On model checking data-independent systems with arrays without reset

A system is data-independent with respect to a data type X iff the operations it can perform on values of type X are restricted to just equality testing. The system may also store, input and output values of type X. We study model checking of systems which are data-independent with respect to two distinct type variables X and Y, and may in addition use arrays with indices from X and values from Y . Our main interest is the following parameterised model-checking problem: whether a given program satisfies a given temporal-logic formula for all non-empty nite instances of X and Y . Initially, we consider instead the abstraction where X and Y are infinite and where partial functions with finite domains are used to model arrays. Using a translation to data-independent systems without arrays, we show that the u-calculus model-checking problem is decidable for these systems. From this result, we can deduce properties of all systems with finite instances of X and Y . We show that there is a procedure for the above parameterised model-checking problem of the universal fragment of the u-calculus, such that it always terminates but may give false negatives. We also deduce that the parameterised model-checking problem of the universal disjunction-free fragment of the u-calculus is decidable. Practical motivations for model checking data-independent systems with arrays include verification of memory and cache systems, where X is the type of memory addresses, and Y the type of storable values. As an example we verify a fault-tolerant memory interface over a set of unreliable memories.Comment: Appeared in Theory and Practice of Logic Programming, vol. 4, no. 5&6, 200

Captivated In Time

Not included

MHD Turbulence Revisited

Kraichnan (1965) proposed that MHD turbulence occurs as a result of collisions between oppositely directed Alfv\'en wave packets. Recent work has generated some controversy over the nature of non linear couplings between colliding Alfv\'en waves. We find that the resolution to much of the confusion lies in the existence of a new type of turbulence, intermediate turbulence, in which the cascade of energy in the inertial range exhibits properties intermediate between those of weak and strong turbulent cascades. Some properties of intermediate MHD turbulence are: (i) in common with weak turbulent cascades, wave packets belonging to the inertial range are long lived; (ii) however, components of the strain tensor are so large that, similar to the situation in strong turbulence, perturbation theory is not applicable; (iii) the breakdown of perturbation theory results from the divergence of neighboring field lines due to wave packets whose perturbations in velocity and magnetic fields are localized, but whose perturbations in displacement are not; (iv) 3--wave interactions dominate individual collisions between wave packets, but interactions of all orders $n\geq 3$ make comparable contributions to the intermediate turbulent energy cascade; (v) successive collisions are correlated since wave packets are distorted as they follow diverging field lines; (vi) in common with the weak MHD cascade, there is no parallel cascade of energy, and the cascade to small perpendicular scales strengthens as it reaches higher wave numbers; (vii) For an appropriate weak excitation, there is a natural progression from a weak, through an intermediate, to a strong cascade.Comment: 25 pages, to appear in The Astrophysical Journa

On the Dynamical Stability of the Solar System

A long-term numerical integration of the classical Newtonian approximation to the planetary orbital motions of the full Solar System (sun + 8 planets), spanning 20 Gyr, was performed. The results showed no severe instability arising over this time interval. Subsequently, utilizing a bifurcation method described by Jacques Laskar, two numerical experiments were performed with the goal of determining dynamically allowed evolutions for the Solar System in which the planetary orbits become unstable. The experiments yielded one evolution in which Mercury falls onto the Sun at ~1.261Gyr from now, and another in which Mercury and Venus collide in ~862Myr. In the latter solution, as a result of Mercury's unstable behavior, Mars was ejected from the Solar System at ~822Myr. We have performed a number of numerical tests that confirm these results, and indicate that they are not numerical artifacts. Using synthetic secular perturbation theory, we find that Mercury is destabilized via an entrance into a linear secular resonance with Jupiter in which their corresponding eigenfrequencies experience extended periods of commensurability. The effects of general relativity on the dynamical stability are discussed. An application of the bifurcation method to the outer Solar System (Jupiter, Saturn, Uranus, and Neptune) showed no sign of instability during the course of 24Gyr of integrations, in keeping with an expected Uranian dynamical lifetime of 10^(18) years.Comment: 37 pages, 18 figures, accepted for publication in the Astrophysical Journa

Characterisation of two alcohol acyltransferases from kiwifruit (Actinidia spp.) reveals distinct substrate preferences.

Volatile esters are key compounds of kiwifruit flavour and are formed by alcohol acyltransferases that belong to the BAHD acyltransferase superfamily. Quantitative RT-PCR was used to screen kiwifruitderived expressed sequence tags with proposed acyltransferase function in order to select ripeningspecific sequences and test their involvement in alcohol acylation. The screening criterion was for at least 10-fold increased transcript accumulation in ripe compared with unripe kiwifruit and in response to ethylene. Recombinant expression in yeast revealed alcohol acyltransferase activity for Actinidia-derived AT1, AT16 and the phylogenetically distinct AT9, using various alcohol and acyl-CoA substrates. Functional characterisation of AT16 and AT9 demonstrated striking differences in their substrate preferences and apparent catalytic efficiencies ðV0 max K�1 m Þ. Thus revealing benzoyl-CoA:alcohol O-acyltransferase activity for AT16 and acetyl-CoA:alcohol O-acyltransferase activity for AT9. Both kiwifruit-derived enzymes displayed higher reaction rates with butanol compared with ethanol, even though ethanol is the main alcohol in ripe fruit. Since ethyl acetate and ethyl benzoate are major esters in ripe kiwifruit, we suggest that fruit characteristic volatile profiles result from a combination of substrate availability and specificity of individual alcohol acyltransferases

Social Balance on Networks: The Dynamics of Friendship and Enmity

How do social networks evolve when both friendly and unfriendly relations exist? Here we propose a simple dynamics for social networks in which the sense of a relationship can change so as to eliminate imbalanced triads--relationship triangles that contains 1 or 3 unfriendly links. In this dynamics, a friendly link changes to unfriendly or vice versa in an imbalanced triad to make the triad balanced. Such networks undergo a dynamic phase transition from a steady state to "utopia"--all friendly links--as the amount of network friendliness is changed. Basic features of the long-time dynamics and the phase transition are discussed.Comment: 16 pages, 11 figures, paper based on an invited talk at Dyonet06, Dynamics on Complex Networks and Applications, Dresden, Germany, Feburary 200

The Heider balance - a continuous approach

The Heider balance (HB) is investigated in a fully connected graph of $N$ nodes. The links are described by a real symmetric array r(i,j), i,j=1,...,N. In a social group, nodes represent group members and links represent relations between them, positive (friendly) or negative (hostile). At the balanced state, r(i,j)r(j,k)r(k,i)>0 for all the triads (i,j,k). As follows from the structure theorem of Cartwright and Harary, at this state the group is divided into two subgroups, with friendly internal relations and hostile relations between the subgroups. Here the system dynamics is proposed to be determined by a set of differential equations. The form of equations guarantees that once HB is reached, it persists. Also, for N=3 the dynamics reproduces properly the tendency of the system to the balanced state. The equations are solved numerically. Initially, r(i,j) are random numbers distributed around zero with a symmetric uniform distribution of unit width. Calculations up to N=500 show that HB is always reached. Time to get the balanced state varies with the system size N as N^{-1/2}. The spectrum of relations, initially narrow, gets very wide near HB. This means that the relations are strongly polarized. In our calculations, the relations are limited to a given range around zero. With this limitation, our results can be helpful in an interpretation of somestatistical data.Comment: 9 pages, 4 figures. Int. J. Mod. Phys. C (2005), in prin

Identifying Target Populations for Screening or Not Screening Using Logic Regression

Colorectal cancer remains a significant public health concern despite the fact that effective screening procedures exist and that the disease is treatable when detected at early stages. Numerous risk factors for colon cancer have been identified, but none are very predictive alone. We sought to determine whether there are certain combinations of risk factors that distinguish well between cases and controls, and that could be used to identify subjects at particularly high or low risk of the disease to target screening. Using data from the Seattle site of the Colorectal Cancer Family Registry (C-CFR), we fit logic regression models to combine risk factor information. Logic regression is a methodology that identifies subsets of the population, described by Boolean combinations of binary coded risk factors. This method is well suited to situations in which interactions between many variables result in differences in disease risk. Neither the logic regression models nor stepwise logistic regression models fit for comparison resulted in criteria that could be used to direct subjects to screening. However, we believe that our novel statistical approach could be useful in settings where risk factors do discriminate between cases and controls, and illustrate this with a simulated dataset

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu