Analysis of E. coli soluble proteins by non‐denaturing micro 2‐DE/3‐DE and MALDI‐MS‐PMF

Escherichia coli (strain K‐12)‐soluble proteins were analyzed by nondenaturing micro 2‐DE and MALDI‐MS‐PMF. The reported conditions of nondenaturing IEF in agarose column gels [Jin, Y., Manabe, T., Electrophoresis 2009, 30, 939–948] were modified to optimize the resolution of cellular soluble proteins. About 300 CBB‐stained spots, the apparent molecular masses of which ranged from ca. 6000 to 10 kDa, were detected. All the spots on two reference 2‐DE gels (one for wide mass range and one for low‐molecular‐mass range) were numbered and subjected to MALDI‐MS‐PMF for the assignment of constituting polypeptides. Most of the spots (310 spots out of 329) provided significant match (p<0.05) with polypeptides in Swiss‐Prot database and totally 228 polypeptide species were assigned. Activity staining of enzymes such as alkaline phosphatase and catalases was performed on the 2‐DE gels and the locations of the activity spots matched well with those of the MS‐assigned polypeptides of the enzymes. Most of the polypeptides with subunit information in Swiss‐Prot (119 polypeptides as homo‐multimers and 25 as hetero‐multimers out of the 228), such as pyruvate dehydrogenase complex which is composed of three enzymatic components, were detected at the apparent mass positions of their polymers, suggesting that the proteins were separated retaining their subunit structures. When a nondenaturing 2‐DE gel was vertically cut into 2 mm strips and one of the strips was subjected to a third‐dimension micro SDS‐PAGE (micro 3‐DE), about 190 CBB‐stained spots were detected. The assignment of the polypeptides separated on the 3‐DE gel would further provide information on protein/polypeptide interactions.     

考虑意外事件对交通流影响的元胞自动机交通流模型

在NaSh模型的基础上,考虑交通事故和养护路段等意外事件对高速公路交通流的影响,建立了有意外事件影响的在车道管制下的高速公路交通流元胞自动机模型,并进行数值模拟. 研究发现:意外事件对高速公路交通流有明显影响,并且意外事件对交通流的影响在某一密度值范围内尤其明显,且意外事件堵塞点在第一车道比在第二车道对交通流的影响小;同时,在该密度值范围内,意外事件堵塞时间和堵塞路段长度越长,对交通流的影响就越大. 关键词： 元胞自动机 交通流 意外事件     

On the Tutte–Krushkal–Renardy polynomial for cell complexes

Recently V. Krushkal and D. Renardy generalized the Tutte polynomial from graphs to cell complexes. We show that evaluating this polynomial at the origin gives the number of cellular spanning trees in the sense of A. Duval, C. Klivans, and J. Martin. Moreover, after a slight modification, the Tutte–Krushkal–Renardy polynomial evaluated at the origin gives a weighted count of cellular spanning trees, and therefore its free term can be calculated by the cellular matrix-tree theorem of Duval et al. In the case of cell decompositions of a sphere, this modified polynomial satisfies the same duality identity as the original polynomial. We find that evaluating the Tutte–Krushkal–Renardy along a certain line gives the Bott polynomial. Finally we prove skein relations for the Tutte–Krushkal–Renardy polynomial.     

Emergence of density dynamics by surface interpolation in elementary cellular automata

A classic problem in elementary cellular automata (ECAs) is the specification of numerical tools to represent and study their dynamical behaviour. Mean field theory and basins of attraction have been commonly used; however, although the first case gives the long term estimation of density, frequently it does not show an adequate approximation for the step-by-step temporal behaviour; mainly for non-trivial behaviour. In the second case, basins of attraction display a complete representation of the evolution of an ECA, but they are limited up to configurations of 32 cells; and for the same ECA, one can obtain tens of basins to analyse. This paper is devoted to represent the dynamics of density in ECAs for hundreds of cells using only two surfaces calculated by the nearest-neighbour interpolation. A diversity of surfaces emerges in this analysis. Consequently, we propose a surface and histogram based classification for periodic, chaotic and complex ECA.     

有超车规则的交通流的元胞自动机模型

分析和评论了2014年美国大学生数学建模竞赛（MCM）A题,以及获得outstanding winner奖的6篇论文。首先对试题进行分析,并结合已有文献指出A题的主要解题思路;然后,通过评述获奖论文,指出学生论文的优点及存在的问题;最后,对今年赛题的某些问题进行讨论。     

细胞神经网络的指数稳定性

该文研究了具有可变时滞的随机细胞神经网络的指数 稳定性,应用Razumikhin定理与Lyapunov函数,建立了这种细胞神经网络均方指数稳定与几乎必然指数稳定的两类判据,一类是时滞无关而另一类是时滞相关.     

Lattice games without rational strategies

We show that the lattice games of Guo and Miller support universal computation, disproving their conjecture that all lattice games have rational strategies. We also state an explicit counterexample to that conjecture: a three dimensional lattice game whose set of winning positions does not have a rational generating function.     

Three-dimensional cellular automaton simulation of tumour growth in inhomogeneous oxygen environment

Cellular automaton theory has previously been used to study cell growth. In this study, we present a three-dimensional cellular automaton model performing the growth simulation of normal and cancerous cells. The necessary nutrient supply is provided by an artificial arterial tree which is generated by constrained constructive optimization. Spatial oxygen diffusion is approximated again by a cellular automaton model. All results could be illustrated dynamically by three-dimensional volume visualization. Because of the chosen modelling approach, an extension of the model to simulate angiogenic processes is possible.     

Evolution of groups with a hierarchical structure

The universal occurrence of a hierarchical structure and its dynamic behavior in various types of group, living or abstract, are discussed. Here the word “group” refers not only to tangible aggregation but also to invisible aggregation of social psychological and of geopolitical meaning. The evolution of these groups is simulated using a model of agents distributed on the lattices of cellular grids. It is assumed that agents, fearing isolation, interact asymmetrically with each other with regard to exchange of “power”. As an indicator of hierarchy, the Gini coefficient is introduced. Example calculations are made for the aggregation, fusion and fission of animal groups, and for the appearance of a powerful empire and the rise and fall of supremacy. It is shown that such abstract objects evolve with time in accordance with the universal rules of groups common to birds and fish.