Rewriting Logic Semantics of a Plan Execution Language

The Plan Execution Interchange Language (PLEXIL) is a synchronous language developed by NASA to support autonomous spacecraft operations. In this paper, we propose a rewriting logic semantics of PLEXIL in Maude, a high-performance logical engine. The rewriting logic semantics is by itself a formal interpreter of the language and can be used as a semantic benchmark for the implementation of PLEXIL executives. The implementation in Maude has the additional benefit of making available to PLEXIL designers and developers all the formal analysis and verification tools provided by Maude. The formalization of the PLEXIL semantics in rewriting logic poses an interesting challenge due to the synchronous nature of the language and the prioritized rules defining its semantics. To overcome this difficulty, we propose a general procedure for simulating synchronous set relations in rewriting logic that is sound and, for deterministic relations, complete. We also report on two issues at the design level of the original PLEXIL semantics that were identified with the help of the executable specification in Maude

Theory of Cylindrical Tubules and Helical Ribbons of Chiral Lipid Membranes

We present a general theory for the equilibrium structure of cylindrical tubules and helical ribbons of chiral lipid membranes. This theory is based on a continuum elastic free energy that permits variations in the direction of molecular tilt and in the curvature of the membrane. The theory shows that the formation of tubules and helical ribbons is driven by the chirality of the membrane. Tubules have a first-order transition from a uniform state to a helically modulated state, with periodic stripes in the tilt direction and ripples in the curvature. Helical ribbons can be stable structures, or they can be unstable intermediate states in the formation of tubules.Comment: 43 pages, including 12 postscript figures, uses REVTeX 3.0 and epsf.st

Equation of state and phonon frequency calculations of diamond at high pressures

The pressure-volume relationship and the zone-center optical phonon frequency of cubic diamond at pressures up to 600 GPa have been calculated based on Density Functional Theory within the Local Density Approximation and the Generalized Gradient Approximation. Three different approaches, viz. a pseudopotential method applied in the basis of plane waves, an all-electron method relying on Augmented Plane Waves plus Local Orbitals, and an intermediate approach implemented in the basis of Projector Augmented Waves have been used. All these methods and approximations yield consistent results for the pressure derivative of the bulk modulus and the volume dependence of the mode Grueneisen parameter of diamond. The results are at variance with recent precise measurements up to 140 GPa. Possible implications for the experimental pressure determination based on the ruby luminescence method are discussed.Comment: 10 pages, 6 figure

Phase equilibria and glass transition in colloidal systems with short-ranged attractive interactions. Application to protein crystallization

We have studied a model of a complex fluid consisting of particles interacting through a hard core and a short range attractive potential of both Yukawa and square-well form. Using a hybrid method, including a self-consistent and quite accurate approximation for the liquid integral equation in the case of the Yukawa fluid, perturbation theory to evaluate the crystal free energies, and mode-coupling theory of the glass transition, we determine both the equilibrium phase diagram of the system and the lines of equilibrium between the supercooled fluid and the glass phases. For these potentials, we study the phase diagrams for different values of the potential range, the ratio of the range of the interaction to the diameter of the repulsive core being the main control parameter. Our arguments are relevant to a variety of systems, from dense colloidal systems with depletion forces, through particle gels, nano-particle aggregation, and globular protein crystallization.Comment: 20 pages, 10 figure

Evo-devo of human adolescence: beyond disease models of early puberty

Despite substantial heritability in pubertal development, much variation remains to be explained, leaving room for the influence of environmental factors to adjust its phenotypic trajectory in the service of fitness goals. Utilizing evolutionary development biology (evo-devo), we examine adolescence as an evolutionary life-history stage in its developmental context. We show that the transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, other environmental cues, social needs of adolescence and maturation toward youth and adulthood. Using the evolutionary theory of socialization, we show that familial psychosocial stress fosters a fast life history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. Here we explore implications of an evolutionary-developmental-endocrinological-anthropological framework for theory building, while illuminating new directions for research

A previously undescribed variant of the confluence of sinuses

An 8-year-old female with a history of chronic headaches and uncertain papilloedema was found to have a variant of the posterior intracranial dural venous sinuses on magnetic resonance imaging assessment of the brain. Magnetic resonance venography included in the imaging revealed a circular formation of the confluence of sinuses and absent right-sided transverse sinus. The confluence of sinuses is a highly variable structure; however, to the authors’ knowledge, a circular confluence of sinuses variant has not been reported in the literature

Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Creatine and guanidinoacetate reference values in a French population

Creatine and guanidinoacetate are biomarkers of creatine metabolism. Their assays in body fluids may be used for detecting patients with primary creatine deficiency disorders (PCDD), a class of inherited diseases. Their laboratory values in blood and urine may vary with age, requiring that reference normal values are given within the age range. Despite the long known role of creatine for muscle physiology, muscle signs are not necessarily the major complaint expressed by PCDD patients. These disorders drastically affect brain function inducing, in patients, intellectual disability, autistic behavior and other neurological signs (delays in speech and language, epilepsy, ataxia, dystonia and choreoathetosis), being a common feature the drop in brain creatine content. For this reason, screening of PCDD patients has been repeatedly carried out in populations with neurological signs. This report is aimed at providing reference laboratory values and related age ranges found for a large scale population of patients with neurological signs (more than 6 thousand patients) previously serving as a background population for screening French patients with PCDD. These reference laboratory values and age ranges compare rather favorably with literature values for healthy populations. Some differences are also observed, and female participants are discriminated from male participants as regards to urine but not blood values including creatine on creatinine ratio and guanidinoacetate on creatinine ratio values. Such gender differences were previously observed in healthy populations; they might be explained by literature differential effects of testosterone and estrogen in adolescents and adults, and by estrogen effects in prepubertal age on SLC6A8 function. Finally, though they were acquired on a population with neurological signs, the present data might reasonably serve as reference laboratory values in any future medical study exploring abnormalities of creatine metabolism and transport

Mechanistic framework to link root growth models with weather and soil physical properties, including example applications to soybean growth in Brazil

Background and aimsRoot elongation is generally limited by a combination of mechanical impedance and water stress in most arable soils. However, dynamic changes of soil penetration resistance with soil water content are rarely included in models for predicting root growth. Better modelling frameworks are needed to understand root growth interactions between plant genotype, soil management, and climate. Aim of paper is to describe a new model of root elongation in relation to soil physical characteristics like penetration resistance, matric potential, and hypoxia.MethodsA new diagrammatic framework is proposed to illustrate the interaction between root elongation, soil management, and climatic conditions. The new model was written in Matlab®, using the root architecture model RootBox and a model that solves the 1D Richards equations for water flux in soil. Inputs: root architectural parameters for Soybean; soil hydraulic properties; root water uptake function in relation to matric flux potential; root elongation rate as a function of soil physical characteristics. Simulation scenarios: (a) compact soil layer at 16 to 20 cm; (b) test against a field experiment in Brazil during contrasting drought and normal rainfall seasons.Results(a) Soil compaction substantially slowed root growth into and below the compact layer. (b) Simulated root length density was very similar to field measurements, which was influenced greatly by drought. The main factor slowing root elongation in the simulations was evaluated using a stress reduction function.ConclusionThe proposed framework offers a way to explore the interaction between soil physical properties, weather and root growth. It may be applied to most root elongation models, and offers the potential to evaluate likely factors limiting root growth in different soils and tillage regimes