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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

A Continuing Career in Biocatalysis: Frances H. Arnold

On the occasion of Professor Frances H. Arnold’s recent acceptance of the 2018 Nobel Prize in Chemistry, we honor her numerous contributions to the fields of directed evolution and biocatalysis. Arnold pioneered the development of directed evolution methods for engineering enzymes as biocatalysts. Her highly interdisciplinary research has provided grounds not only for understanding the mechanisms of enzyme evolution but also for developing commercially viable enzyme biocatalysts and biocatalytic processes. In this Account, we highlight some of her notable contributions in the past three decades in the development of foundational directed evolution methods and their applications in the design and engineering of enzymes with desired functions for biocatalysis. Her work has created a paradigm shift in the broad catalysis field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Layer by Layer Photo-Cross-Linked Environmental Functional hydrogel Thin Films Based on Vanillin: Part 3

The present work emphasizes the preparation of new monomer from the family of vanillin acrylate. It has been prepared in two steps the name of the final product is [2-((ditert-butylamino) methyl)-4-formyl-6-methoxyphenyl acrylate] and abbreviated by TBAMVA, both products were evaluated by {sup 1}H, {sup 13}C NMR and FTIR and they were in the logic case with the chemical structure. The next step was the preparation of three different pH and temperature responsive copolymers by free radical polymerization of 5, 10, 20 mol% of TBAMVA and 5 mol% of maleimide photo-cross-linker with N-isopropylacrylamide. Polymers were chemically and physically characterized indicating the presence of the aldehyde group in the main chain. The lower critical solution temperature of polymers has been determined by two methods; the first one using turbidity measurements by UV–Vis Spectroscopy, another method using micro-DSC. The last step was the formation of pH-Temperature responsive hydrogel layer over gold and studying the swelling properties response to pH and temperature using surface plasmon resonance with the optical waveguide. In the present work, we focused on synthesizing new environmental functional polymers and hydrogel thin films used as biosensor as a target for many biological molecules in biosynthesis, drug delivery, and bio-separation.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Accurate lattice geometrical parameters and bulk moduli from a semilocal density functional

Accurate prediction of lattice constants is very important in applications of density functional theory. In this work, we assess the efficacy of a non-empirical meta-generalized gradient approximation proposed by Tao and Mo (TM) by calculating the lattice constants as well as bulk moduli of 33 crystalline semiconductors within the TM scheme. We find that the TM functional is able to produce very accurate lattice constants, with a mean absolute error of 0.038 Å, and bulk moduli with a mean absolute error of 3.2 GPa, improving upon commonly-used semilocal density functionals, such as the LSDA, PBE, SOGGA, PBEsol, TPSS, M06L, and SCAN. The high computational efficiency and remarkable agreements with the corresponding experimental values suggest that the TM functional can be a very competitive candidate in electronic structure theory. We attribute the accuracy of the TM functional to be the result of its satisfaction of many exact or nearly-exact conditions related to the exchange-correlation energy and the associated hole, leading to an improved description of the short- as well as intermediate-range van der Waals interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Modification at the C2'-O-Position with 2-Methylbenzothiophene Induces Unique Structural Changes and Thermal Transitions on Duplexes of RNA and DNA

Oligonucleotides can be chemically modified for a variety of applications that include their use as biomaterials, in therapeutics, or as tools to understand biochemical processes, among others. This work focuses on the functionalization of oligonucleotides of RNA and DNA (12- or 14-nucleotides long) with methylbenzothiophene (BT), at the C2'-O-position, which led to unique structural features. Circular dichroism (CD) analyses showed that positioning the BT units on one strand led to significant thermal destabilization, while duplexes where each strand contained 4-BT rings formed a distinct arrangement with cooperativity/interactions among the modifications (evidenced from the appearance of a band with positive ellipticity at 235 nm). Interestingly, the structural arrays displayed increased duplex stabilization (>10 °C higher than the canonical analogue) as a function of [Na + ] with an unexpected structural rearrangement at temperatures above 50 °C. Density functional theory–polarizable continuum model (DFT-PCM) calculations were carried out, and the analyses were in agreement with induced structural changes as a function of salt content. A model was proposed where the hydrophobic surface allows for an internal nucleobase rearrangement into a more thermodynamically stable structure, before undergoing full denaturation, with increased heat. While this behavior is not common, B- to Z-form duplex transitions can occur and are dependent on parameters that were probed in this work, i.e., temperature, nature of modification, or ionic content. To take advantage of this phenomenon, we probed the ability of the modified duplexes to be recognized by Zα (an RNA binding protein that targets Z-form RNA) via electrophoretic analysis and CD. Interestingly, the protein did not bind to canonical duplexes of DNA or RNA; however, it recognized the modified duplexes, in a [monovalent/divalent salt] dependent manner. Overall, the findings describe methodology to attain unique structural motifs of modified duplexes of DNA or RNA, and control their behavior as a function of salt concentration. While their affinity to RNA binding proteins, and the corresponding mechanism of action, requires further exploration, the tunable properties can be of potential use to study this, and other, types of modifications. The novel arrays that formed, under the conditions described herein, provide a useful way to explore the structure and behavior of modified oligonucleotides, in general.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

First-Principles Dissociation Pathways of BCl 3 on the Si(100)-2 × 1 Surface

BCl 3 is a promising acceptor precursor for atomic-precision δ-doping of silicon, as it has been observed to rapidly dissociate into boron doped into the silicon surface and surface chlorine, which can be removed upon annealing. The chemical pathway and the resulting kinetics, through which BCl 3 adsorbs and dissociates on silicon, however, have only been partially explained. Here, in this work, we use density functional theory to expand the dissociation reactions of BCl 3 to include reactions that take place across multiple silicon dimer rows and reactions which end in a bare B atom either at the surface, substituted for a surface silicon, or in a subsurface position. We further simulate the resulting scanning tunneling microscopy images for each of these BCl x dissociation fragments, demonstrating that they often display distinct features that may allow for relatively confident experimental identification. Finally, we input the full dissociation pathway for BCl 3 into a kinetic Monte Carlo model, which simulates realistic reaction pathways as a function of environmental conditions, such as the pressure and temperature of dosing. We find that BCl 2 is broadly dominant at low temperatures, while high temperatures and ample space on the silicon surface for dissociation encourage the formation of bridging BCl fragments and B substitutions on the surface. This work provides the chemical mechanisms for understanding atomic-precision doping of Si with B, enabling a number of relevant quantum applications, such as bipolar nanoelectronics, acceptor-based qubits, and superconducting Si.

Campbell, Quinn T. [Sandia National Laboratories (↗
DOE OSTI2020

Monitoring Local Electric Fields using Stark Shifts on Napthyl Nitrile-Functionalized Silicon Photoelectrodes

in this paper, we report spectroscopic measurements of the local electric field using vibrational Stark shifts of napthyl nitrile-functionalized silicon under electrochemical working conditions. The C$\equiv$N bond is particularly sensitive to applied electric fields and serves as a good probe for the local electric fields at the silicon–aqueous interface. Here, surface-enhanced Raman spectra (SERS) are collected at a silicon surface using a water immersion lens as a function of the reference potential in a three-terminal potentiostat. In deionized (DI) water and KCl solutions, the nitrile (i.e., C$\equiv$N) stretch downshifts by 4.7 and 8.6 cm –1 , respectively, under an applied potential of –1 V vs Ag/AgCl. Density functional theory (DFT) calculations of the napthyl nitrile complex carried out under various electric fields establish the Stark tuning rate to be 0.5622 cm–1/(MV cm –1 ). Based on this relation, electric fields of –8.4 and –15.2 MV/cm were obtained under negative applied potentials. These measurements report the electric field strength within the double (i.e., Helmholtz) layer, which is responsible for pulling positively charged ions (e.g., H + ) toward the surface in reduction reaction processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Addressing Issues with Working Memory in Video Object Segmentation

Contemporary state-of-the-art video object segmentation (VOS) models compare incoming unannotated images to a history of image-mask relations via affinity or cross-attention to predict object masks. We refer to the internal memory state of the initial image-mask pair and past image-masks as a working memory buffer. While the current state of the art models perform very well on clean video data, their reliance on a working memory of previous frames leaves room for error. Affinity-based algorithms include the inductive bias that there is temporal continuity between consecutive frames. To account for inconsistent camera views of the desired object, working memory models need an algorithmic modification that regulates the memory updates and avoid writing irrelevant frames into working memory. A simple algorithmic change is proposed that can be applied to any existing working memory-based VOS model to improve performance on inconsistent views, such as sudden camera cuts, frame interjections, and extreme context changes. The resulting model performances show significant improvement on video data with these frame interjections over the same model without the algorithmic addition. Our contribution is a simple decision function that determines whether working memory should be updated based on the detection of sudden, extreme changes and the assumption that the object is no longer in frame. By implementing algorithmic changes, such as this, we can increase the real-world applicability of current VOS models.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A study of the role of the PDF uncertainty on the LHC W -boson mass measurement

The determination of the W -boson mass through an analysis of the decay charged-lepton transverse momentum distribution has a sizable uncertainty due to the imperfect knowledge of the relevant parton distribution functions (PDFs). In this work, a quantitative assessment of the W -boson mass uncertainty at the LHC resulting from the PDF uncertainty is examined. We use the CT14 NNLO PDFs with a NNLL + NNLO calculation (ResBos) to simulate the W -boson production and decay kinematics. The uncertainty of the W -boson mass determination is then determined as a function of the boson and lepton kinematics. For W + production using $P^{W}_{T}$ < 15 GeV and 35 < $P^{l}_{T}$ (GeV) < 45, PDF uncertainties lead (at the 68% CL) to a mass uncertainty for the $M^{+}_{W}$ of $^{+16.0}_{-17.5}$ MeV, $^{+13.9}_{-14.8}$ MeV, and $^{+12.2}_{-19.2}$ MeV, are determined at 7 TeV, 8 TeV and 13 TeV, respectively. The uncertainties of $M^{-}_{W}$ for the same cuts are found to be $^{+15.9}_{-15.6}$ MeV, $^{+15.0}_{-12.7}$ MeV and $^{+14.8}_{-15.3}$ MeV at 7 TeV, 8 TeV and 13 TeV, respectively.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Gibbs mixing of partially distinguishable photons with a polarising beamsplitter membrane

For a thought experiment concerning the mixing of two classical gases, Gibbs concluded that the work that can be extracted from mixing is determined by whether or not the gases can be distinguished by a semi-permeable membrane; that is, the mixing work is a discontinuous function of how similar the gases are. Here we describe an optomechanical setup that generalises Gibbs’ thought experiment to partially distinguishable quantum gases. Specifically, we model the interaction between a polarisation dependent beamsplitter, that plays the role of a semi-permeable membrane, and two photon gases of non-orthogonal polarisation. We find that the work arising from the mixing of the gases is related to the potential energy associated with the displacement of the microscopic membrane, and we derive a general quantum mixing work expression, valid for any two photon gases with the same number distribution. The quantum mixing work is found to change continuously with the distinguishability of the two polarised gases. In addition, fluctuations of the work on the microscopic membrane become important, which we calculate for Fock and thermal states of the photon gases. Our findings generalise Gibbs’ mixing to the quantum regime and open the door for new quantum thermodynamic (thought) experiments with quantum gases with non-orthogonal polarisations and microscopic pistons that can distinguish orthogonal polarisations.

distinguishability↗
DOE OSTI2020

Electrochemical reduction of europium(iii) using tetra- n -octyl diglycolamide functionalized ordered mesoporous carbon microelectrodes

This work investigates the one-electron reduction of Eu(III) to Eu(II) with ordered mesoporous carbon (OMC) in cavity microelectrode (CME) systems. OMC materials with and without tetra-n-octyl diglycolamide (TODGA) functionalization were subjected to voltammetric measurements and compared with commercial carbon black Vulcan® XC-72. The electrochemical reduction of solution Eu(III) with unfunctionalized OMC, XC-72, and TODGA-functionalized OMC—both within the electrode matrix and on the electrode surface—is reported. The complexation of Eu(III) by TODGA-functionalized OMC prior to electrode preparation incorporates Eu(III) as part of the bulk electrode matrix. Under these conditions, the high capacitance obscures the Eu(III)/Eu(II) redox couple. A signal emerges above the background (capacitive) currents when 2-octanol is added to the TODGA-functionalized OMC as a wetting agent. In contrast, surface Eu(III)–TODGA complexation, when Eu(III) contacts the electrode surface exclusively after electrode preparation, provides a strong response. The addition of 2-octanol to TODGA reduces the capacitance of the electrode and narrows the Eu(III)/Eu(II) redox peak widths. In conclusion, the desorption by reductive stripping of Eu(II) was demonstrated using a 2-octanol modified TODGA OMC CME, opening the possibility for selective separation of Eu from adjacent trivalent lanthanides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Representing plant diversity in land models: An evolutionary approach to make “Functional Types” more functional

Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. Here we review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A novel technique for minimizing energy functional using neural networks

An energy functional describes the equilibrium state of a system. In this work, we present a novel technique, Functional Optimization using Neural Networks (FONN), for minimizing the system’s energy. FONN utilizes neural networks to process information at discrete grid points, considering their interactions with neighboring grid points, to update the state of the system. The training process involves formulating a loss function based on the system’s energy, and with the help of multiple fine-tuning steps, the method employs a progressive energy reduction technique that decreases the energy in multiple steps. FONN’s effectiveness is demonstrated across various problems, including the minimization of the heat and Lyapunov energy. Furthermore, the paper explores the minimization of the elastic bending energy with an area constraint.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

How Accurate Are Approximate Density Functionals for Noncovalent Interaction of Very Large Molecular Systems?

Noncovalent intermolecular interactions are very important in many research areas. Therefore, it is vital to understand the extent to which approximate density functionals give a proper description of noncovalent interactions. Previous research has demonstrated that some approximate density functionals can predict usefully accurate interaction energies for many noncovalent systems; however, most of that work is limited to small and moderate-sized molecules. Very recently though, accurate benchmarks have become available for some very large molecules. Here, the present work applies 21 approximate density functionals to compute the binding energies of seven large molecular systems that have a number of atoms ranging from 200 to 910. The results are judged by comparison to the recently published CIM-DLPNO-CCSD(T) results, which are assumed to provide a reliable benchmark. The five most accurate methods among those tested are found to be PW6B95-D4, PW6B95-D3(BJ), revM11, M06-L, and MN15.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Workhorse minimally empirical dispersion-corrected density functional with tests for weakly bound systems: r 2 SCAN + rVV 10

SCAN+rVV10 has been demonstrated to be a versatile van der Waals (vdW) density functional that delivers good predictions of both energetic and structural properties for many types of bonding. Recently, the r 2 SCAN functional was devised as a revised form of SCAN with improved numerical stability. In this work, we refit the rVV10 functional to optimize the r 2 SCAN+rVV10 vdW density functional and test its performance for molecular interactions and layered materials. Our molecular tests demonstrate that r 2 SCAN+rVV10 outperforms its predecessor SCAN+rVV10 in both efficiency (numerical stability) and accuracy. This good performance is also found in lattice-constant predictions. In comparison with benchmark results from higher-level theories or experiments, r 2 SCAN+rVV10 yields excellent interlayer binding energies and phonon dispersions for layered materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Growth functions of periodic space tessellations

This work analyzes the rules governing the growth of the numbers of vertices, edges and faces in all possible periodic tessellations of the 2D Euclidean space, and encodes those rules in several types of polynomial growth functions. These encodings map the geometric, combinatorial and topological properties of the tessellations into sets of integer coefficients. Several general statements about these encodings are given with rigorous mathematical proof. The variation of the growth functions is represented graphically and analyzed in orphic diagrams, so named because of their similarity to orphic art. Several examples of 3D space groups are included, to emphasize the complexity of the growth functions in higher dimensions. A freely available Python library is presented to facilitate the discovery of the growth functions and the generation of orphic diagrams.

Chemistry↗
DOE OSTI2020

Machine learning defect properties in Cd-based chalcogenides

Impurity energy levels in the band gap can have serious consequences for a semiconductor's performance as a photovoltaic absorber. Data-driven approaches can help accelerate the prediction of point defect properties in common semiconductors, and thus lead to the identification of potential deep lying impurity states. In this work, we use density functional theory (DFT) to compute defect formation energies and charge transition levels of hundreds of impurities in CdX chalcogenide compounds, where X = Te, Se or S. We apply machine learning techniques on the DFT data and develop on-demand predictive models for the formation energy and relevant transition levels of any impurity atom in any site. The trained ML models are general and accurate enough to predict the properties of any possible point defects in any Cd-based chalcogenide, as we prove by testing on a few selected defects in mixed chalcogen compounds CdTe 0.5 Se 0.5 and CdSe 0.5 S 0.5 . The ML framework used in this work can be extended to any class of semiconductors.

density functional theory↗
DOE OSTI2021

CrI 3 revisited with a many-body ab initio theoretical approach

CrI 3 has recently been shown to exhibit low-dimensional, long-range magnetic ordering from few layers to single layers of CrI 3 . The properties of CrI 3 bulk and few layered systems are uniquely defined by a combination of short-range intralayer and long-range interlayer interactions; including strong correlations, exchange and spin orbit coupling. Unfortunately, both the long-range van der Waals interactions, which are driven by dynamic, many-body electronic correlations and the competing strong intralayer correlations, present a formidable challenging for the local or semi local mean-field approximations employed in workhorse electronic structure approaches like density functional theory. In this work, we employ a sophisticated many-body approach that can simultaneously describe long- and short-range correlations. Herein, we establish that the fixed-node diffusion Monte Carlo (FNDMC) method reproduces the experimental interlayer separation distance of bulk CrI 3 for the high-temperature, monoclinic phase, with a reliable prediction of the interlayer binding energy. We subsequently employed, the FNDMC results to benchmark the accuracy of several density functional theory exchange-correlation approximations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The role of coverage effects on the structure–sensitivity of formic acid electrooxidation on Pd surfaces

Direct formic acid (FA) fuel cells (DFAFCs) with Pd anode catalysts are promising for small portable applications. During the electrooxidation of formic acid (FAO), CO accumulates on the Pd electrocatalyst, thereby decreasing its performance. In this work, we use density functional theory (DFT; RPBE) to elucidate the significance of coverage effects on the structure–sensitivity of FAO over four low–index Pd surfaces: Pd(1 1 1), Pd(1 0 0), Pd(1 1 0), and Pd(2 1 1). We construct coverage–dependent Gibbs free energy diagrams and in agreement with experiment, predict that Pd(1 0 0) and Pd(2 1 1) are the most active surfaces. Additionally, we find that the presence of CO spectator species can alter the preferred electrooxidation pathway under different applied potentials. Furthermore, such pathway transitions appear to be critical for rationalizing experimental trends regarding electrocatalytic activity and are only captured when coverage effects are accounted for. Insights derived from this work may facilitate the design of improved FAO electrocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗