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.     

小世界网络中的删边扩容效应

不同于无标度网络,小世界网络中体现负载特性的介数分布和体现连接特征的度分布这两种结构差异很大,依据这个差异,我们提出了有效的删边扩容方法并进行了仿真实验,并进一步从容量与最大介数的关系理论分析确证了实验结果.接着,我们分析了小世界网络中介数分布的差异性与删边扩容效果的相关性,把基于介数的基尼系数变化用于度量删边扩容的效果,指出了结构差异是导致删边扩容效应的必要条件.还指出了无论从容量与介数的定义、仿真结果、结构差异与删边扩容效果的关系来看,都应该从介数入手来实现删边扩容方法,这种方法反直觉,有很多变种,并且实现方便、节省成本,作为一类新的路由策略可以广泛地应用于各类通信网络和交通网络等领域.     

Betweenness estimation in OLSR-based multi-hop networks for distributed filtering

In traditional networks special efforts are put to secure the perimeter with firewalls: particular routers that analyze and filter the traffic to separate zones with different levels of trust. In wireless multi-hop networks the perimeter is a concept extremely hard to identify, thus, it is much more effective to enforce control on the nodes that will route more traffic. But traffic filtering and traffic analysis are costly activities for the limited resources of mesh nodes, so a trade-off must be reached limiting the number of nodes that enforce them. This work shows how, using the OLSR protocol, the centrality of groups of nodes with reference to traffic can be estimated with high accuracy independently of the network topology or size. We also show how this approach greatly limits the impact of an attack to the network using a number of firewalls that is only a fraction of the available nodes.     

基于线路阻抗短时调节的多直流连锁换相失败抑制方法

连锁换相失败是交直流混联电网的新型连锁故障形式之一。结合连锁关系在换相失败相关现象中的体现和参与环节,文中提出了一种在关键线路短时调节阻抗以降低耦合的抑制策略,重点讨论了策略的实施位置。在加权网络模型的基础上,基于直流分群界定了换相失败的连锁范围。在直流群内搜索对直流耦合关系影响较大的关键路径,并采用潮流介数比较各线路阻抗变化对系统运行状态的冲击,以避免在重要线路采取措施。针对不同的扰动,利用换相电压时间面积判断需要启动策略的直流群,从而实现有差别的连锁换相失败抑制。在修改的IEEE 39节点系统和某省市电网算例中,利用PSCAD/EMTDC开展仿真,结果均验证了关键线路阻抗短时调节策略抑制连锁换相失败的效率和有效性。     

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。     

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.     

复杂河流网络节点重要度分析

流域中,具有一定水力联系的河流、交叉口、水利工程设施等纵横交错地构成了一个复杂的河流网络.应用复杂网络理论,建立了河流网络模型,并描述了节点的重要度.将该网络模型应用于海河流域,建立了含有565个节点的海河流域网络.计算了海河流域网络节点的度指标和介数指标,并分别划分为8个等级和12个等级,对不同等级的节点进行节点重要度分析.通过对比分析节点的度指标和介数指标,证明了介数指标更能准确刻画河流网络节点的重要性.复杂网络中节点重要度分析可以为水利规划提供理论依据.     

一种利用BC方法的关键词自动提取算法研究

通过分析几种常见关键词自动抽取方法的特点和不足，以KeyGraph算法思想为基础，构建词语网络并利用网络节点中心度（Betweenness Centrality）理论，提出了一种新的自动抽取关键词算法．通过分析和比较，新算法提取的关键词更能体现文档内容，并且相对低频而意义重要的关键词也能被提取出．最后，通过与TF和TFIDF算法的比较和分析，获得了令人满意的结果．     

基于综合重要度的电网关键线路辨识方法

更加精准快速识别出电网关键线路，对提高电网运行的稳定程度以及预防电网连锁故障具有重要意义。文章首先基于复杂网络理论提出改进潮流介数指标，从结构角度判别系统受到功率扰动后线路的脆弱程度；然后基于熵理论，提出计及线路负载率的加权潮流转移熵指标，克服原有指标中只考虑转移潮流分布均匀性的不足；最后建立包括以上2种指标的综合重要度评估指标，更加全面地衡量线路在电力系统中的重要程度。通过对IEEE 39节点系统进行仿真，得出了不同攻击方式下系统的改进网络传输效率变化曲线图，证明了综合重要度指标的有效性，对预防电力系统连锁故障具有重要意义。