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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 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Efficient continuous Energy-Multigroup hybrid depletion scheme using the Shift Monte Carlo code. Part I: Energy condensation sensitivity analysis

Monte Carlo (MC) codes coupled to depletion solvers are increasingly used to provide high fidelity fuel cycle modeling capabilities. Here, these coupled depletion-MC tools produce accurate results in general but can experience nonphysical spatial oscillations when time steps are large or when a system’s dominance ratio approaches unity. Two substepping techniques have been developed previously to remedy and dampen these spatial oscillations without needing to reduce step sizes. The first approach relied on higher-order techniques to account for spectral changes within steps (extrapolation and interpolation techniques). The second approach used the first order perturbation (FOP) theory to account for the change in the one-group spatial flux distribution within steps. This paper develops a hybrid depletion methodology which, in a way, combines how the flux is handled in both substepping techniques. Specifically, the multigroup (MG) MC Shift code is used to update the flux distribution within steps rather than a one-group FOP solver. A fully reflected pincell is investigated, which is not spatially dependent in the MG representation. Thus, the analysis in this paper is an initial demonstration of hybrid depletion. An upcoming companion paper will focus on how the hybrid depletion dampens spatial oscillations. The hybrid depletion approach is verified to be consistent with previous constant extrapolation depletion (CED) methods. This paper finds that the hybrid CED exhibits some error in the eigenvalue and one group constants within macro steps. To address this discrepancy, a simple interpolation scheme (CELI) is investigated. This work found that CELI sufficiently addresses the discrepancy in spectrum for macro steps up to 100 days. Overall, this work demonstrates that the hybrid depletion method can significantly reduce the number of high fidelity MC executions in a MC-coupled depletion with an acceptable eigenvalue error.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

Transient Multiphysics Simulations with Pin Power Reconstruction in the Griffin Reactor Physics Code

This work introduces the pin power reconstruction capability available in the Griffin reactor physics code. This capability is implemented in an unstructured mesh framework, and the methods introduced are applied to the 2D SIMBA reactor core, which has assemblies and pins arranged in a hexagonal lattice. Since this reactor has a non-Cartesian geometry and also operates in the thermal spectrum, a general approach to pin power reconstruction is adopted, where SPH-based equivalence is leveraged to preserve assembly-wise reaction rates, while computing full-core form functions to preserve pin-wise fission production rates within the fuel pins of the reactor core. In a 2D microreactor benchmark problem, this pin power reconstruction approach was shown to reproduce pin powers compared to the Serpent2 Monte Carlo code for fixed temperature conditions and control drum rotation angles, yielding a core-wide RMS error level of 0.6\% and a maximum absolute pin error of 2.3\%. In addition, a tabulated library of multigroup cross sections, SPH factors, and form functions was generated to demonstrate the applicability of pin power reconstruction to a thermal feedback problem. Finally, a control drum transient was successfully simulated, showcasing the application of pin power reconstruction in a transient multiphysics feedback problem.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Non-coding RNAs and heme oxygenase-1 in vaccinia virus infection

Highlights: • Heme oxygenase-1 (HO-1) induction inhibited vaccinia virus infection of macrophages. • Reduced infectivity inversely correlated with increased expression of non-coding RNAs. • The regulation of HO-1 and ncRNAs suggests a novel host defense response against vaccinia virus infection. - Abstract: Small nuclear RNAs (snRNAs) are <200 nucleotide non-coding uridylate-rich RNAs. Although the functions of many snRNAs remain undetermined, a population of snRNAs is produced during the early phase of infection of cells by vaccinia virus. In the present study, we demonstrate a direct correlation between expression of the cytoprotective enzyme heme oxygenase-1 (HO-1), suppression of selective snRNA expression, and inhibition of vaccinia virus infection of macrophages. Hemin induced HO-1 expression, completely reversed virus-induced host snRNA expression, and suppressed vaccinia virus infection. This involvement of specific virus-induced snRNAs and associated gene clusters suggests a novel HO-1-dependent host-defense pathway in poxvirus infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Long non-coding RNA ANRIL is up-regulated in bladder cancer and regulates bladder cancer cell proliferation and apoptosis through the intrinsic pathway

Antisense non-coding RNA in the INK4 locus (ANRIL) is a member of long non-coding RNAs and has been reported to be dysregulated in several human cancers. However, the role of ANRIL in bladder cancer remains unclear. This present study aimed to investigate whether and how ANRIL involved in bladder cancer. Our results showed up-regulation of ANRIL in bladder cancer tissues versus the corresponding adjacent non-tumor tissues. To explore the specific mechanisms, ANRIL was silenced by small interfering RNA or short hairpin RNA transfection in human bladder cancer T24 and EJ cells. Knockdown of ANRIL repressed cell proliferation and increased cell apoptosis, along with decreased expression of Bcl-2 and increased expressions of Bax, cytoplasmic cytochrome c and Smac and cleaved caspase-9, caspase-3 and PARP. However, no change of cleaved caspase-8 level was observed. Furthermore, in vivo experiment confirmed that knockdown of ANRIL inhibited tumorigenic ability of EJ cells in nude mice. Meanwhile, in accordance with in vitro study, knockdown of ANRIL inhibited expression of Bcl-2 and up-regulated expressions of Bax and cleaved caspase-9, but did not affect cleaved caspase-8 level. In conclusion, we first report that ANRIL possibly serves as an oncogene in bladder cancer and regulates bladder cancer cell proliferation and apoptosis through the intrinsic apoptosis pathway. - Highlights: • We first report the role of ANRIL in bladder cancer. • ANRIL is obviously up-regulated in bladder cancer tissues. • ANRIL regulates bladder cancer cell proliferation and cell apoptosis through the intrinsic pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Targeting long non-coding RNA ASBEL with oligonucleotide antagonist for breast cancer therapy

Long non-coding RNAs (lncRNAs) are defined as a class of RNA transcripts longer than 200 nucleotides encoded by mammalian genomes that lack protein-coding potential. LncRNA ASBEL has been identified as an anti-sense transcript of BTG3 (B cell translocation gene 3) gene, which encodes an anti-proliferation protein. Remarkable down-regulation of BTG3 has been reported in triple-negative breast cancer (TNBC). In the present study, a number of single-stranded modified anti-sense DNA oligonucleotides (antago) were designed, synthesized and screened for specific lncRNA ASBEL knockdown. We showed here that anti-ASBEL antago played a significant tumor suppressive role in TNBC by effective down-regulating lncRNA ASBEL, which in turn led to increased BTG3 expression. The obtained data suggest lncRNA ASBEL as a novel therapeutic target in TNBC. - Highlights: • LncRNA ASBEL is a promising therapeutic target in TNBC. • Antago is more powerful than siRNA in modulating lncRNA. • Antago3 is a useful therapeutic tool for TNBC treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long non-coding RNA XIST inhibited breast cancer cell growth, migration, and invasion via miR-155/CDX1 axis

Highlights: • LncRNA XIST was significantly down-regulated in breast cancer. • LncRNA XIST depressed the growth, migration and invasion of breast cancer. • MiR-155 was a direct target of XIST. • LncRNA XIST exerted its function via miR-155/CDX1 axis. Long non-coding RNA (lncRNA) is an important member of non-coding RNA family and emerging evidence has indicated that it plays a pivotal role in many physiological and pathological processes. The lncRNA X inactive specific transcript (XIST) is a potential tumour suppressor in some types of cancers. However, the expression and function of XIST in breast cancer remain largely unclear. The objective of this study was to evaluate the expression and biological role of XIST in breast cancer. The results showed that XIST was significantly down-regulated in breast cancer tissues and cell lines. Further functional analysis indicated that overexpression of XIST remarkably inhibited breast cancer cell growth, migration, and invasion. The results of luciferase reporter assays verified that miR-155 was a direct target of XIST in breast cancer. Moreover, caudal-type homeobox 1 (CDX1) was identified as a direct target of miR-155 and miR-155/CDX1 rescued the effects of XIST in breast cancer cells. Taken together, our results suggest that XIST is down-regulated in breast cancer and suppresses breast cancer cell growth, migration, and invasion via the miR-155/CDX1 axis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Long non-coding RNA TTN-AS1 promotes cell growth and metastasis in cervical cancer via miR-573/E2F3

Long non-coding RNAs (lncRNAs) are a crucial member of non-coding RNA family, and increasing evidence demonstrates that lncRNAs participate in the initiation and progression of cancers. Our study aimed to explore the role of lncRNA TTN-AS1 in cervical cancer (CC) development. In the present study, our results showed that TTN-AS1 was substantially increased in CC tissues and cell lines, high expression of TTN-AS1 was correlated with advanced FIGO stage, poor differentiation, lymph node metastasis, and poor overall survival of CC patients. Function assays showed that TTN-AS1 inhibition decreased the proliferation and invasion of CC cells both in vitro and in vivo. Mechanistically, we revealed that TTN-AS1 could positively modulate E2F3 expression via sponging miR-573 in CC cells. Together, our study revealed that lncRNA TTN-AS1 was involved in the progression of CC cells by regulation of miR-573-E2F3 axis, which offered a new insight into the treatment strategies of CC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Sost , independent of the non-coding enhancer ECR5, is required for bone mechanoadaptation

Here, sclerostin ( Sost ) is a negative regulator of bone formation that acts upon the Wnt signaling pathway. Sost is mechanically regulated at both mRNA and protein level such that loading represses and unloading enhances Sost expression, in osteocytes and in circulation. The non-coding evolutionarily conserved enhancer ECR5 has been previously reported as a transcriptional regulatory element required for modulating Sost expression in osteocytes. Here we explored the mechanisms by which ECR5 , or several other putative transcriptional enhancers regulate Sost expression, in response to mechanical stimulation. We found that in vivo ulna loading is equally osteoanabolic in wildtype and Sost –/– mice, although Sost is required for proper distribution of load-induced bone formation to regions of high strain. Using Luciferase reporters carrying the ECR5 non-coding enhancer and heterologous or homologous h SOST promoters, we found that ECR5 is mechanosensitive in vitro and that ECR5 -driven Luciferase activity decreases in osteoblasts exposed to oscillatory fluid flow. Yet, ECR5 –/– mice showed similar magnitude of load-induced bone formation and similar periosteal distribution of bone formation to high-strain regions compared to wildtype mice. Further, we found that in contrast to Sost –/– mice, which are resistant to disuse-induced bone loss, ECR5 –/– mice lose bone upon unloading to a degree similar to wildtype control mice. ECR5 deletion did not abrogate positive effects of unloading on Sost , suggesting that additional transcriptional regulators and regulatory elements contribute to load-induced regulation of Sost .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Upgrading aminoacyl-tRNA synthetases for genetic code expansion

Synthesis of proteins with non-canonical amino acids via genetic code expansion is at the forefront of synthetic biology. Progress in this field has enabled site-specific incorporation of over 200 chemically and structurally diverse amino acids into proteins in an increasing number of organisms. This has been facilitated by our ability to repurpose aminoacyl-tRNA synthetases to attach non-canonical amino acids to engineered tRNAs. Current efforts in the field focus on overcoming existing limitations to the simultaneous incorporation of multiple non-canonical amino acids or amino acids that differ from the l-α-amino acid structure (e.g. d-amino acid or β-amino acid). Here, we summarize the progress and challenges in developing more selective and efficient aminoacyl-tRNA synthetases for genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Nexus: a modular workflow management system for quantum simulation codes

The management of simulation workflows is a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantum chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

The iEBE-VISHNU code package for relativistic heavy-ion collisions

The iEBE-VISHNU code package performs event-by-event simulations for relativistic heavy-ion collisions using a hybrid approach based on (2 + 1)-dimensional viscous hydrodynamics coupled to a hadronic cascade model. We present the detailed model implementation, accompanied by some numerical code tests for the package. iEBE-VISHNU forms the core of a general theoretical framework for model-data comparisons through large scale Monte-Carlo simulations. A numerical interface between the hydrodynamically evolving medium and thermal photon radiation is also discussed. Finally, this interface is more generally designed for calculations of all kinds of rare probes that are coupled to the temperature and flow velocity evolution of the bulk medium, such as jet energy loss and heavy quark diffusion.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Transfer reaction code with nonlocal interactions

Here, we present a suite of codes (NLAT for nonlocal adiabatic transfer) to calculate the transfer cross section for single-nucleon transfer reactions, (d,N) or (N,d), including nonlocal nucleon-target interactions, within the adiabatic distorted wave approximation. For this purpose, we implement an iterative method for solving the second order nonlocal differential equation, for both scattering and bound states. The final observables that can be obtained with NLAT are dif- ferential angular distributions for the cross sections of A(d,N)B or B(N,d)A. Details on the implementation of the T-matrix to obtain the final cross sections within the adiabatic distorted wave approximation method are also provided. This code is suitable to be applied for deuteron induced reactions in the range of E d = 10–70 MeV, and provides cross sections with 4% accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Temporal parallelization of edge plasma simulations using the parareal algorithm and the SOLPS code

We show that numerical modelling of edge plasma physics may be successfully parallelized in time. The parareal algorithm has been employed for this purpose and the SOLPS code package coupling the B2.5 finite-volume fluid plasma solver with the kinetic Monte-Carlo neutral code Eirene has been used as a test bed. The complex dynamics of the plasma and neutrals in the scrape-off layer (SOL) region makes this a unique application. It is demonstrated that a significant computational gain (more than an order of magnitude) may be obtained with this technique. The use of the IPS framework for event-based parareal implementation optimizes resource utilization and has been shown to significantly contribute to the computational gain.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

DMFTwDFT: An open-source code combining Dynamical Mean Field Theory with various density functional theory packages

We report Dynamical Mean Field Theory (DMFT) is a successful method to compute the electronic structure of strongly correlated materials, especially when it is combined with density functional theory (DFT). Here, we present an open-source computational package (and a library) combining DMFT with various DFT codes interfaced through the Wannier90 package. The correlated subspace is expanded as a linear combination of Wannier functions introduced in the DMFT approach as local orbitals. In particular, we provide a library mode for computing the DMFT density matrix. This library can be linked and then internally called from any DFT package, assuming that a set of localized orbitals can be generated in the correlated subspace. The existence of this library allows developers of other DFT codes to interface with our package and achieve the charge-self-consistency within DFT+DMFT loops. To test and check our implementation, we computed the density of states and the band structure of well-known solid-state correlated materials, namely LaNiO, SrVO, and NiO. The obtained results are compared to those obtained from other DFT+DMFT implementations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

HiPACE++: A portable, 3D quasi-static particle-in-cell code

Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static, three-dimensional particle-in-cell code HiPACE++. By decomposing all the computation of a 3D domain in successive 2D transverse operations and choosing appropriate memory management, HiPACE++ demonstrates orders-of-magnitude speedups on modern scientific GPUs over CPU-only implementations. The 2D transverse operations are performed on a single GPU, avoiding time-consuming communications. The longitudinal parallelization is done through temporal domain decomposition, enabling near-optimal strong scaling from 1 to 512 GPUs. HiPACE++ is a modular, open-source code enabling efficient modeling of plasma accelerators from laptops to state-of-the-art supercomputers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

TTDFT: A GPU accelerated Tucker tensor DFT code for large-scale Kohn-Sham DFT calculations

We present the Tucker tensor DFT (TTDFT) code which uses a tensor-structured algorithm with graphic processing unit (GPU) acceleration for conducting ground-state DFT calculations on large-scale systems. The Tucker tensor DFT algorithm uses a localized Tucker tensor basis computed from an additive separable approximation to the Kohn-Sham Hamiltonian. The discrete Kohn-Sham problem is solved using Chebyshev filtered subspace iteration method that relies on matrix-matrix multiplications of a sparse symmetric Hamiltonian matrix and a dense wavefunction matrix, expressed in the localized Tucker tensor basis. These matrix-matrix multiplication operations, which constitute the most computationally intensive step of the solution procedure, are GPU accelerated providing ~8-fold GPU-CPU speedup for these operations on the largest systems studied. In conclusion, the computational performance of the TTDFT code is presented using benchmark studies on aluminum nano-particles and silicon quantum dots with system sizes ranging up to ~7,000 atoms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

MSTor 2023 : A new version of the computer code for multistructural torsional anharmonicity, now with automatic torsional identification using redundant internal coordinates

The MSTor program is a computer program for calculating partition functions and thermodynamic functions of complex gas-phase molecules with multiple torsions; the multi-structural approximation with torsional anharmonicity (MS-T) can be used based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic (MS-LH) approximation or multi-structural local quasiharmonic (MS-LQ) approximation or by the dual-level MS-T method. Furthermore, the program package includes eight utility codes that can be used as stand-alone programs to help the user to generate the input files for the code or to generate comparison results. The 2023 version of MSTor includes a new capability, namely automatic identification of torsional modes with redundant internal coordinates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

HFBTHO-AD: Differentiation of a nuclear energy density functional code

The HFBTHO code implements a nuclear energy density functional solver to model the structure of atomic nuclei. HFBTHO has previously been used to calibrate energy functionals and perform sensitivity analysis by using derivative-free methods. To enable derivative-based optimization and uncertainty quantification approaches, we must compute the derivatives of HFBTHO outputs with respect to the parameters of the energy functional, which are a subset of all input parameters of the code. Here, we use the algorithmic/automatic differentiation (AD) tool Tapenade to differentiate HFBTHO. We compare the derivatives obtained using AD against finite-difference approximation and examine the performance of the derivative computation.

Algorithmic differentiation↗