The Living Application: a Self-Organising System for Complex Grid Tasks

We present the living application, a method to autonomously manage applications on the grid. During its execution on the grid, the living application makes choices on the resources to use in order to complete its tasks. These choices can be based on the internal state, or on autonomously acquired knowledge from external sensors. By giving limited user capabilities to a living application, the living application is able to port itself from one resource topology to another. The application performs these actions at run-time without depending on users or external workflow tools. We demonstrate this new concept in a special case of a living application: the living simulation. Today, many simulations require a wide range of numerical solvers and run most efficiently if specialized nodes are matched to the solvers. The idea of the living simulation is that it decides itself which grid machines to use based on the numerical solver currently in use. In this paper we apply the living simulation to modelling the collision between two galaxies in a test setup with two specialized computers. This simulation switces at run-time between a GPU-enabled computer in the Netherlands and a GRAPE-enabled machine that resides in the United States, using an oct-tree N-body code whenever it runs in the Netherlands and a direct N-body solver in the United States.Comment: 26 pages, 3 figures, accepted by IJHPC

Formal executable descriptions of biological systems

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells

Towards Designing Artificial Universes for Artificial Agents under Interaction Closure

We are interested in designing artificial universes for artificial agents. We view artificial agents as networks of highlevel processes on top of of a low-level detailed-description system. We require that the high-level processes have some intrinsic explanatory power and we introduce an extension of informational closure namely interaction closure to capture this. Then we derive a method to design artificial universes in the form of finite Markov chains which exhibit high-level processes that satisfy the property of interaction closure. We also investigate control or information transfer which we see as an building block for networks representing artificial agent

Using simulations and artificial life algorithms to grow elements of construction

'In nature, shape is cheaper than material', that is a common truth for most of the plants and other living organisms, even though they may not recognize that. In all living forms, shape is more or less directly linked to the influence of force, that was acting upon the organism during its growth. Trees and bones concentrate their material where thy need strength and stiffness, locating the tissue in desired places through the process of self-organization. We can study nature to find solutions to design problems. That’s where inspiration comes from, so we pick a solution already spotted somewhere in the organic world, that closely resembles our design problem, and use it in constructive way. First, examining it, disassembling, sorting out conclusions and ideas discovered, then performing an act of 'reverse engineering' and putting it all together again, in a way that suits our design needs. Very simple ideas copied from nature, produce complexity and exhibit self-organization capabilities, when applied in bigger scale and number. Computer algorithms of simulated artificial life help us to capture them, understand well and use where needed. This investigation is going to follow the question : How can we use methods seen in nature to simulate growth of construction elements? Different ways of extracting ideas from world of biology will be presented, then several techniques of simulated emergence will be demonstrated. Specific focus will be put on topics of computational modelling of natural phenomena, and differences in developmental and non-developmental techniques. Resulting 3D models will be shown and explained

Robot life: simulation and participation in the study of evolution and social behavior.

This paper explores the case of using robots to simulate evolution, in particular the case of Hamilton's Law. The uses of robots raises several questions that this paper seeks to address. The first concerns the role of the robots in biological research: do they simulate something (life, evolution, sociality) or do they participate in something? The second question concerns the physicality of the robots: what difference does embodiment make to the role of the robot in these experiments. Thirdly, how do life, embodiment and social behavior relate in contemporary biology and why is it possible for robots to illuminate this relation? These questions are provoked by a strange similarity that has not been noted before: between the problem of simulation in philosophy of science, and Deleuze's reading of Plato on the relationship of ideas, copies and simulacra

Don't Believe Everything You Hear : Preserving Relevant Information by Discarding Social Information

Integrating information gained by observing others via Social Bayesian Learning can be beneficial for an agent’s performance, but can also enable population wide information cascades that perpetuate false beliefs through the agent population. We show how agents can influence the observation network by changing their probability of observing others, and demonstrate the existence of a population-wide equilibrium, where the advantages and disadvantages of the Social Bayesian update are balanced. We also use the formalism of relevant information to illustrate how negative information cascades are characterized by processing increasing amounts of non-relevant informatio

Development and validation of detailed building, plant and controller modelling to demonstrate interactive behaviour of system components

As plant modelling becomes capable of more complexity and detailed resolution, new opportunities arise for the virtual evaluation of discrete plant components such as flow control and energy conversion devices, and controllers. Such objects are conventionally developed and tested at the prototype stage in a laboratory environment. Designers now seek to use modelling technology to extend their understanding from limited laboratory test results to full building and plant system analysis. This paper describes the development of a modelling system, using ESP-r, for typical United Kingdom domestic house types with hydronic gas or oil fired central heating including radiator and underfloor heating systems, and with a variety of conventional or advanced control types. It demonstrates the ability of detailed building and plant modelling to reveal unexpected insights into how real control systems perform in combination with other plant items and in different building types, including estimation of their influence on annual energy consumption. Comparisons with measurements taken in test rooms confirm that the observed behaviour of controls is realised in practice. The authors conclude that the complex dynamic interactions that take place between the various elements that make up a real building energy system have an important influence on its overall energy performance, revealing causes of variance that cannot be identified by laboratory testing alone, or by simplistic energy assessment tools