14,814 research outputs found
StochKit-FF: Efficient Systems Biology on Multicore Architectures
The stochastic modelling of biological systems is an informative, and in some
cases, very adequate technique, which may however result in being more
expensive than other modelling approaches, such as differential equations. We
present StochKit-FF, a parallel version of StochKit, a reference toolkit for
stochastic simulations. StochKit-FF is based on the FastFlow programming
toolkit for multicores and exploits the novel concept of selective memory. We
experiment StochKit-FF on a model of HIV infection dynamics, with the aim of
extracting information from efficiently run experiments, here in terms of
average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag
Towards homeostatic architecture: simulation of the generative process of a termite mound construction
This report sets out to the theme of the generation of a âlivingâ,
homeostatic and self-organizing architectural structure. The main research
question this project addresses is what innovative techniques of design,
construction and materials could prospectively be developed and eventually
applied to create and sustain human-made buildings which are mostly
adaptive, self-controlled and self-functioning, without option to a vast supply
of materials and peripheral services. The hypothesis is that through the
implementation of the biological building behaviour of termites, in terms of
collective construction mechanisms that are based on environmental stimuli,
we could achieve a simulation of the generative process of their adaptive
structures, capable to inform in many ways human construction. The essay
explicates the development of the 3-dimensional, agent-based simulation of
the termite collective construction and analyzes the results, which involve
besides physical modelling of the evolved structures. It finally elucidates the
potential of this emerging and adaptive architectural performance to be
translated to human practice and thus enlighten new ecological engineering
and design methodologies
On Designing Multicore-aware Simulators for Biological Systems
The stochastic simulation of biological systems is an increasingly popular
technique in bioinformatics. It often is an enlightening technique, which may
however result in being computational expensive. We discuss the main
opportunities to speed it up on multi-core platforms, which pose new challenges
for parallelisation techniques. These opportunities are developed in two
general families of solutions involving both the single simulation and a bulk
of independent simulations (either replicas of derived from parameter sweep).
Proposed solutions are tested on the parallelisation of the CWC simulator
(Calculus of Wrapped Compartments) that is carried out according to proposed
solutions by way of the FastFlow programming framework making possible fast
development and efficient execution on multi-cores.Comment: 19 pages + cover pag
Digital Ecosystems: Ecosystem-Oriented Architectures
We view Digital Ecosystems to be the digital counterparts of biological
ecosystems. Here, we are concerned with the creation of these Digital
Ecosystems, exploiting the self-organising properties of biological ecosystems
to evolve high-level software applications. Therefore, we created the Digital
Ecosystem, a novel optimisation technique inspired by biological ecosystems,
where the optimisation works at two levels: a first optimisation, migration of
agents which are distributed in a decentralised peer-to-peer network, operating
continuously in time; this process feeds a second optimisation based on
evolutionary computing that operates locally on single peers and is aimed at
finding solutions to satisfy locally relevant constraints. The Digital
Ecosystem was then measured experimentally through simulations, with measures
originating from theoretical ecology, evaluating its likeness to biological
ecosystems. This included its responsiveness to requests for applications from
the user base, as a measure of the ecological succession (ecosystem maturity).
Overall, we have advanced the understanding of Digital Ecosystems, creating
Ecosystem-Oriented Architectures where the word ecosystem is more than just a
metaphor.Comment: 39 pages, 26 figures, journa
Wall Orientation and Shear Stress in the Lattice Boltzmann Model
The wall shear stress is a quantity of profound importance for clinical
diagnosis of artery diseases. The lattice Boltzmann is an easily parallelizable
numerical method of solving the flow problems, but it suffers from errors of
the velocity field near the boundaries which leads to errors in the wall shear
stress and normal vectors computed from the velocity. In this work we present a
simple formula to calculate the wall shear stress in the lattice Boltzmann
model and propose to compute wall normals, which are necessary to compute the
wall shear stress, by taking the weighted mean over boundary facets lying in a
vicinity of a wall element. We carry out several tests and observe an increase
of accuracy of computed normal vectors over other methods in two and three
dimensions. Using the scheme we compute the wall shear stress in an inclined
and bent channel fluid flow and show a minor influence of the normal on the
numerical error, implying that that the main error arises due to a corrupted
velocity field near the staircase boundary. Finally, we calculate the wall
shear stress in the human abdominal aorta in steady conditions using our method
and compare the results with a standard finite volume solver and experimental
data available in the literature. Applications of our ideas in a simplified
protocol for data preprocessing in medical applications are discussed.Comment: 9 pages, 11 figure
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