Cluster Analysis Based on Bipartite Network

Clustering data has a wide range of applications and has attracted considerable attention in data mining and artificial intelligence. However it is difficult to find a set of clusters that best fits natural partitions without any class information. In this paper, a method for detecting the optimal cluster number is proposed. The optimal cluster number can be obtained by the proposal, while partitioning the data into clusters by FCM (Fuzzy c-means) algorithm. It overcomes the drawback of FCM algorithm which needs to define the cluster number c in advance. The method works by converting the fuzzy cluster result into a weighted bipartite network and then the optimal cluster number can be detected by the improved bipartite modularity. The experimental results on artificial and real data sets show the validity of the proposed method

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism