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.     

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。     

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.     

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)...     

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。     

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。