7,129 research outputs found
General Iteration graphs and Boolean automata circuits
This article is set in the field of regulation networks modeled by discrete
dynamical systems. It focuses on Boolean automata networks. In such networks,
there are many ways to update the states of every element. When this is done
deterministically, at each time step of a discretised time flow and according
to a predefined order, we say that the network is updated according to
block-sequential update schedule (blocks of elements are updated sequentially
while, within each block, the elements are updated synchronously). Many
studies, for the sake of simplicity and with some biologically motivated
reasons, have concentrated on networks updated with one particular
block-sequential update schedule (more often the synchronous/parallel update
schedule or the sequential update schedules). The aim of this paper is to give
an argument formally proven and inspired by biological considerations in favour
of the fact that the choice of a particular update schedule does not matter so
much in terms of the possible and likely dynamical behaviours that networks may
display
On the effects of firing memory in the dynamics of conjunctive networks
Boolean networks are one of the most studied discrete models in the context
of the study of gene expression. In order to define the dynamics associated to
a Boolean network, there are several \emph{update schemes} that range from
parallel or \emph{synchronous} to \emph{asynchronous.} However, studying each
possible dynamics defined by different update schemes might not be efficient.
In this context, considering some type of temporal delay in the dynamics of
Boolean networks emerges as an alternative approach. In this paper, we focus in
studying the effect of a particular type of delay called \emph{firing memory}
in the dynamics of Boolean networks. Particularly, we focus in symmetric
(non-directed) conjunctive networks and we show that there exist examples that
exhibit attractors of non-polynomial period. In addition, we study the
prediction problem consisting in determinate if some vertex will eventually
change its state, given an initial condition. We prove that this problem is
{\bf PSPACE}-complete
Internal Diffusion-Limited Aggregation: Parallel Algorithms and Complexity
The computational complexity of internal diffusion-limited aggregation (DLA)
is examined from both a theoretical and a practical point of view. We show that
for two or more dimensions, the problem of predicting the cluster from a given
set of paths is complete for the complexity class CC, the subset of P
characterized by circuits composed of comparator gates. CC-completeness is
believed to imply that, in the worst case, growing a cluster of size n requires
polynomial time in n even on a parallel computer.
A parallel relaxation algorithm is presented that uses the fact that clusters
are nearly spherical to guess the cluster from a given set of paths, and then
corrects defects in the guessed cluster through a non-local annihilation
process. The parallel running time of the relaxation algorithm for
two-dimensional internal DLA is studied by simulating it on a serial computer.
The numerical results are compatible with a running time that is either
polylogarithmic in n or a small power of n. Thus the computational resources
needed to grow large clusters are significantly less on average than the
worst-case analysis would suggest.
For a parallel machine with k processors, we show that random clusters in d
dimensions can be generated in O((n/k + log k) n^{2/d}) steps. This is a
significant speedup over explicit sequential simulation, which takes
O(n^{1+2/d}) time on average.
Finally, we show that in one dimension internal DLA can be predicted in O(log
n) parallel time, and so is in the complexity class NC
An event-based architecture for solving constraint satisfaction problems
Constraint satisfaction problems (CSPs) are typically solved using
conventional von Neumann computing architectures. However, these architectures
do not reflect the distributed nature of many of these problems and are thus
ill-suited to solving them. In this paper we present a hybrid analog/digital
hardware architecture specifically designed to solve such problems. We cast
CSPs as networks of stereotyped multi-stable oscillatory elements that
communicate using digital pulses, or events. The oscillatory elements are
implemented using analog non-stochastic circuits. The non-repeating phase
relations among the oscillatory elements drive the exploration of the solution
space. We show that this hardware architecture can yield state-of-the-art
performance on a number of CSPs under reasonable assumptions on the
implementation. We present measurements from a prototype electronic chip to
demonstrate that a physical implementation of the proposed architecture is
robust to practical non-idealities and to validate the theory proposed.Comment: First two authors contributed equally to this wor
Computer architecture for efficient algorithmic executions in real-time systems: New technology for avionics systems and advanced space vehicles
Improvements and advances in the development of computer architecture now provide innovative technology for the recasting of traditional sequential solutions into high-performance, low-cost, parallel system to increase system performance. Research conducted in development of specialized computer architecture for the algorithmic execution of an avionics system, guidance and control problem in real time is described. A comprehensive treatment of both the hardware and software structures of a customized computer which performs real-time computation of guidance commands with updated estimates of target motion and time-to-go is presented. An optimal, real-time allocation algorithm was developed which maps the algorithmic tasks onto the processing elements. This allocation is based on the critical path analysis. The final stage is the design and development of the hardware structures suitable for the efficient execution of the allocated task graph. The processing element is designed for rapid execution of the allocated tasks. Fault tolerance is a key feature of the overall architecture. Parallel numerical integration techniques, tasks definitions, and allocation algorithms are discussed. The parallel implementation is analytically verified and the experimental results are presented. The design of the data-driven computer architecture, customized for the execution of the particular algorithm, is discussed
Mean-Field and Non-Mean-Field Behaviors in Scale-free Networks with Random Boolean Dynamics
We study two types of simplified Boolean dynamics over scale-free networks,
both with synchronous update. Assigning only Boolean functions AND and XOR to
the nodes with probability and , respectively, we are able to analyze
the density of 1's and the Hamming distance on the network by numerical
simulations and by a mean-field approximation (annealed approximation). We show
that the behavior is quite different if the node always enters in the dynamic
as its own input (self-regulation) or not. The same conclusion holds for the
Kauffman KN model. Moreover, the simulation results and the mean-field ones (i)
agree well when there is no self-regulation, and (ii) disagree for small
when self-regulation is present in the model.Comment: 12 pages, 7 figure
q-State Potts model metastability study using optimized GPU-based Monte Carlo algorithms
We implemented a GPU based parallel code to perform Monte Carlo simulations
of the two dimensional q-state Potts model. The algorithm is based on a
checkerboard update scheme and assigns independent random numbers generators to
each thread. The implementation allows to simulate systems up to ~10^9 spins
with an average time per spin flip of 0.147ns on the fastest GPU card tested,
representing a speedup up to 155x, compared with an optimized serial code
running on a high-end CPU. The possibility of performing high speed simulations
at large enough system sizes allowed us to provide a positive numerical
evidence about the existence of metastability on very large systems based on
Binder's criterion, namely, on the existence or not of specific heat
singularities at spinodal temperatures different of the transition one.Comment: 30 pages, 7 figures. Accepted in Computer Physics Communications.
code available at:
http://www.famaf.unc.edu.ar/grupos/GPGPU/Potts/CUDAPotts.htm
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