Undecidable Properties of Limit Set Dynamics of Cellular Automata

Cellular Automata (CA) are discrete dynamical systems and an abstract model of parallel computation. The limit set of a cellular automaton is its maximal topological attractor. A well know result, due to Kari, says that all nontrivial properties of limit sets are undecidable. In this paper we consider properties of limit set dynamics, i.e. properties of the dynamics of Cellular Automata restricted to their limit sets. There can be no equivalent of Kari's Theorem for limit set dynamics. Anyway we show that there is a large class of undecidable properties of limit set dynamics, namely all properties of limit set dynamics which imply stability or the existence of a unique subshift attractor. As a consequence we have that it is undecidable whether the cellular automaton map restricted to the limit set is the identity, closing, injective, expansive, positively expansive, transitive

Direct Product Primality Testing of Graphs is GI-hard

We investigate the computational complexity of the graph primality testing problem with respect to the direct product (also known as Kronecker, cardinal or tensor product). In [1] Imrich proves that both primality testing and a unique prime factorization can be determined in polynomial time for (finite) connected and nonbipartite graphs. The author states as an open problem how results on the direct product of nonbipartite, connected graphs extend to bipartite connected graphs and to disconnected ones. In this paper we partially answer this question by proving that the graph isomorphism problem is polynomial-time many-one reducible to the graph compositeness testing problem (the complement of the graph primality testing problem). As a consequence of this result, we prove that the graph isomorphism problem is polynomial-time Turing reducible to the primality testing problem. Our results show that connectedness plays a crucial role in determining the computational complexity of the graph primality testing problem

An Easily Checkable Algebraic Characterization of Positive Expansivity for Additive Cellular Automata over a Finite Abelian Group

We provide an easily checkable algebraic characterization of positive expansivity for Additive Cellular Automata over a finite abelian group. First of all, an easily checkable characterization of positive expansivity is provided for the non trivial subclass of Linear Cellular Automata over the alphabet $(\Z/m\Z)^n$. Then, we show how it can be exploited to decide positive expansivity for the whole class of Additive Cellular Automata over a finite abelian group.Comment: 12 page

A Heuristic for Direct Product Graph Decomposition

In this paper we describe a heuristic for decomposing a directed graph into factors according to the direct product (also known as Kronecker, cardinal or tensor product). Given a directed, unweighted graph G with adjacency matrix Adj(G), our heuristic aims at identifying two graphs G 1 and G 2 such that G = G 1 × G 2 , where G 1 × G 2 is the direct product of G 1 and G 2 . For undirected, connected graphs it has been shown that graph decomposition is “at least as difficult” as graph isomorphism; therefore, polynomial-time algorithms for decomposing a general directed graph into factors are unlikely to exist. Although graph factorization is a problem that has been extensively investigated, the heuristic proposed in this paper represents – to the best of our knowledge – the first computational approach for general directed, unweighted graphs. We have implemented our algorithm using the MATLAB environment; we report on a set of experiments that show that the proposed heuristic solves reasonably- sized instances in a few seconds on general-purpose hardware. Although the proposed heuristic is not guaranteed to find a factorization, even if one exists; however, it always succeeds on all the randomly-generated instances used in the experimental evaluation

From Linear to Additive Cellular Automata

This paper proves the decidability of several important properties of additive cellular automata over finite abelian groups. First of all, we prove that equicontinuity and sensitivity to initial conditions are decidable for a nontrivial subclass of additive cellular automata, namely, the linear cellular automata over \u207f, where is the ring \u2124/m\u2124. The proof of this last result has required to prove a general result on the powers of matrices over a commutative ring which is of interest in its own. Then, we extend the decidability result concerning sensitivity and equicontinuity to the whole class of additive cellular automata over a finite abelian group and for such a class we also prove the decidability of topological transitivity and all the properties (as, for instance, ergodicity) that are equivalent to it. Finally, a decidable characterization of injectivity and surjectivity for additive cellular automata over a finite abelian group is provided in terms of injectivity and surjectivity of an associated linear cellular automata over \u207f

Additive Cellular Automata Over Finite Abelian Groups: Topological and Measure Theoretic Properties

We study the dynamical behavior of D-dimensional (D >= 1) additive cellular automata where the alphabet is any finite abelian group. This class of discrete time dynamical systems is a generalization of the systems extensively studied by many authors among which one may list [Masanobu Ito et al., 1983; Giovanni Manzini and Luciano Margara, 1999; Giovanni Manzini and Luciano Margara, 1999; Jarkko Kari, 2000; Gianpiero Cattaneo et al., 2000; Gianpiero Cattaneo et al., 2004]. Our main contribution is the proof that topologically transitive additive cellular automata are ergodic. This result represents a solid bridge between the world of measure theory and that of topology theory and greatly extends previous results obtained in [Gianpiero Cattaneo et al., 2000; Giovanni Manzini and Luciano Margara, 1999] for linear CA over Z_m i.e. additive CA in which the alphabet is the cyclic group Z_m and the local rules are linear combinations with coefficients in Z_m. In our scenario, the alphabet is any finite abelian group and the global rule is any additive map. This class of CA strictly contains the class of linear CA over Z_m^n, i.e.with the local rule defined by n x n matrices with elements in Z_m which, in turn, strictly contains the class of linear CA over Z_m. In order to further emphasize that finite abelian groups are more expressive than Z_m we prove that, contrary to what happens in Z_m, there exist additive CA over suitable finite abelian groups which are roots (with arbitrarily large indices) of the shift map. As a consequence of our results, we have that, for additive CA, ergodic mixing, weak ergodic mixing, ergodicity, topological mixing, weak topological mixing, topological total transitivity and topological transitivity are all equivalent properties. As a corollary, we have that invertible transitive additive CA are isomorphic to Bernoulli shifts. Finally, we provide a first characterization of strong transitivity for additive CA which we suspect it might be true also for the general case

Strictly Temporally Periodic Points in Cellular Automata

We study the set of strictly periodic points in surjective cellular automata, i.e., the set of those configurations which are temporally periodic for a given automaton but they not spatially periodic. This set turns out to be dense for almost equicontinuous surjective cellular automata while it is empty for the positively expansive ones. In the class of additive cellular automata, the set of strictly periodic points can be either dense or empty. The latter happens if and only if the cellular automaton is topologically transitive

Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

<p>Abstract</p> <p>Background</p> <p>The present knowledge of protein structures at atomic level derives from some 60,000 molecules. Yet the exponential ever growing set of hypothetical protein sequences comprises some 10 million chains and this makes the problem of protein structure prediction one of the challenging goals of bioinformatics. In this context, the protein representation with contact maps is an intermediate step of fold recognition and constitutes the input of contact map predictors. However contact map representations require fast and reliable methods to reconstruct the specific folding of the protein backbone.</p> <p>Methods</p> <p>In this paper, by adopting a GRID technology, our algorithm for 3D reconstruction FT-COMAR is benchmarked on a huge set of non redundant proteins (1716) taking random noise into consideration and this makes our computation the largest ever performed for the task at hand.</p> <p>Results</p> <p>We can observe the effects of introducing random noise on 3D reconstruction and derive some considerations useful for future implementations. The dimension of the protein set allows also statistical considerations after grouping per SCOP structural classes.</p> <p>Conclusions</p> <p>All together our data indicate that the quality of 3D reconstruction is unaffected by deleting up to an average 75% of the real contacts while only few percentage of randomly generated contacts in place of non-contacts are sufficient to hamper 3D reconstruction.</p