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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

CHIR99021 promotes self-renewal of mouse embryonic stem cells by modulation of protein-encoding gene and long intergenic non-coding RNA expression

Embryonic stem cells (ESCs) can proliferate indefinitely in vitro and differentiate into cells of all three germ layers. These unique properties make them exceptionally valuable for drug discovery and regenerative medicine. However, the practical application of ESCs is limited because it is difficult to derive and culture ESCs. It has been demonstrated that CHIR99021 (CHIR) promotes self-renewal and enhances the derivation efficiency of mouse (m)ESCs. However, the downstream targets of CHIR are not fully understood. In this study, we identified CHIR-regulated genes in mESCs using microarray analysis. Our microarray data demonstrated that CHIR not only influenced the Wnt/β-catenin pathway by stabilizing β-catenin, but also modulated several other pluripotency-related signaling pathways such as TGF-β, Notch and MAPK signaling pathways. More detailed analysis demonstrated that CHIR inhibited Nodal signaling, while activating bone morphogenetic protein signaling in mESCs. In addition, we found that pluripotency-maintaining transcription factors were up-regulated by CHIR, while several developmental-related genes were down-regulated. Furthermore, we found that CHIR altered the expression of epigenetic regulatory genes and long intergenic non-coding RNAs. Quantitative real-time PCR results were consistent with microarray data, suggesting that CHIR alters the expression pattern of protein-encoding genes (especially transcription factors), epigenetic regulatory genes and non-coding RNAs to establish a relatively stable pluripotency-maintaining network. - Highlights: • Combined use of CHIR with LIF promotes self-renewal of J1 mESCs. • CHIR-regulated genes are involved in multiple pathways. • CHIR inhibits Nodal signaling and promotes Bmp4 expression to activate BMP signaling. • Expression of epigenetic regulatory genes and lincRNAs is altered by CHIR.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

A SQL to C compiler in 500 lines of code

Abstract We present the design and implementation of a SQL query processor that outperforms existing database systems and is written in just about 500 lines of Scala code – a convincing case study that high-level functional programming can handily beat C for systems-level programming where the last drop of performance matters. The key enabler is a shift in perspective toward generative programming. The core of the query engine is an interpreter for relational-algebra operations, written in Scala. Using the open-source lightweight modular staging framework, we turn this interpreter into a query compiler with very low effort. To do so, we capitalize on an old and widely known result from partial evaluation: the first Futamura projection, which states that a process that can specialize an interpreter to any given input program is equivalent to a compiler. In this context, we discuss lightweight modular staging programming patterns such as mixed-stage data structures (e.g., data records with static schema and dynamic field components) and techniques to generate low-level C code, including specialized data structures and data loading primitives.

Computer Science↗
DOE OSTI2026

The CP-PAW Code Package for First-Principles Calculations from a User’s Perspective

CP-PAW is a combined electronic structure and ab initio molecular dynamics code to perform mixed quantum and classical simulations of atomistic condensed phase systems, such as solids, liquids, and molecular systems. As the name suggests, the CP-PAW code unifies the all-electron projector augmented-wave (PAW) method with the Car–Parrinello (CP) approach to determine not only the electronic and nuclear ground states of condensed matter but also to study their properties and dynamics. In addition to briefly outlining the underlying theory, the focus will be on the unique aspects of CP-PAW and how to correctly employ them as a user. How to install CP-PAW using the new build system will also be briefly mentioned.

Blöchl, Peter E [Institute for Theoretical Physic↗
DOE OSTI2026

Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment

The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. Here, we identify two non-coding structural variants in individuals with FOXG1 syndrome-like features, allowing us to delineate a ~ 124 kb commonly affected regulatory region. Using epigenomic profiling and in vivo enhancer assays, we characterize and validate regulatory elements within the commonly affected regulatory region and wider FOXG1 TAD. We see strong activation of previously validated forebrain enhancers, and identify an enhancer cluster and progenitor-specific enhancer region that are strongly activated during forebrain-directed neural progenitor cell differentiation, a process in which FOXG1 is an important regulator. Perturbation of these elements results in varying degrees of reduced FOXG1 transcription in forebrain neural progenitor cells and in population shifts within these cells, while removal of the TAD boundary leads to aberrant expression of the neighbouring PRKD1 gene. Our findings characterize enhancer and architectural elements essential for proper FOXG1 transcription during neurodevelopment, therefore improving variant interpretation in this region.

Hamerlinck, Lisa↗
DOE OSTI2021

Code interoperability extends the scope of quantum simulations

The functionality of many materials is critically dependent on the integration of dissimilar components and on the interfaces that arise between them. The description of such heterogeneous components requires the development and deployment of first principles methods, coupled to appropriate dynamical descriptions of matter and advanced sampling techniques, in order to capture all the relevant length and time scales of importance to the materials’ performance. It is thus essential to build simple, streamlined computational schemes for the prediction and design of multiple properties of broad classes of materials, by developing interoperable codes which can be efficiently coupled to each other to perform complex tasks. We discuss the use of interoperable codes to simulate the structural and spectroscopic characterization of materials, including chemical reactions for catalysis, the description of defects for quantum information science, and heat and charge transport.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Electron–phonon physics from first principles using the EPW code

EPW is an open-source software for ab initio calculations of electron–phonon interactions and related materials properties. The code combines density functional perturbation theory and maximally localized Wannier functions to efficiently compute electron–phonon coupling matrix elements, and to perform predictive calculations of temperature-dependent properties and phonon-assisted quantum processes in bulk solids and low-dimensional materials. Here, we report on significant developments in the code since 2016, namely: a transport module for the calculation of charge carrier mobility under electric and magnetic fields using the Boltzmann transport equation; a superconductivity module for calculations of phonon-mediated superconductors using the anisotropic multi-band Eliashberg theory; an optics module for calculations of phonon-assisted indirect transitions; a module for the calculation of small and large polarons without supercells; and a module for calculating band structure renormalization and temperature-dependent optical spectra using the special displacement method. For each capability, we outline the methodology and implementation and provide example calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Dynamics in a stellar convective layer and at its boundary: Comparison of five 3D hydrodynamics codes

Our ability to predict the structure and evolution of stars is in part limited by complex, 3D hydrodynamic processes such as convective boundary mixing. Hydrodynamic simulations help us understand the dynamics of stellar convection and convective boundaries. However, the codes used to compute such simulations are usually tested on extremely simple problems and the reliability and reproducibility of their predictions for turbulent flows is unclear. We define a test problem involving turbulent convection in a plane-parallel box, which leads to mass entrainment from, and internal-wave generation in, a stably stratified layer. We compare the outputs from the codes FLASH, MUSIC, PPMSTAR, PROMPI, and SLH, which have been widely employed to study hydrodynamic problems in stellar interiors. The convection is dominated by the largest scales that fit into the simulation box. All time-averaged profiles of velocity components, fluctuation amplitudes, and fluxes of enthalpy and kinetic energy are within ≲3σ of the mean of all simulations on a given grid (128 3 and 256 3 grid cells), where σ describes the statistical variation due to the flow’s time dependence. They also agree well with a 512 3 reference run. The 128 3 and 256 3 simulations agree within 9% and 4%, respectively, on the total mass entrained into the convective layer. The entrainment rate appears to be set by the amount of energy that can be converted to work in our setup and details of the small-scale flows in the boundary layer seem to be largely irrelevant. Our results lend credence to hydrodynamic simulations of flows in stellar interiors. We provide in electronic form all outputs of our simulations as well as all information needed to reproduce or extend our study.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Electromagnetic simulations of JET ICRF ITER-like antenna with TOPICA and SSWICH asymptotic codes

Multi-megawatt Ion Cyclotron Range of Frequencies (ICRF) heating is routinely used in the JET tokamak. To increase the ICRF heating power available from the A2 antennas, the ICRF ITER-Like Antenna (ILA) was reinstalled for the 2015 JET ITER-like wall experimental campaign. The application of high levels of ICRF power typically results in increased plasma wall interaction which leads to the observation of enhanced influx of metallic impurities in the plasma edge. It is assumed that the impurity production is mainly driven by the parallel component of the Radio-Frequency (RF) antenna electric near-field, E// (parallel to the confinement magnetic field of the tokamak), that is rectified in a thin boundary layer (RF sheath). Torino Polytechnic Ion Cyclotron Antenna (TOPICA) code was used to compute E // field maps in front of the ILA and between its poloidal limiters in the presence of plasma using measured density profiles and various antenna feedings. E // field maps calculated between the poloidal limiters were used to estimate the poloidal distribution of RF-sheath Direct Current (DC) potential in this private region of the ILA and make relative comparison of various antenna electrical settings. For this purpose we used the asymptotic version of the Self-consistent Sheaths and Waves for Ion Cyclotron Heating Slow-Wave (SSWICH-SW) code. These estimations can help to study the formation of RF sheaths around the antenna and even at distant locations (~3m away).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Preliminary Result of Neoclassical Impurity Transport Affected by ICRH with a 4-D Fokker-Planck Code

To understand the role of ion cyclotron resonance heating (ICRH) in mitigating tungsten accumulation, we evaluate the impact of ICRH-induced poloidal asymmetries on neoclassical impurity transport using a newly developed 4-D Fokker–Planck code (FP4D). Unlike conventional approaches that separate RF heating and transport modelling, FP4D solves both fast-ion distribution formation and impurity transport self-consistently without bounce-averaging. Benchmarking against the NEO code confirms the accuracy of the neoclassical physics in FP4D. Using FP4D, we analyze anisotropic and non-Maxwellian minority distributions under ICRH and their effects on the equilibrium potential and tungsten transport. Results show that anisotropy induced poloidal potential variations can reduce inward tungsten flux, depending on the modelling approach. Our findings highlight the importance of resolving the full velocity and poloidal structure of minority species in predicting impurity transport under strong RF heating conditions.

Jeong, Yunho [Hanyang Univ., Seoul (Korea, Republi↗
DOE OSTI2026

Simulations of ICRF Heating for SPARC during First Campaign and Primary Reference-Like Discharge using the Stix Code

High magnetic field tokamaks, like SPARC, rely on ion cyclotron radio frequency heating (ICRF) to reach fusion relevant temperatures. The SPARC tokamak will have 14 ICRF antennas in 7 toroidal locations delivering > 20 MW of power to the plasma. New capabilities with the full wave cold plasma solver, Stix, now allow for resolving the wave-particle resonances using lower order thermal corrections to capture core absorption of Landau damping and ion resonances in devices like SPARC. Favorable comparisons to the TORIC codes give confidence in the single pass absorption of this model to accurately capture the strength of edge interactions of the RF. Using this new dielectric formulation in the Stix code, simulations of the 2D poloidal cross section of SPARC are completed for the first campaign and primary reference-like discharges (PRD-like). A scan of the minority ion concentrations of helium-3 is performed and shows the expected behavior that as the helium-3 decreases the amount of single pass absorption also decreases which is seen in both scenarios. Additionally, both scenarios show only slight differences in single-pass absorption for the range of 3% to 5% helium-3 allowing for more flexibility in experiments. This study also highlights the differences between the first campaign and PRD-like with the first campaign discharges showing much more multi-pass absorption and an effect of confining the wave to a smaller portion of the cross-section due to the fast wave cut-off. This latter result suggests that far-field sheath rectification at the high-field side would be minimal for the first campaign scenario.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Language and design evolution of the OpenMC Monte Carlo particle transport code

The OpenMC Monte Carlo particle transport code has been continuously developed for 13 years by a large community of contributors. In that time span, the codebase has undergone significant changes that have redefined what OpenMC is and made it an enduring presence in the nuclear science and engineering community. In this paper, we discuss the evolution of programming language use in OpenMC, trends in the overall design of the programming interfaces, and implications for the future of the code.

Romano, Paul (ORCID:000000021147045X)↗
DOE OSTI2014

Edge equilibrium code for tokamaks

The edge equilibrium code (EEC) described in this paper is developed for simulations of the near edge plasma using the finite element method. It solves the Grad-Shafranov equation in toroidal coordinate and uses adaptive grids aligned with magnetic field lines. Hermite finite elements are chosen for the numerical scheme. A fast Newton scheme which is the same as implemented in the equilibrium and stability code (ESC) is applied here to adjust the grids.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Coded aperture imaging for fluorescent x-rays

We employ a coded aperture pattern in front of a pixilated charge couple device detector to image fluorescent x-rays (6–25 KeV) from samples irradiated with synchrotron radiation. Coded apertures encode the angular direction of x-rays, and given a known source plane, allow for a large numerical aperture x-ray imaging system. The algorithm to develop and fabricate the free standing No-Two-Holes-Touching aperture pattern was developed. The algorithms to reconstruct the x-ray image from the recorded encoded pattern were developed by means of a ray tracing technique and confirmed by experiments on standard samples.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Simulation of magnetic island dynamics under resonant magnetic perturbation with the TEAR code and validation of the results on T-10 tokamak data

Simulation of the magnetic island evolution under Resonant Magnetic Perturbation (RMP) in rotating T-10 tokamak plasma is presented with intent of TEAR code experimental validation. In the T-10 experiment chosen for simulation, the RMP consists of a stationary error field, a magnetic field of the eddy current in the resistive vacuum vessel and magnetic field of the externally applied controlled halo current in the plasma scrape-off layer (SOL). The halo-current loop consists of a rail limiter, plasma SOL, vacuum vessel, and external part of the circuit. Effects of plasma resistivity, viscosity, and RMP are taken into account in the TEAR code based on the two-fluid MHD approximation. Radial distribution of the magnetic flux perturbation is calculated with account of the externally applied RMP. A good agreement is obtained between the simulation results and experimental data for the cases of preprogrammed and feedback-controlled halo current in the plasma SOL.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

High-frequency combination coding-based steady-state visual evoked potential for brain computer interface

This study presents a new steady-state visual evoked potential (SSVEP) paradigm for brain computer interface (BCI) systems. The goal of this study is to increase the number of targets using fewer stimulation high frequencies, with diminishing subject’s fatigue and reducing the risk of photosensitive epileptic seizures. The new paradigm is High-Frequency Combination Coding-Based High-Frequency Steady-State Visual Evoked Potential (HFCC-SSVEP).Firstly, we studied SSVEP high frequency(beyond 25 Hz)response of SSVEP, whose paradigm is presented on the LED. The SNR (Signal to Noise Ratio) of high frequency(beyond 40 Hz) response is very low, which is been unable to be distinguished through the traditional analysis method; Secondly we investigated the HFCC-SSVEP response (beyond 25 Hz) for 3 frequencies (25Hz, 33.33Hz, and 40Hz), HFCC-SSVEP produces n{sup n} with n high stimulation frequencies through Frequence Combination Code. Further, Animproved Hilbert-huang transform (IHHT)-based variable frequency EEG feature extraction method and a local spectrum extreme target identification algorithmare adopted to extract time-frequency feature of the proposed HFCC-SSVEP response.Linear predictions and fixed sifting (iterating) 10 time is used to overcome the shortage of end effect and stopping criterion,generalized zero-crossing (GZC) is used to compute the instantaneous frequency of the proposed SSVEP respondent signals, the improved HHT-based feature extraction method for the proposed SSVEP paradigm in this study increases recognition efficiency, so as to improve ITR and to increase the stability of the BCI system. what is more, SSVEPs evoked by high-frequency stimuli (beyond 25Hz) minimally diminish subject’s fatigue and prevent safety hazards linked to photo-induced epileptic seizures, So as to ensure the system efficiency and undamaging.This study tests three subjects in order to verify the feasibility of the proposed method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Neural coding using telegraphic switching of magnetic tunnel junction

In this work, we present a synaptic transmission representing neural coding with spike trains by using a magnetic tunnel junction (MTJ). Telegraphic switching generates an artificial neural signal with both the applied magnetic field and the spin-transfer torque that act as conflicting inputs for modulating the number of spikes in spike trains. The spiking probability is observed to be weighted with modulation between 27.6% and 99.8% by varying the amplitude of the voltage input or the external magnetic field. With a combination of the reverse coding scheme and the synaptic characteristic of MTJ, an artificial function for the synaptic transmission is achieved.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Estimation of sheath potentials in front of ASDEX upgrade ICRF antenna with SSWICH asymptotic code

Multi-megawatt Ion Cyclotron Range of Frequencies (ICRF) heating became problematic in ASDEX Upgrade (AUG) tokamak after coating of ICRF antenna limiters and other plasma facing components by tungsten. Strong impurity influx was indeed produced at levels of injected power markedly lower than in the previous experiments. It is assumed that the impurity production is mainly driven by parallel component of Radio-Frequency (RF) antenna electric near-field E// that is rectified in sheaths. In this contribution we estimate poloidal distribution of sheath Direct Current (DC) potential in front of the ICRF antenna and simulate its relative variations over the parametric scans performed during experiments, trying to reproduce some of the experimental observations. In addition, relative comparison between two types of AUG ICRF antenna configurations, used for experiments in 2014, has been performed. For this purpose we use the Torino Polytechnic Ion Cyclotron Antenna (TOPICA) code and asymptotic version of the Self-consistent Sheaths and Waves for Ion Cyclotron Heating (SSWICH) code. Further, we investigate correlation between amplitudes of the calculated oscillating sheath voltages and the E// fields computed at the lateral side of the antenna box, in relation with a heuristic antenna design strategy at IPP Garching to mitigate RF sheaths.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Research on effect of emission uniformity on X-band relativistic backward oscillator using conformal PIC code

Explosive emission cathodes (EECs) are adopted in relativistic backward wave oscillators (RBWOs) to generate intense relativistic electron beam. The emission uniformity of the EEC can render saturation of the power generation unstable and the output mode impure. However, the direct measurement of the plasma parameters on the cathode surface is quite difficult and there are very few related numerical study reports about this issue. In this paper, a self-developed three-dimensional conformal fully electromagnetic particle in cell code is used to study the effect of emission uniformity on the X-band RBWO; the electron explosive emission model and the field emission model are both implemented in the same cathode surface, and the local field enhancement factor is also considered in the field emission model. The RBWO with a random nonuniform EEC is thoroughly studied using this code; the simulation results reveal that when the area ratio of cathode surface for electron explosive emission is 80%, the output power is unstable and the output mode is impure. When the annular EEC does not emit electron in the angle range of 30°, the RBWO can also operate normally.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗