46,526 research outputs found
Software for Embedded Control Systems
The research of our team deals with the realization of control schemes on digital computers. As such the emphasis is on embedded control software implementation. Applications are in the field of mechatronic devices, using a mechatronic design approach (the integrated and optimal design of a mechanical system and its embedded control system). The ultimate goal is to support the application developer (i.e. mechatronic design engineer) such that implementing control software according to Ă°o it the first time rightÂż becomes business as usual
Constrained Allocation Flux Balance Analysis
New experimental results on bacterial growth inspire a novel top-down
approach to study cell metabolism, combining mass balance and proteomic
constraints to extend and complement Flux Balance Analysis. We introduce here
Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic
costs associated to growth are accounted for in an effective way through a
single additional genome-wide constraint. Its roots lie in the experimentally
observed pattern of proteome allocation for metabolic functions, allowing to
bridge regulation and metabolism in a transparent way under the principle of
growth-rate maximization. We provide a simple method to solve CAFBA efficiently
and propose an "ensemble averaging" procedure to account for unknown protein
costs. Applying this approach to modeling E. coli metabolism, we find that, as
the growth rate increases, CAFBA solutions cross over from respiratory,
growth-yield maximizing states (preferred at slow growth) to fermentative
states with carbon overflow (preferred at fast growth). In addition, CAFBA
allows for quantitatively accurate predictions on the rate of acetate excretion
and growth yield based on only 3 parameters determined by empirical growth
laws.Comment: 21 pages, 6 figures (main) + 33 pages, various figures and tables
(supporting); for the supplementary MatLab code, see
http://tinyurl.com/h763es
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Multiscale and inhomogeneous molecular systems are challenging topics in the
field of molecular simulation. In particular, modeling biological systems in
the context of multiscale simulations and exploring material properties are
driving a permanent development of new simulation methods and optimization
algorithms. In computational terms, those methods require parallelization
schemes that make a productive use of computational resources for each
simulation and from its genesis. Here, we introduce the heterogeneous domain
decomposition approach which is a combination of an heterogeneity sensitive
spatial domain decomposition with an \textit{a priori} rearrangement of
subdomain-walls. Within this approach, the theoretical modeling and
scaling-laws for the force computation time are proposed and studied as a
function of the number of particles and the spatial resolution ratio. We also
show the new approach capabilities, by comparing it to both static domain
decomposition algorithms and dynamic load balancing schemes. Specifically, two
representative molecular systems have been simulated and compared to the
heterogeneous domain decomposition proposed in this work. These two systems
comprise an adaptive resolution simulation of a biomolecule solvated in water
and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure
Refining SCJ Mission Specifications into Parallel Handler Designs
Safety-Critical Java (SCJ) is a recent technology that restricts the
execution and memory model of Java in such a way that applications can be
statically analysed and certified for their real-time properties and safe use
of memory. Our interest is in the development of comprehensive and sound
techniques for the formal specification, refinement, design, and implementation
of SCJ programs, using a correct-by-construction approach. As part of this
work, we present here an account of laws and patterns that are of general use
for the refinement of SCJ mission specifications into designs of parallel
handlers used in the SCJ programming paradigm. Our notation is a combination of
languages from the Circus family, supporting state-rich reactive models with
the addition of class objects and real-time properties. Our work is a first
step to elicit laws of programming for SCJ and fits into a refinement strategy
that we have developed previously to derive SCJ programs.Comment: In Proceedings Refine 2013, arXiv:1305.563
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