Algorithms for finding transposons in gene sequences

With the process of evolution, some genes will change their relative positions in gene sequence. These "jumping genes" are called transposons. Through some intuitive rules, we give a criterion to determine transposons among gene sequences of different individuals of the same species. Then we turn this problem into graph theory and give algorithms for different situations with acceptable time complexities. One of these algorithms has been reported briefly as the "iteration algorithm" in Kang et al.'s paper (in this paper, transposon is called "core-gene-defined genome organizational framework", cGOF). This paper provides the omitted details and discussions on general cases.Comment: 5 pages, 2 figure

The observation of diffraction phases in matter wave scattering

We study the diffraction phase of different orders via the Dyson expansion series, for ultracold atomic gases scattered by a standing-wave pulse. As these diffraction phases are not observable in a single pulse scattering process, a temporal Talbot-Lau interferometer consisting of two standing-wave pulses is demonstrated experimentally with a Bose-Einstein condensate to explore this physical effect. The role of the diffraction phases is clearly shown by the second standing-wave pulse in the relative population of different momentum states. Our experiments demonstrate obvious effects beyond the Raman-Nath method, while agree well with our theory by including the diffraction phases. In particular, the observed asymmetry in the dependence of the relative population on the interval between two standing-wave pulses reflects the diffraction phase differences. The role of interatomic interaction in the Talbot-Lau interferometer is also discussed.Comment: 7 pages, 3 figures, accepted by Phys. Rev.

Asymmetric superradiant scattering and abnormal mode amplification induced by atomic density distortion

The superradiant Rayleigh scattering using a pump laser incident along the short axis of a Bose-Einstein condensate with a density distortion is studied, where the distortion is formed by shocking the condensate utilizing the residual magnetic force after the switching-off of the trapping potential. We find that very small variation of the atomic density distribution would induce remarkable asymmetrically populated scattering modes by the matter-wave superradiance with long time pulse. The optical field in the diluter region of the atomic cloud is more greatly amplified, which is not an ordinary mode amplification with the previous cognition. Our numerical simulations with the density envelop distortion are consistent with the experimental results. This supplies a useful method to reflect the geometric symmetries of the atomic density profile by the superradiance scattering.Comment: 7pages,4 figures, Optical Express 21,(2013)1437

Manipulating the momentum state of a condensate by sequences of standing wave pulses

We analyze the effects of sequences of standing wave pulses on a Bose-Einstein condensate (BEC). Experimental observations are in good agreement with a numerical simulation based on the band structure theory in the optical lattice. We also demonstrate that a coherent control method based on such sequences of pulses is very efficient for experimentally designing specific momentum states.Comment: 6 pages; 5 figures; submitted to PR

Cluster Attack: Query-based Adversarial Attacks on Graphs with Graph-Dependent Priors

While deep neural networks have achieved great success in graph analysis, recent work has shown that they are vulnerable to adversarial attacks. Compared with adversarial attacks on image classification, performing adversarial attacks on graphs is more challenging because of the discrete and non-differential nature of the adjacent matrix for a graph. In this work, we propose Cluster Attack -- a Graph Injection Attack (GIA) on node classification, which injects fake nodes into the original graph to degenerate the performance of graph neural networks (GNNs) on certain victim nodes while affecting the other nodes as little as possible. We demonstrate that a GIA problem can be equivalently formulated as a graph clustering problem; thus, the discrete optimization problem of the adjacency matrix can be solved in the context of graph clustering. In particular, we propose to measure the similarity between victim nodes by a metric of Adversarial Vulnerability, which is related to how the victim nodes will be affected by the injected fake node, and to cluster the victim nodes accordingly. Our attack is performed in a practical and unnoticeable query-based black-box manner with only a few nodes on the graphs that can be accessed. Theoretical analysis and extensive experiments demonstrate the effectiveness of our method by fooling the node classifiers with only a small number of queries.Comment: IJCAI 2022 (Long Presentation

On the Convergence of Solutions for SPDEs under Perturbation of the Domain

We investigate the effect of domain perturbation on the behavior of mild solutions for a class of semilinear stochastic partial differential equations subject to the Dirichlet boundary condition. Under some assumptions, we obtain an estimate for the mild solutions under changes of the domain

Polymers of Intrinsic Microporosity (PIMs) in Sensing and in Electroanalysis

Polymers of intrinsic microporosity (PIMs) provide high surface area materials (typically 1000 m2 g-1 apparent BET surface area) that are processable from organic solvents to give glassy films or composite coatings. Multi-functionality for sensing with these materials is achieved (i) based on the polymer backbone itself being fluorescent or chemically active or (ii) based on guest species (chromophores, nano-catalysts, nano-photo-catalysts, etc.) that are readily embedded into PIMs and accessible through micropores in the polymer host. The ease of forming uniform microporous films or composite films is linked to molecular rigidity and highlighted here for sensing/electroanalytical applications