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2. Efficient Tsunami Modeling on Adaptive Grids with Graphics Processing Units (GPUs)

Author

Qin, Xinsheng, LeVeque, Randall, and Motley, Michael

Subjects
Physics - Computational Physics, Computer Science - Computational Engineering, Finance, and Science, Physics - Atmospheric and Oceanic Physics, Physics - Geophysics
Abstract

Solving the shallow water equations efficiently is critical to the study of natural hazards induced by tsunami and storm surge, since it provides more response time in an early warning system and allows more runs to be done for probabilistic assessment where thousands of runs may be required. Using Adaptive Mesh Refinement (AMR) speeds up the process by greatly reducing computational demands, while accelerating the code using the Graphics Processing Unit (GPU) does so through using faster hardware. Combining both, we present an efficient CUDA implementation of GeoClaw, an open source Godunov-type high-resolution finite volume numerical scheme on adaptive grids for shallow water system with varying topography. The use of AMR and spherical coordinates allows modeling transoceanic tsunami simulation. Numerical experiments on several realistic tsunami modeling problems illustrate the correctness and efficiency of the code, which implements a simplified dimensionally-split version of the algorithms. This implementation is shown to be accurate and faster than the original when using CPUs alone. The GPU implementation, when running on a single GPU, is observed to be 3.6 to 6.4 times faster than the original model running in parallel on a 16-core CPU. Three metrics are proposed to evaluate relative performance of the model, which shows efficient usage of hardware resources.

Published
2019

4. Accelerating wave-propagation algorithms with adaptive mesh refinement using the Graphics Processing Unit (GPU)

Author

Qin, Xinsheng, LeVeque, Randall J., and Motley, Michael R.

Subjects
Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Numerical Analysis, Mathematics - Numerical Analysis
Abstract

Clawpack is a library for solving nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. It supports Adaptive Mesh Refinement (AMR), which is essential in solving multi-scale problems. Recently, we added capabilities to accelerate the code by using the Graphics Process Unit (GPU). Routines that manage CPU and GPU AMR data and facilitate the execution of GPU kernels are added. Customized and CPU thread-safe memory managers are designed to manage GPU and CPU memory pools, which is essential in eliminating the overhead of memory allocation and de-allocation. A global reduction is conducted every time step for dynamically adjusting the time step based on Courant number restrictions. Some small GPU kernels are merged into bigger kernels, which greatly reduces kernel launching overhead. A speed-up between $2$ and $3$ for the total running time is observed in an acoustics benchmark problem.

Published
2018

6. Dual-Responsive "Egg-Box" Shaped Microgel Beads Based on W 1 /O/W 2 Double Emulsions for Colon-Targeted Delivery of Synbiotics.

Author

He, Xian, Qin, Yunyun, Liu, Haoyue, Cheng, Kang, Yang, Wanshui, and Qin, Xinsheng

Subjects
FOURIER transform infrared spectroscopy, HYDROGEN bonding interactions, MICROSCOPY, CONTACT angle, ALIMENTARY canal, PECTINS
Abstract

In this study, for enhancing the resistance of probiotics to environmental factors, we designed a microgel beads delivery system loaded with synbiotics. Multiple droplets of W1/O/W2 emulsions stabilized with zein–apple pectin hybrid nanoparticles (ZAHPs) acted as the inner "egg," whereas a three-dimensional network of poly-L-lysine (PLL)-alginate-CaCl2 (Ca) crosslinked gel layers served as the outermost "box." ZAHPs with a mass ratio of 2:1 zein-to-apple pectin showed excellent wettability (three-phase contact angle = 89.88°). The results of the ζ-potentials and Fourier transform infrared spectroscopy demonstrate that electrostatic interaction forces and hydrogen bonding were the main forces involved in the formation of ZAHPs. On this basis, we prepared W1/O/W2 emulsions with other preparation parameters and observed their microstructures by optical microscopy and confocal laser scanning microscope. The multi-chambered structures of W1/O/W2 emulsions were successfully visualized. Finally, the W1/O/W2 emulsions were coated with PLL-alginate-Ca using the solution extrusion method. The results of the in vitro colonic digestion stage reveal that the survival rate of probiotics in the microgel beads was about 75.11%, which was significantly higher than that of the free. Moreover, probiotics encapsulated in microgel beads also showed positive storage stability. Apple pectin would serve as both an emulsifier and a prebiotic. Thus, the results indicate that the "egg-box" shaped microgel beads, designed on the basis of pH-sensitive and enzyme-triggered mechanisms, can enhance the efficiency of probiotics translocation in the digestive tract and mediate spatiotemporal controlled release. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Placenta-Related Parameters at Delivery in Relation to Folic Acid Supplementation in Different Pregnancies.

Author

Ren, Yating, Yang, Maoyuan, Ren, Siyi, Ge, Zhihao, Cao, Yu, Qin, Xinsheng, Sheng, Jie, and Wang, Sufang

Abstract

Folic acid plays an important role in the synthesis, repair, and methylation of deoxyribonucleic acid (DNA). Currently, most studies have focused on the effects of periconceptional folic acid (FA) supplementation on fetal development, and there is still a lack of population-based research exploring the association between FA use during pregnancy and placental development. This study aimed to investigate the impacts of FA supplementation in different pregnancies on placenta-related parameters at delivery. The study included 2708 pregnant women recruited from Ma'anshan City, Anhui Province, China, between May 2013 and September 2014. Information on FA use from one month before conception to delivery was collected. Placental length, width, and thickness were measured. Multivariable logistic regression analysis was used to assess the effects of FA supplementation in different pregnancies on placenta-related parameters. Based on multiple regression analysis, propensity score weighting was adopted to enhance comparability between different FA supplementation groups. Compared with FA non-users, FA supplementation before conception was associated with increased placental width (0.241 cm, 95%CI: 0.052–0.429, p = 0.013) and increased placental surface area (6.398 cm2, 95%CI: 1.407–11.389, p = 0.012), and FA use in early/middle pregnancy was, respectively, related with increased placental thickness (0.061 cm, 95%CI: 0.004–0.117, p = 0.036; 0.066 cm, 95%CI: 0.004–0.129, p = 0.038). FA use before conception could increase placental width and area, and FA use in early/middle pregnancy could increase placental thickness. To confirm the findings, further investigations are needed. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Spatial distribution patterns and association of two Apocynaceae plants in the tropical mountain rainforests of Jianfengling, Hainan Island, China

Author

Xu Han, Tang GuangDa, He Zengli, Qin Xinsheng, and Li Yide

Subjects
Ecology, Apocynaceae, biology, Alstonia rostrata, Rainforest, biology.organism_classification, Tabernaemontana bufalina, Geography, Spatial distribution pattern, China, Ecology, Evolution, Behavior and Systematics, Allelopathy, Nature and Landscape Conservation
Published
2017

19. A comparison of a two-dimensional depth-averaged flow model and a three-dimensional RANS model for predicting tsunami inundation and fluid forces

Author

Qin, Xinsheng, Motley, Michael, LeVeque, Randall, Gonzalez, Frank, Mueller, Kaspar, Qin, Xinsheng, Motley, Michael, LeVeque, Randall, Gonzalez, Frank, and Mueller, Kaspar

Abstract

The numerical modeling of tsunami inundation that incorporates the built environment of coastal communities is challenging for both 2-D and 3-D depth-integrated models, not only in modeling the flow but also in predicting forces on coastal structures. For depth-integrated 2-D models, inundation and flooding in this region can be very complex with variation in the vertical direction caused by wave breaking on shore and interactions with the built environment, and the model may not be able to produce enough detail. For 3-D models, a very fine mesh is required to properly capture the physics, dramatically increasing the computational cost and rendering impractical the modeling of some problems. In this paper, comparisons are made between Geo-Claw, a depth-integrated 2-D model based on the nonlinear shallow-water equations (NSWEs), and OpenFOAM, a 3-D model based on Reynolds-averaged Navier-Stokes (RANS) equation for tsunami inundation modeling. The two models were first validated against existing experimental data of a bore impinging onto a single square column. Then they were used to simulate tsunami inundation of a physical model of Seaside, Oregon. The resulting flow parameters from the models are compared and discussed, and these results are used to extrapolate tsunami-induced force predictions. It was found that the 2-D model did not accurately capture the important details of the flow near initial impact due to the transiency and large vertical variation of the flow. Tuning the drag coefficient of the 2-D model worked well to predict tsunami forces on structures in simple cases, but this approach was not always reliable in complicated cases. The 3-D model was able to capture transient characteristic of the flow, but at a much higher computational cost; it was found this cost can be alleviated by subdividing the region into reasonably sized subdomains without loss of accuracy in critical regions., QC 20181008

Published
2018
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22. A New Species of Manglietia (Magnoliaceae) from China

Author

Zhou Renzhang, Xing FuWu, and Qin Xinsheng

Subjects
Gynoecium, White (horse), Botany, Stamen, Manglietia, Plant Science, Biology, biology.organism_classification, China, Ecology, Evolution, Behavior and Systematics, Magnoliaceae
Abstract

Manglietia albistaminea Law, R. Z. Zhou & X. S. Qin, a new species from China, is described and illustrated. This species is similar to M. fordiana Oliver and M. hainanensis Dandy, from which it differs by fine short hairs on both leaf surfaces, white stamens, and white pilose carpels.

Published
2006

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