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At least 721 records · Page 40

System-based identification of toxicity pathways associated with multi-walled carbon nanotube-induced pathological responses

The fibrous shape and biopersistence of multi-walled carbon nanotubes (MWCNT) have raised concern over their potential toxicity after pulmonary exposure. As in vivo exposure to MWCNT produced a transient inflammatory and progressive fibrotic response, this study sought to identify significant biological processes associated with lung inflammation and fibrosis pathology data, based upon whole genome mRNA expression, bronchoaveolar lavage scores, and morphometric analysis from C57BL/6J mice exposed by pharyngeal aspiration to 0, 10, 20, 40, or 80 μg MWCNT at 1, 7, 28, or 56 days post-exposure. Using a novel computational model employing non-negative matrix factorization and Monte Carlo Markov Chain simulation, significant biological processes with expression similar to MWCNT-induced lung inflammation and fibrosis pathology data in mice were identified. A subset of genes in these processes was determined to be functionally related to either fibrosis or inflammation by Ingenuity Pathway Analysis and was used to determine potential significant signaling cascades. Two genes determined to be functionally related to inflammation and fibrosis, vascular endothelial growth factor A (vegfa) and C-C motif chemokine 2 (ccl2), were confirmed by in vitro studies of mRNA and protein expression in small airway epithelial cells exposed to MWCNT as concordant with in vivo expression. This study identified that the novel computational model was sufficient to determine biological processes strongly associated with the pathology of lung inflammation and fibrosis and could identify potential toxicity signaling pathways and mechanisms of MWCNT exposure which could be used for future animal studies to support human risk assessment and intervention efforts. - Highlights: • A novel computational model identified toxicity pathways matching in vivo pathology. • Systematic identification of MWCNT-induced biological processes in mouse lungs • MWCNT-induced functional networks of lung inflammation and fibrosis were revealed. • Two functional, representative genes, ccl2 and vegfa, were validated in vitro.

60 APPLIED LIFE SCIENCES↗

Modeling and simulation of vascular tumors embedded in evolving capillary networks

Here in this work, we present a coupled 3D–1D model of solid tumor growth within a dynamically changing vascular network to facilitate realistic simulations of angiogenesis. Additionally, the model includes erosion of the extracellular matrix, interstitial flow, and coupled flow in blood vessels and tissue. We employ continuum mixture theory with stochastic Cahn–Hilliard type phase-field models of tumor growth. The interstitial flow is governed by a mesoscale version of Darcy’s law. The flow in the blood vessels is controlled by Poiseuille flow, and Starling’s law is applied to model the mass transfer in and out of blood vessels. The evolution of the network of blood vessels is orchestrated by the concentration of the tumor angiogenesis factors (TAFs); blood vessels grow towards the increasing TAFs concentrations. This process is not deterministic, allowing random growth of blood vessels and, therefore, due to the coupling of nutrients in tissue and vessels, makes the growth of tumors stochastic. We demonstrate the performance of the model by applying it to a variety of scenarios. Numerical experiments illustrate the flexibility of the model and its ability to generate satellite tumors. Simulations of the effects of angiogenesis on tumor growth are presented as well as sample-independent features of cancer.

3D–1D coupled blood flow models↗

A Feature-Based Stochastic Permeability of Shale: Part 1—Validation and Two-Phase Permeability in a Utica Shale Sample

Estimate of permeability plays a crucial role in flow-based studies of fractured tight-rocks. It is well known that most of the flow through tight-rocks (e.g., shales) is controlled by permeable features (e.g., fractures, laminations, etc.), and there is negligible flow through the matrix. However, current approaches in the literature to model permeability of tight-rocks do not account for such features present within the rock ranging from micro-scale to field-scale. Current permeability modeling approach assumes a single continuum without considering the presence of permeable features within the matrix (e.g., micro-fractures) or outside the matrix (e.g., natural fractures). Although the laboratory-measured permeability implicitly captures discrete features present in that sample (e.g., fractures, laminations, micro-fractures), most of the permeability models proposed for shale do not account for these features. Fracture permeability in the literature is typically modeled using an ideal slit assumption; however, this highly overestimates its permeability because fractures in real medium are non-ideal in terms of their porosity and tortuosity, which affect their permeability. Additionally, the transition zone between fracture and matrix also affects the permeability of fracture. Here in this study, part of a two-part series, a new method to predict permeability of fractured shale by discretizing the medium into matrix (inorganic and organic) and fractures is presented. New analytical expressions of permeability are derived to account for non-ideal nature of porous medium and two-phase flow in fractures. Rock feature in each cell of the grid is identified as one of the three elements (organic matter, inorganic matter, or fracture), and permeability of that cell is estimated using a suitable analytical expression. This method allows estimating permeability at any scale of interest and more robustly than by a pure analytical approach. The proposed method is validated against local and global-scale measurements on three fractured samples from laboratory. Finally, the method is used to predict two-phase flow permeability of supercritical CO 2 displacing water within a fracture in a Utica shale sample. The proposed two-phase flow permeability equations can be used as a quick analytical tool to predict relative permeability estimates of two-phase flow in fractured shale samples. In Part 2, the proposed method is used to estimate field-scale permeability through an optimization process that uses field-scale production and other readily available information.

58 GEOSCIENCES↗

Characterizing the performance of node-aware strategies for irregular point-to-point communication on heterogeneous architectures

Supercomputer architectures are trending toward higher computational throughput due to the inclusion of heterogeneous compute nodes. These multi-GPU nodes increase on-node computational efficiency, while also increasing the amount of data to be communicated and the number of potential data flow paths. In this work, we characterize the performance of irregular point-to-point communication with MPI on heterogeneous compute environments through performance modeling, demonstrating the limitations of standard communication strategies for both device-aware and staging-through-host communication techniques. Presented models suggest staging communicated data through host processes then using node-aware communication strategies for high inter-node message counts. Notably, the models also predict that node-aware communication utilizing all available CPU cores to communicate inter-node data leads to the most performant strategy when communicating with a high number of nodes. Furthermore, model validation is provided via a case study of irregular point-to-point communication patterns in distributed sparse matrix–vector products. Importantly, we include a discussion on the implications model predictions have on communication strategy design for emerging supercomputer architectures.

97 MATHEMATICS AND COMPUTING↗

Extracting and Interpreting Electrochemical Impedance Spectra (EIS) from Physics-Based Models of Lithium-Ion Batteries

This paper implements a highly efficient algorithm to extract electrochemical impedance spectra (EIS) from physics-based battery models (e.g., a P2D model). The mathematical approach is different from how EIS is practiced experimentally. Experimentally, the voltage (current) is harmonically perturbed over a wide range of frequencies and the amplitude and phase shift of the corresponding current (voltage) is measured. The experimental approach can be implemented in simulation software, but is computationally expensive. The approach here is to determine locally linear state-space models from the full physical model. The four Jacobian matrices that are the basis of the state-space models can be derived by numerical differentiation of the physical model. The EIS is then extracted from the state-space model using computationally efficient matrix-manipulation techniques. The algorithm can evaluate the full EIS at an instant in time during a transient, independent of whether the battery is in a stationary state. The approach is also able to separate the full-cell impedance to evaluate partial EIS, such as for a battery anode alone. Although such partial EIS is difficult to measure experimentally, the partial EIS provides valuable insights in interpreting the full-cell EIS.

25 ENERGY STORAGE↗

Enhanced superconductivity by near-neighbor attraction in the doped extended Hubbard model

A recent experiment has unveiled an anomalously strong electron-electron attraction in the one-dimensional copper-oxide chain Ba 2–x Sr x CuO 3+δ . While the effect of the near-neighbor electron attraction V in the one-dimensional extended Hubbard chain has been examined recently, its effect in the Hubbard model beyond the one-dimensional chain remains unclear. Here, in this work, we report a density matrix renormalization group study of the extended Hubbard model on long four-leg cylinders on the square lattice. We find that the near-neighbor electron attraction V can notably enhance the long-distance superconducting correlations while simultaneously suppressing the charge-density-wave (CDW) correlations. Specifically, for a modestly strong electron attraction, the superconducting correlations become dominant over the CDW correlations with a Luttinger exponent K sc ~1 and strong divergent superconducting susceptibility. Our results provide a promising way to realize long-range superconductivity in the doped Hubbard model. The relevance of our numerical results to cuprate materials is also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Diagonalization of transfer matrix of supersymmetry U{sub q}(sl-caret(M+1|N+1)) chain with a boundary

We study the supersymmetry U{sub q}(sl-caret(M+1|N+1)) analogue of the supersymmetric t-J model with a boundary. Our approach is based on the algebraic analysis method of solvable lattice models. We diagonalize the commuting transfer matrix by using the bosonizations of the vertex operators associated with the quantum affine supersymmetry U{sub q}(sl-caret(M+1|N+1)).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A generalized 3D elastic model for nanoscale, self-assembled oxide-metal thin films with pillar-in-matrix configurations

In recent years, functional oxide-metal based vertically aligned nanocomposite (VAN) thin films have gained interest due to their intriguing physical properties and multifunctionalities stemming from the complex interactions between the two phases in the film and the substrate. In this work, we develop a model for studying the energetics of these thin film systems, including the effects of both lattice mismatch and capillary forces due to interface curvature. Each phase is incorporated into the model using a phase indicator function, and we introduce the capillary forces as body forces using a vector density representation of the interface. The model is implemented using the finite element method to study the deformation of the thin film which is composed of Au nanopillars embedded in a La 0.7 Sr 0.3 MnO 3 (LSMO) matrix on an SrTiO 3 (STO) substrate. Further, the results suggest that the total energy is lowest for random configurations of pillars compared to ordered square and hexagonal lattice configurations, consistent with the random distribution of pillars found in experiments. Furthermore, we find that the interfacial energy dominates the total energy of each configuration, suggesting that interfacial energy in the system is an important design parameter for nanocomposite growth, along with the lattice mismatch.

36 MATERIALS SCIENCE↗

SiC/SiC Cladding Materials Properties Handbook

When a new class of material is considered for a nuclear core structure, the in-pile performance is usually assessed based on multi-physics modeling in coordination with experiments. This report aims to provide data for the mechanical and physical properties and environmental resistance of silicon carbide (SiC) fiber–reinforced SiC matrix (SiC/SiC) composites for use in modeling for their application as accidenttolerant fuel cladding for light water reactors (LWRs). The properties are specific for tube geometry, although many properties can be predicted from planar specimen data. This report presents various properties, including mechanical properties, thermal properties, chemical stability under normal and offnormal operation conditions, hermeticity, and irradiation resistance. Table S.1 summarizes those properties mainly for nuclear-grade SiC/SiC composites fabricated via chemical vapor infiltration (CVI). While most of the important properties are available, this work found that data for the in-pile hydrothermal corrosion resistance of SiC materials and for thermal properties of tube materials are lacking for evaluation of SiC-based cladding for LWR applications.

36 MATERIALS SCIENCE↗

SUBSURFACE CHARACTERIZATION OF 67P/CHURYUMOV–GERASIMENKO’S ABYDOS SITE

On 2014 November 12, the ESA/ Rosetta descent module Philae landed on the Abydos site of comet 67P/Churyumov–Gerasimenko. Aboard this module, the Ptolemy mass spectrometer measured a CO/CO{sub 2} ratio of 0.07 ± 0.04, which differs substantially from the value obtained in the coma by the Rosetta /ROSINA instrument, suggesting a heterogeneity in the comet nucleus. To understand this difference, we investigated the physicochemical properties of the Abydos subsurface, leading to CO/CO{sub 2} ratios close to that observed by Ptolemy at the surface of this region. We used a comet nucleus model that takes into account different water ice phase changes (amorphous ice, crystalline ice, and clathrates) as well as diffusion of molecules throughout the pores of the matrix. The input parameters of the model were optimized for the Abydos site, and the ROSINA CO/CO{sub 2} measured ratio is assumed to correspond to the bulk value in the nucleus. We find that all considered structures of water ice are able to reproduce the Ptolemy observation with a time difference not exceeding ∼50 days, i.e., lower than ∼2% on 67P/Churyumov–Gerasimenko’s orbital period. The suspected heterogeneity of 67P/Churyumov–Gerasimenko’s nucleus is also found possible only if it is constituted of crystalline ices. If the icy phase is made of amorphous ice or clathrates, the difference between Ptolemy and ROSINA’s measurements would rather originate from the spatial variations in illumination on the nucleus surface. An eventual new measurement of the CO/CO{sub 2} ratio at Abydos by Ptolemy could be decisive to distinguish between the three water ice structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multicontinuum Flow Models for Assessing Two-Phase Flow in Containment Science

We present a new pre-processor tool written in Python that creates multicontinuum meshes for PFLOTRAN to simulate two-phase flow and transport in both the fracture and matrix continua. We discuss the multicontinuum modeling approach to simulate potentially mobile water and gas in the fractured volcanic tuffs at Aqueduct Mesa, at the Nevada National Security Site.

58 GEOSCIENCES↗

Theory for transport in magnetized plasmas

We present a two fluid model for anomalous thermal, particle and momentum transport which has been derived from kinetic theory using a small parameter ε~10-2. This small parameter can come from either the ratio of wave frequency to cyclotron frequency or the ratio of potential to thermal energies. This fluid model is strongly nonlinear and has an exact closure within the accuracy ε. It can be used to simulate the full radius of a tokamak including internal and edge transport barriers at the same time without introducing any local assumptions for physics model or grid size. It involves a full transport matrix, thus giving possibility for both density and heat pinches. The model can be derived from the Vlasov equation, adding also close collisions and includes particle pinches of the type found in the magnetosphere and in the Massachusetts Institute of Technology elevated dipole machine. Pinches are also in agreement for the heat pinch experiments on Doublet III D including simultaneous particle and heat pinches. For tokamaks it gives the right scaling of confinement time versus heating power. Finally, we have also recovered the Turbulent Equipartition result that the density scales as inverse safety factor q in typical simulations. Thus this model is both fundamental and of high practical use.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Code Benchmark of the HTTF Pressurized Conduction Cooldown Test Using SAM

The High Temperature Test Facility (HTTF) at Oregon State University is an integral system test facility to simulate postulated reactor transients of prismatic high-temperature gas-cooled reactors(HTGRs). A series of test campaigns was launched, providing abundant test data that could be used to benchmark reactor system analysis codes like the System Analysis Module (SAM). In this study, a SAM model of the facility is developed based on the two-dimensional (2D) ring model approach. All components including the ceramic matrix, graphite heaters, helium coolant channels, core barrel, upcomer, pressure vessel, and reactor cavity cooling system are modeled as concentric cylindrical rings. The model is used to simulate one of the benchmark problems-Pressurized Conduction Cooldown (PCC)-within the scope of the Organisation for Economic Co-operation and Development Nuclear Energy Agency International HTTF Benchmark. The simulations consist of two parts. In the first part, operating and boundary conditions as well as thermophysical properties of materials are specified for the benchmark problem. In this work, results from the first part will be used in code-to-code comparison. In the second part, the SAM model is used to simulate Test PG-27, which is the first PCC test carried out in the HTTF, with only two of the ten heater banks activated. The results in the second part are used for code-to-data comparison. Because the helium coolant flow rate is not measured in this facility, it is estimated using the input power and inlet/outlet coolant temperatures. Additionally, radial heat flow in the ceramic blocks is complicated by hundreds of cylindrical coolant channels and heater rods embedded in them. As such, it is necessary to deduce an effective thermal conductivity for the ceramic to analyze the core thermal behavior. SAM predictions of the helium coolant and ceramic temperatures are compared with test data measured in three equivalent sectors. Overall, the SAM results agree reasonably well with test data within the variation of data among the three sectors, which demonstrates SAM's capability in capturing transient effects in HTGR using the simplified 2D ring model.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Linear Solver for Electromagnetic Simulation of General Distribution Feeders

High-fidelity electromagnetic transient (EMT) modeling is required for accurate simulation and analysis of power system dynamics in modern distribution feeders. However, the high-fidelity of EMT models often leads to significant computational challenges, particularly in terms of computational resources and simulation time. This paper investigates the development and application of a detailed EMT model for general distribution feeders, with a focus on improving computational efficiency. A direct linear solver is proposed for a bordered block diagonal (BBD) matrix structure commonly encountered in a EMT model of distribution feeders. The solver integrates the Schur complement method with the block tridiagonal matrix algorithm to enhance the computational performance. The proposed solver is validated using the primary feeder of the IEEE 342-node test system, demonstrating its accuracy and efficiency in EMT simulations. Furthermore, the solver’s performance is benchmarked against MATLAB’s built-in linear solvers, showing significant improvements in computation time while maintaining high fidelity and accuracy in simulation results.

Choi, Jongchan [ORNL] (ORCID:000000025952455X)↗

Reservoir-scale model of geologic hydrogen production from serpentinization: Cyclic injection in a dual-permeability fracture-matrix system

Geologic hydrogen (GeoH 2 ) from serpentinization is a promising low-carbon resource, but its reservoir-scale behavior remains poorly understood. We develop a dual-permeability reactive transport model for an injector–producer well pair in ultramafic rock that couples multiphase flow, heat transfer, geochemistry, and porosity–permeability evolution. Here, the model is calibrated to olivine flow-through experiments and upscaled to two-year long simulations with continuous injection and cyclic injection with shut-in-to-injection ratios (SIR = 1, 0.5, 0.1). Olivine reacts along high-flux pathways to form lizardite and magnetite, increasing pH; H 2 (aq) and H 2 (g) peak early and then decline as exsolution and advective export outpace local generation. Continuous injection yields the highest cumulative H 2 but the lowest water-use efficiency (1.138 x 10 –6 mol/kgw). Cyclic injection increases this ratio to 1.35 x 10 –6 , 1.377 x 10 –6 , and 1.182 x 10 –6 mol/kgw for SIR = 1, 0.5, and 0.1, respectively; SIR = 0.5 provides a ~20% improvement over continuous injection and the best compromise for pilot design.

08 HYDROGEN↗

On the solvability of the quantum Rabi model and its 2-photon and two-mode generalizations

We study the solvability of the time-independent matrix Schrödinger differential equations of the quantum Rabi model and its 2-photon and two-mode generalizations in Bargmann Hilbert spaces of entire functions. We show that the Rabi model and its 2-photon and two-mode analogs are quasi-exactly solvable. We derive the exact, closed-form expressions for the energies and the allowed model parameters for all the three cases in the solvable subspaces. Up to a normalization factor, the eigenfunctions for these models are given by polynomials whose roots are determined by systems of algebraic equations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A quantitative phase-field model for gas bubble evolution in UO2

Due to the large formation energy of vacancies and noble gas atoms in the form of interstitials or substitutional atoms in nuclear fuel (UO2), the thermodynamic equilibrium concentrations of these species are very low in the nuclear fuel matrix even at very high temperatures, which imposes difficulties upon the quantitative study of bubble evolution via the phase-field method. In this study, a quantitative phase-field model is proposed to deal with this problem. The system’s free energy density is derived according to the principles of thermodynamics, with consideration of the elastic effect and with the use of real material parameters from experiments. The model is useful for the study of the kinetics of gas bubble growth with very dilute concentrations of vacancy and gas atoms in the matrix. This model is applied to study single bubble growth and multiple bubble growth under various concentrations of vacancy and gas atoms and at various temperatures. The elastic effect and the effects of the generation rate of vacancies and gas atoms on bubble growth are analyzed.

low defect concentration, nuclear fuel, gas bubble↗