1,734 research outputs found
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
Concurrent constraint programming with process mobility
We propose an extension of concurrent constraint programming with primitives for process migration within a hierarchical network, and we study its semantics. To this purpose, we first investigate a "pure " paradigm for process migration, namely a paradigm where the only actions are those dealing with transmissions of processes. Our goal is to give a structural definition of the semantics of migration; namely, we want to describe the behaviour of the system, during the transmission of a process, in terms of the behaviour of the components. We achieve this goal by using a labeled transition system where the effects of sending a process, and requesting a process, are modeled by symmetric rules (similar to handshaking-rules for synchronous communication) between the two partner nodes in the network. Next, we extend our paradigm with the primitives of concurrent constraint programming, and we show how to enrich the semantics to cope with the notions of environment and constraint store. Finally, we show how the operational semantics can be used to define an interpreter for the basic calculus.
Graphical Encoding of a Spatial Logic for the pi-Calculus
This paper extends our graph-based approach to the verification of spatial properties of π-calculus specifications. The mechanism is based on an encoding for mobile calculi where each process is mapped into a graph (with interfaces) such that the denotation is fully abstract with respect to the usual structural congruence, i.e., two processes are equivalent exactly when the corresponding encodings yield isomorphic graphs. Behavioral and structural properties of π-calculus processes expressed in a spatial logic can then be verified on the graphical encoding of a process rather than on its textual representation. In this paper we introduce a modal logic for graphs and define a translation of spatial formulae such that a process verifies a spatial formula exactly when its graphical representation verifies the translated modal graph formula
Atomic and Molecular Data for Interstellar Studies: A Status Report
Most interstellar species have a large fraction of their electronic transitions at far ultraviolet wavelengths. Observations at these wavelengths reveal spectra rich in absorption lines seen against the continuum of a background source, such as a hot star in our Galaxy, a supernova in a nearby galaxy, or even a bright nucleus in an active galaxy. Most of the observations continue to be made with space-borne instruments, but recent work includes measurements of extragalactic material at large redshifts obtained at high resolution with large ground-based telescopes (e.g., the Keck Telescope). The combination of precise experimental oscillator strengths, large-scale computations, and astronomical spectra with high signal-to-noise ratios are yielding a set of self-consistent-values that span a range in strength in excess of 100 for more and more species. The large range is important for studies involving the different environments probed by the various background sources. This review highlights recent work on the atomic species. Si II, S I, and Fe II, and on the molecules, CO and C2
Syntactic Markovian Bisimulation for Chemical Reaction Networks
In chemical reaction networks (CRNs) with stochastic semantics based on
continuous-time Markov chains (CTMCs), the typically large populations of
species cause combinatorially large state spaces. This makes the analysis very
difficult in practice and represents the major bottleneck for the applicability
of minimization techniques based, for instance, on lumpability. In this paper
we present syntactic Markovian bisimulation (SMB), a notion of bisimulation
developed in the Larsen-Skou style of probabilistic bisimulation, defined over
the structure of a CRN rather than over its underlying CTMC. SMB identifies a
lumpable partition of the CTMC state space a priori, in the sense that it is an
equivalence relation over species implying that two CTMC states are lumpable
when they are invariant with respect to the total population of species within
the same equivalence class. We develop an efficient partition-refinement
algorithm which computes the largest SMB of a CRN in polynomial time in the
number of species and reactions. We also provide an algorithm for obtaining a
quotient network from an SMB that induces the lumped CTMC directly, thus
avoiding the generation of the state space of the original CRN altogether. In
practice, we show that SMB allows significant reductions in a number of models
from the literature. Finally, we study SMB with respect to the deterministic
semantics of CRNs based on ordinary differential equations (ODEs), where each
equation gives the time-course evolution of the concentration of a species. SMB
implies forward CRN bisimulation, a recently developed behavioral notion of
equivalence for the ODE semantics, in an analogous sense: it yields a smaller
ODE system that keeps track of the sums of the solutions for equivalent
species.Comment: Extended version (with proofs), of the corresponding paper published
at KimFest 2017 (http://kimfest.cs.aau.dk/
The importance of root interactions in field bean/triticale intercrops
To highlight the contribution of belowground interactions to biomass and N and P yields,
field bean and triticale were grown in a P-poor soil as sole crops and as replacement intercrops at two
N levels. The shoots were always in contact, while the roots of adjacent rows were free to interact
or were completely separated. This allowed simultaneous testing the intraspecific and interspecific
competition between rows, which to our knowledge has not been studied before. Root biomass,
distribution in soil, morphometry, and functional traits were determined, together with the nodule
number and biomass. The Land Equivalent Ratio for shoot biomass and N and P yield were higher
than 1 when roots were in contact, and markedly lower when they were separated. This demonstrates
the positive contribution of root interactions, which in field bean, consisted of increased root elongation
without changes in biomass and nutrient status; in triticale, of increased N and P uptake eciency and
reduced biomass partitioning to roots. The soil-plant processes underlying intercrop advantage led to
complementarity in N sources with low N inputs and facilitated N and P uptake with high N inputs,
which demonstrates that intercropping could be profitable in both low and high input agriculture
Atomic Physics with the Goddard High-Resolution Spectrograph on the Hubble Space Telescope
Interstellar spectra toward zeta Oph acquired with the Goddard High-Resolution Spectrograph were used to obtain oscillator strengths for approximately two dozen S I lines. This analysis was possible because precisely determined experimental oscillator strengths are available for several multiplets, including one with a weak interstellar line. The self-consistent set of oscillator strengths then was obtained from a curve of growth based on line strengths spanning a range of a factor of 100. The derived f-values for a number of multiplets differ from values quoted by Morton (1991) but are generally consistent with the suite of available experimental and theoretical results
Esca symptoms appearance in Vitis vinifera L.: influence of climate, pedo-climatic conditions and rootstock/cultivar combination
This study investigated the appearance of esca symptoms in relation to environmental factors and the rootstock/cultivar combination in an experimental setting between 2004 and 2009. Among the common genotypes showing susceptibility to the esca disease, four cultivars were considered: ‘Cabernet Sauvignon’, ‘Sangiovese’, ‘Trebbiano Toscano’ and ‘Chardonnay’. These cultivars were studied own-rooted and in combination with two rootstocks: Kober 5BB and 1103 Paulsen. The difference in susceptibility of cultivars to esca appeared negatively related to the graft. No clear relation was found between esca appearance and environmental factors. Moreover, an unexpected discordance between esca incidence percentage and mortality rate was observed.
Biochar impact on the estimation of the colorimetric-based enzymatic assays of soil
This study was carried out in order to assess the influence of biochar applications on
the estimation of colorimetric-based
enzymatic assays and to verify the effectiveness
of the most common methods. Since most methods used to determine enzymatic
activities in the soil are based on colorimetry, biochar may absorb substrates and/
or coloured products thereby distorting the analytical result. Biochar was added to
two soils, with different textures and cation exchangeable capacities, at a rate of
2% (w/w), and seven enzyme activities were determined following standard methods.
The biochar amendment lowered the spectrophotometer reading of the activity
of FDAase and dehydrogenase in the sandy soil. In the three enzymatic activities
based on p-nitrophenol
production (β-glucosidase,
phosphatase and arylsulphatase),
the addition of biochar did not change the enzyme assays. The biochar led to an
overestimation in terms of the protease and urease activities in the sandy soil. In the
clay loamy soil, biochar did not change the response of any of the enzyme activities
tested. A biochar dose of up to 2% only guarantees the effectiveness of the most common
spectrophotometric methods for not excessively sandy soils
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