Simulating FAS-induced apoptosis by using P systems

In contrast to differential equations, P systems are an unconventional model of computation which takes into consideration the discrete character of the quantity of components and the inherent randomness that exists in biological phenomena. The key feature of P systems is their compartmentalised structure which represents the heterogeneity of the structural organisation of the cells, and where one can take into account the role played by membranes in the functioning of the system, for example signalling at the cell surface, selective uptake of substances from the media, diffusion across different compartments, etc. We show here that P systems can be a reliable tool for Systems Biology and could even outperform in some cases the current simulation techniques based on differential equations. We will also use a strategy based on the well known Gillespie algorithm but running on more than one compartment called Multi-compartmental Gillespie Algorithm.     

P systems with array objects and array rewriting rules

Array P systems were introduced by Paun Gh. which is linking the two areas of membrane computing and picture grammars. Puzzle grammars were introduced by us for generating connected picture arrays in the two-dimensional plane, motivated by the problem of tiling the plane. On the other hand, incorporating into arrays the developmental type of generation used in the well-known biologically motivated L systems, Siromoney and Siromoney proposed a very general rectangular array generating model, called extended controlled tabled L array system (ECTLAS). In this paper we introduce two variations of the array P system, called BPG array P system and parallel array P system. The former has in the regions array objects and basic puzzle grammar rules (BPG), which are a specific kind of puzzle grammar rules. In the latter, the regions have rectangular array objects and tables of context-free rules. We examine these two types of P systems for their array generative power.     

Phylogenetic relationships of native and introduced Bemisia tabaci (Homoptera:Aleyrodidae) from China and India based on mtCOI DNA sequencing and host plant comparisons

Phylogenetic relationships for Bemisia tabaci were reconstructed by analysis of a ～780 bp fragment of the mitochondrial cytochrome oxidase I (mtCOI) gene with an emphasis on geographic range and distribution among eight eudicot plant families that are common hosts of B. tabaci worldwide to elucidate key phylogeographic linkages between populations extant in China (n=31) and India (n=34). Bootstrap values for the Maximum Parsimony tree were highly robust for all major nodes involving the major Asian clade, subgroups, and sister groups within, at 92%—100%. Between-clade distances for the Southeast Asia and three other major clades, e.g. from sub-Sahara Africa, North Africa-Mediterranean, and the Americas, were approximately >16% divergent. Two major Asian subgroups (I, II) were resolved, which represented populations indigenous to the region, comprising two (I a, I b) and five (II a—e) sister groups, respectively, which diverged by 11%. Two distinct populations from sunflower in Hyderabad grouped separately within the two Asian subgroups. All other populations grouped uniquely within Asian subgroup II or I. The “B” biotype was identified in 23 collections from China at 97.3%—99.5% nucleotide identity with “B” biotype reference sequences; it was not identified in collections from India. The majority of haplotypes were associated with 3—4 plant families, with one exception that for sister group IId (sesame, India), it might be monophagous. Thus, B. tabaci from the southeastern and near eastern regions of the Asian continent comprise of a large number of ancestral, richly divergent, mostly polyphagous populations. This region is therefore hypothesized to constitute an important Old World center of diversification for the B. tabaci complex, together with sub-Saharan Africa.     

分布式Alamouti空时码的信道容量分析

针对分布式Alamouti空时码（DASTC）系统的信道容量求解问题，提出了一种求解DASTC系统的信道容量闭式解及其上界的方法．该方法根据DASTC系统利用多节点联合发送信息的特点，选择距离信源节点最近的空闲节点作为中继节点构建了DASTC系统的无线中继信道模型，采用网络信息论中的最大割最小流定理，将DASTC信道模型分为广播信道模型和多接入信道模型，     

荧光法在对-二苯氨基苯基硼酸(DPBA)对单糖的识别作用中的应用

采用荧光光谱法研究了具有分子内电荷转移性质的一种新型硼酸衍生物,对-二苯氨基苯基硼酸(DPBA)与羧甲基-β-环糊精(CM-β-CD)的包合行为,并考察了包合物DPBA在CM-β-CD存在下与四种单糖分子的识别作用,实验结果表明,DPBA与果糖,葡萄糖,半乳糖,甘露糖分子的结合计量比均为1∶1,结合常数从大到小的顺序为:D-果糖>>D-甘露糖>D-半乳糖≈D-葡萄糖.CM-β-CD对DPBA具有增溶增敏性,从而能够在水溶液中更好地对糖分子进行识别.     

中国五加科羽叶参属和五加属的新组合和新异名

在编写《Flora of China》五加科英文版时，查阅了当今国内、外的主要植物标本室中的馆藏标本，包拈五加科的模式、副模式及其他的大量标本，笔者得到一些新的认识和发现。在此主要报道羽叶参属和五加属中新修订的一些分类群，其中有1个新组合Penta panax longipes Shang et C．F．Ji；1个新的等级Eleuthero—coccus leucorrhizus var．setchuenensis（Harms）Shang＆J．Y．Huang;1个新变种E．trifoliatus var．inte—gerrimus Shang＆P．Lowry。另外还对20个植物名称进行了分类讨论，将它们分别置于正确的种名之下，作为异名处理。     

Nonlinear interactions between gravity waves and background winds

Using the nonlinear propagating gravity waves (GW) model in the two-dimensional compressible atmosphere and the linear GW theory, the process of GW propagation in different background winds, e.g. the direction of the background wind is opposite to (dead wind) or the same as (tail wind) the direction of the horizontal phase velocity of GW, is studied. The results show that the dead wind prolongs the vertical wavelength and accelerates GW propagation. Therefore, GW propagates up to a higher height becomes instable in a short time and eventually induces an inverse jet flow. Then, the vertical wavelength is becoming short due to the nonlinear interactions between GW and the inverse jet flow. The vertical wavelength and group velocity decrease after GW propagates into the tail wind. The initial instable time is delayed. Although most of GW is trapped in the instable region, some of GW propagates above the instable region. Compared with GW propagation in the tail wind, the nonlinear interactions between GW and the dead wind are also strong. In contrast, the linear GW theory predicts that GW can propagate freely in the dead wind. The vertical wavelength simulated by the nonlinear numerical model is different from that predicted by the linear theory greatly after GW propagates into the dead wind.     

Comparing the biological coherence of network clusters identified by different detection algorithms

Protein-protein interaction networks serve to carry out basic molecular activity in the cell. Detecting the modular structures from the protein-protein interaction network is important for understanding the organization, function and dynamics of a biological system. In order to identify functional neighbor- hoods based on network topology, many network cluster identification algorithms have been devel- oped. However, each algorithm might dissect a network from a different aspect and may provide dif- ferent insight on the network partition. In order to objectively evaluate the performance of four com- monly used cluster detection algorithms: molecular complex detection (MCODE), NetworkBlast, shortest-distance clustering (SDC) and Girvan-Newman (G-N) algorithm, we compared the biological coherence of the network clusters found by these algorithms through a uniform evaluation framework. Each algorithm was utilized to find network clusters in two different protein-protein interaction net- works with various parameters. Comparison of the resulting network clusters indicates that clusters found by MCODE and SDC are of higher biological coherence than those by NetworkBlast and G-N algorithm.     

Selective Smoothed Finite Element Method

The paper examines three selective schemes for the smoothed finite element method (SFEM) which was formulated by incorporating a cell-wise strain smoothing operation into the standard compatible finite element method (FEM). These selective SFEM schemes were formulated based on three selective integration FEM schemes with similar properties found between the number of smoothing cells in the SFEM and the number of Gaussian integration points in the FEM. Both scheme 1 and scheme 2 are free of nearly incompressible locking, but scheme 2 is more general and gives better results than scheme 1. In addition, scheme 2 can be applied to anisotropic and nonlinear situations, while scheme 1 can only be applied to isotropic and linear situations. Scheme 3 is free of shear locking. This scheme can be applied to plate and shell problems. Results of the numerical study show that the selective SFEM schemes give more accurate results than the FEM schemes.     

BEM Analysis of Wave Propagation in a Water-Filled Borehole in an Anisotropic Solid

This paper describes a time-domain boundary element method developed to analyze the interactions of acoustic and elastic waves near the interfaces between water and an anisotropic elastic solid. Two models are analyzed with one being the interface between two half spaces of fluid and solid and the other being a fluid region sandwiched by half space domains of anisotropic elastic solids. Both monopole and dipole point sources are used to generate an initial pressure wave in the fluid. Some snapshots of the transient wave behavior near the fluid-solid interfaces are given. The effect of the anisotropy in the solid on the pressure waveforms in the fluid is discussed. The numerical results allow detailed arrival identification and interpretation of acoustic and elastic waves propagating along the fluid-solid interfaces.