Scientific modelling can be accessible, interoperable and user friendly: A case study for pasture and livestock modelling in Spain

This article describes the adaptation of a non-spatial model of pastureland dynamics, including vegetation life cycle, livestock management and nitrogen cycle, for use in a spatially explicit and modular modelling platform (k.LAB) dedicated to make data and models more interoperable. The aim is to showcase to the social-ecological modelling community the delivery of an existing, monolithic model, into a more modular, transparent and accessible approach to potential end users, regional managers, farmers and other stakeholders. This also allows better usability and adaptability of the model beyond its originally intended geographical scope (the Cantabrian Region in the North of Spain). The original code base (written in R in 1,491 lines of code divided into 13 files) combines several algorithms drawn from the literature in an opaque fashion due to lack of modularity, non-semantic variable naming and implicit assumptions. The spatiotemporal rewrite is structured around a set of 10 namespaces called PaL (Pasture and Livestock), which includes 198 interoperable and independent models. The end user chooses the spatial and temporal context of the analysis through an intuitive web-based user interface called k.Explorer. Each model can be called individually or in conjunction with the others, by querying any PaL-related concepts in a search bar. A scientific dataflow and a provenance diagram are produced in conjunction with the model results for full transparency. We argue that this work demonstrates key steps needed to create more Findable, Accessible, Interoperable and Reusable (FAIR) models beyond the selected example. This is particularly essential in environments as complex as agricultural systems, where multidisciplinary knowledge needs to be integrated across diverse spatial and temporal scales in order to understand complex and changing problems. © 2023 Marquez Torres et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The authors would like to thank Joan Busqué who created and shared the original Puerto model and the team lead by José Barquín at the Hydrological Institute of Cantabria (IHC). Special thanks to Simone Langhans and Ken Bagstad who suggested revisions to the article. Robinson et al. (2014) for logistic support for EarthEnv-DEM90

The FIT-pull Method: an experimental tool to monitor the track measurements and the B proper time.

In this note we describe a statistical tool, the \textit{FIT-pull method}, that can test the reliability of the measurements of the tracks and the vertices on real and Monte-Carlo data without knowledge of the truth information. The basic mathematical formalism is derived from the Lagrange Multipliers method and briefly described. Several tests are performed to prove its validity in different situations. %KDifferent useful examples are discussed. In particular, by using Monte-Carlo simulation, we demonstrate that the method can be applied to check if the measured tracks or vertices have biases or incorrect covariance matrices. For correct input measurements we obtain pull distributions with a normal Gaussian statistical form. In this case the B proper time value and its error, which is a function of the track and vertex measurements, are correctly calculated. However, in the case of incorrect measurements, for example due to a systematic error or to a scale factor of the covariance matrix, the pull distributions studied deviate from normal Gaussians and the B proper time measurement can be affected. In principle the method can, if necessary, be used to recover information from corrupted measurements. Its potential in this capacity is demonstrated for the particular case of the decay channel $B^0_d \to \pi^+ \pi^-$ with the reconstructed Monte-Carlo data produced in 2004

Excitation properties of photopigments and their possible dependence on the host star

Photosynthesis is a plausible pathway for the sustenance of a substantial biosphere on an exoplanet. In fact, it is also anticipated to create distinctive biosignatures detectable by next-generation telescopes. In this work, we explore the excitation features of photopigments that harvest electromagnetic radiation by constructing a simple quantum-mechanical model. Our analysis suggests that the primary Earth-based photopigments for photosynthesis may not function efficiently at wavelengths >1.1 mu m. In the context of (hypothetical) extrasolar photopigments, we calculate the potential number of conjugated pi-electrons (N-*) in the relevant molecules, which can participate in the absorption of photons. By hypothesizing that the absorption maxima of photopigments are close to the peak spectral photon flux of the host star, we utilize the model to estimate N-*. As per our formalism, N-* is modulated by the stellar temperature, and is conceivably higher (lower) for planets orbiting stars cooler (hotter) than the Sun; exoplanets around late-type M-dwarfs might require an N-* twice that of the Earth. We conclude the analysis with a brief exposition of how our model could be empirically tested by future observations

Affine equation of state from quintessence and k-essence fields

We explore the possibility that a scalar field with appropriate Lagrangian can mimic a perfect fluid with an affine barotropic equation of state. The latter can be thought of as a generic cosmological dark component evolving as an effective cosmological constant plus a generalized dark matter. As such, it can be used as a simple, phenomenological model for either dark energy or unified dark matter. Furthermore, it can approximate (up to first order in the energy density) any barotropic dark fluid with arbitrary equation of state. We find that two kinds of Lagrangian for the scalar field can reproduce the desired behaviour: a quintessence-like with a hyperbolic potential, or a purely kinetic k-essence one. We discuss the behaviour of these two classes of models from the point of view of the cosmological background, and we give some hints on their possible clustering properties.Comment: 9 pages, 6 figures. Minor updates, accepted by CQ

Coupled cluster simulation of impulsive stimulated X-ray Raman scattering

Time-dependent equation-of-motion coupled cluster (TD-EOM-CC) is used to simulate impulsive stimulated x-ray Raman scattering (ISXRS) of ultrashort laser pulses by neon, carbon monoxide, pyrrole, and p-aminophenol. The TD-EOM-CC equations are expressed in the basis of field-free EOM-CC states, where the calculation of the core-excited states is simplified through the use of the core-valence separation (CVS) approximation. The transfer of electronic population from the ground state to the core- and valence-excited states is calculated for different numbers of included core- and valence-excited states, as well as for electric field pulses with different polarizations and carrier frequencies. The results indicate that Gaussian pulses can transfer significant electronic populations to the valence states through the Raman process. The sensitivity of this population transfer to the model parameters is analyzed. The time-dependent electronic density for p-aminophenol is also showcased, supporting the interpretation that ISXRS involves localized core excitations and can be used to rapidly generate valence wavepackets.Comment: 10 pages, 5 figure

Redshift Drift in LTB Void Universes

We study the redshift drift, i.e., the time derivative of the cosmological redshift in the Lema\^itre-Tolman-Bondi (LTB) solution in which the observer is assumed to be located at the symmetry center. This solution has often been studied as an anti-Copernican universe model to explain the acceleration of cosmic volume expansion without introducing the concept of dark energy. One of decisive differences between LTB universe models and Copernican universe models with dark energy is believed to be the redshift drift. The redshift drift is negative in all known LTB universe models, whereas it is positive in the redshift domain $z \lesssim 2$ in Copernican models with dark energy. However, there have been no detailed studies on this subject. In the present paper, we prove that the redshift drift of an off-center source is always negative in the case of LTB void models. We also show that the redshift drift can be positive with an extremely large hump-type inhomogeneity. Our results suggest that we can determine whether we live near the center of a large void without dark energy by observing the redshift drift.Comment: 16 pages, 2 figure

Implications for quintessence models from MAXIMA-1 and BOOMERANG-98

Prompted by the recent MAXIMA-1 and BOOMERANG-98 measurements of the cosmic microwave background (CMB) anisotropy power spectrum, and motivated by the results from the observation of high-redshift Type Ia supernovae, we investigate CMB anisotropies in quintessence models in order to characterize the nature of the dark energy today. We perform a Bayesian likelihood analysis, using the MAXIMA-1 and BOOMERANG-98 published bandpowers, in combination with COBE/DMR, to explore the space of quintessence parameters: the quintessence energy density \Omega_\phi and equation of state w_\phi. We restrict our analysis to flat, scale-invariant, inflationary adiabatic models. We find that this simple class of inflationary models, with a quintessence component \Omega_\phi < ~0.7, -1 < = w_\phi < ~-0.5, is in good agreement with the data. Within the assumptions of our analysis, pure quintessence models seem to be slightly favored, although the simple cosmological constant scenario is consistent with the data.Comment: 4 pages, 3 figures. Reflects version accepted for publication by ApJ Letter