First Steps Towards a Runtime Comparison of Natural and Artificial Evolution

Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1)EA. We show that SSWM can have a moderate advantage over the (1+1)EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1)EA by taking advantage of information on the fitness gradient

Contactless pick-and-place of millimetric objects using inverted near-field acoustic levitation

We model and realize an ultrasonic contactless pick-and-place device capable of picking, self-centering, self-orienting, translating, and releasing flat millimetric objects. The device is an ultrasonic Langevin transducer operating at 21 kHz that radiates into air through a tapered tip. Objects are trapped few micrometers below the tip due to the near-field acoustic levitation phenomenon. We first investigate the conditions to achieve an attractive force on the object depending on its size and the device operating frequency. Second, we use a 3D acoustic model that describes the converging forces and torque that provide the self-centering and self-orienting capabilities. Third, a more advanced Computational Fluid Dynamics model based on the Navier-Stokes equations explains the small gap between the tip and the trapped object. The contactless manipulation capabilities of the device are demonstrated by picking, transporting, and releasing a Surface Mount Device in air. The presented manipulation concept can be an interesting alternative for manipulating delicate objects such as microelectromechanical devices, silicon dies, or micro-optical devices.This research was supported by the São Paulo Research Foundation—FAPESP (Grant Nos. 2017/27078-0 and 2018/04101-0)

A molecular dynamics framework to explore the structure and dynamics of layered double hydroxides

It is presented a straightforward procedure based on the CLAYFF force field to perform molecular dynamics (MD) computer simulations with the GROMACS open source package of layered double hydroxide (LDH) materials with different intercalated anions. This procedure enables running very long simulations of systems where all atomic positions are allowed to move freely, while maintaining the integrity of the LDH structure intact. Therefore, it has the potential to model different important applications of LDH involving ion-exchange and interlayer equilibrium processes in diverse areas as drug delivery, water purification, and corrosion protection. The magnesium-aluminium based LDH with a metallic ratio 2:1 (Mg2Al) was chosen to validate our computer simulation framework, because of the comprehensive experimental and computational studies reported in the literature devoted to the understanding of the structure of Mg2Al LDH. Potential parameters from the literature were used to model the Mg2Al LDH with different intercalated anions using a new set of atomic point charges calculated with the DDEC6 formalism. Once the model was validated through careful comparisons of the simulated and experimental structures, the procedure was adapted to the Zn2Al LDH materials. Lennard-Jones parameters had to be developed for zinc (II) cations and calibrated using the experimental structural data found in the literature for Zn2Al LDH and the height of the galleries determined experimentally in this work for Zn2Al with intercalated nitrate anions. The consistency of the model is proved by carrying out MD simulations to reproduce in the computer the typical experimental conditions in which the Zn2Al LDH is immersed in a sodium chloride water solution to act as a nanotrap for aggressive anions in corrosion protection applications. The LDH structure is maintained in the MD simulation in which the LDH is free to move alongside the solution and allowing a natural anion exchange between the LDH and the solution as well as dehydration/hydration of the basal space.publishe

VineSens: An Eco-Smart Decision-Support Viticulture System

[Abstract] This article presents VineSens, a hardware and software platform for supporting the decision-making of the vine grower. VineSens is based on a wireless sensor network system composed by autonomous and self-powered nodes that are deployed throughout a vineyard. Such nodes include sensors that allow us to obtain detailed knowledge on different viticulture processes. Thanks to the use of epidemiological models, VineSens is able to propose a custom control plan to prevent diseases like one of the most feared by vine growers: downy mildew. VineSens generates alerts that warn farmers about the measures that have to be taken and stores the historical weather data collected from different spots of the vineyard. Such data can then be accessed through a user-friendly web-based interface that can be accessed through the Internet by using desktop or mobile devices. VineSens was deployed at the beginning in 2016 in a vineyard in the Ribeira Sacra area (Galicia, Spain) and, since then, its hardware and software have been tested to prevent the development of downy mildew, showing during its first season that the system can led to substantial savings, to decrease the amount of phytosanitary products applied, and, as a consequence, to obtain a more ecologically sustainable and healthy wine.Ministerio de Economía y Competitividad; TEC2013-47141-C4-1-RMinisterio de Economía y Competitividad; TEC2016-75067-C4-1-R

Hypothyroidism decreases the biogenesis in free mitochondria and neuronal oxygen consumption in the cerebral cortex of developing rats

Thyroid hormone plays a critical role in mitochondrial biogenesis in two areas of the developing brain, the cerebral cortex and the striatum. Here we analyzed, in the cerebral cortex of neonatal rats, the effect of hypothyroidism on the biogenesis in free and synaptosomal mitochondria by analyzing, in isolated mitochondria, the activity of respiratory complex I, oxidative phosphorylation, oxygen consumption, and the expression of mitochondrial genome. In addition, we studied the effect of thyroid hormone in oxygen consumption in vivo by determining metabolic flow through C-13 nuclear magnetic resonance spectroscopy. Our results clearly show that in vivo, hypothyroidism markedly reduces oxygen consumption in the neural population of the cerebral cortex. This effect correlates with decreased free mitochondria biogenesis. In contrast, no effect was observed in the biogenesis in synaptosomal mitochondria. The parameters analyzed were markedly improved after T-3 administration. These results suggest that a reduced biogenesis and the subsequent reduction of respiratory capacity in free mitochondria could be the underlying cause of decreased oxygen consumption in the neurons of the cerebral cortex of hypothyroid neonates.This work was supported by Ministerio de Educaciín y Ciencia Grants SAF2004-06263-CO2-02 (to A.S.), SAF2004-06263-CO2-01, and SAF2007-62811 and Comunidad de Madrid Grant GR/SAL/0033/2004 (to A.P.-C.). Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas is funded by the Instituto de Salud Carlos III. T.B.R. is a recipient of a fellowship from the Fundaçâo para a Ciência e Tecnologia, Portugal (SFRH/BPD/26881/2006).Peer reviewe

The crystal structure of p-type transparent conductive oxide CuBO2

We employed ab initio global structural prediction algorithms to obtain the ground-state structure of CuBO2 This is a very promising p-type transparent conductive oxide that was synthesized recently, and thought to belong to the delafossite family. We proved that the true ground state is certainly not the delafossite structure, and that the most promising candidate is a low symmetry monoclinic phase. This is still a layered structure, but with boron and copper having a different coordination with respect to the delafossite phas

Food talk : 40-Hz fin whale calls are associated with prey biomass

Funding: This work was supported by Fundação para a Ciência eTecnologia (FCT) Azores 2020 Operational Programme and Fundo Regional da Ciência e Tecnologia (FRCT) through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011) and AWARENESS (PTDC/BIA-BMA/30514/2017), co-funded by FEDER, COMPETE, QREN, POPH, ERDF, ESF, the Lisbon Regional Operational Programme and the Portuguese Ministry for Science and Education. Okeanos R&D Centre is supported by FCT through the strategic fund (UIDB/05634/2020). M.R. was supported by a DRCT doctoral grant (M3.1.a/F/028/2015). S.P.J. was funded by EC funds (SUMMER H2020-EU.3.2.3.1), I.C. by FCT through AWARENESS–(PTDC/BIA-BMA/30514/2017). H.M. acknowledges support by CMAF-CIO (funded by FCT, Portugal, through the projects UID/MAT/00006/2013 and UIDB/04561/2020, respectively). A.P. was supported by AWARENESS project (PTDC/BIA-BMA/30514/2017) and UIDB/50019/2020–I.D.L. and T.A.M. by CEAUL and the LMR ACCURATE project (contract no. N3943019C2176). M.A.S. was funded by FCT and EC funds (IF/00943/2013, SUMMER H2020-EU.3.2.3.1, GA 817806).Animals use varied acoustic signals that play critical roles in their lives. Understanding the function of these signals may inform about key life-history processes relevant for conservation. In the case of fin whales (Balaenoptera physalus), that produce different call types associated with different behaviours, several hypotheses have emerged regarding call function, but the topic still remains in its infancy. Here, we investigate the potential function of two fin whale vocalizations, the song-forming 20-Hz call and the 40-Hz call, by examining their production in relation to season, year and prey biomass. Our results showed that the production of 20-Hz calls was strongly influenced by season, with a clear peak during the breeding months, and secondarily by year, likely due to changes in whale abundance. These results support the reproductive function of the 20-Hz song used as an acoustic display. Conversely, season and year had no effect on variation in 40-Hz calling rates, but prey biomass did. This is the first study linking 40-Hz call activity to prey biomass, supporting the previously suggested food-associated function of this call. Understanding the functions of animal signals can help identifying functional habitats and predict the negative effects of human activities with important implications for conservation.Publisher PDFPeer reviewe

The Si-Ge substitutional series in the chiral STW Zeolite Structure Type

The whole compositional range (Ge$_f$ = Ge/(Ge+Si)= 0 to 1) of zeolite STW has been synthesized and studied by a comprehensive combined experimental--theoretical approach. The yield of zeolite goes through a maximum and then drops at the GeO$_2$ side of the series, following the inverse of the calculated free energy curve. The unit cell generally expands, roughly linearly, as the Ge$_f$ increases, but a notable resilience to expansion is observed at the high silica side. This can be attributed to the more rigid character of SiO$_2$ and the ability of Ge units to deform. Density functional theory calculations provide a new assignment of the previously controversial $^{19}$F MAS NMR resonances for occluded fluoride, which is based not only in the number of Ge atoms in the double-4-ring units but also on the way they are associated (namely, no Ge, isolated Ge, Ge pairs or closed Ge clusters). While we found an overall good agreement between the experimental and theoretical trends in preferential occupation by Ge of different crystallographic sites, the theoretical models show more sharp and abrupt tendencies, likely due both to limitations of the approach and to kinetic factors that allow metastable configurations to actually exist.Comment: 26 page

Unveiling the local structure of 2-mercaptobenzothiazole intercalated in (Zn2Al) layered double hydroxides

The structure and composition of a zinc-aluminum layered double hydroxide (Zn2Al LDH) with the intercalated 2-mercaptobenzothiazole corrosion inhibitor (a.k.a. benzo[d]thiazole-2-thiol) are interpreted by means of atomistic molecular dynamics (MD) simulations. The results concerning the proportion of intercalated 2-mercaptobenzothiazole and water species in the Zn2Al LDH interlayer were correlated with experimental X-ray diffraction (XRD) and thermogravimetric analysis (TGA) data of samples obtained at pH 8.5, 10 and 11.5. While the sample synthesized at the lowest pH is almost free of contaminants, the sample obtained at the highest pH is contaminated by a small fraction of a material with intercalated OH-. The comparison of the calculated and XRD interlayer distances suggests that the most stable structure has a ratio of ~4.5 water molecules per intercalated organic species, which is higher than the ratio of ~2 typically reported in the literature. The distribution of molecules in the LDH interlayer consists of a layer of water near the hydroxides, a second layer grown over the first layer, with the 2-mercaptobenzothiazole species adopting conformations with the sulfur of the thioamide group facing the hydroxide/water layers and the 6-member ring oriented towards the middle of the interlayer. Different structural analyses were done to explain the equilibria between the different species in the interlayer space, and their molecular interactions with the LDH metal hydroxide layers.publishe

Deep-diving beaked whales dive together but forage apart

Funding: Data collection and analysis were performed with funds from the U.S. Office of Naval Research (ONR), the US National Oceanographic Partnership Program (NOPP), the US Strategic Environmental Research Development Program (SERDP) and the Spanish Government National Projects CETOBAPH (CGL2009-13112) and DEEPCOM (CTM2017-88686-P). J.A.T. is currently the recipient of a FPU Doctoral Scholarship (FPU16/00490) from the Spanish Ministry of Universities. M.J. is supported by the Aarhus University Research Foundation and the EU H2020 research and innovation programme under Marie Skłodowska-Curie grant 754513. P.A. is funded by an Agustín de Bethencourt fellowship from the Cabildo Insular de Tenerife and NAS by a Ramón y Cajal fellowship from the Spanish Government. V.E.W. is funded by a University of Auckland Doctoral Scholarship. C.J.P.G. is partially funded by the Ministry of Science and Innovation (MICINN) of Spain under Grant PID2019-110442GB-I00. T.A.M. thanks partial support from CEAUL (funded by FCT - Fundação para a Ciência e a Tecnologia, Portugal, through the project UIDB/00006/2020).Echolocating animals that forage in social groups can potentially benefit from eavesdropping on other group members, cooperative foraging or social defence, but may also face problems of acoustic interference and intra-group competition for prey. Here, we investigate these potential trade-offs of sociality for extreme deep-diving Blainville′s and Cuvier's beaked whales. These species perform highly synchronous group dives as a presumed predator-avoidance behaviour, but the benefits and costs of this on foraging have not been investigated. We show that group members could hear their companions for a median of at least 91% of the vocal foraging phase of their dives. This enables whales to coordinate their mean travel direction despite differing individual headings as they pursue prey on a minute-by-minute basis. While beaked whales coordinate their echolocation-based foraging periods tightly, individual click and buzz rates are both independent of the number of whales in the group. Thus, their foraging performance is not affected by intra-group competition or interference from group members, and they do not seem to capitalize directly on eavesdropping on the echoes produced by the echolocation clicks of their companions. We conclude that the close diving and vocal synchronization of beaked whale groups that quantitatively reduces predation risk has little impact on foraging performance.PostprintPeer reviewe