Browsing by Author "Xu, Y."
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Item Bright Solitons in a Two-Dimensional Spin-Orbit-Coupled Dipolar Bose-Einstein Condensate(American Physical Society, 2015-07-27) Xu, Y.; Zhang, Y.; Zhang, Chuanwei; Zhang, ChuanweiWe study a two-dimensional spin-orbit-coupled dipolar Bose-Einstein condensate with repulsive contact interactions by both the variational method and the imaginary-time evolution of the Gross-Pitaevskii equation. The dipoles are completely polarized along one direction in the two-dimensional plane to provide an effective attractive dipole-dipole interaction. We find two types of solitons as the ground states arising from such attractive dipole-dipole interactions: a plane-wave soliton with a spatially varying phase and a stripe soliton with a spatially oscillating density for each component. Both types of solitons possess smaller size and higher anisotropy than the soliton without spin-orbit coupling. Finally, we discuss the properties of moving solitons, which are nontrivial because of the violation of Galilean invariance.Item Cofunctional Subpathways were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue(Hindawi Publishing Corporation) Su, F.; Shang, D.; Xu, Y.; Feng, L.; Yang, H.; Liu, B.; Su, Shengyang; Chen, L.; Li, X.; Su, ShengyangDissecting the characteristics of the transcription factor (TF) regulatory subpathway is helpful for understanding the TF underlying regulatory function in complex biological systems. To gain insight into the influence of TFs on their regulatory subpathways, we constructed a global TF-subpathways network (TSN) to analyze systematically the regulatory effect of common-motif, common-family, or common-tissue TFs on subpathways. We performed cluster analysis to show that the common-motif, common-family, or common-tissue TFs that regulated the same pathway classes tended to cluster together and contribute to the same biological function that led to disease initiation and progression. We analyzed the Jaccard coefficient to show that the functional consistency of subpathways regulated by the TF pairs with common motif, common family, or common tissue was significantly greater than the random TF pairs at the subpathway level, pathway level, and pathway class level. For example, HNF4A (hepatocyte nuclear factor 4, alpha) and NR1I3 (nuclear receptor subfamily 1, group I, member 3) were a pair of TFs with common motif, common family, and common tissue. They were involved in drug metabolism pathways and were liver-specific factors required for physiological transcription. In short, we inferred that the cofunctional subpathways were regulated by common-motif, common-family, or common-tissue TFs.