Overcoming controllability problems in distributed testing from an input output transition system

This is the Pre-print version of the Article. The official published version can be accessed from the link below - Copyright @ 2012 Springer VerlagThis paper concerns the testing of a system with physically distributed interfaces, called ports, at which it interacts with its environment. We place a tester at each port and the tester at port p observes events at p only. This can lead to controllability problems, where the observations made by the tester at a port p are not sufficient for it to be able to know when to send an input. It is known that there are test objectives, such as executing a particular transition, that cannot be achieved if we restrict attention to test cases that have no controllability problems. This has led to interest in schemes where the testers at the individual ports send coordination messages to one another through an external communications network in order to overcome controllability problems. However, such approaches have largely been studied in the context of testing from a deterministic finite state machine. This paper investigates the use of coordination messages to overcome controllability problems when testing from an input output transition system and gives an algorithm for introducing sufficient messages. It also proves that the problem of minimising the number of coordination messages used is NP-hard

Television screen time, but not computer use and reading time, is associated with cardio-metabolic biomarkers in a multiethnic Asian population: A cross-sectional study

10.1186/1479-5868-10-70International Journal of Behavioral Nutrition and Physical Activity10

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Mean-atom-trajectory model for the velocity autocorrelation function of monatomic liquids

We present a model for the motion of an average atom in a liquid or supercooled liquid state and apply it to calculations of the velocity autocorrelation function $Z(t)$ and diffusion coefficient $D$. The model trajectory consists of oscillations at a distribution of frequencies characteristic of the normal modes of a single potential valley, interspersed with position- and velocity-conserving transits to similar adjacent valleys. The resulting predictions for $Z(t)$ and $D$ agree remarkably well with MD simulations of Na at up to almost three times its melting temperature. Two independent processes in the model relax velocity autocorrelations: (a) dephasing due to the presence of many frequency components, which operates at all temperatures but which produces no diffusion, and (b) the transit process, which increases with increasing temperature and which produces diffusion. Because the model provides a single-atom trajectory in real space and time, including transits, it may be used to calculate all single-atom correlation functions.Comment: LaTeX, 8 figs. This is an updated version of cond-mat/0002057 and cond-mat/0002058 combined Minor changes made to coincide with published versio

Granular discharge and clogging for tilted hoppers

We measure the flux of spherical glass beads through a hole as a systematic function of both tilt angle and hole diameter, for two different size beads. The discharge increases with hole diameter in accord with the Beverloo relation for both horizontal and vertical holes, but in the latter case with a larger small-hole cutoff. For large holes the flux decreases linearly in cosine of the tilt angle, vanishing smoothly somewhat below the angle of repose. For small holes it vanishes abruptly at a smaller angle. The conditions for zero flux are discussed in the context of a {\it clogging phase diagram} of flow state vs tilt angle and ratio of hole to grain size

Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Microscopic Description of Band Structure at Very Extended Shapes in the A ~ 110 Mass Region

Recent experiments have confirmed the existence of rotational bands in the A \~ 110 mass region with very extended shapes lying between super- and hyper-deformation. Using the projected shell model, we make a first attempt to describe quantitatively such a band structure in 108Cd. Excellent agreement is achieved in the dynamic moment of inertia J(2) calculation. This allows us to suggest the spin values for the energy levels, which are experimentally unknown. It is found that at this large deformation, the sharply down-sloping orbitals in the proton i_{13/2} subshell are responsible for the irregularity in the experimental J(2), and the wave functions of the observed states have a dominant component of two-quasiparticles from these orbitals. Measurement of transition quadrupole moments and g-factors will test these findings, and thus can provide a deeper understanding of the band structure at very extended shapes.Comment: 4 pages, 3 eps figures, final version accepted by Phys. Rev. C as a Rapid Communicatio

The critical amplitude ratio of the susceptibility in the random-site two-dimensional Ising model

We present a new way of probing the universality class of the site-diluted two-dimensional Ising model. We analyse Monte Carlo data for the magnetic susceptibility, introducing a new fitting procedure in the critical region applicable even for a single sample with quenched disorder. This gives us the possibility to fit simultaneously the critical exponent, the critical amplitude and the sample dependent pseudo-critical temperature. The critical amplitude ratio of the magnetic susceptibility is seen to be independent of the concentration $q$ of the empty sites for all investigated values of $q\le 0.25$. At the same time the average effective exponent $\gamma_{eff}$ is found to vary with the concentration $q$, which may be argued to be due to logarithmic corrections to the power law of the pure system. This corrections are canceled in the susceptibility amplitude ratio as predicted by theory. The central charge of the corresponding field theory was computed and compared well with the theoretical predictions.Comment: 6 pages, 4 figure

Universality of the Crossing Probability for the Potts Model for q=1,2,3,4

The universality of the crossing probability $\pi_{hs}$ of a system to percolate only in the horizontal direction, was investigated numerically by using a cluster Monte-Carlo algorithm for the $q$-state Potts model for $q=2,3,4$ and for percolation $q=1$. We check the percolation through Fortuin-Kasteleyn clusters near the critical point on the square lattice by using representation of the Potts model as the correlated site-bond percolation model. It was shown that probability of a system to percolate only in the horizontal direction $\pi_{hs}$ has universal form $\pi_{hs}=A(q) Q(z)$ for $q=1,2,3,4$ as a function of the scaling variable $z= [ b(q)L^{\frac{1}{\nu(q)}}(p-p_{c}(q,L)) ]^{\zeta(q)}$. Here, $p=1-\exp(-\beta)$ is the probability of a bond to be closed, $A(q)$ is the nonuniversal crossing amplitude, $b(q)$ is the nonuniversal metric factor, $\zeta(q)$ is the nonuniversal scaling index, $\nu(q)$ is the correlation length index. The universal function $Q(x) \simeq \exp(-z)$. Nonuniversal scaling factors were found numerically.Comment: 15 pages, 3 figures, revtex4b, (minor errors in text fixed, journal-ref added

Fluctuations of an evaporating black hole from back reaction of its Hawking radiation: Questioning a premise in earlier work

This paper delineates the first steps in a systematic quantitative study of the spacetime fluctuations induced by quantum fields in an evaporating black hole. We explain how the stochastic gravity formalism can be a useful tool for that purpose within a low-energy effective field theory approach to quantum gravity. As an explicit example we apply it to the study of the spherically-symmetric sector of metric perturbations around an evaporating black hole background geometry. For macroscopic black holes we find that those fluctuations grow and eventually become important when considering sufficiently long periods of time (of the order of the evaporation time), but well before the Planckian regime is reached. In addition, the assumption of a simple correlation between the fluctuations of the energy flux crossing the horizon and far from it, which was made in earlier work on spherically-symmetric induced fluctuations, is carefully analyzed and found to be invalid. Our analysis suggests the existence of an infinite amplitude for the fluctuations of the horizon as a three-dimensional hypersurface. We emphasize the need for understanding and designing operational ways of probing quantum metric fluctuations near the horizon and extracting physically meaningful information.Comment: 10 pages, REVTeX; minor changes, a few references added and a brief discussion of their relevance included. To appear in the proceedings of the 10th Peyresq meeting. Dedicated to Rafael Sorkin on the occasion of his 60th birthda