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NASA NTRS1999

Gravisensing, apoptosis, and drug recovery in Taxus cell suspensions

Haploid and diploid cell suspensions of Taxus spp. were examined for their adaptive plasticity in response to simulated microgravity, unit gravity, and hypergravity. Cell suspensions produced the taxane, paclitaxel, (TAXOL (R)), which is useful for the treatment of various cancers. Amyloplasts contributed to taxane ring biosynthesis and to drug release at the cell wall. Drug-producing cells reacted as gravisensing osmotic tensiometers. In stressed cells, amyloplasts docked and fused in clusters to sites on the plasmalemma before taxane discharge into the culture medium. In simulated microgravity and compared to all other treatments, taxane production was reduced nearly 100-fold. The percent paclitaxel of total taxanes remained 3-to 6-fold greater, and biomass doubled. When p53-independent programmed cell death was induced, taxanes were released into the culture medium as free molecules (soluble and insoluble) or bound to membranes, nuclear fragments, xylan residues, and other particulate materials. Unit gravity and especially hypergravity promoted xylogenesis and significant drug overproduction. A model relating families of >touch = (TCH), taxane early response (TER), nuclear cycling, and apoptosis-regulating genes to gravisensing, cell wall modifications, and to taxane recovery accounted for most but not all of the observations.

Paclitaxel/biosynthesis↗

NASA NTRSDate not supplied

The Pheno-Evo Model: Evolution of Microbial Phenotypic Diversity in 2D Space

Biologists appreciate microbes for their simplicity and predictability: we assume that a population of genetically identical cells in a uniform environment will all behave the same way. While this assumption is often useful, it is also often wrong. Not only might microbes in a clonal population act differently from one another, the differences may be categorical (growing v. non-growing; toxin-sensitive v. tolerant), and this diversity might be an evolved trait conferring increased fitness on the population. How does such phenotypic heterogeneity evolve? And how does a population find the optimal distribution of phenotypes for a given environment? Efforts at modeling microbial phenotypic heterogeneity often focus on populations with two discrete phenotypic types; phenotypes in continuous distributions remain poorly explored. To address this gap and to explore the role of spatial relationships, we use agent-based modeling to simulate a phenotypically diverse population of microbial cells evolving in the presence of periodic toxic stress. Cells on patches in a 2D grid may degrade toxin, suffer damage from toxin, switch phenotype, and reproduce. An individual's phenotype its toxin degradation rate-- for which there is a tradeoff with reproduction-- and the genotype encodes the distribution of phenotypic values in the population. The rate of toxin diffusion determines how individuals influence their neighbors' environments. We examine the effects of toxin concentration, diffusion rate, and environmental predictability on the survival success of populations with different phenotype distributions, and populations' evolutionary trajectories when phenotype distribution is allowed to evolve. We conduct all simulations on the platform NetLogo, which provides a friendly interface allowing users of any experience level to tweak parameters and run their own simulations. We have also created custom tools in R for analyzing and visualizing the results of multiple runs.

microbial evolution↗

DOE OSTI2020

Low Cost (CAPEX and variable): Tool design for cell and module fabrication with thin, free-standing silicon wafers

This project aimed to develop technologies that can potentially enable free-standing thin (<80 μm) wafer in today’s manufacturing lines with high production yield, and thereby reduce capex barriers of silicon photovoltaics cells and modules. One of the major benefits is that thin wafer dramatically reduces the amount of polysilicon required. As a result, it can lead to reduction in the capital expenditures associated with polysilicon refining and wafer fabrication, which together are more than half of the total capital expenditure to manufacture Si PV module. We focused our efforts on developing the tools needed to enable high yield fabrication of wafer, cell, and module with thin silicon wafers. However, as the wafer thickness reduces, the major challenge is that wafer breakage increases significantly. Three technological areas were explored in this project to improve the production yield of the silicon wafer, namely detection of edge cracks via dark-field near-infrared (NIR) scattering; (2) wafer handling using controlled temperature profiles; (3) manufacturable low-stress cell interconnection for multiwire. First, the formation of wafer cracks in submillimeter length is one of the reasons that causes wafer breakages. Crack detection tools are needed to enable us to locate and track the wafer crack during manufacturing, so that we can improve the process to reduce initialization. The state-of-the-art crack detection technique cannot fulfill the need for measuring submillimeter edge cracks detrimental for thin wafers. The prototype developed in this project demonstrates the scanning of microcracks near wafer edges. With a semi-automatic laboratory setup, the submillimeter cracks were reliably detected near the edges in multi-Si wafers. The smallest detectable crack is 200 µm in length in slow scans; and submillimeter cracks are detected in high-throughput scans at the scan speed of >0.5 m/s, which is compatible with the inline detection of a manufacturing line at least 1 sec/wafer. This detection limit is a significant advancement in comparison to the benchmarked industrial tool. Second, wafer handling with the well-controlled temperature profile was thought to be the solution to reduce crack initiation and propagation during the manufacturing. However, without crack detection being widely adopted in production line, we did not find a strong industrial pull toward this technology. We did an initial literature survey and then diverted our efforts to the other tasks. Third, the innovation on low-stress multi-wire interconnection tackles a fundamental problem in the standard interconnection scheme. The standard over-under “zig-zag” interconnection induces a significant amount of stress into the soldering point on the cell whenever PV module is under stress, e.g., thermal cycling, transportation, and installation. Therefore, the interconnection process was re-designed in this project to allow for significant movement between adjacent solar cells, e.g., due to thermal expansion, without building up stresses on the solar cells or solder joints. The new interconnection method with the cross-connect wire also simplifies the tabbing and stringing process by replacing the standard over-under method with an off-cell interconnect from top to bottom. A manual tabbing and stringing tool for this new process was prototyped in the lab to demonstrate the fabrication of this new interconnection design. During the test with brass sheets as our “testing cells”, it was found that the mechanical cycling test only broke the interconnection after more than 50,000 cycles, which is equivalent to more than 130 years of the day-and-night thermal cycles. Lastly, throughout the project, we continuously analyzed the PV market with techno-economic analysis to identify the opportunity for thin Si adoption. Even though the drastic cost reduction has already happened in the past five years, our analysis results indicated that we can still save quite significantly in both manufacturing cost and factory capex, Particularly, in order to grow the PV manufacturing capacity to multi-terawatt level, reducing the thickness of silicon wafer is one of the most effective ways to quickly reduce factory capex, and sustain the high growth rate. The technologies developed in this project are readily available to provide some assistances in tackling the production yield problem.

14 SOLAR ENERGY↗

DOE OSTI2022

Control of deviatoric stress in the diamond anvil cell through thermal expansion mismatch stress in thin films

Elastic and plastic properties of materials and phase transitions at extreme conditions vary with both hydrostatic pressure and deviatoric stress. To generate and measure controlled deviatoric stress at pressures beyond those accessible with large volume differential and rotational presses and optical access for spectroscopy, experiments tested the combination of diamond anvil cell and thin film technology. Thin films of polycrystalline Cr-doped Al 2 O 3 ruby were prepared using pulsed laser deposition on single-crystal substrates of either Al 2 O 3 sapphire or yttria-stabilized cubic zirconia for contrasting initial film stress, and loaded in diamond anvil cells for confining stress. The piezospectroscopic response of the ruby films demonstrates consistently higher deviatoric stress in the film on zirconia relative to the film on the control sapphire, and an increase in deviatoric stress with applied load. Complementary synchrotron X-ray diffraction of the zirconia substrate confirmed that no pressure-induced phase transitions impacted the stress state of the ruby film, but differences in compressibility of film and substrate result in changes in film stress analogous to thermal expansion mismatch. Furthermore, this technique may be applied to evaluate elastic and plastic response of thin films of a variety of materials under extreme stress.

36 MATERIALS SCIENCE↗

NASA NTRS1991

Reverse bias voltage testing of 8 cm x 8cm silicon solar cells

A study is described of the reverse I-V characteristics of the largest space qualified silicon solar cells currently available (8 x 8 cm) and of reverse bias voltage (RBV) testing performed on these cells. This study includes production grade cells, both with and without cover glass. These cells span the typical output range seen in production. Initial characteristics of these cells are measured at both 28 and 60 C. These measurements show weak correlation between cell output and reverse characteristics. Analysis is presented to determine the proper conditions for RBV stress to simulate shadowing effects on a particular array design. After performing the RBV stress the characteristics of the stressed cells are remeasured. The degradation in cell performance is highly variable which exacerbates cell mismatching over time. The effect of this degradation on array lifetime is also discussed. Generalization of these results to other array configurations is also presented.

Woike, T.↗

DOE OSTI2024

Uniaxial stress effect on the electronic structure of quantum materials

Uniaxial stress has proven to be a powerful experimental tuning parameter for effectively controlling lattice, charge, orbital, and spin degrees of freedom in quantum materials. In addition, its ability to manipulate the symmetry of materials has garnered significant attention. Recent technical progress to combine uniaxial stress cells with quantum oscillation and angle-resolved photoemission techniques allowed to study the electronic structure as function of uniaxial stress. This review provides an overview on experimental advancements in methods and examines studies on diverse quantum materials, encompassing the semimetal WTe 2 , the unconventional superconductor Sr 2 RuO 4 , Fe-based superconductors, and topological materials.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Uniaxial stress effect on the electronic structure of quantum materials

Uniaxial stress has proven to be a powerful experimental tuning parameter for effectively controlling lattice, charge, orbital, and spin degrees of freedom in quantum materials. In addition, its ability to manipulate the symmetry of materials has garnered significant attention. Recent technical progress to combine uniaxial stress cells with quantum oscillation and angle-resolved photoemission techniques allowed to study the electronic structure as function of uniaxial stress. This review provides an overview on experimental advancements in methods and examines studies on diverse quantum materials, encompassing the semimetal WTe2, the unconventional superconductor Sr2RuO4, Fe-based superconductors, and topological materials.

FOS: Physical sciences↗

NASA NTRS1996

Accumulation of Dissolved DMSP by Marine Bacteria and its Degradation Via Bacterivory

Several bacterial isolates enriched from seawater using complex media were able to accumulate dimethylsulfoniopropionate (DMSP) from media into cells over several hours without degrading it. Uptake only occurred in metabolically active cells, and was repressed in some strains by the presence of additional carbon sources. Accumulation was also more rapid in osmotically-stressed cells, suggesting DMSP is used as an osmotic solute. Uptake could be blocked by inhibitors of active transport systems (2,4-dinitrophenol, azide, arsenate) and of protein synthesis (chloramphenicol). Some structural analogs such as glycine betaine and S-methyl methionine also blocked DMSP uptake, suggesting that the availability of alternate organic osmolytes may influence DMSP uptake. Stresses such as freezing, heating, or osmotic down shock resulted in partial release of DMSP back to the medium. One strain which contained a DMSP-lyase was also able to accumulate DMSP, and DMS was only produced in the absence of alternate carbon sources. Bacteria containing DMSP were prepared as prey for bacterivorous ciliates and flagellates, to examine the fate of the DMSP during grazing. In all cases, predators metabolized the DMSP in bacteria. In some cases, DMS was produced, but it is not clear if this was due to the predators or to associated bacteria in the non-axenic grazer cultures. Bacterivores may influence DMSP cycling by either modulating populations of DMSP-metabolizing bacteria, or by metabolizing DMSP accumulated by bacterial prey.

Wolfe, Gordon V.↗

NASA NTRS1994

Plasmodesmal-mediated cell-to-cell transport in wheat roots is modulated by anaerobic stress

Cell-to-cell transport of small molecules and ions occurs in plants through plasmodesmata. Plant roots are frequently subjected to localized anaerobic stress, with a resultant decrease in ATP. In order to determine the effect of this stress on plasmodesmal transport, fluorescent dyes of increasing molecular weight (0.46 to 1OkDa) were injected into epidermal and cortical cells of 3-day-old wheat roots, and their movement into neighboring cells was determined by fluorescence microscopy. Anaerobiosis was generated by N2 gas or simulated by the presence of sodium azide, both of which reduced the ATP levels in the tissue by over 80%. In the absence of such stress, the upper limit for movement, or size exclusion limit (SEL), of cortical plasmodesmata was <1 kDa. The ATP analogue TNP-ADP (mw 681) moved across the plasmodesmata of unstressed roots, indicating that plasmodesmata may be conduits for nucleotide (ATP and ADP) exchange between cells. Upon imposition of stress, the SEL rose to between 5 and 10 kDa. This response of plasmodesmata to a decrease in the level of ATP suggests that they are constricted by an ATP-dependent process so as to maintain a restricted SEL. When roots are subjected to anaerobic stress, an increase in SEL may permit enhanced delivery of sugars to the affected cells of the root where anaerobic respiration could regenerate the needed ATP.

NASA Discipline Plant Biology↗

DOE OSTI2021

Extracellular vesicles promote epithelial-to-mesenchymal transition of lens epithelial cells under oxidative stress

Posterior capsule opacification (PCO), resulting from residual lens epithelial cell (LEC) epithelial–mesenchymal transition (EMT), abnormal proliferation, and migration, is the most common complication of cataract surgery. A recent study determined that extracellular vesicles (EVs) and reactive oxygen species (ROS) regulate the EMT process during cutaneous wound healing and tumour metastasis. However, their underlying mechanism in PCO is unclear. In this study, we examined the secreted EVs from a scratch model in vitro. We found that the production of ROS was increased after mechanical injury, especially at the wound edge, and there was an increased viability of LECs, which can be blocked by diphenyleneiodonium, an NADPH oxidase inhibitor. Cell viability and migration were increased upon treatment with 1 μM H{sub 2}O{sub 2}, but significantly reduced when the concentration of H{sub 2}O{sub 2} increased to 100 μM. Transwell assay showed that both post-surgery LECs and LECs treated with 1 μM H{sub 2}O{sub 2} significantly induced the migration of normal LECs by EV secretion. Extraction and quantification of EVs derived from injured and H{sub 2}O{sub 2}-treated LECs showed a similar increase in production. Co-incubation of EVs from both injured and H{sub 2}O{sub 2}-treated LECs with normal LECs and organ-cultured mouse lenses activated EMT, which was attenuated by a ROS inhibitor. These results suggest that EVs participate in ROS-induced lens EMT, making EVs a potential target for treating PCO.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Recent Advances in the Roles of HSFs and HSPs in Heat Stress Response in Woody Plants

A continuous increase in ambient temperature caused by global warming has been considered a worldwide threat. As sessile organisms, plants have evolved sophisticated heat shock response (HSR) to respond to elevated temperatures and other abiotic stresses, thereby minimizing damage and ensuring the protection of cellular homeostasis. In particular, for perennial trees, HSR is crucial for their long life cycle and development. HSR is a cell stress response that increases the number of chaperones including heat shock proteins (HSPs) to counter the negative effects on proteins caused by heat and other stresses. There are a large number of HSPs in plants, and their expression is directly regulated by a series of heat shock transcription factors (HSFs). Therefore, understanding the detailed molecular mechanisms of woody plants in response to extreme temperature is critical for exploring how woody species will be affected by climate changes. In this review article, we summarize the latest findings of the role of HSFs and HSPs in the HSR of woody species and discuss their regulatory networks and cross talk in HSR. In addition, strategies and programs for future research studies on the functions of HSFs and HSPs in the HSR of woody species are also proposed.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

A Multi Targeted Dietary Supplement as a Potential Countermeasure for Prolonged, Deep Space Exploration

Deep space exploration, particularly to the Moon and Mars, are currently major goals of NASA and other international space agencies. Long-term space flight presents unique challenges to the human physiology from microgravity, social isolation, altered circadian rhythm and radiation. Oxidative stress has been implicated as a crucial factor in space environment induced injury. Elucidating these detrimental effects on the central nervous system and brain is a primary objective, as they may result in adverse changes in astronaut behavior, mood and performance of critical tasks. We were recently funded by HRP Human Factors Behavioral Performance (HFBP) Element to test the hypothesis that Galactic Cosmic Ray Simulation (GCRsim) Ionizing Radiation (IR), microgravity and social isolation combine synergistically to trigger an oxidative stress response that alters immune homeostasis, brain structure and function, and neurobehavioral and cognitive performance. This project will identify potential biomarkers for, and mechanisms underlying, structural and functional changes in the immune and nervous systems leading to behavioral/cognitive performance deficits, and its potential application to develop effective countermeasures to mitigate negative health effects of long duration space habitation. Countermeasures to offset neurological damaged and cognitive deficits are paramount for protecting astronauts during deep space transits, but many countermeasures have been found to be unsuitable in ground-based model studies. We have developed a multi targeted dietary supplement (MTDS) designed to simultaneously ameliorate oxidative stress, inflammatory processes, energetic shortfalls, and membrane and mitochondrial deterioration. Administration of this MTDS has improved cognition and longevity in age accelerated and normal aging mice. Specifically, the MTDS was found to prevent a decline in mitochondrial complex III activity and cell loss, as well as prevent an increase in protein carbonyls and mitochondrial 3-nitrotyrosine in the brain of these mice. Further, administration of the MTDS was also found to reduce bone marrow chromosomal aberrations, DNA damage, lymphocyte apoptosis after whole body exposure of 2 Gy γ radiation. Mice exposed to a high dose cranially (10 Gy) had decreased cognitive responses (seen as increased latency time to uncover buried food and decreased novel object recognition), increased plasma 8-OHdG levels, increased markers of cell stress in the brain, decreased hippocampal brain-derived neurotrophic factor (BDNF) protein and decreased plasma levels of cytokines, all of which were ameliorated with treatment of the MTDS. As we have shown the supplement is protective in models of cognitive damage similar space environment stressors, particularly increased oxidative stress, we propose it may be a suitable countermeasure for upcoming deep space exploration.

radiation↗

NASA NTRSDate not supplied

A MULTI TARGETED DIETARY SUPPLEMENT AS A POTENTIAL COUNTERMEASURE FOR DEEP SPACE EXPLORATION

Future deep space exploration to the Moon and Mars and beyond are currently major goals of NASA. Space flight presents unique challenges to the human physiology from the combined effects of microgravity, social isolation, altered circadian rhythm and radiation. Oxidative stress has been implicated as a crucial factor in space environment induced injury. Elucidating these detrimental effects on the central nervous system and brain is a primary objective, as they may result in adverse changes in astronaut behavior, mood and performance of critical tasks. We were recently funded by HRP Human Factors Behavioral Performance (HFBP) Element to test the hypothesis that Galactic Cosmic Ray Simulation (GCRsim) Ionizing Radiation (IR), microgravity and social isolation combine synergistically to trigger an oxidative stress response that alters immune homeostasis, brain structure and function, and neurobehavioral and cognitive performance. This project will identify potential biomarkers for, and mechanisms underlying, structural and functional changes in the immune and nervous systems leading to behavioral/cognitive performance deficits, and its potential application to develop effective countermeasures to mitigate negative health effects of long duration space habitation. Countermeasures to offset neurological damaged and cognitive deficits are paramount for protecting astronauts during deep space transits, but many countermeasures have been found to be unsuitable in ground-based model studies. We have developed a multi targeted dietary supplement (MTDS) designed to simultaneously ameliorate oxidative stress, inflammatory processes, energetic shortfalls, and membrane and mitochondrial deterioration. Administration of this MTDS has improved cognition and longevity in age accelerated and normal aging mice. Specifically, the MTDS was found to prevent a decline in mitochondrial complex III activity and cell loss, as well as prevent an increase in protein carbonyls and mitochondrial 3-nitrotyrosine in the brain of these mice. Further, administration of the MTDS was also found to reduce bone marrow chromosomal aberrations, DNA damage, lymphocyte apoptosis after whole body exposure of 2 Gy γ radiation. Mice exposed to a high dose cranially (10 Gy) had decreased cognitive responses (seen as increased latency time to uncover buried food and decreased novel object recognition), increased plasma 8-OHdG levels, increased markers of cell stress in the brain, decreased hippocampal brain-derived neurotrophic factor (BDNF) protein and decreased plasma levels of cytokines, all of which were ameliorated with treatment of the MTDS. As we have shown the supplement is protective in models of cognitive damage similar space environment stressors, particularly increased oxidative stress, we propose it may be a suitable countermeasure for upcoming deep space exploration.

Stephanie Puukila↗

NASA NTRS2001

Shear stress reduces protease activated receptor-1 expression in human endothelial cells

Shear stress has been shown to regulate several genes involved in the thrombotic and proliferative functions of endothelial cells. Thrombin receptor (protease-activated receptor-1: PAR-1) increases at sites of vascular injury, which suggests an important role for PAR-1 in vascular diseases. However, the effect of shear stress on PAR-1 expression has not been previously studied. This work investigates effects of shear stress on PAR-1 gene expression in both human umbilical vein endothelial cells (HUVECs) and microvascular endothelial cells (HMECs). Cells were exposed to different shear stresses using a parallel plate flow system. Northern blot and flow cytometry analysis showed that shear stress down-regulated PAR-1 messenger RNA (mRNA) and protein levels in both HUVECs and HMECs but with different thresholds. Furthermore, shear-reduced PAR-1 mRNA was due to a decrease of transcription rate, not increased mRNA degradation. Postshear stress release of endothelin-1 in response to thrombin was reduced in HUVECs and HMECs. Moreover, inhibitors of potential signaling pathways applied during shear stress indicated mediation of the shear-decreased PAR-1 expression by protein kinases. In conclusion, shear stress exposure reduces PAR-1 gene expression in HMECs and HUVECs through a mechanism dependent in part on protein kinases, leading to altered endothelial cell functional responses to thrombin.

Non-NASA Center↗

DOE OSTI2022

Mixed heavy metal stress induces global iron starvation response

Abstract Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

The endomembrane sheath: a key structure for understanding the plant cell?

Recent evidence suggests that integrin is abundant in endomembranes of plant cells, and the endomembranes are clad by a sheath of cytoskeleton including F-actin. A role for endomembrane integrin and the endomembrane sheath is proposed: this system might orchestrate metabolic regulation by providing and modulating loci for channelling, and might accelerate channeling as needed by dragging the endoplasmic reticulum (ER) and organelles through the cytoplasm. To accomplish this "streaming", F-actin might lever against the rest of the endomembrane sheath and the ER might also lever against adhesion sites (i.e., plasmodesmata and plasmalemmal control centers). As an important agent in the control of cellular activities, according to this model, the endomembrane sheath would play a major part in responses to diverse signals and stresses, and under extreme stress cell survival would depend on the ability of the system to maintain enough integrity to direct critical syntheses and degradations.

NASA Discipline Plant Biology↗

NASA NTRS1982

Investigation of reliability attributes and accelerated stress factors on terrestrial solar cells

The accelerated stress test results obtained on all terrestrial solar cells since the inception of the program are summarized. Tested cells were grouped according to the method used to form the conductive metallization layer: solder dipped, vacuum deposited, screen printed, and copper plated. Although metallization systems within each group were quite similar, they differed in numerous details according to the procedures employed by each manufacturer. Test results were summarized for all cells according to both electrical degradation and catastrophic mechanical changes. These results indicated a variability within each metallization category which was dependent on the manufacturer. Only one manufacturer was represented in the copper plated category and, although these showed no signs of detrimental copper diffusion during high temperature testing, their metallization was removed easily during high humidity pressure cooker testing. Preliminary testing of encapsulated cells showed no major differences between encapsulated and unencapsulated cells when subjected to accelerated testing.

Lathrop, J. W.↗

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↗