Harnessing modern parallel computing resources to achieve complex multiphysics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such ...development by providing simplified interfaces for specification of partial differential equations, boundary conditions, material properties, and all aspects of a simulation without the need to consider the parallel, adaptive, nonlinear, finite element solve that is handled internally. Through the use of interfaces and inheritance, each portion of a simulation becomes reusable and composable in a manner that allows disparate research groups to share code and create an ecosystem of growing capability that lowers the barrier for the creation of multiphysics simulation codes. Included within the framework is a unique capability for building multiscale, multiphysics simulations through simultaneous execution of multiple sub-applications with data transfers between the scales. Other capabilities include automatic differentiation, scaling to a large number of processors, hybrid parallelism, and mesh adaptivity. To date, MOOSE-based applications have been created in areas of science and engineering such as nuclear physics, geothermal science, magneto-hydrodynamics, seismic events, compressible and incompressible fluid flow, microstructure evolution, and advanced manufacturing processes.
Logical development of the cell ontology Meehan, Terrence F; Masci, Anna Maria; Abdulla, Amina ...
BMC bioinformatics,
01/2011, Letnik:
12, Številka:
1
Journal Article
Recenzirano
Odprti dostop
The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. ...By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL.
Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types.
Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.
In this work, we investigate the production of highly oxidative species in solutions exposed to a self-pulsed corona discharge in air. We examine how the properties of the target solution (pH, ...conductivity) and the discharge power affect the discharge stability and the production of H
2
O
2
. Indigo carmine, a common organic dye, is used as an indicator of oxidative strength and in particular, hydroxyl radical (OH
·
) production. The observed rate of indigo oxidation in contact with the discharge far exceeds that predicted from reactions based on concentrations of species measured in the bulk solution. The generation of H
2
O
2
and the oxidation of indigo carmine indicate a high concentration of highly oxidizing species such as OH
·
at the plasma–liquid interface. These results indicate that reactions at the air plasma–liquid interface play a dominant role in species oxidation during direct non-equilibrium atmospheric pressure plasma treatment.
Abstract
We present extensive multifrequency Karl G. Jansky Very Large Array (VLA) and Very Long Baseline Array (VLBA) observations of the radio-bright supernova (SN) IIb SN 2004C that span ∼40–2793 ...days post-explosion. We interpret the temporal evolution of the radio spectral energy distribution in the context of synchrotron self-absorbed emission from the explosion’s forward shock as it expands in the circumstellar medium (CSM) previously sculpted by the mass-loss history of the stellar progenitor. VLBA observations and modeling of the VLA data point to a blastwave with average velocity ∼0.06
c
that carries an energy of ≈10
49
erg. Our modeling further reveals a flat CSM density profile
ρ
CSM
∝
R
−0.03±0.22
up to a break radius
R
br
≈ (1.96 ± 0.10) × 10
16
cm, with a steep density gradient following
ρ
CSM
∝
R
−2.3±0.5
at larger radii. We infer that the flat part of the density profile corresponds to a CSM shell with mass ∼0.021
M
☉
, and that the progenitor’s effective mass-loss rate varied with time over the range (50–500) × 10
−5
M
☉
yr
−1
for an adopted wind velocity
v
w
= 1000 km s
−1
and shock microphysical parameters
ϵ
e
= 0.1,
ϵ
B
= 0.01. These results add to the mounting observational evidence for departures from the traditional single-wind mass-loss scenarios in evolved, massive stars in the centuries leading up to core collapse. Potentially viable scenarios include mass loss powered by gravity waves and/or interaction with a binary companion.
Fusion reactors depend on the blanket material to breed and release tritium at the same rate or faster than it is consumed by the fusion reaction. Cellular ceramic breeders (CCBs) are dense materials ...that can maintain a high tritium breeding ratio while promoting tritium release because of highly connected pores. Assessing the tritium breeding capabilities of these materials requires a combination of extensive experimental and modeling efforts. In this work, we develop and calibrate a multiphysics model of tritium transport. This novel model accounts for ceramic and pore diffusion, trapping and detrapping, and several surface reactions at the pore surface. We perform a sensitivity analysis and calibrate the model by comparing its predictions against experimental measurements of deuterium absorption. The calibrated model is then used to model tritium absorption in samples with different pore microstructures to investigate the effect of pore interconnectivity on tritium absorption. The model is part of the development of the multiscale, multiphysics framework for tritium transport i.e., the Tritium Migration Analysis Program (TMAP8), which is itself built on top of the finite-element multiphysics framework multiphysics object-oriented simulation environment (MOOSE). This study demonstrates some of TMAP8's capabilities and is the first step toward assessing the tritium breeding capabilities of ceramic breeder material designs.
As the scope of additive manufacturing broadens, interest has developed in 3D-printed objects that are derived from recyclable resins with chemical and mechanical tunability. Dynamic covalent bonds ...have the potential to not only increase the sustainability of 3D-printed objects, but also serve as reactive sites for postprinting derivatization. In this study, we use boronate esters as a key building block for the development of catalyst-free, 3D-printing resins with the ability to undergo room-temperature exchange at the cross-linking sites. The orthogonality of boronate esters is exploited in fast-curing, oxygen-tolerant thiol–ene resins in which the dynamic character of 3D-printed objects can be modulated by the addition of a static, covalent cross-linker with no room-temperature bond exchange. This allows the mechanical properties of printed parts to be varied between those of a traditional thermoset and a vitrimer. Objects printed with a hybrid dynamic/static resin exhibit a balance of structural stability (residual stress = 18%) and rapid exchange (characteristic relaxation time = 7 s), allowing for interfacial welding and postprinting functionalization. Modulation of the cross-linking density postprinting is enabled by selective hydrolysis of the boronate esters to generate networks with swelling capacities tunable from 1.3 to 3.3.
Abstract Youth screen media activity is a growing concern, though few studies include objective usage data. Through the longitudinal, U.S.-based Adolescent Brain Cognitive Development (ABCD) Study, ...youth (m age = 14; n = 1415) self-reported their typical smartphone use and passively recorded three weeks of smartphone use via the ABCD-specific Effortless Assessment Research System (EARS) application. Here we describe and validate passively-sensed smartphone keyboard and app use measures, provide code to harmonize measures across operating systems, and describe trends in adolescent smartphone use. Keyboard and app-use measures were reliable and positively correlated with one another ( r = 0.33) and with self-reported use ( r s = 0.21–0.35). Participants recorded a mean of 5 h of daily smartphone use, which is two more hours than they self-reported. Further, females logged more smartphone use than males. Smartphone use was recorded at all hours, peaking on average from 8 to 10 PM and lowest from 3 to 5 AM. Social media and texting apps comprised nearly half of all use. Data are openly available to approved investigators ( https://nda.nih.gov/abcd/ ). Information herein can inform use of the ABCD dataset to longitudinally study health and neurodevelopmental correlates of adolescent smartphone use.
The frequency and intensity of wildfires have been increasing over the last 50 years and negatively impacted the wine industry. Previous methods of smoke mitigation during grape processing have shown ...little impact in reducing smoke taint in wines. Therefore, a novel method of using edible spray coatings for vineyard application was developed to help prevent volatile smoke phenol uptake in wine grapes. Four cellulose nanofiber‐based coating suspensions incorporated with chitosan and/or β‐cyclodextrin were evaluated. Films derived from the coating suspensions were exposed to volatile phenols found in wildfire smoke (guaiacol, 4‐methyl guaiacol, m‐cresol, o‐cresol, p‐cresol, syringol, and 4‐methyl syringol) and evaluated with ultraviolet‐visible spectroscopy where the results indicated that the coatings could uptake smoke phenols in varying degrees. The coatings were also applied in a vineyard at three different application times during grape growth: pea‐sized, pre‐bunch closure, and both at pea‐sized and pre‐bunch closure. The results showed that the application time did not have a significant (p < 0.05) effect on berry size, weight, °Brix, pH, or titratable acidity. The type of coating, time of application and washing were found to impact the number of volatile phenols in the grapes after a smoke event. Results from this study indicated that edible coatings could help mitigate smoke uptake in wine grapes without sacrificing the growth and key composition parameters of wine grapes.
Practical Application
This research provides a novel spray coating that can be applied to wine grapes in the vineyard to potentially mitigate volatile smoke compounds in wine grapes without impacting fruit growth and key compositional parameters of wine grapes, thus maintaining high quality of wines for consumers. Results from this study can also be potentially applied to other agricultural commodities to solve the issues caused by the wildfire smoke.
The last 2 years have been a period of unprecedented growth for the MOOSE community and the software itself. The number of monthly visitors to the website has grown from just over 3,000 to now ...averaging 5,000. In addition, over 1,800 pull requests have been merged since the beginning of 2020, and the new discussions forum has averaged 600 unique visitors per month. The previous publication has been cited over 200 times since it was published 2 years ago. This paper serves as an update on some of the key additions and changes to the code and ecosystem over the last 2 years, as well as recognizing contributions from the community.
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