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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Long non-coding RNA SBF2-AS1 promotes hepatocellular carcinoma progression through regulation of miR-140-5p-TGFBR1 pathway

Highlights: • LncRNA SBF2-AS1 was overexpressed in HCC tissues and cell lines. • Up-regulation of lncRNA SBF2-AS1 was associated with poor clinical features and prognosis in HCC patients. • Knockdown of lncRNA SBF2-AS1 suppressed HCC progression by regulation of miR-140-5p-TGFBR1 pathway. A growing number of studies has suggested that long non-coding RNAs (lncRNAs) exert essential roles in the development and progression of hepatocellular carcinoma (HCC). However, the roles of lncRNA and its molecular mechanism in HCC are largely unknown. In the present study, the functions and molecular mechanisms of a novel lncRNA, SET-binding factor 2 (SBF2) antisense RNA1 (SBF2-AS1), were investigated in HCC tissues and cell lines. We found that the expression levels of SBF2-AS1 were significantly up-regulated in HCC tissues and correlated with poor prognosis. SBF2-AS1 knockdown could inhibit the proliferation of HCC cells and attenuate the development of HCC tumor in vivo. Moreover, wound healing and Transwell assays revealed that down-regulation of SBF2-AS1 suppressed the migration and invasion of HCC cells by modulating epithelial-mesenchymal transition (EMT) ability. Mechanistically, we observed that SBF2-AS1 served as a competing endogenous RNA (ceRNA) of miR-140–5p. Subsequently, transforming growth factor beta receptor 1 (TGFBR1) was certified as a direct target of miR-140–5p and enforcing SBF2-AS1 expression elevated TGFBR1 expression in HCC. Taken together, our study suggested that SBF2-AS1 modulated TGFBR1 through sponging miR-140–5p in HCC development and progression indicating that SBF2-AS1 might be further chosen as a potential anticancer therapeutic target and a promising prognostic biomarker for HCC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Knockdown of long non-coding RNA TP73-AS1 suppresses triple negative breast cancer cell vasculogenic mimicry by targeting miR-490-3p/TWIST1 axis

Triple negative breast cancer (TNBC) is among the most clinically aggressive subtypes of breast cancer. Despite the availability of new drugs, patients suffering TNBC bear disheartening prognosis. Vasculogenic mimicry (VM) is a malignant tumor specific non-endothelial vascular network, which provide oxygen and nutrients to tumor cells and facilitate tumor progression. Therefore targeting TNBC VM formation may contribute to tumor treatment. In this study, we found that long non-coding RNA TP73 antisense RNA 1 (TP73-AS1) was upregulated in VM positive TNBC tissues. Knockdown of TP73-AS1 suppressed TNBC cell line MDA-MB-231 cell VM formation in vitro. In addition, RNA immunoprecipitation assay and dual luciferase reporter assay showed that TP73-AS1 bound to miR-490-3p in a sequence-specific manner. miR-490-3p was downregulated in VM positive tissues and was involved in TP73-AS1-mediated MDA-MB-231 cell VM formation. Furthermore, TWIST1 was a target of miR-490-3p and participated in TP73-AS1/miR-490-3p-modulated MDA-MB-231 cell VM formation. Findings in this study may provide insight in TNBC management.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long non-coding RNA EPIC1 promotes cholangiocarcinoma cell growth

Highlights: • Lnc-EPIC1 expression is elevated in cholangiocarcinoma tissues, compared to adjacent tissues. • Lnc-EPIC1 promotes CCA cancer cell growth. • MYC directly interacts with Lnc-EPIC1 in CCA cancer cells. Cholangiocarcinoma (CCA) is the as the most frequently observed biliary tract malignancy, which has low survival rate in addition to constrained treatment options. However, the fundamental molecular mechanism underlying malignant progression of CCA is quite ambiguous. Recent studies reported that long non-coding RNA (lncRNA) might play critical roles in regulating chemo-resistant of multiple types of cancer. In this study, our results indicate that the LncRNA-EPIC1 expression were significantly increased in cholangiocarcinoma tissues, compared to adjacent normal tissues. And also, its expression also increased in several CCA cancer cell lines than that in human normal immortalized cholangiocyte cell. Loss-and-gain of Lnc-EPIC1 contributes to the CCA cell growth, colony formation, cell apoptosis and also cell cycle. Myc has been reported to directly interact with Lnc-EPIC1 in several cancer cells. Myc targets, including Cyclin A/D and CDK9 were downregulated by Lnc-EPIC1 siRNA. Myc knockout also suppresses the CCA cell growth, colony formation and cell apoptosis. However, Lnc-EPIC1 knockdown failed to enhance the Myc-KO-induced suppression of CCA tumor progression. RNA immunoprecipitation (RIP) results showed the direct interaction between Lnc-EPIC1 and Myc. Taken together, our results show that Lnc-EPIC1 promotes CCA cancer progression by targeting Myc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long non-coding RNA FLVCR1-AS1 contributes to the proliferation and invasion of lung cancer by sponging miR-573 to upregulate the expression of E2F transcription factor 3

Lung cancer is one of the most common causes of cancer-related death all over the world. In recent years, long non-coding RNAs (lncRNAs) have been reported to play critical roles in the development and progression of human malignancies. In the present study, we aimed to study the role and mechanism of FLVCR1-AS1 in human non-small cell lung cancer (NSCLC). Results revealed that FLVCR1-AS1 was markedly upregulated in NSCLC tissues and cell lines. Knockdown of FLVCR1-AS1 significantly inhibited the proliferation, migration, invasion and promoted apoptosis of NSCLC cells, and suppressed tumor growth of NSCLC in vivo. Moreover, we explored regulatory mechanism, and found that FLVCR1-AS1 functioned as a competing endogenous RNA (ceRNA) by directly binding to miRNA-573, and E2F transcription factor 3 (E2F3) was identified as a down-stream target of miR-573. FLVCR1-AS1 positively regulated E2F3 expression through inhibiting miR-573 in NSCLC cells. Our findings suggested that FLVCR1-AS1/miR-573/E2F3 axis was an important signaling pathway in mediating tumorigenesis and progression of NSCLC, and further indicated that FLVCR1-AS1 could be a novel diagnostic biomarker and therapeutic target for NSCLC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long non-coding RNA, Bmcob, regulates osteoblastic differentiation of bone marrow mesenchymal stem cells

Disordered osteoblastic differentiation of bone marrow mesenchymal stem cells (BMSCs) contributes to bone loss. The underlying mechanisms are complicated and not fully understood. Long non-coding RNAs (lncRNAs) are emerging as an important regulatory factors on bone metabolism. Here, we discovered a novel lncRNA, Bmcob, which modulated osteogenic differentiation of primary mouse BMSCs. Expression levels of Bmcob were significantly upregulated in early-to-mid stages during osteoblast differentiation. Silencing of Bmcob suppressed osteoblastic differentiation of BMSCs in vitro, whereas its overexpression protected BMSCs from oxidative stress induced inhibition on osteogenesis. Subsequently, we discovered that selenoprotein P (Sepp1), which is located next to the Bmcob gene, was partly responsible for the regulatory effects of Bmcob. In addition, a series of selenoproteins were downregulated in BMSCs with Bmcob knockdown. Mechanistically, we found Bmcob was associated with selenocysteine insertion sequence binding protein 2 (SBP2), a critical trans-acting factor for selenoprotein synthesis. Finally, we suggest an explanatory hypothesis that through modulating nucleocytoplasmic shuttling of SBP2, Bmcob regulates a number of selenoproteins expression, including sepp1, and then mediates osteogenesis of BMSCs. Taken together, our results revealed a novel mechanism regulating osteogenesis of BMSCs and may function as a potential target for treating osteoporosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Surface tension models for a multi-material ALE code with AMR

A number of surface tension models have been implemented in a 3D multi-physics multi-material code, ALE–AMR, which combines Arbitrary Lagrangian Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR). ALE–AMR is unique in its ability to model hot radiating plasmas, cold fragmenting solids, and most recently, the deformation of molten material. The surface tension models implemented include a diffuse interface approach with special numerical techniques to remove parasitic flow and a height function approach in conjunction with a volume-fraction interface reconstruction package. These surface tension models are benchmarked with a variety of test problems. In conclusion, based on the results, the height function approach using volume fractions was chosen to simulate droplet dynamics associated with extreme ultraviolet (EUV) lithography.

42 ENGINEERING↗
DOE OSTI2025

3D mesh regularization within an ALE code using a weighted line sweeping method

The Lagrangian formalism is widely used to simulate hydrodynamic responses in complex engineering applications, particularly those involving strong shock waves. However, as the mesh moves with the fluid, it can become highly distorted, requiring a regularization step. This involves constructing a new grid and remapping conservative quantities onto it to restore mesh quality. This work introduces a regularization method for block-structured meshes within a 3D ALE (Arbitrary Lagrangian-Eulerian) code. The proposed approach prevents mesh tangling while preserving the anisotropic features of the initial Lagrangian mesh. This regularization technique incorporates aspect ratio-based weights to control mesh smoothing. Unlike uniform rezoning techniques, this weighted approach maintains proximity to the Lagrangian mesh while improving mesh quality. Here, the method effectively handles concave geometries by mitigating the grid attraction phenomenon, which typically leads to mesh concentration along concave edges. Numerical experiments demonstrate its efficiency in regularizing severely deformed meshes, and its integration within the ALE framework is validated on challenging hydrodynamic test cases, including the triple point problem.

42 ENGINEERING↗
DOE OSTI2014

A block-tridiagonal solver with two-level parallelization for finite element-spectral codes

Two-level parallelization is introduced to solve a massive block-tridiagonal matrix system. One-level is used for distributing blocks whose size is as large as the number of block rows due to the spectral basis, and the other level is used for parallelizing in the block row dimension. The reason for the added parallelization dimension is to retard the saturation of the scaling due to communication overhead and inefficiencies in the single-level parallelization only distributing blocks. As a technique for parallelizing the tridiagonal matrix, the combined method of “Partitioned Thomas method” and “Cyclic Odd–Even Reduction” is implemented in an MPI-Fortran90 based finite element-spectral code (TORIC) that calculates the propagation of electromagnetic waves in a tokamak. The two-level parallel solver using thousands of processors shows more than 5 times improved computation speed with the optimized processor grid compared to the single-level parallel solver under the same conditions. Three-dimensional RF field reconstructions in a tokamak are reflected as examples of the physics simulations that have been enabled by this algorithmic advance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

The accurate particle tracer code

The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runaway electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world’s fastest computer, the Sunway TaihuLight supercomputer, by supporting master–slave architecture of Sunway many-core processors. Here, based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

HTR solver: An open-source exascale-oriented task-based multi-GPU high-order code for hypersonic aerothermodynamics

In this study, the open-source Hypersonics Task-based Research (HTR) solver for hypersonic aerothermodynamics is described. The physical formulation of the code includes thermochemical effects induced by high temperatures (vibrational excitation and chemical dissociation). The HTR solver uses high-order TENO-based spatial discretization on structured grids and efficient time integrators for stiff systems, is highly scalable in GPU-based supercomputers as a result of its implementation in the Regent/Legion stack, and is designed for direct numerical simulations of canonical hypersonic flows at high Reynolds numbers. Additionally, the performance of the HTR solver is tested with benchmark cases including inviscid vortex advection, low- and high-speed laminar boundary layers, inviscid one-dimensional compressible flows in shock tubes, supersonic turbulent channel flows, and hypersonic transitional boundary layers of both calorically perfect gases and dissociating air.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Fission fragment decay simulations with the CGMF code

The CGMF code implements the Hauser-Feshbach statistical nuclear reaction model to follow the de-excitation of fission fragments by successive emissions of prompt neutrons and γ rays. The Monte Carlo technique is used to facilitate the analysis of complex distributions and correlations among the prompt fission observables. Starting from initial configurations for the fission fragments in mass, charge, kinetic energy, excitation energy, spin, and parity, Y(A,Z,KE,U,J,π), CGMF samples neutron and γ-ray probability distributions at each stage of the decay process, conserving energy, spin and parity. Nuclear structure and reaction input data from the RIPL3 library are used to describe fission fragment properties and decay probabilities. Characteristics of prompt fission neutrons, prompt fission γ rays, and independent fission yields can be studied consistently. Correlations in energy, angle and multiplicity among the emitted neutrons and γ rays can be easily analyzed as a function of the emitting fragments. Finally, in its current version, CGMF is limited to certain spontaneous fission reactions on Pu and Cf isotopes, as well as neutron-induced fission reactions up to 20 MeV on U, Np, and Pu isotopes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

DFT-FE 1.0: A massively parallel hybrid CPU-GPU density functional theory code using finite-element discretization

In this work, we present DFT-FE 1.0, building on DFT-FE 0.6 [Comput. Phys. Commun. 246, 106853 (2020)], to conduct fast and accurate large-scale density functional theory (DFT) calculations (reaching ~ 100,000 electrons) on both many-core CPU and hybrid CPU-GPU computing architectures. This work involves improvements in the real-space formulation—via an improved treatment of the electrostatic interactions that substantially enhances the computational efficiency—as well high-performance computing aspects, including the GPU acceleration of all the key compute kernels in DFT-FE. We demonstrate the accuracy by comparing the ground-state energies, ionic forces and cell stresses on a wide-range of benchmark systems against those obtained from widely used DFT codes. Further, we demonstrate the numerical efficiency of our implementation, which yields ~ 20× CPU-GPU speed-up by using GPU acceleration on hybrid CPU-GPU nodes. Notably, owing to the parallel-scaling of the GPU implementation, we obtain wall-times of 80–140 seconds for full ground-state calculations, with stringent accuracy, on benchmark systems containing ~ 6, 000 – 15,000 electrons.

pseudopotential↗
DOE OSTI2023

Implementation and verification of a model linearized multi-species collision operator in the COGENT code

We implement the multi-species linearized model collision operator, based on the approach proposed by Kolesnikov, in the full-f continuum gyrokinetic code COGENT. We describe the operator and use it in several COGENT simulations of highly collisional plasmas. We analyze simulation results with the Braginskii fluid model to illustrate that COGENT recovers both friction and thermal forces. Finally, we simulate the neoclassical transport of heavy impurities with COGENT and illustrate agreement with previously published theoretical results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Verification and validation of the open-source plasma fluid code: Zapdos

Zapdos is an open-source finite element plasma fluid solver based on the MOOSE multiphysics framework. This paper outlines Zapdos verification, benchmarking, and validation efforts for 1D and 2D RF capacitively coupled plasma discharge models for mid-range pressures (0.1 - 1 Torr). The verification process involved using the method of manufactured solutions to assess Zapdos spatial and temporal error convergence. L2 errors ranged from 10 -2 to 10 -4 , while the convergence’s slope were in agreement with the predicted slopes for the tested variable and time integration orders. The benchmarking process involved comparisons to previously results from the validated finite element code, LSODI. These works included 1D and 2D simulations for a range of plasma parameters (densities, temperatures, voltage, etc.). For the 1D cases, Zapdos and LSODI results were in very good agreement. In the 2D cases, variable behaviors matched, with slight discrepancies in peak values. The validation process involved comparisons to experimental works including electron density measurements by microwave interferometry and metastable density measurements by planar laser-induced fluorescence imaging. Results shown reasonable agreement at higher pressure, with results starting to diverge at low pressures. Furthermore, probable causes for this diverges are the limitation of the fluid assumption for plasmas at low pressure, or the need for more robust boundary conditions. Overall, Zapdos shown reasonable results for the verification, benchmarking, and validation efforts, and Zapdos can be downloaded at https://github.com/shannon-lab/zapdos.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Considerations and code for partial volume correcting [ 18 F]-AV-1451 tau PET data

[ 18 F]-AV-1451 is a leading tracer used with positron emission tomography (PET) to quantify tau pathology. However, [ 18 F]-AV-1451 shows “off target” or non-specific binding, which we define as binding of the tracer in unexpected areas unlikely to harbor aggregated tau based on autopsy literature. Along with caudate, putamen, pallidum and thalamus nonspecific binding, we have found binding in the superior portion of the cerebellar gray matter, leading us to use inferior cerebellar gray as the reference region. We also addressed binding in the posterior portion of the choroid plexus. PET signal unlikely to be associated with tau also occurs in skull, meninges and soft tissue. We refer to [ 18 F]- AV-1451 binding in the skull and meninges as extra-cortical hotspots (ECH) and find them near lateral and medial orbitofrontal, lateral occipital, inferior and middle temporal, superior and inferior parietal, and inferior cerebellar gray matter. Lastly, the choroid plexus also shows nonspecific binding that bleeds into hippocampus. We are providing the code (http://www.runmycode.org/companion/view/2798) used to create different regions of interest (ROIs) that we then used to perform Partial Volume Correction (PVC) using the Rousset geometric transfer matrix method. This method was used in the companion article, “Comparison of multiple tau-PET measures as biomarkers in aging and Alzheimer's Disease” (DOI 10.1016/j.neuroimage.2017.05.058).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Use of system code to estimate equilibrium tritium inventory in fusion DT machines, such as ARIES-AT and components testing facilities

ITER is under construction and will begin operation in 2020. This is the first 500 MWfusion class DT device, and since it is not going to breed tritium, it will consume most of the limited supply of tritium resources in the world. Yet, in parallel, DT fusion nuclear component testing machines will be needed to provide technical data for the design of DEMO. It becomes necessary to estimate the tritium burn-up fraction and corresponding initial tritium inventory and the doubling time of these machines for the planning of future supply and utilization of tritium. With the use of a system code, tritium burn-up fraction and initial tritium inventory for steady state DT machines can be estimated. Estimated tritium burn-up fractions of FNSF-AT, CFETR-R and ARIES-AT are in the range of 1–2.8%. Corresponding total equilibrium tritium inventories of the plasma flow and tritium processing system, and with the DCLL blanket option are 7.6 kg, 6.1 kg, and 5.2 kg for ARIES-AT, CFETR-R and FNSF-AT, respectively.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2017

Review of the 9th NLTE code comparison workshop

Here, we review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Cross-Code verification and sensitivity analysis to effectively model the electrothermal instability

This manuscript presents verification cases that are developed to study the electrothermal instability (ETI). Specific verification cases are included to ensure that the unit physics components necessary to model the ETI are accurate, providing a path for fluid-based codes to effectively simulate ETI in the linear and nonlinear growth regimes. Two software frameworks with different algorithmic approaches are compared for accuracy in their ability to simulate diffusion of a magnetic field, linear growth of the ETI, and a fully nonlinear ETI evolution. The nonlinear ETI simulations show early time agreement, with some differences emerging, as noted in the wavenumber spectrum, late into the nonlinear development of ETI. Here, a sensitivity study explores the role of equation-of-state (EOS), vacuum density, and vacuum resistivity. EOS and vacuum resistivity are found to be the most critical factors in the modeling of nonlinear ETI development.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗