the same test at two different times. After the first test, they received negative feedback (a higher than real time) in order to check the effects on the second test. The results of this study were expected to replicate the study published by Seligman at Berkeley University in 1990. Interestingly, after such negative feedback, pessimists showed significant differences between the first and second tests. In contrast, although not statistically significant, our results indicate that all the swimmers whose performance improved in the second test had optimistic profiles. Finally, we discuss the use of evaluating and providing training in optimism for enhanced performance in competitive sports