Simulation of Mobile Ambients by P Systems. Part 2

Ambient calculus is a theory which deals with mobile computing and computation and encompasses such notions as mobile agents, the ambients where the agents interact and the mobility of the ambients themselves. P systems is a formalism which abstracts from the structure and functioning of living cells and describes distributed parallel computing devices with multiset of objects processing. Ambient calculus and membrane computing are based on the same concepts and structures though they are developed in di®erent areas of computer science. The purpose of our work now is to express ambient calculus by means of P systems, namely by tissue P systems with dynamic network of membranes

Bigraphical models for protein and membrane interactions

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes

A framework for protein and membrane interactions

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences

Mutual Mobile Membranes with Timers

A feature of current membrane systems is the fact that objects and membranes are persistent. However, this is not true in the real world. In fact, cells and intracellular proteins have a well-defined lifetime. Inspired from these biological facts, we define a model of systems of mobile membranes in which each membrane and each object has a timer representing their lifetime. We show that systems of mutual mobile membranes with and without timers have the same computational power. An encoding of timed safe mobile ambients into systems of mutual mobile membranes with timers offers a relationship between two formalisms used in describing biological systems

Slow rotation of a spherical particle inside an elastic tube

In this paper, we present an analytical calculation of the rotational mobility functions of a particle rotating on the centerline of an elastic cylindrical tube whose membrane exhibits resistance towards shearing and bending. We find that the correction to the particle rotational mobility about the cylinder axis depends solely on membrane shearing properties while both shearing and bending manifest themselves for the rotational mobility about an axis perpendicular to the cylinder axis. In the quasi-steady limit of vanishing frequency, the particle rotational mobility nearby a no-slip rigid cylinder is recovered only if the membrane possesses a non-vanishing resistance towards shearing. We further show that for the asymmetric rotation along the cylinder radial axis, a coupling between shearing and bending exists. Our analytical predictions are compared and validated with corresponding boundary integral simulations where a very good agreement is obtained.Comment: 23 pages, 7 figures and 107 references. Revised manuscript resubmitted to Acta Mec

A Patterned Single Layer Graphene Resistance Temperature Sensor

Micro-fabricated single-layer graphenes (SLGs) on a silicon dioxide (SiO2)/Si substrate, a silicon nitride (SiN) membrane, and a suspended architecture are presented for their use as temperature sensors. These graphene temperature sensors act as resistance temperature detectors, showing a quadratic dependence of resistance on the temperature in a range between 283 K and 303 K. The observed resistance change of the graphene temperature sensors are explained by the temperature dependent electron mobility relationship (~T−4) and electron-phonon scattering. By analyzing the transient response of the SLG temperature sensors on different substrates, it is found that the graphene sensor on the SiN membrane shows the highest sensitivity due to low thermal mass, while the sensor on SiO2/Si reveals the lowest one. Also, the graphene on the SiN membrane reveals not only the fastest response, but also better mechanical stability compared to the suspended graphene sensor. Therefore, the presented results show that the temperature sensors based on SLG with an extremely low thermal mass can be used in various applications requiring high sensitivity and fast operation

Security Policies as Membranes in Systems for Global Computing

We propose a simple global computing framework, whose main concern is code migration. Systems are structured in sites, and each site is divided into two parts: a computing body, and a membrane which regulates the interactions between the computing body and the external environment. More precisely, membranes are filters which control access to the associated site, and they also rely on the well-established notion of trust between sites. We develop a basic theory to express and enforce security policies via membranes. Initially, these only control the actions incoming agents intend to perform locally. We then adapt the basic theory to encompass more sophisticated policies, where the number of actions an agent wants to perform, and also their order, are considered