VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations.

We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and uncertainty quantication (UQ). It enables users to verify key aspects of their applications, systematically compare and validate the simulation outputs against observational or benchmark data, and run simulations conveniently on any platform from the desktop to current multi-petascale computers. In this sequel to our paper on VECMAtk which we presented last year [1] we focus on a range of functional and performance improvements that we have introduced, cover newly introduced components, and applications examples from seven different domains such as conflict modelling and environmental sciences. We also present several implemented patterns for UQ/SA and V&V, and guide the reader through one example concerning COVID-19 modelling in detail. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

Probing negatively charged and neutral excitons in MoS2/hBN and hBN/MoS2/hBN van der Waals heterostructures.

High-quality van der Waals heterostructures assembled from hBN-encapsulated monolayer transition metal dichalcogenides enable observations of subtle optical and spin-valley properties whose identification was beyond the reach of structures exfoliated directly on standard SiO2/Si substrates. Here, we describe different van der Waals heterostructures based on uncapped single-layer MoS2 stacked onto hBN layers of different thicknesses and hBN-encapsulated monolayers. Depending on the doping level, they reveal the fine structure of excitonic complexes, i.e. neutral and charged excitons. In the emission spectra of a particular MoS2/hBN heterostructure without an hBN cap we resolve two trion peaks, T1 and T2, energetically split by about 10 meV, resembling the pair of singlet and triplet trion peaks (T S and T T ) in tungsten-based materials. The existence of these trion features suggests that monolayer MoS2 has a dark excitonic ground state, despite having a 'bright' single-particle arrangement of spin-polarized conduction bands. In addition, we show that the effective excitonic g-factor significantly depends on the electron concentration and reaches the lowest value of -2.47 for hBN-encapsulated structures, which reveals a nearly neutral doping regime. In the uncapped MoS2 structures, the excitonic g-factor varies from -1.15 to -1.39 depending on the thickness of the bottom hBN layer and decreases as a function of rising temperature.

Room temperature multi-phonon upconversion photoluminescence in monolayer semiconductor WS2.

Photon upconversion is an anti-Stokes process in which an absorption of a photon leads to a reemission of a photon at an energy higher than the excitation energy. The upconversion photoemission has been already demonstrated in rare earth atoms in glasses, semiconductor quantum wells, nanobelts, carbon nanotubes and atomically thin semiconductors. Here, we demonstrate a room temperature upconversion photoluminescence process in a monolayer semiconductor WS2, with energy gain up to 150 meV. We attribute this process to transitions involving trions and many phonons and free exciton complexes. These results are very promising for energy harvesting, laser refrigeration and optoelectronics at the nanoscale.

Persistent Müllerian duct syndrome (PMDS) in the Polish free-ranged bull populations of the European bison (Bison bonasus L.).

This study describes the diversity of vestigial male uteri of the European bison (Eb) examined for: (1) morphology, (2) glycoprotein localization, (3) total protein and glycoprotein profiles, (4) steroid concentrations, and (5) PMDS based on the mutation of AMH and AMHR2 genes. Uteri of adult bulls (5-12 years old) were compared to a uterus of a juvenile female (6 months old). Male uterine proteins were analyzed in parallel to secretory endometrial proteins of pseudo-pregnant pig (PsEND) and BSA used as profile-controls. Hematoxylin/eosin-staining revealed the diversity of male uterine morphology, including lumen size/shape, endometrial (END) gland density, luminal knob-like epithelial structures and multiple intrauterine cells proliferating within the lumen. PAS-staining revealed the presence of glycoproteins restricted to luminal epithelial cells and END glands. Heterologous total protein PAGE-profiles (20-66kDa) revealed two dominant fractions (66 and 45kDa), similar to PAS-profiles (67 and 47kDa) in male and female uterine tissues. In male uterine tissues, androstendione and progesterone, but not testosterone, estrone or estradiol concentrations were lower than in the female. Sequencing of AMH- and AMHR2-like amplicons allowed identification of these gene mutations in Eb. Our results provide novel data regarding PMDS, demonstrating the diversity of uterine morphology, glycoprotein mass/profile, steroid concentration and AMH/AMHR2 mutations in Eb bulls.

Cord atrophy separates early primary progressive and relapsing remitting multiple sclerosis.

BACKGROUND AND OBJECTIVE: The onset of multiple sclerosis is relapsing remitting or primary progressive. An improved understanding of the causes of early progressive disability in primary progressive multiple sclerosis (PPMS) could provide mechanistic targets for therapeutic intervention. METHODS: Five magnetic resonance imaging (MRI) parameters that could potentially cause progressive disability were investigated in 43 patients with early PPMS and in 37 patients with early relapsing remitting multiple sclerosis (RRMS): atrophy in brain, both grey matter and white matter; intrinsic abnormality in brain, both grey matter and white matter (measured by the magnetisation transfer ratio (MTR)); and atrophy of the upper cervical spinal cord. Both groups were also compared with controls. RESULTS: Patients with PPMS were older and more likely to be men. Both patient groups had atrophy of brain grey matter and white matter, and intrinsic abnormality in MTR of normal-appearing grey matter and white matter. Cord atrophy was present only in the PPMS (mean cord area: PPMS, 67.8 mm2; RRMS, 72.7 mm2; controls, 73.4 mm2; p = 0.007). This was confirmed by multivariate analysis of all five MRI parameters, age and sex. CONCLUSION: Grey matter and white matter of the brain are abnormal in both early RRMS and PPMS, but cord atrophy is present only in PPMS. This is concordant with myelopathy being the usual clinical presentation of PPMS. Measurement of cord atrophy seems to be clinically relevant in PPMS treatment trials.

Noninvasive evaluation of somatic embryogenesis.

Callus Suspension Cultures of Ipomea batates Poir. cv. White Star were grown in an airlift bioreactor. A machine vision system was used to monitor nondestructively callus growth during a 10 day culture period. Growth data obtained with this system included the overall reactor population and population estimates for the 200-1200-microm fractions at 200-microm intervals. A model of callus growth was developed to explain the mechanics of callus enlargement. The model was based on the assumptions that (1) the calli could not subdivide or shrink, (2) there was a fixed percentage of the initial population for each fraction that was nonviable, and (3) growth rates did not vary with time during the culture period. It was determined that the growth rates and nonviable ratios decreased as fraction size increased.

A mathematical model of lung parenchyma.

The geometry of the proposed model of the parenchyma of a mammalian lung reproduces a cluster of alveoli arranged around a lowest-level air duct. The alveolar walls are assumed to be nonlinear elastic membranes, whose properties are described in terms of a strain energy function which reflects the hardening character of the stress-strain curve. The effect of the surfactant is included in terms of a variable (area-dependent) surface tension. Analyses of various mechanical processes in the parenchyma are performed with the aid of the finite element method, with the geometric and physical nonlinearities of the problem taken into account.