A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks

We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model. Within this setup, we tackle the Bayesian estimation of a subset of the model parameters. Specifically, we compare three Monte Carlo based numerical methods for the approximation of the posterior probability density function of the unknown parameters given a set of partial and noisy observations of the system. The schemes we assess are the particle Metropolis-Hastings (PMH) algorithm, the nonlinear population Monte Carlo (NPMC) method and the approximate Bayesian computation sequential Monte Carlo (ABC-SMC) scheme. We present an extensive numerical simulation study, which shows that while the three techniques can effectively solve the problem there are significant differences both in estimation accuracy and computational efficiency

Northernmost (Subarctic) and deepest record of Paleodictyon: paleoecological and biological implications

The data were collected in the framework of the AleutBio project of BMBF grant 03G0293A to Prof. Dr. Angelika Brandt, Senckenberg Research Institute and Natural History Museum Frankfurt, Germany. The research of O. Miguez-Salas was funded by a Humboldt Postdoctoral Fellowship from the Humboldt Foundation and a Margarita Salas Fellowship from the Ministry of Spain and EU Next Generations projects. The research of F.J. Rodríguez-Tovar was supported by grant PID2019- 104625RB-100 funded by MCIN/AEI/ https://doi.org/10.13039/501100011033.The online version contains supplementary material available at https://doi.org/10.1038/s41598-023-34050-wPaleodictyon is one of the most iconic and widespread of trace fossils in the geological record. However, modern examples are less well known and restricted to deep-sea settings at relatively low latitudes. Here, we report the distribution of Paleodictyon at six abyssal sites near the Aleutian Trench. This study reveals for the first time the presence of Paleodictyon at Subarctic latitudes (51°–53°N) and at depths over 4500 m, although the traces were not observed at stations deeper than 5000 m suggesting that there is some bathymetric constraint for the trace maker. Two small Paleodictyon morphotypes were recognized (average mesh size of 1.81 cm), one having a central hexagonal pattern, the other being characterized by a non-hexagonal pattern. Within the study area, Paleodictyon shows no apparent correlation with local environmental parameters. Finally, based on a worldwide morphological comparison, we conclude that the new Paleodictyon specimens represent distinct ichnospecies that are associated with the relatively eutrophic conditions in this region. Their smaller size may reflect this more eutrophic setting in which sufficient food can be obtained from a smaller area in order to satisfy the energetic requirements of the tracemakers. If so, then Paleodictyon size may provide some assistance when interpreting paleoenvironmental conditions.EU Next Generations PID2019-104625RB-100Ministry of SpainWolfgang BorchertAlexander von Humboldt-Stiftung AvHBundesministerium für Bildung und Forschung 03G0293A BMBFMinisterio de Ciencia e Innovación MICINNAgencia Estatal de Investigación AE

Fully stable numerical calculations for finite onedimensional structures: mapping the Transfer Matrix method

We design a fully stable numerical solution of the Maxwell´s equations with the Transfer Matrix Method (TMM) to understand the interaction between an electromagnetic field and a finite, one-dimensional, nonperiodic structure. Such an exact solution can be tailored from a conventional solution by choosing an adequate transformation between its reference systems, which induces a mapping between its associated TMMs. The paper demonstrates theoretically the numerical stability of the TMM for the exact solution within the framework of Maxwell´s equations, but the same formalism can efficiently be applied to resolve other classical or quantum linear wave-propagation interaction in one, two, and three dimensions. This is because the formalism is exclusively built up for an in depth analysis of the TMM´s symmetriesPeer reviewe

The complex case of Macaronichnus trace fossil affecting rock porosity

Bioturbation is an important factor for reservoir quality due to the modification of host rock petrophysical properties (i.e., porosity, permeability, and connectivity). However, there is no predictable relationship between bioturbation and its effect on rock properties, due to the variability of the involved ichnological features. A detailed ichnological analysis is necessary to determine how bioturbation affects petrophysical properties in a bioturbated reservoir. Traditionally, ichnological features such as density, tiering, size, orientation, architecture, and fill, have been considered. However, other properties have been undervalued as is the case of lining. Here, we present a detailed study on the effects of Macaronichnus burrows, an ichnotaxon usually related to hydrocarbon exploration due to its high concentration in rock notably affecting petrophysical properties. Macaronichnus, a subhorizontal cylindrical burrow, is characterized by a well-defined and developed outer rim surrounding the tube core. Our data indicates a clear zonation in porosity according to burrow structure, with the lowest porosity in the tube core and higher values associated with the surrounded rim. This duality is determined by the tracemaker grain selective feeding activity and the consequent concentrated cementation. The organism concentrates the lighter minerals in the tube core fill during feeding, favoring post-depositional cementation during diagenesis and this results in lower porosity than the host rock. However, heavy minerals, mainly glauconite, are located in the rim, showing higher porosity. Our results support the view that ichnological analyses are essential to determine reservoir quality in bioturbated reservoirs, evidencing that other ichnological properties in addition to those traditionally considered must be evaluated.EU's Horizon 2020 research and innovation program under the Marie Skodowska-Curie Grant 792314Ministerio de Educación, Cultura y Deporte, SpainSecretaria de Estado de I+D+I, Spain CGL2015-66835-P PID2019-104625RB-100Junta de Andalucía B-RNM-072-UGR18 P18-RT-4074Scientific Excellence Unit (UGR) UCE-2016-0

Dynamics of Turing patterns under spatio-temporal forcing

We study, both theoretically and experimentally, the dynamical response of Turing patterns to a spatio-temporal forcing in the form of a travelling wave modulation of a control parameter. We show that from strictly spatial resonance, it is possible to induce new, generic dynamical behaviors, including temporally-modulated travelling waves and localized travelling soliton-like solutions. The latter make contact with the soliton solutions of P. Coullet Phys. Rev. Lett. {\bf 56}, 724 (1986) and provide a general framework which includes them. The stability diagram for the different propagating modes in the Lengyel-Epstein model is determined numerically. Direct observations of the predicted solutions in experiments carried out with light modulations in the photosensitive CDIMA reaction are also reported.Comment: 6 pages, 5 figure

Resonant Photocurrent Generation in Dye-Sensitized Periodically Nanostructured Photoconductors by Optical Field Confinement Effects

Herein we show experimental evidence of resonant photocurrent generation in dye-sensitized periodically nanostructured photoconductors, which is achieved by spectral matching of the sensitizer absorption band to different types of localized photon modes present in either periodic or broken symmetry structures. Results are explained in terms of the calculated spatial distribution of the electric field intensity within the configurations under analysis.Unión Europea FP7 / 2007-2013Convenio de subvención ERC 307081 (POLIGHT)Ministerio de Economía y Competitividad MAT2011- 23593CONSOLIDER HOPE CSD2007-00007Junta de Andalucía FQM3579Junta de Andalucía FQM524

A broken socioeconomic promotion: Palma del Río and the case of the morisco Alonso de Almerique

Aunque todavía sabemos poco acerca de los moriscos granadinos que fueron expulsados a Castilla entre 1570 y 1610, algo que empieza a quedar claro es la existencia de una fuerte estructuración interna, tema ignorado hasta hace pocos años. Este artículo se centra en la figura del morisco Alonso Fernández de Almerique, asentado en la villa cordobesa de Palma del Río, quien no sólo consiguió enriquecerse gracias a muy diversas actividades económicas, sino que casi logró hacer olvidar su condición originaria.We still do not know much about the moriscos who were expelled from Granada to Castile between 1570 and 1610, something that is becoming clear, though, is the existence of a strong internal structure, an unkown issue until recent years. This paper focuses on Alonso Fernández de Almerique, a morisco settled in the cordovan town of Palma del Río, who not only got rich thanks to various economic activities, but even nearly managed to make forget his origins

On the Physical Vapour Deposition (PVD): Evolution of Magnetron Sputtering Processes for Industrial Applications

Advanced coatings play an important role in a wide range of industrial applications. These coatings are commonly used in machining tools due to their high hardness and wear resistance, but also can be applied in jewellery and decorative purposes. Deposition techniques have seen a strong evolution as result of the directly related devices, control evolution and software. Several variants have been developed around the main techniques: arc evaporation and sputtering. The coatings produced present significant differences in their characteristics, namely in terms of structure, mechanical properties and surface morphology. Depending on the substrate material and application, the deposition process needs to be properly selected, providing the particular characteristics requested. This paper intends to do a critical review of the evolution of the advanced coatings deposition process, mainly focused on the Physical Vapour Deposition (PVD) process, particularly in the Magnetron Sputtering technique, which is able to produce smooth surfaces, using lower temperatures, presenting excellent mechanical and tribological properties and having very good adhesion to the main materials used as substrate.info:eu-repo/semantics/publishedVersio

A critical review on the numerical simulation related to Physical Vapour Deposition

Physical Vapour Deposition (PVD) is a process usually used for the production of advanced coatings regarding its application in several industrial and current products, such as optical lens, moulds and dies, decorative parts or tools. This process has several variants due to its strong evolution along the last decades. The process is commonly assisted by plasma, creating a particular low pressure and medium temperature atmosphere, which is responsible for the transition of atomic particles between the target and the parts to be coated into a vacuum reactor. Several parameters are directly affecting the deposition, namely the substrate temperature, pressure inside the reactor, assisting gases used, type of current, power supply, bias, substrate and target materials, samples holder and corresponding rotation, deposition time, among others. Many mathematical models have been developed in order to allow the generation of numerical simulation applications, trying to combine parameters and expect the corresponding results. Numerical simulation applications were created around the mathematical models previously developed, which can play an important role in the prediction of the coating properties and structure. This paper intends to describe the numerical simulation evolution in the last years, namely the use of Finite Elements Method (FEM) and Computational Fluid Dynamics (CFD).info:eu-repo/semantics/publishedVersio