In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila,Persephonella marina,Thermosulfidibacter takaii,and Thermus thermophilus

Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO₂ sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO₂ binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn²⁺. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO₂ sequestration agents.     

一种网络社团划分的评价及改进方法

主要从节点在所属群体内的相对重要程度出发, 尝试性地给出一种网络社团结构的新定义, 并在此基础上构建了一种网络社团划分的评价及改进方法。该方法既可以与现有的社团划分算法进行组合, 形成新的网络社团划分算法, 也可以独立使用, 对网络社团的划分结果进行评价与改进。最后, 通过MCL、GN、Factions等方法及算例对提出的算法进行了验证与分析。     

PSN网络中基于社会属性的消息路由

PSN（pocket switched network）网络作为一种特殊的DTN（Delay Tolerance Network）网络,除了具有不包含持续端到端连接、高传输时延及节点资源受限的特点以外,具有更强的社会规律性.本文在研究了现有的算法的基础上,提出了一种基于社会信息的路由算法—BridgingCom.为使消息尽快从本地传递到目标节点,我们选择桥接中心度（Bridging Centrality）作为中继节点的选择依据.实验结果表明,与已有相关算法相比,本改进算法能够在网络负载较低的情况下获得较高的传输效率,较低的传输延迟.     

Protein interaction networks: centrality,modularity, dynamics,and applications

In the post-genomic era, proteomics has achieved significant theoretical and practical advances with the development of high-throughput technologies. Especially the rapid accumulation of protein-protein interactions (PPIs) provides a foundation for constructing protein interaction networks (PINs), which can furnish a new perspective for understanding cellular organizations, processes, and functions at network level. In this paper, we present a comprehensive survey on three main characteristics of PINs: centrality, modularity, and dynamics. 1) Different centrality measures, which are used to calculate the importance of proteins, are summarized based on the structural characteristics of PINs or on the basis of its integrated biological information; 2) Different modularity definitions and various clustering algorithms for predicting protein complexes or identifying functional modules are introduced; 3) The dynamics of proteins, PPIs and sub-networks are discussed, respectively. Finally, the main applications of PINs in the complex diseases are reviewed, and the challenges and future research directions are also discussed.     

Virtual network embedding based on real-time topological attributes

As a great challenge of network virtualization, virtual network embedding/mapping is increasingly important. It aims to successfully and efficiently assign the nodes and links of a virtual network (VN)...     

邮件挖掘技术在社会网络分析中的研究与应用

邮件挖掘是数据挖掘领域中一项新兴的技术,它的出现源于电子邮件在人们生活中的广泛使用以及数据挖掘技术的日益成熟.介绍分析了这项技术及其崭新的一个应用--社会网络分析SNA,并根据当前国际研究现状与发展趋势,提出了社会关系网络的构建方法以及社团挖掘改进算法和相关优化策略.描述了社会网络分析系统框架结构的设计与搭建.     

复杂社会网络的介数性质近似计算方法研究

随着计算机和互联网的迅猛发展,面向互联网的社会网络挖掘和分析成为一个新的课题。从互联网挖掘的社会网络往往规模巨大,这对网络分析算法的性能提出了更高的要求 。介数值作为图的重要结构性质,广泛应用于基于图的聚类、分类算法,如何降低其计算的复杂性是急需解决的问题。目前,常用的方法是利用对最短路径长度的近似来降低低网络分析算法的复杂性,但已有的近似方法没有考虑现实大规模网络的复杂网络特性,对最短路径长度的近似方 近似计算方法,其基本思想是结合复杂网络的结构特性,利用通过网络中枢节点的路径来近似最短路径,以近似的最短路径求得介数的近似值。这为图的结构性质的近似估算算提供了一种新颖的思路。通过与传统的介数计算方法和近的分析得到了若干有益的结论,为进一步的研究工作奠定了基础。     

一种面向度中心性及重叠网络社区的发现算法

针对社会网络中存在较多以度中心节点为中心并且具有多社区重叠节点的网络社区结构,提出了一种面向度中心性及重叠网络社区的两阶段发现算法。第一阶段发现初始社区:选取度最大的Top-k个节点作为候选中心节点,并将每个节点与其邻居节点形成候选初始社区,其中如果某候选社区与已形成的初始社区的重叠度低于阈值,则形成一个新的初始社区;第二阶段调整社区划分:通过偏离度机制进行调整,将偏离度最大值对应的节点划分到连接紧密的相应社区内,形成最终社区划分。实验表明,该方法不仅能够揭示网络中以某个节点为中心的密集的社区结构,还能有效处理初始社区不同程度的重叠问题。相比现有算法,所提方法对预先输入的候选初始社区数k值不敏感,并具有较高的准确性和灵活性。     

Finding groups with maximum betweenness centrality

In this paper we consider the problem of identifying the most influential (or central) group of nodes (of some predefined size) in a network. Such a group has the largest value of betweenness centrality or one of its variants, for example, the length-scaled or the bounded-distance betweenness centralities. We demonstrate that this problem can be modelled as a mixed integer program (MIP) that can be solved for reasonably sized network instances using off-the-shelf MIP solvers. We also discuss interesting relations between the group betweenness and the bounded-distance betweenness centrality concepts. In particular, we exploit these relations in an algorithmic scheme to identify approximate solutions for the original problem of identifying the most central group of nodes. Furthermore, we generalize our approach for identification of not only the most central groups of nodes, but also central groups of graph elements that consists of either nodes or edges exclusively, or their combination according to some pre-specified criteria. If necessary, additional cohesiveness properties can also be enforced, for example, the targeted group should form a clique or a κ-club. Finally, we conduct extensive computational experiments with different types of real-life and synthetic network instances to show the effectiveness and flexibility of the proposed framework. Even more importantly, our experiments reveal some interesting insights into the properties of influential groups of graph elements modelled using the maximum betweenness centrality concept or one of its variations.     

基于内容热度与节点介数的NDN网络缓存策略

缓存技术是数据命名网络（Named data networking,NDN）的关键技术之一. NDN传统的LCE缓存策略会造成较大的冗余. 改进的RCOne策略采用随机放置的方法,没有利用任何内容、节点信息,对网络缓存性能的提升有限. Betw策略只考虑到节点介数,导致高介数节点缓存更替频繁,当节点缓存容量远小于内容总量时,缓存性能下降. 为了解决这些问题,本文提出一种结合内容热度与节点介数的新型缓存策略HotBetw（Hot content placed on node with high Betweenness）,充分利用内容与节点信息选择最佳的位置放置缓存. 仿真实验表明相对于典型NDN缓存策略,HotBetw缓存策略在提高缓存命中率、降低平均跳数方面具有很好的效果.