33,269 research outputs found
Looking for Simple Common Schemes to Design Recognizer P Systems with Active Membranes That Solve Numerical Decision Problems
Earlier solutions to decision problems by means of P systems
used many counter objects to control the synchronization of different
stages in a computation (usually as many counters as the stage must
last in the worst case). In this paper we propose a way to replace those
counters with some spacial objects for each stage. Furthermore, following
the ideas presented in [1], in order to have a common scheme to attack
numerical problems, all instances of a problem with the same size are
solved by the same P system (which depends on the size) given an input
which describes the corresponding instance of the problem. We illustrate
these ideas with a cellular solution to the Subset-Sum problem
Spiking Neural P Systems with Structural Plasticity: Attacking the Subset Sum Problem
Spiking neural P systems with structural plasticity (in short,
SNPSP systems) are models of computations inspired by the function and
structure of biological neurons. In SNPSP systems, neurons can create
or delete synapses using plasticity rules. We report two families of solutions:
a non-uniform and a uniform one, to the NP-complete problem
Subset Sum using SNPSP systems. Instead of the usual rule-level nondeterminism
(choosing which rule to apply) we use synapse-level nondeterminism
(choosing which synapses to create or delete). The nondeterminism
due to plasticity rules have the following improvements from a
previous solution: in our non-uniform solution, plasticity rules allowed
for a normal form to be used (i.e. without forgetting rules or rules with
delays, system is simple, only synapse-level nondeterminism); in our uniform
solution the number of neurons and the computation steps are
reduced.Ministerio de Economía y Competitividad TIN2012-3743
Fast Hardware Implementations of Static P Systems
In this article we present a simulator of non-deterministic static P systems
using Field Programmable Gate Array (FPGA) technology. Its major feature
is a high performance, achieving a constant processing time for each transition. Our
approach is based on representing all possible applications as words of some regular
context-free language. Then, using formal power series it is possible to obtain the
number of possibilities and select one of them following a uniform distribution, in
a fair and non-deterministic way. According to these ideas, we yield an implementation
whose results show an important speed-up, with a strong independence from
the size of the P system.Ministry of Science and Innovation of the Spanish Government under the project TEC2011-27936 (HIPERSYS)European Regional Development Fund (ERDF)Ministry of Education of Spain (FPU grant AP2009-3625)ANR project SynBioTI
Characterizing PSPACE with Shallow Non-Confluent P Systems
In P systems with active membranes, the question of understanding the
power of non-confluence within a polynomial time bound is still an open problem. It is
known that, for shallow P systems, that is, with only one level of nesting, non-con
uence
allows them to solve conjecturally harder problems than con
uent P systems, thus reaching PSPACE. Here we show that PSPACE is not only a bound, but actually an exact
characterization. Therefore, the power endowed by non-con
uence to shallow P systems
is equal to the power gained by con
uent P systems when non-elementary membrane
division and polynomial depth are allowed, thus suggesting a connection between the
roles of non-confluence and nesting depth
Characterizing PSPACE with Shallow Non-Confluent P Systems
In P systems with active membranes, the question of understanding the
power of non-confluence within a polynomial time bound is still an open problem. It is
known that, for shallow P systems, that is, with only one level of nesting, non-con
uence
allows them to solve conjecturally harder problems than con
uent P systems, thus reaching PSPACE. Here we show that PSPACE is not only a bound, but actually an exact
characterization. Therefore, the power endowed by non-con
uence to shallow P systems
is equal to the power gained by con
uent P systems when non-elementary membrane
division and polynomial depth are allowed, thus suggesting a connection between the
roles of non-confluence and nesting depth
A Comprehensive Three-Dimensional Model of the Cochlea
The human cochlea is a remarkable device, able to discern extremely small
amplitude sound pressure waves, and discriminate between very close
frequencies. Simulation of the cochlea is computationally challenging due to
its complex geometry, intricate construction and small physical size. We have
developed, and are continuing to refine, a detailed three-dimensional
computational model based on an accurate cochlear geometry obtained from
physical measurements. In the model, the immersed boundary method is used to
calculate the fluid-structure interactions produced in response to incoming
sound waves. The model includes a detailed and realistic description of the
various elastic structures present.
In this paper, we describe the computational model and its performance on the
latest generation of shared memory servers from Hewlett Packard. Using compiler
generated threads and OpenMP directives, we have achieved a high degree of
parallelism in the executable, which has made possible several large scale
numerical simulation experiments that study the interesting features of the
cochlear system. We show several results from these simulations, reproducing
some of the basic known characteristics of cochlear mechanics.Comment: 22 pages, 5 figure
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
An efficient parallel immersed boundary algorithm using a pseudo-compressible fluid solver
We propose an efficient algorithm for the immersed boundary method on
distributed-memory architectures, with the computational complexity of a
completely explicit method and excellent parallel scaling. The algorithm
utilizes the pseudo-compressibility method recently proposed by Guermond and
Minev [Comptes Rendus Mathematique, 348:581-585, 2010] that uses a directional
splitting strategy to discretize the incompressible Navier-Stokes equations,
thereby reducing the linear systems to a series of one-dimensional tridiagonal
systems. We perform numerical simulations of several fluid-structure
interaction problems in two and three dimensions and study the accuracy and
convergence rates of the proposed algorithm. For these problems, we compare the
proposed algorithm against other second-order projection-based fluid solvers.
Lastly, the strong and weak scaling properties of the proposed algorithm are
investigated
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