Membrane automata with priorities

In this paper the one-way P automata with priorities are introduced. Such automata are P systems where the membranes are only allowed to consume objects from parent membranes, under the given conditions. The result of computation of these systems is the set of multiset sequences consumed by skin membrane into the system. The rules associated in some order with each membrane cannot modify any objects, they can only move them through membrane. We show that P automata with priorities and two membranes can accept every recursively enumerated language.     

Encoding Catalytic P Systems in π@

P systems are theoretical computing devices abstracted away from the biological architecture of the cell, introduced some years ago by Gheorghe Păun and now intensely studied. In the area of concurrent systems, process calculi have recently been applied and extended with similar aim, to simulate (and formalise) the behaviour of the cell. Although many common points can be found between the two approaches, no formal and exhaustive comparison has been carried out yet.π@ is a new calculus, strongly π-Calculus based, well-suited to easily encode biologically inspired process calculi. In this paper the encoding in π@ of one variant of P systems is proposed, thus allowing a better understanding of similarities between P systems and bio-inspired process calculi.     

Perfect Simulation of a Class of Stochastic Hybrid Systems with an Application to Peer to Peer Systems

In this paper we present a class of hybrid systems made of deterministic differential equations and random discrete jumps. We then show how to construct a simulation of such a stochastic hybrid system that provides perfect samples of its asymptotic behavior based on the extension to continuous state-space of coupling-from-the-past techniques introduced by Foss and Tweedie (Stoch Models 14:187–204, 1998) and using suitable envelope trajectories to tackle non-monotonicity. The applicability of the method is illustrated by showing how this framework can be used to model the Squirrel peer to peer system and by reporting a simulation study based on this approach. This paper provides both a framework on how to carry simulation based experimental studies of large and complex hybrid systems and its application in the Squirrel model demonstrating how versatile and powerful this approach can be over a typical example.

A Simple Calculus for Proteins and Cells

The use of process calculi to represent biological systems has led to the design of different calculi such as brane calculi [Luca Cardelli. Brane calculi. In CMSB, pages 257–278, 2004] and κ-calculus [Vincent Danos and Cosimo Laneve. Formal molecular biology. Theoritical Computer Science, 325(1):69–110, 2004]. Both have proved to be useful to model different types of biological systems.As an attempt to unify the two directions, we introduce the bioκ-calculus, a simple calculus for describing proteins and cells, in which bonds are represented by means of shared names and interactions are modelled at the domain level. Protein-protein interactions have to be at most binary and cell interactions have to fit with sort constraints.We define the semantics of bioκ-calculus, analyse its properties, and discuss its expressiveness by modelling two significant examples: a signalling pathway and a virus infection.     

Finite Horizon Minimax Optimal Control of Nonlinear Continuous Time Systems with Stochastic Uncertainty

This paper develops a general continuous-time stochastic framework for robustness analysis and robust control synthesis. We consider a stochastic minimax optimization problem for general stochastic uncertain systems. A general method is presented for converting problems of performance analysis or controller synthesis into unconstrained optimization problems.     

计算系统生物学中并行随机仿真方法研究进展

随机仿真是计算系统生物学中对随机离散模型进行仿真研究的一类重要方法。本文对随机仿真方法的原理及并行化研究的进展进行了论述,指出了并行化是解决随机仿真性能开销问题的重要途径,并依照细粒度并行和粗粒度并行分类,阐述了当前并行随机仿真方法的研究现状,重点针对空间并行性,介绍了反应-扩散系统随机仿真的方法和相关工具。最后,对并行随机仿真方法研究未来发展进行了展望。     

随机系统的切换控制

基于线性矩阵不等式和控制理论,针对由一组由随机微分方程描述的子系统组成的切换系统,给出此类切换系统稳定的充分条件,并给出控制器的设计方法。仿真结果表明,所设计的两类控制器及相应的控制策略均能保证闭环系统在一定意义下的稳定。     

Fuzzy Optimal Control for Bilinear Stochastic Systems with Fuzzy Parameters

In this paper we consider the control problem for a class of partially observed bilinear stochastic systems with fuzzy parameters. Using Takagi–Sugeno fuzzy model, the problem is described by three sets of fuzzy stochastic differential equations: one for the state process, one for the observed process and one for the controller which is assumed to be driven by the observed process. With this formulation, the original stochastic control problem can be treated as a deterministic identification problem in which the controller parameters and the corresponding membership functions are the unknowns. Using a suitable performance index, we have developed a set of necessary conditions for determining the parameters of the controller and the corresponding membership functions. Finally, some numerical simulations are presented to illustrate the effectiveness of the proposed fuzzy control scheme.     

Membrane Computing and Brane Calculi (Some Personal Notes)

This is a very short discussion of similarities and dissimilarities between membrane computing and brane calculi, insisting mainly on some recent ideas of bridging the two areas of research (from this last point of view, the bibliography tries to be as complete as possible) and proving that, in fact, there is no real dissimilarity...     

生化网络的随机Petri网建模与分析

细胞的行为是随机性的,学习细胞中的随机性有助于理解细胞的组织,设计和进化。建立、确认和分析随机的生化网络模型是当前计算系统生物学领域的一个重要研究主题。当前,标准的Petri网模型已经成为生化网络模拟和定性分析的有力工具。尝试使用随机Petri网对生化网络进行建模与分析,简单描述了随机Petri网理论对标准Petri网的扩充,通过对二聚作用和肌动蛋白这两个典型例子的建模与演化模拟,介绍、论证了随机Petri网理论的新应用。     

系统生物学的分析与建模

要从系统水平上理解生物系统，必需建立一个新的框架．这个新的框架就是系统生物学，其目的在于在系统水平上阐述和理解生物系统．本文试图以系统控制学科的视点，评述系统生物学的分析与建模的主要思路和方法，以及系统生物学发展现状和可能的发展前景．     

带反脉冲的同质脉冲神经膜系统

脉冲神经膜系统是一种膜系统中吸收了脉冲神经网络特点的新型生物计算装置,具有强大的计算能力.带反脉冲的同质脉冲神经膜系统是使用了两种对象(称为脉冲和反脉冲)、且其中每个神经元具有相同规则集合的一种脉冲神经膜系统的变体.本文研究了无延迟规则和突触权值情况下的带反脉冲同质脉冲神经膜系统的计算通用性问题,证明了这种P系统无论是工作在产生模式,还是接收模式下都是计算通用的.本文解答了曾湘祥等人提出的关于是否存在无延迟规则的同质脉冲神经膜系统和如何移除突触权值的两个公开问题.     

Optimal Control of Switching Times in Switched Stochastic Systems

In this paper, we solve an optimal control problem for switched stochastic systems using calculus of variations, where the objective is to minimize a cost functional defined on the state and the switching times are the sole control variables. In particular, we focus on the problem in which a pre‐specified sequence of active subsystems is given. For one switching time case, the derivative of the cost functional with respect to the switching time is derived, which has an especially simple form and can be directly used in gradient descent algorithms to locate the optimal switching instant. Then, we propose an approach to deal with the problem with multi‐switching times case. Finally, two numerical examples are given, highlighting the viability and advantages of the proposed methodology.     

基于LMIs的不确定随机切换系统的H∞鲁棒控制

基于线性矩阵不等式和控制理论,针对由一组由随机微分方程描述的子系统组成的切换系统,研究此类切换系统在任意切换策略下的鲁棒控制问题,并给出控制器的设计方法。仿真结果表明,所设计,扮控制器能保证闭环系统在一定意义下的随机稳定。     

对带控制器饱和的Markovian跳跃双线性系统稳定时滞估计

研究了带有饱和控制器的时滞Markovian跳跃双线性系统随机镇定问题. 文章先给出了采用无记忆控制的相应无时滞系统局部指数稳定的充分性条件, 然后给出了采用该无记忆控制的时滞系统保持随机稳定性的最大时滞上界估计. 数值算例验证了该方法的有效性.     

Comparison of Hybrid Systems and Fluid Stochastic Petri Nets

Hybrid Systems are modelsof interacting digital and continuous devices with applicationsin the control of aircraft, computers, or modern cars for instance.Concurrently, Fluid Stochastic Petri Nets (FSPNs) have been introducedas an extension of stochastic Petri nets to model physical systemsthat contain continuous fluid quantities controlled by discretelogic, as well as a means to deal with the possible state explosionof discrete models. Of course, an FSPN is by definition a hybridsystem but in this paper, we compare a general hybrid systemsformalism with FSPN formalism. The conclusion of this paper,suplemented by some examples, is that fluid stochastic Petrinets and hybrid system formalism can be converted from one tothe other. Although there is a price to pay for such a conversion,the conversion can transfer the solution methods from one tothe other and thus help the development of both formalisms.     

Mixture of Automatically- and Manually-controlled Vehicles in Intelligent Transport Systems

This paper presents a technology which allows for the existence of mixed traffic, as a first step towards intelligent transport systems. We begin by designing an automatic driving controller called the intelligent vehicle driving system (IVDS). This is a two-layer system: the higher layer analyzes the current scenario and infers the control objective that associates with a certain index function; the lower layer optimizes the function provided by the upper layer. IVDS only uses the measurement of a vehicle's speed and distance relative to the vehicle in front, together with measurements of the vehicle's own state. Consequently, the vehicles equipped with the IVDS can operate together with manually-controlled vehicles. Next, a mathematical rule-based model for human drivers is developed. This model attempts to mimic human driver's behavior in vehicle following and lane-changing. Finally, we examine the control performance of the proposed controller and the potential benefits of mixed traffic by implementing the human driver model and IVDS on an automated highway simulator.     

Translating Mobile Ambients into P Systems

We present a translation of the mobile ambients without communication and replication into P systems with mobile membranes. We introduce a set of developmental rules over membranes, and describe the correspondence between the behaviour of an ambient and the evolution of its translated membrane system. We give an operational correspondence result between the mobile ambients and P systems.