Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular replacement”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11

Adsorption Processes during Electrochemical Atomic Layer Deposition of Gold

Electrochemical atomic layer deposition (e-ALD) technique offers a simple and effective "wet chemistry" approach enabling high-precision monolayer-by-monolayer deposition of metal films. The process of e-ALD of Au involves lead underpotential deposition (PbUPD) followed by its redox replacement by a Au monolayer. The time evolution of the deposit mass during "one-pot" Au e-ALD is known to exhibit a unique three-stage response that is presently not well understood. In this work, we probe this response using voltammetry, electrochemical quartz crystal microgravimetry (e-QCM), and chronoamperometry to unravel the underlying mechanistic events during Au e-ALD. Furthermore, the presence of adsorbed Au +3 -ligand complex(es) (Au-L) on the Au surface is established. In stage I of e-ALD, this Au-L adsorbed layer is reduced to Au while a Pb UPD adlayer is formed. In stage II, the Pb UPD adlayer undergoes spontaneous surface-limited redox replacement by nobler Au under open-circuit conditions. Finally, in stage III, re-adsorption of the Au-L occurs on the newly deposited Au. Quantitative analysis of the deposit mass transients obtained under a variety of conditions provides an estimate of the Au-L mass and its molecular weight.

36 MATERIALS SCIENCE↗

Unification of nonequilibrium molecular dynamics and the mode-resolved phonon Boltzmann equation for thermal transport simulations

Nano-size confinement induces many intriguing non-Fourier heat conduction phenomena, such as nonlinear temperature gradients, temperature jumps near the contacts, and size-dependent thermal conductivity. Over the past decades, these effects have been studied and interpreted by nonequilibrium molecular dynamics (NEMD) and phonon Boltzmann transport equation (BTE) simulations separately, but no theory that unifies these two methods has ever been established. In this work, we unify these methods using a quantitative mode-level comparison and demonstrate that they are equivalent for various thermostats. We show that different thermostats result in different non-Fourier thermal transport characteristics due to the different mode-level phonon excitations inside the thermostats, which explains the different size-dependent thermal conductivities calculated using different reservoirs, even though they give the same bulk thermal conductivity. Specifically, the Langevin thermostat behaves like a thermalizing boundary in phonon BTE and provides mode-level thermal-equilibrium phonon outlets, while the Nose-Hoover chain thermostat and velocity rescaling method behave like biased reservoirs, which provide a spatially uniform heat generation and mode-level nonequilibrium phonon outlets. These findings explain why different experimental measurement methods can yield different size-dependent thermal conductivity. They also indicate that the thermal conductivity of materials can be tuned for various applications by specifically designing thermostats. Finally, the unification of NEMD and phonon BTE will largely facilitate the study of thermal transport in complex systems in the future by, e.g., replacing computationally unaffordable first-principles NEMD simulations with computationally less expensive spectral BTE simulations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Overcoming Fundamental Limitations in Adsorbent Design: Alkene Adsorption by Non‐porous Copper(I) Complexes

Abstract Purifying alkenes from alkanes requires cryogenic distillation. This consumes energy equivalent to countries of ca. 5 million people. Replacing distillation with adsorption processes would significantly increase energy efficiency. Trade‐offs between kinetics, selectivity, capacity, and heat of adsorption have prevented production of an optimal adsorbent. We report adsorbents that overcome these trade‐offs. [Cu‐Br] 3 and [Cu‐H] 3 are air‐stable trinuclear complexes that undergo reversible solid‐state inter‐molecular rearrangements to produce dinuclear [Cu‐Br⋅(alkene)] 2 and [Cu‐H⋅(alkene)] 2 . The reversible solid‐state rearrangement, confirmed in situ using powder X‐ray diffraction, allows adsorbent design trade‐offs to be overcome, coupling low heat of adsorption (−10 to −17 kJ mol −1 alkene ), high alkene:alkane selectivity (47; 29), and uptake capacity (>2.5 mol alkene mol −1 Cu3 ). Most remarkably, [Cu‐H] 3 displays fast uptake and regenerates capacity within 10 minutes.

Parasar, Devaborniny↗

Fractionated and purified hybrid poplar lignins as a polyol replacement in rigid polyurethane/polyisocyanurate foams

This study introduces fractionated lignin as an innovative component in the formulation of rigid polyurethane/polyisocyanurate (PUR/PIR) foams. Low-density PUR/PIR rigid foams were prepared by replacing 80% of the petrochemical-based polyol with a hybrid poplar (HP) lignin, recovered via alkaline pretreatment, and also with a fraction of this lignin, isolated via the Aqueous Lignin Purification with Hot Agents (ALPHA) process. The as-recovered HP and ALPHA-fractionated HP lignins were characterized to determine hydroxyl content, molecular weight (Mw) distribution, and pH. Both lignin-based foams met minimum standard requirements in terms of closed cell content, compression strength, and thermal conductivity. Notably, the foams made with ALPHA-based lignin outperformed the as-recovered lignin-based foams in all measured foam properties. Moreover, the ALPHA-based foam had comparable performance to the control foam (without lignin) except for density and even surpassed the control foam in closed cell content and compressive strength. This investigation of the molecular properties of lignin suggests that significant reductions in lignin average molecular weight and polydispersity (PDI) can positively impact the properties of lignin-based rigid foams.

09 BIOMASS FUELS↗

Benchmarking the performance of uncertainty quantification methods for neural network-based interatomic potentials

Machine-learned interatomic potentials (ML-IAPs) continue to gain popularity as accurate, computationally efficient replacements for traditional, physics-based interatomic potentials and expensive ab initio methods. Uncertainty quantification (UQ) of ML-IAPs is a growing area of research as UQ is critical in many applications of IAPs, such as developing curated datasets, active learning-based data augmentation, self-improving models, and estimating the uncertainty of molecular dynamics simulations. In this paper, we construct and benchmark a series of different neural network potentials (NNPs) with varying network architectures to determine the performance of these models with respect to both the mean and uncertainty calibration error. Each NNP method is specifically designed to predict either epistemic or aleatoric uncertainty with particular focus on the differences in behavior between the epistemic and aleatoric uncertainty estimates. We benchmark these methods using multiple datasets common in the ML-IAP literature. The results show that the aleatoric uncertainty from single-shot model architectures is a competitive alternative to ensemble-based epistemic uncertainty predictions in regions of sufficient data-density. However, in regions where the representative data is sparse, aleatoric uncertainty models tend to overpredict and epistemic methods tend to underpredict the actual model error. We conclude that the type of UQ is crucial when discussing performance of probabilistic model results as different methods have different performance characteristics depending on the regime in which they are evaluated. Therefore, the type of UQ method should be carefully evaluated against both the data characteristics and requirements for the intended application.

97 MATHEMATICS AND COMPUTING↗

Molecular-Level Overhaul of y-Aminopropyl Aminosilicone/Triethylene Glycol Post-Combustion CO2-Capture Solvents

Capturing carbon dioxide (CO2) from post-combustion gas streams is an energy-intensive process that is required prior to either converting or sequestering CO2. There are a few commercial offerings of 1st and 2nd generation aqueous amine technologies, however the cost of capturing CO2 with these technologies remains high. To decrease costs of capture, researchers are designing efficient solvent systems with the goal of being drop-in replacements for 1st and 2nd generation infrastructure. One approach has seen the development of water-lean solvents that aim to increase efficiency by reducing the water content in solution. Water-lean solvents such as GE’s GAP/TEG are promising technologies, with potential to halve the parasitic load to a coal-fired power plant, only if the intrinsically high solution viscosities and hydrolysis of the siloxane moieties could be mitigated. We present here, an integrated multidisciplinary approach to overhaul the GAP/TEG solvent system at the molecular level to mitigate hydrolysis while also reducing viscosity. We present molecular-level insights into chemical speciation of CO2-containing ions, showing that co-solvents and diluents have a negligible effect on reducing viscosity and are not needed. This finding allowed for the design of singlecomponent siloxane-free diamine derivatives with site-specific incorporation of selective chemical moieties for direct placement and orientation of hydrogen bonding to reduce viscosity. Ultimately, we present new single-component diamine formulations less susceptible to hydrolysis that exhibit up to a 98% reduction in viscosity compared to the initial GAP/TEG formulation.

Cantu Cantu, David↗

Molecular cloning and characterization of a tumor-associated, growth-related, and time-keeping hydroquinone (NADH) oxidase (tNOX) of the HeLa cell surface

NOX proteins are growth-related cell surface proteins that catalyze both hydroquinone or NADH oxidation and protein disulfide interchange and exhibit prion-like properties. The two enzymatic activities alternate to generate a regular period length of about 24 min. Here we report the expression, cloning, and characterization of a tumor-associated NADH oxidase (tNOX). The cDNA sequence of 1830 bp is located on gene Xq25-26 with an open reading frame encoding 610 amino acids. The activities of the bacterially expressed tNOX oscillate with a period length of 22 min as is characteristic of tNOX activities in situ. The activities are inhibited completely by capsaicin, which represents a defining characteristic of tNOX activity. Functional motifs identified by site-directed mutagenesis within the C-terminal portion of the tNOX protein corresponding to the processed plasma membrane-associated form include quinone (capsaicin), copper and adenine nucleotide binding domains, and two cysteines essential for catalytic activity. Four of the six cysteine to alanine replacements retained enzymatic activity, but the period lengths of the oscillations were increased. A single protein with two alternating enzymatic activities indicative of a time-keeping function is unprecedented in the biochemical literature.

NASA Discipline Cell Biology↗

Characterizing the Self-Assembly Properties of Monoolein Lipid Isosteres

Living cells feature lipid compartments which exhibit a variety of shapes and structures that assist essential cellular processes. Many natural cell compartments frequently adopt convoluted nonlamellar lipid architectures that facilitate specific biological reactions. Improved methods for controlling the structural organization of artificial model membranes would facilitate investigations into how membrane morphology affects biological functions. Monoolein (MO) is a single-chain amphiphile which forms nonlamellar lipid phases in aqueous solution and has wide applications in nanomaterial development, the food industry, drug delivery, and protein crystallization. However, even if MO has been extensively studied, simple isosteres of MO, while readily accessible, have seen limited characterization. An improved understanding of how relatively minor changes in lipid chemical structure affect self assembly and membrane topology could instruct the construction of artificial cells and organelles for modeling biological structures and facilitate nanomaterial-based applications. Here, we investigate the differences in self-assembly and large-scale organization between MO and two MO lipid isosteres. We show that replacing the ester linkage between the hydrophilic headgroup and hydrophobic hydrocarbon chain with a thioesther or amide functional group results in the assembly of lipid structures with different phases not resembling those formed by MO. Using light and cryo-electron microscopy, small-angle X-ray scattering, and infrared spectroscopy, we demonstrate differences in the molecular ordering and large-scale architectures of the self-assembled structures made from MO and its isosteric analogues. These results improve our understanding of the molecular underpinnings of lipid mesophase assembly and may facilitate the development of MO-based materials for biomedicine and as model lipid compartments.

60 APPLIED LIFE SCIENCES↗

Rigorous Oxidation State Assignments for Supported Ga-Containing Catalysts Using Theory-Informed X-ray Absorption Spectroscopy Signatures from Well-Defined Ga(I) and Ga(III) Compounds

Gallium-based heterogeneous catalysts originally developed for commercial use in propane dehydroaromatization have been explored extensively as potential replacements for Pt- and Cr-based catalysts used in propane dehydrogenation for on-demand propylene production. In a large number of experimental and theoretical studies, active sites with a variety of Ga nuclearities, coordination environments, and oxidation states have been proposed. Isolated Ga(I) ions are often invoked, despite the scarcity of well-defined molecular species and their well-documented instability. In this study, we investigate the appearance of a high-intensity, low-energy white line at the Ga K-edge upon reduction of Ga/HZSM-5 by H 2 at a temperature of ca. 500 °C, accompanied by a dramatic reduction in the extended X-ray absorption fine structure (EXAFS) intensity. In contrast, Ga/γ-Al 2 O 3 does not show such behavior. In order to lay a rigorous foundation for characterizing these types of systems and to establish experimental signatures for the elusive Ga(I) oxidation state, we recorded Ga K-edge X-ray absorption spectra [including high-energy-resolution fluorescence detection-X-ray absorption near-edge spectroscopy (HERFD-XANES)] for several well-defined molecular and crystalline Ga(I) compounds. XANES is essential to establishing the presence of Ga(I), despite the overlap in edge energies with organoGa(III) compounds, because Ga(I)-containing oxide materials show very weak EXAFS scattering. Compared to the XANES of trigonal Ga(III)-containing materials, Ga(I) spectra display a significantly more intense white line feature. Theoretical simulations agree well with this experimental observation and reveal that the strong XANES intensity originates from the superposition of transitions to several empty, nearly degenerate p-like states. Finally, these signatures provide compelling evidence for assigning the intense white line and dramatic loss of EXAFS intensity in Ga/HZSM-5 to the near-quantitative reduction of Ga(III) to Ga(I), while the weaker white line and conventional EXAFS signal of Ga/γ-Al 2 O 3 point to, at most, a minor fraction of Ga(I) sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reducing sputter induced stress and damage for efficient perovskite/silicon tandem solar cells

Reducing damages caused by sputtering of transparent conductive oxide (TCO) electrodes is critical in achieving highly efficient and stable perovskite/silicon tandem solar cells. Here we study the sputter caused damage to bathocuproine (BCP), which is widely used in highly efficient p-i-n structure single junction perovskite solar cells. While BCP buffer layer protects the underneath layers from damage, itself can be damaged by sputtering of TCOs at a wide range of target-substrate distances, supported by molecular dynamic simulation. More intriguingly, it is observed that TCO easily peeled off after sputtering when the sputtering target is close to substrate. This is ascribed to formation of stress during cooling down process after sputtering due to different thermal expansion coefficients of the layers. Our studies explain why tin oxide (SnO2) made by atomic layer deposition can replace BCP for a much better tandem device performance. SnO2 has high affinity with sputtered TCO electrode to suppress peeling-off issue and has higher bond energy to resist sputter induced damage, thus it allows a wider window of target-substrate distances than BCP during TCO sputtering. Ultimately, we demonstrate an efficient perovskite/silicon monolithic tandem solar cell with efficiency of 26.0% to illustrate the beneficial effects of reduced stress and damage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Myocardialization of the cardiac outflow tract

During development, the single-circuited cardiac tube transforms into a double-circuited four-chambered heart by a complex process of remodeling, differential growth, and septation. In this process the endocardial cushion tissues of the atrioventricular junction and outflow tract (OFT) play a crucial role as they contribute to the mesenchymal components of the developing septa and valves in the developing heart. After fusion, the endocardial ridges in the proximal portion of the OFT initially form a mesenchymal outlet septum. In the adult heart, however, this outlet septum is basically a muscular structure. Hence, the mesenchyme of the proximal outlet septum has to be replaced by cardiomyocytes. We have dubbed this process "myocardialization." Our immunohistochemical analysis of staged chicken hearts demonstrates that myocardialization takes place by ingrowth of existing myocardium into the mesenchymal outlet septum. Compared to other events in cardiac septation, it is a relatively late process, being initialized around stage H/H28 and being basically completed around stage H/H38. To unravel the molecular mechanisms that are responsible for the induction and regulation of myocardialization, an in vitro culture system in which myocardialization could be mimicked and manipulated was developed. Using this in vitro myocardialization assay it was observed that under the standard culture conditions (i) whole OFT explants from stage H/H20 and younger did not spontaneously myocardialize the collagen matrix, (ii) explants from stage H/H21 and older spontaneously formed extensive myocardial networks, (iii) the myocardium of the OFT could be induced to myocardialize and was therefore "myocardialization-competent" at all stages tested (H/H16-30), (iv) myocardialization was induced by factors produced by, most likely, the nonmyocardial component of the outflow tract, (v) at none of the embryonic stages analyzed was ventricular myocardium myocardialization-competent, and finally, (vi) ventricular myocardium did not produce factors capable of supporting myocardialization. Copyright 1999 Academic Press.

NASA Discipline Cardiopulmonary↗

Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)

Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.

Biochemistry & Molecular Biology↗

Overcoming Fundamental Limitations in Adsorbent Design: Alkene Adsorption by Non-porous Copper(I) Complexes

Purifying alkenes from alkanes requires cryogenic distillation. This consumes energy equivalent to countries of ca. 5 million people. Replacing distillation with adsorption processes would significantly increase energy efficiency. Trade-offs between kinetics, selectivity, capacity, and heat of adsorption have prevented production of an optimal adsorbent. Here, we report adsorbents that overcome these trade-offs. [Cu-Br] 3 and [Cu-H] 3 are air-stable trinuclear complexes that undergo reversible solid-state inter-molecular rearrangements to produce dinuclear [Cu-Br∙(alkene)] 2 and [Cu-H∙(alkene)] 2 . The reversible solid-state rearrangement, confirmed in situ using powder X-ray diffraction, allows adsorbent design trade-offs to be overcome, coupling low heat of adsorption (-10 to -17 kJ mol -1 alkene ), high alkene:alkane selectivity (47; 29), and uptake capacity (>2.5 molalkene mol -1 Cu3 ). Most remarkably, [Cu-H] 3 displays fast uptake and regenerates capacity within 10 minutes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward a mechanistic understanding of electrocatalytic nanocarbon

Electrocatalytic nanocarbon (EN) is a class of material receiving intense interest as a potential replacement for expensive, metal-based electrocatalysts for energy conversion and chemical production applications. The further development of EN will require an intricate knowledge of its catalytic behaviors, however, the true nature of their electrocatalytic activity remains elusive. This review highlights work that contributed valuable knowledge in the elucidation of EN catalytic mechanisms. Experimental evidence from spectroscopic studies and well-defined molecular models, along with the survey of computational studies, is summarized to document our current mechanistic understanding of EN-catalyzed oxygen, carbon dioxide and nitrogen electrochemistry. We hope this review will inspire future development of synthetic methods and in situ spectroscopic tools to make and study well-defined EN structures.

36 MATERIALS SCIENCE↗

CALIPSO Lidar Calibration at 532 nm: Version 4 Nighttime Algorithm

Data products from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) on board Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) were recently updated following the implementation of new (version 4) calibration algorithms for all of the level 1 attenuated backscatter measurements. In this work we present the motivation for and the implementation of the version 4 nighttime 532 nm parallel channel calibration. The nighttime 532 nm calibration is the most fundamental calibration of CALIOP data, since all of CALIOP’s other radiometric calibration procedures – i.e., the 532 nm daytime calibration and the 1064 nm calibrations during both nighttime and daytime – depend either directly or indirectly on the 532 nm nighttime calibration. The accuracy of the 532 nm nighttime calibration has been significantly improved by raising the molecular normalization altitude from 30-34 km to 36-39 km to substantially reduce stratospheric aerosol contamination. Due to the greatly reduced molecular number density and consequently reduced signal-to-noise ratio (SNR) at these higher altitudes, the signal is now averaged over a larger number of samples using data from multiple adjacent granules. As well, an enhanced strategy for filtering the radiation-induced noise from high energy particles was adopted. Further, the meteorological model used in the earlier versions has been replaced by the improved MERRA-2 model. An aerosol scattering ratio of 1.01 ± 0.01 is now explicitly used for the calibration altitude. These modifications lead to globally revised calibration coefficients which are, on average, 2-3% lower than in previous data releases. Further, the new calibration procedure is shown to eliminate biases at high altitudes that were present in earlier versions and consequently leads to an improved representation of stratospheric aerosols. Validation results using airborne lidar measurements are also presented. Biases relative to collocated measurements acquired by the Langley Research Center (LaRC) airborne high spectral resolution lidar (HSRL) are reduced from 3.6% ± 2.2% in the version 3 data set to 1.6% ± 2.4 % in the version 4 release.

Jayanta Kar↗

Tetracene Functionalized Si(111) Achieves Enhanced Solar-to-Chemical Energy Conversion via Molecular Acceptor States

The properties of semiconductor|liquid interfaces play a critical role in determining the efficiency of solar-to-hydrogen (STH) conversion. Here, we investigate how molecular functionalization of Si(111) and Si(111)|TiO 2 surfaces impacts photoelectrochemical (PEC) hydrogen production efficiency. We find that functionalization of ∼3% of the atop sites of Si(111) with either 9-anthracene (Anth) or 5-tetracene (Tet), with the remaining sites passivated by methyl groups, provides substrates with high electronic quality and low surface oxide densities, as determined by X-ray photoelectron spectroscopy (XPS) measurements. Surface photovoltage (SPV) spectroscopy shows that surfaces modified with Anth or Tet exhibit an increased photovoltage, with Tet-functionalized surfaces yielding an additional 192 meV relative to methyl-terminated Si(111), indicating improved charge separation for Si-Tet. Further improvement in onset potential was achieved by replacing a nitrogen-containing TiO 2 atomic layer deposition (ALD) precursor (TDMAT) with a precursor lacking nitrogen (TTIP), which eliminates the parasitic defect band in the TiO 2 overlayer (p-Si(111)-Tet|TTIP-TiO 2 |Pt: V OC = +0.283 ± 0.041 V vs RHE). Density functional theory (DFT) analysis demonstrates that compared with Anth-modified Si(111), the Tet-modified surface exhibits more hybridized Si(111)-Tet states closer to the silicon band edges. Mercury contact current–voltage (I–V, dark) measurements quantified the relative interfacial density of states of Si-Tet, Si-Anth and Si-Me surfaces─revealing that the interfacial state density was highest for Si-Tet. This suggests that such hybridized interfaces serve to capture better photoexcited charge, which enables facile electron transfer to molecular acceptors in solution. Altogether, the data indicate that beneficial hybrid molecular LUMO surface states interacting with the Si conduction band edge results in improved hydrogen evolution (HER) performance for p-Si devices.

Group theory↗