现代优化计算方法在蛋白质结构预测中的应用

现代优化计算方法在蛋白质结构预测中占有重要地位.简要地介绍了模拟退火算法,遗传算法,人工神经网络和图论算法在蛋白质结构预测中的应用.对国内外近年来应用这些算法,特别是在蛋白质构象搜索问题中,解决蛋白质结构预测的研究作了回顾,并分析、比较了这几种算法的效果和特点.     

Non-Parametric Regression Methods

The nature of the financial time series is complex, continuous interchange of stochastic and deterministic regimes. Therefore, it is difficult to forecast with parametric techniques. Instead of parametric models, we propose three techniques and compare with each other. Neural networks and support vector regression (SVR) are two universally approximators. They are data-driven non parametric models. ARCH/GARCH models are also investigated. Our assumption is that the future value of Istanbul Stock Exchange 100 index daily return depends on the financial indicators although there is no known parametric model to explain this relationship. This relationship comes from the technical analysis. Comparison shows that the multi layer perceptron networks overperform the SVR and time series model (GARCH).     

A fluid system with coupled input and output,and its application to bottlenecks in ad hoc networks

This paper studies a fluid queue with coupled input and output. Flows arrive according to a Poisson process, and when n flows are present, each of them transmits traffic into the queue at a rate c/(n+1), where the remaining c/(n+1) is used to serve the queue. We assume exponentially distributed flow sizes, so that the queue under consideration can be regarded as a system with Markov fluid input. The rationale behind studying this queue lies in ad hoc networks: bottleneck links have roughly this type of sharing policy. We consider four performance metrics: (i) the stationary workload of the queue, (ii) the queueing delay, i.e., the delay of a ‘packet’ (a fluid particle) that arrives at the queue at an arbitrary point in time, (iii) the flow transfer delay, i.e., the time elapsed between arrival of a flow and the epoch that all its traffic has been put into the queue, and (iv) the sojourn time, i.e., the flow transfer time increased by the time it takes before the last fluid particle of the flow is served. For each of these random variables we compute the Laplace transform. The corresponding tail probabilities decay exponentially, as is shown by a large-deviations analysis. F. Roijers’ work has been carried out partly in the SENTER-NOVEM funded project Easy Wireless.     

Identifying Linking-Pin Organizations in Inter-Organizational Networks

Within the large literature on inter-organizational networks, there has been some discussion of linking-pin organizations and the role they play in integrating these networks. Based on this verbal specification of linking-pin organizations, we construct operational criteria and empirical methods for identifying these structurally important organizations in potentially large and complex inter-organizational networks. These methods are based on ideas drawn from blockmodeling, structural holes, centrality and centralization of networks, and identifying cut-points in networks. These methods are applied to a constructed example and then to real empirical inter-organizational networks. Implications and contrasts with other methods are discussed, together with some open problems.     

A model of fads,fashions, and group formation

I develop a model of consumer behavior where agents purchase goods in order to signify personal characteristics. Agents purchase goods in order to imitate agents similar to them and agents they want to emulate. Depending on parameter values of consumer preferences the model generates stable groups, fads, and fashion cycles, or a mixture of both. The model is unique to the economic literature on fads in that the extinction of fads occurs endogenously in the model. © 2004 Wiley Periodicals, Inc. Complexity 9: 51–61, 2004     

Viscoelastic properties of nanostructured natural rubber/polystyrene interpenetrating polymer networks

The effects of the blend ratio and initiating system on the viscoelastic properties of nanostructured natural rubber/polystyrene‐based interpenetrating polymer networks (IPNs) were investigated in the temperature range of ?80 to 150 °C. The studies were carried out at different frequencies (100, 50, 10, 1, and 0.1 Hz), and their effects on the damping and storage and loss moduli were analyzed. In all cases, tan δ and the storage and loss moduli showed two distinct transitions corresponding to natural rubber and polystyrene phases, which indicated that the system was not miscible on the molecular level. However, a slight inward shift was observed in the IPNs, with respect to the glass‐transition temperatures (T_g's) of the virgin polymers, showing a certain degree of miscibility or intermixing between the two phases. When the frequency increased from 0.1 to 100 Hz, the T_g values showed a positive shift in all cases. In a comparison of the three initiating systems (dicumyl peroxide, benzoyl peroxide, and azobisisobutyronitrile), the dicumyl peroxide system showed the highest modulus. The morphology of the IPNs was analyzed with transmission electron microscopy. The micrographs indicated that the system was nanostructured. An attempt was made to relate the viscoelastic behavior to the morphology of the IPNs. Various models, such as the series, parallel, Halpin–Tsai, Kerner, Coran, Takayanagi, and Davies models, were used to model the viscoelastic data. The area under the linear loss modulus curve was larger than that obtained by group contribution analysis; this showed that the damping was influenced by the phase morphology, dual‐phase continuity, and crosslinking of the phases. Finally, the homogeneity of the system was further evaluated with Cole–Cole analysis. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1680–1696, 2003     

Networks, Fields and Organizations: Micro-Dynamics, Scale and Cohesive Embeddings

Social action is situated in fields that are simultaneously composed of interpersonal ties and relations among organizations, which are both usefully characterized as social networks. We introduce a novel approach to distinguishing different network macro-structures in terms of cohesive subsets and their overlaps. We develop a vocabulary that relates different forms of network cohesion to field properties as opposed to organizational constraints on ties and structures. We illustrate differences in probabilistic attachment processes in network evolution that link on the one hand to organizational constraints versus field properties and to cohesive network topologies on the other. This allows us to identify a set of important new micro-macro linkages between local behavior in networks and global network properties. The analytic strategy thus puts in place a methodology for Predictive Social Cohesion theory to be developed and tested in the context of informal and formal organizations and organizational fields. We also show how organizations and fields combine at different scales of cohesive depth and cohesive breadth. Operational measures and results are illustrated for three organizational examples, and analysis of these cases suggests that different structures of cohesive subsets and overlaps may be predictive in organizational contexts and similarly for the larger fields in which they are embedded. Useful predictions may also be based on feedback from level of cohesion in the larger field back to organizations, conditioned on the level of multiconnectivity to the field.     

酵母蛋白质网络的动力学性质

蛋白质-蛋白质、蛋白质-DNA相互作用网络决定了细胞中各种关键功能的执行．基于芽殖酵母(budding yeast saccharomyces cerevisiae)的蛋白质-蛋白质相互作用网络数据和相关的实验文献，我们建立了调控细胞周期和生命周期(cell cycle and life cycle)的蛋白质网络，并利用离散模型研究了该网络的动力学性质，研究表明：细胞周期网络的动力学性质具有很强的稳定性，约94％的蛋白质初态将演化到对应于生物学G1基态的稳定态，使其成为惟一的全局吸引点；同时，绝大多数的初态的演化路径都通过由G1激发态到G1基态的细胞周期演化路径，使细胞周期路径成为全局性的“吸引”路径。     

Preparation and properties of homogeneous V2O5-SiO2 xerogel composite based on interpenetrating polymer network

In this paper, we report the conducting and electrochemical properties of a homogeneous V₂O₅-SiO₂ xerogel composite obtained from the simultaneous polymerization in both inorganic components (Si-O and V-O based polymers) forming an interpenetrating polymer network, where a mutual “solubility” due to cross-links and entanglements was observed. The presence of V₂O₅ inside the silica matrix has a strong effect on electrical conductivity; measurements showed room temperature conductivity almost 1000 times higher than what is found in the literature. In addition, the electrochemical behavior is quite similar to that found in V₂O₅ xerogel. Moreover, the effects of thermal treatment on the conducting and electrochemical properties were investigated. It was found that both properties were improved with no significant effect on V₂O₅ xerogel layered structure.     

Delay-dependent stochastic stability of delayed Hopfield neural networks with Markovian jump parameters

In this paper, the problem of stochastic stability for a class of time-delay Hopfield neural networks with Markovian jump parameters is investigated. The jumping parameters are modeled as a continuous-time, discrete-state Markov process. Without assuming the boundedness, monotonicity and differentiability of the activation functions, some results for delay-dependent stochastic stability criteria for the Markovian jumping Hopfield neural networks (MJDHNNs) with time-delay are developed. We establish that the sufficient conditions can be essentially solved in terms of linear matrix inequalities.