The LifeV library: engineering mathematics beyond the proof of concept

LifeV is a library for the finite element (FE) solution of partial differential equations in one, two, and three dimensions. It is written in C++ and designed to run on diverse parallel architectures, including cloud and high performance computing facilities. In spite of its academic research nature, meaning a library for the development and testing of new methods, one distinguishing feature of LifeV is its use on real world problems and it is intended to provide a tool for many engineering applications. It has been actually used in computational hemodynamics, including cardiac mechanics and fluid-structure interaction problems, in porous media, ice sheets dynamics for both forward and inverse problems. In this paper we give a short overview of the features of LifeV and its coding paradigms on simple problems. The main focus is on the parallel environment which is mainly driven by domain decomposition methods and based on external libraries such as MPI, the Trilinos project, HDF5 and ParMetis. Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar

Upgrading of Biobased Glycerol to Glycerol Carbonate as a Tool to Reduce the CO2 Emissions of the Biodiesel Fuel Life Cycle

With regards to oil-based diesel fuel, the adoption of bio-derived diesel fuel was estimated to reduce CO2 emissions by approximately 75%, considering the whole life cycle. In this paper, we present a novel continuous-flow process able to transfer an equimolar amount of CO2 (through urea) to glycerol, producing glycerol carbonate. This represents a convenient tool, able to both improve the efficiency of the biodiesel production through the conversion of waste streams into added-value chemicals and to beneficially contribute to the whole carbon cycle. By means of a Design of Experiments approach, the influence of key operating variables on the product yield was studied and statistically modeled

Extended LaSalle's invariance principle for full-range cellular neural networks

In several relevant applications to the solution of signal processing tasks in real time, a cellular neural network (CNN) is required to be convergent, that is, each solution should tend toward some equilibrium point. The paper develops a Lyapunov method, which is based on a generalized version of LaSalle's invariance principle, for studying convergence and stability of the differential inclusions modeling the dynamics of the full-range (FR) model of CNNs. The applicability of the method is demonstrated by obtaining a rigorous proof of convergence for symmetric FR-CNNs. The proof, which is a direct consequence of the fact that a symmetric FR-CNN admits a strict Lyapunov function, is much more simple than the corresponding proof of convergence for symmetric standard CNNs

Chemo-enzymatic synthesis of new resveratrol-related dimers containing the benzo[b]furan framework and evaluation of their radical scavenger activities

The chemo-enzymatic synthesis and the evaluation of radical scavenger performance of resveratrolrelated dimers with antioxidative power have been investigated. The dimeric compounds, containing the benzo[b]furan framework, were prepared via an oxidative dimerization catalyzed by a laccase from Trametes versicolor, followed by a treatment with the organic oxidant DDQ. This methodology can be useful for the synthesis of various 2,3-diarylbenzo[b]furans derivates, a class of compound that exhibits a wide range of biological activities

Toxicity of the purple mucus of the polychaete Halla parthenopeia (Oenonidae) revealed by a battery of ecotoxicological bioassays

Mucus secretions play a number of functions related to polychaete physiology and ecology. Under stress conditions, the polychaete Halla parthenopeia (Oenonidae) produces a purple mucus after mechanical stimulation, whose function is still unknown. Here, we assessed the toxicity of this purple mucus by means of both acute toxicity bioassays on the polychaete Dinophilus gyrociliatus and commercial ecotoxicological kits (Microtox\uae, Rotoxkit\uae and Artoxkit\uae). Palatability was also tested with the fish Oryzias melastigma. After emitting purple mucus, H. parthenopeia quickly moves away and starts releasing transparent mucus. Acute toxicity bioassays showed that the mucus was harmless (transparent), or lethal even when diluted about 1000 times (purple). Purple mucus was toxic at different concentrations, the LC50 ranging from 0.7-0.3 g l\u20131 for D. gyrociliatus to 76 g l\u20131 for Artemia franciscana (Artoxkit\uae). Freeze-dried brine shrimp coated with transparent or purple muci were both consumed by O. melastigma. We hypothesized that the purple mucus is involved in the chemical defence of H. parthenopeia against competitors and parasites, and that its colour and toxicity are due to hallachrome, a 1,2-anthraquinone found in the skin of H. parthenopeia

Complete Stability of Neural Networks With Extended Memristors

The article considers a large class of delayed neural networks (NNs) with extended memristors obeying the Stanford model. This is a widely used and popular model that accurately describes the switching dynamics of real nonvolatile memristor devices implemented in nanotechnology. The article studies via the Lyapunov method complete stability (CS), i.e., convergence of trajectories in the presence of multiple equilibrium points (EPs), for delayed NNs with Stanford memristors. The obtained conditions for CS are robust with respect to variations of the interconnections and they hold for any value of the concentrated delay. Moreover, they can be checked either numerically, via a linear matrix inequality (LMI), or analytically, via the concept of Lyapunov diagonally stable (LDS) matrices. The conditions ensure that at the end of the transient capacitor voltages and NN power vanish. In turn, this leads to advantages in terms of power consumption. This notwithstanding, the nonvolatile memristors can retain the result of computation in accordance with the in-memory computing principle. The results are verified and illustrated via numerical simulations. From a methodological viewpoint, the article faces new challenges to prove CS since due to the presence of nonvolatile memristors the NNs possess a continuum of nonisolated EPs. Also, for physical reasons, the memristor state variables are constrained to lie in some given intervals so that the dynamics of the NNs need to be modeled via a class of differential inclusions named differential variational inequalities

Convergence of Neural Networks with a Class of Real Memristors with Rectifying Characteristics

The paper considers a neural network with a class of real extended memristors obtained via the parallel connection of an ideal memristor and a nonlinear resistor. The resistor has the same rectifying characteristic for the current as that used in relevant models in the literature to account for diode-like effects at the interface between the memristor metal and insulating material. The paper proves some fundamental results on the trajectory convergence of this class of real memristor neural networks under the assumption that the interconnection matrix satisfies some symmetry conditions. First of all, the paper shows that, while in the case of neural networks with ideal memristors, it is possible to explicitly find functions of the state variables that are invariants of motions, the same functions can be used as Lyapunov functions that decrease along the trajectories in the case of real memristors with rectifying characteristics. This fundamental property is then used to study convergence by means of a reduction-of-order technique in combination with a Lyapunov approach. The theoretical predictions are verified via numerical simulations, and the convergence results are illustrated via the applications of real memristor neural networks to the solution of some image processing tasks in real time

A defective ABC transporter of the MRP family, responsible for the bean lpa1 mutation, affects the regulation of the phytic acid pathway, reduces seed myo-inositol and alters ABA sensitivity

We previously identified the lpa1 (low phytic acid) 280-10 line that carries a mutation conferring a 90% reduction in phytic acid (InsP6) content. In contrast to other lpa mutants, lpa1(280-10) does not display negative pleiotropic effects. In the present paper, we have identified the mutated gene and analysed its impact on the phytic acid pathway. Here, we mapped the lpa1(280-10) mutation by bulk analysis on a segregating F2 population, an then, by comparison with the soybean genome, we identified and sequenced a candidate gene. The InsP6 pathway was analysed by gene expression and quantification of metabolites. The mutated Pvmrp1(280-10) cosegregates with the lpa1(280-10) mutation, and the expression level of several genes of the InsP6 pathway are reduced in the lpa1(280-10) mutant as well as the inositol and raffinosaccharide content. PvMrp2, a very similar paralogue of PvMrp1 was also mapped and sequenced. The lpa1 mutation in beans is likely the result of a defective Mrp1 gene (orthologous to the lpa genes AtMRP5 and ZmMRP4), while its Mrp2 paralog is not able to complement the mutant phenotype in the seed. This mutation appears to down-regulate the InsP6 pathway at the transcriptional level, as well as altering inositol-related metabolism and affecting ABA sensitivity

Effect of s strong rainstorm on the hydrodynamics of the Puerto Princesa underground river (Palawan, Philippines)

Fascinating and fragile environments as are the underground estuaries, need to be studied, understood and protected for present and future generations. Even if wide and abundant bibliography related to tides and their behaviour with respect to the external estuaries is available, none dealed with the estuary caves and the related hydrogeology. This paper aims to partially fill this gap presenting a preliminary study done at the Puerto Princesa Underground River (PPUR), in the Palawan Island (Philippines). The data was collected during the last expedition (November 2016) organised by La Venta, in which some of the authors took part. During the survey, the cave has been instrumented with in continuous diver data-logger devices (CTD) recording temperature (T), electrical conductivity (EC) and water level fluctuations. Longitudinal and vertical water hydrogeological profiles of the cave were realised with the aim of understanding the dynamics of the waters during different hydrogeological regimes in combination with salt water intrusion. In addition, a bathymetric profile was done to better identify the point where to realise the vertical logs. A significant rainstorm occurred during the expedition, lasting for approximately 12 hours resulting in 80 mm of rain, and its effects gave the researchers the opportunity to analyse the hydrodynamics of the flowing waters during a flood. In normal flow conditions, the longitudinal logs highlighted the presence of freshwater inlets and the vertical logs testified to a clear stratification of the waters (freshwaters at the surface and brackish waters at the bottom). During floods, the EC and T data showed evidence of a fast substitution of the resident waters.Key words: anchialine caves, sea water intrusion, hydrodynamics, karst springs, PPUR, Philippines.Učinek močnega naliva na hidrodinamiko podzemske reke Puerto princese (Palawan, Filipini)Očarljivo in občutljivo okolje, kot so podzemni estuariji, je treba preučevati, razumeti in zaščititi za sedanje in prihodnje generacije. Četudi imamo na voljo široko in bogato bibliografijo o plimovanju in delovanju plimovanja v zunanjih estuarijih, nobeno delo ne obravnava estuarskih jam in s tem povezane hidrogeologije. Namen tega članka je delno zapolniti to vrzel in predstaviti predhodno študijo na podzemni reki Puerto Princesa (PPUR) na otoku Palawan (Filipini). Podatki so bili zbrani med zadnjo ekspedicijo (novembra 2016), ki jo je organizirala La Venta, v kateri so sodelovali tudi nekateri avtorji. V raziskavi je bila jama opremljena z zveznimi merilci (CTD) temperature (T), električne prevodnosti (EC) in nihanja nivojev vode. Vzdolžni in navpični hidrogeološki vodni profili jame so bili izmerjeni, da bi razumeli dinamiko voda med različnimi hidrogeološkimi nivoji in med vdori morske vode. Poleg tega je bil opravljen tudi batimetrični profil, da bi lažje določili, kje izvesti navpične meritve. Med ekspedicijo se je zgodil močan naliv, ki je trajal približno 12 ur, padlo je 80 mm dežja, njegov učinek pa je raziskovalcem omogočil analizo hidrodinamike tekočih voda med poplavo. V običajnih vodostajih so vzdolžne meritve pokazale na dotoke sveže vode, vertikalne meritve pa so pokazale  jasno stratifikacijo lastnosti vode (sveža voda na površini in brakična voda na dnu). Med poplavami so podatki EC in T potrdili hitro zamenjavo vode.Ključne besede: anhialine jame, vdor morske vode, hidrodinamika, kraški izviri, PPUR, Filipini. 

Novel Natural Compounds and Their Anatomical Distribution in the Stinging Fireworm Hermodice carunculata (Annelida)

Increasing evidence in the field of bioprospection fosters the necessity of studying poorly investigated poisonous marine invertebrates to expand knowledge on animal venom biology. Among marine annelids, amphinomid fireworms are notorious for their bearded trunk equipped with a powerful stinging capacity. Here, a methodological workflow based on analytical chemistry techniques (compound isolation followed by mass spectrometry and spectroscopy analyses) was applied to gain new insights, leading to the identification and structural elucidation of an array of natural products from Mediterranean specimens of Hermodice carunculata. Eight betaine-derived unprecedented compounds, named "carunculines", were detected, bearing two terminal ammonium groups tri-and disubstituted at the Cα (A, B) and a series of different alkyl chains (I-VIII). The mixture of chemicals was found in all the body parts of H. carunculata, supporting a mechanism of action triggered by their vehiculation inside the dorsal chaetae, and subsequent injection when chaetae break off on contact. Preliminary investigations to understand adaptive features were also performed, showing a trend in carunculine abundance that fits into the evolutionary history of these worms. These findings shed light on the chemical ecology of amphinomids, giving reasons for the success of H. carunculata in benthic environments and providing promising novel metabolites for biotechnological implications