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HACP2 : The Pre-processing Software Tool for the Hybrid Atomistic-Continuum Coupling Simulation
Qian Wang,Wenjing Yang,Fu Li,Xiaoguang Ren,Yuhua Tang 보안공학연구지원센터 2016 International Journal of Hybrid Information Techno Vol.9 No.1
Fluid simulation is an important application of High Performance Computing. The hybrid atomistic-continuum coupling fluid simulation can effectively handle the contradictory of the reduction of the simulation scale and the increase of the computation load when trying to improve the accuracy. The pre-processing procedure of the coupling simulation is quite important in the whole simulation process and requires the support of an efficient, user-friendly interface. Under the demand of efficient coupling fluid simulation, in this paper we design and implement a visualized pre-processing framework HACP2 based on SALOME, for the unified molecular dynamic-computational fluid dynamics modeling and apply it into the coupling simulation process. The experimental verification indicates that our HACP2 framework can offer efficient, easy-to-use pre-processing for the hybrid atomistic-continuum coupling simulation, and effectively improve the efficiency of the coupling simulation.
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Yixin Wang,Long Jin,Jideng Ma,Li Chen,Yuhua Fu,Keren Long,Silu Hu,Yang Song,Dazhi Shang,Qianzi Tang,Xun Wang,Xuewei Li,Mingzhou Li 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.2
Objective: Hemicastration is a unilateral orchiectomy to remove an injured testis, which can induce hormonal changes and compensatory hypertrophy of the remaining testis, and may influence spermatogenesis. However, the underlying molecular mechanisms are poorly understood. Here, we investigated the impact of hemicastration on remaining testicular function. Methods: Prepubertal mice (age 24 days) were hemicastrated, and their growth was monitored until they reached physical maturity (age 72 days). Subsequently, we determined testis DNA methylation patterns using reduced representation bisulfite sequencing of normal and hemicastrated mice. Moreover, we profiled the testicular gene expression patterns by RNA sequencing (RNA-seq) to examine whether methylation changes affected gene expression in hemicastrated mice. Results: Hemicastration did not significantly affect growth or testosterone (p>0.05) compared with control. The genome-wide DNA methylation pattern of remaining testis suggested that substantial genes harbored differentially methylated regions (1,139) in gene bodies, which were enriched in process of protein binding and cell adhesion. Moreover, RNA-seq results indicated that 46 differentially expressed genes (DEGs) involved in meiotic cell cycle, synaptonemal complex assembly and spermatogenesis were upregulated in the hemicastration group, while 197 DEGs were downregulated, which were related to arachidonic acid metabolism. Integrative analysis revealed that proteasome 26S subunit ATPase 3 interacting protein gene, which encodes a protein crucial for homologous recombination in spermatocytes, exhibited promoter hypomethylation and higher expression level in hemicastrated mice. Conclusion: Global profiling of DNA methylation and gene expression demonstrated that hemicastration-induced compensatory response maintained normal growth and testicular morphological structure in mice.
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