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

Effect of sperm concentration and storage temperature on goat spermatozoa during liquid storage

The use of cooled semen is relatively common in goats. There are a number of advantages of cooled semen doses, including easier handling of artificial insemination (AI) doses, transport, more AI doses per ejaculate, and higher fertility rates in comparison with frozen AI doses. However, cooled semen has a short shelf life. The objective of this study was to examine the effect of temperature and sperm concentration on the in vitro sperm quality during liquid storage for 48 h, including sperm motility and kinetics, response to oxidation, mitochondrial membrane potential (MMP) and DNA fragmentation in goats. Three experiments were performed. In the first, the effects of liquid preservation of semen at different temperatures (5 °C or 17 °C), durations (0, 24 and 48 h) and sperm concentrations (250 × 106 sperm/mL (1:2 dilution rate), 166.7 × 106 sperm/mL (1:3 dilution rate) or 50 × 106 sperm/mL (1:10 dilution rate)) on sperm motility and kinetics were studied. In the second experiment, the effect of temperature, sperm washing and concentration on sperm motility and DNA fragmentation was studied. Finally, the effect of sperm concentration and duration of storage at 5 °C on sperm motility, response to oxidative stress and MMP was examined. We found that refrigerated liquid storage of goat sperm impaired sperm quality, such as motility, MMP and response to oxidation, as storage time increased; however, sperm DNA fragmentation index was not significantly affected. Liquid storage at 5 °C preserved higher total motility than at 17 °C. Moreover, we observed that the reduction of sperm concentration below 500 × 106 sperm/mL did not seem to improve the quality of spermatozoa conserved in milk-based extender in the conditions teste

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