Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “atomic structure”

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 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Atomic-Scale Quantification of Interfacial Binding between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite

Using a specific explicitly solvated interface model between a calcium carbonate binding peptide and crystalline aragonite, we investigate the electronic structure, atomic bonding, solvation effect, and the role of hydrogen bonding on the cohesion, stability, and functionality of this complex hybrid system using density functional calculation. The large interface model is strategically constructed using a stepwise procedure followed by ab initio molecular dynamics to obtain the optimal conformation. The calculated data on the electronic structure and bonding are analyzed in terms of three structural parts: aragonite, peptide, and water. Next, we focus on the binding between aragonite (001) surface and the peptide mediated by water. Finally, specific interatomic bonding between the amino acids in peptide and the (001) surface of aragonite is quantified. A single quantum mechanical metric, the total bond order density (TBOD), infers the dynamic interplay of different competing interactions. Four amino acids HIS1, ARG6, MET7, and TRP11 in the peptide sequence have strong interfacial Ca–O bonding and O···H hydrogen bonding between aragonite and peptide. The calculated Young’s modulus 33.37 GPa is in line with the measured value for nacre. Our approach for interfacial study between aragonite and a calcium carbonate binding peptide offers a broad perspective for probing complex interactions between the biomimetic interfaces. Finally, TBOD can be used as an effective parameter in ranking the efficacy of peptide–surface interactions and in providing a programmable design for bio-inspired material interfaces based on computational means.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structure of a complex of uridine phosphorylase from Yersinia pseudotuberculosis with the modified bacteriostatic antibacterial drug determined by X-ray crystallography and computer analysis

Pseudotuberculosis and bubonic plague are acute infectious diseases caused by the bacteria Yersinia pseudotuberculosis and Yersinia pestis. These diseases are treated, in particular, with trimethoprim and its modified analogues. However, uridine phosphorylases (pyrimidine nucleoside phosphorylases) that are present in bacterial cells neutralize the action of trimethoprim and its modified analogues on the cells. In order to reveal the character of the interaction of the drug with bacterial uridine phosphorylase, the atomic structure of the unligated molecule of uridine-specific pyrimidine nucleoside phosphorylase from Yersinia pseudotuberculosis (YptUPh) was determined by X-ray diffraction at 1.7 Å resolution with high reliability (R{sub work} = 16.2, R{sub free} = 19.4%; r.m.s.d. of bond lengths and bond angles are 0.006 Å and 1.005°, respectively; DPI = 0.107 Å). The atoms of the amino acid residues of the functionally important secondary-structure elements—the loop L9 and the helix H8—of the enzyme YptUPh were located. The three-dimensional structure of the complex of YptUPh with modified trimethoprim—referred to as 53I—was determined by the computer simulation. It was shown that 53I is a pseudosubstrate of uridine phosphorylases, and its pyrimidine-2,4-diamine group is located in the phosphate-binding site of the enzyme YptUPh.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Comparative Studies of the Structural and Transport Properties of Molten Salt FLiNaK Using the Machine-Learned Neural Network and Reparametrized Classical Forcefields

Despite surging interest in molten salt reactors and thermal storage systems, knowledge of the physicochemical properties of molten salts are still inadequate due to demanding experiments that require high temperature, impurity control, and corrosion mitigation. Therefore, the ability to predict these properties for molten salts from first-principles computations is urgently needed. Herein, we developed and compared a machine-learned neural network force field (NNFF) and a reparametrized rigid ion model (RIM) for a prototypical molten salt LiF–NaF–KF (FLiNaK). We found that NNFF was able to reproduce both the structural and transport properties of the molten salt with first-principles accuracy and classical-MD computational efficiency. Furthermore, the correlation between the local atomic structures and the dynamics was identified by comparing with RIMs, suggesting the significance of polarization of anions implicitly embedded in the NNFF. Furthermore, this work demonstrated a computational framework that can facilitate the screening of molten salts with different chemical compositions, impurities, and additives, and at different thermodynamic conditions suitable for the next-generation nuclear reactors and thermal energy storage facilities.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Unraveling the origin of antiferromagnetic coupling at YIG/permalloy interface

We investigate the structural and electronic origin of antiferromagnetic (AFM) coupling in the yttrium iron garnet (YIG) and permalloy (Ni 80 ⁢Fe 20 , Py) bilayer system at the atomic level. Ferromagnetic resonance (FMR) spectra reveal unique hybrid modes in samples prepared with surface ion milling, indicative of antiferromagnetic exchange coupling at the YIG/Py interface. Using atomic resolution scanning transmission electron microscopy (STEM), we found that AFM coupling appears at the YIG/Py interface of the tetrahedral YIG surface formed with ion milling. Here, the STEM measurements suggest that the interfacial AFM coupling is predominantly driven by an oxygen-mediated superexchange coupling mechanism, which is confirmed by the density-functional theory (DFT) calculations to be energetically favorable. Thus, the combined experimental and theoretical results reveal the critical role of interfacial atomic structure in determining the type of magnetic coupling in a YIG/ferromagnet heterostructure, and prove that the interfacial structure can be experimentally tuned by surface ion milling.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Theory Aided Design of Active and Durable Nanoscale Cathode Catalysts (Final Report)

One of the greatest technological hurdles to deployment of fuel cells relates to the sluggish activity, low durability and the high cost of the catalysts that are currently employed. For automotive PEM fuel cells to become commercially viable, the Pt-specific power density would need to be reduced to less than 0.2gPt/kW (at cell voltages >0.65 V). This would require the Pt loadings to be less than 0.15 mg Pt /cm 2 MEA within the membrane electrode assembly. This could be achieved by enhancing the catalytic activity at the cathode, thus lowering its overpotential. Various different Pt-alloys have shown 2-4 times enhanced activities over Pt alone but still suffer some of the same durability issues as that of the pure Pt. There is a general loss of active Pt due to dissolution and sintering. While there have been a number of elegant fundamental experimental and theoretical studies on ideal single crystal Pt and Pt alloy surfaces which have helped to elucidate the factors that control the activity, there have been very few fundamental studies focused on the stability, reactivity and durability of well-defined Pt nanoparticles. We carried out ab initio density functional theory together with a novel double reference method that we developed to simulate constant potential electrochemical systems in order to model the electrocatalytic reduction of oxygen over model Pt alloy surfaces and nanoparticles. These simulations were used to probe the factors that control the electrocatalytic activity, guide the potential selection of new materials and test their stability under reaction conditions. Ab initio calculations were used to determine the reaction energies and activation barriers for a comprehensive array of different elementary adsorption, desorption, surface reaction and diffusion steps over Pt and Pt alloys involved in the electroreduction of oxygen as a function of surface coverage, the electrochemical potential and temperature. The calculations were used to simulate the potential dependent adsorption and surface reaction energies along with activation barriers in order to determine the kinetics for different surface structures and structural features (step edge and corner sites) to provide the necessary input for kinetic Monte Carlo simulations to follow the rates of reaction. More coarse-grained simulated annealing methods were used to help establish the lowest energy structures and morphologies for different Pt and Pt-alloy nanoparticles that form. The results from the DFT calculations were used to establish an ab initio-derived kinetic database that was used in both 2D and 3D kinetic Monte Carlo simulations that were used to follow the electrocatalytic performance over different particle sizes, shapes and compositions. The ab initio calculations together with the kinetic Monte Carlo simulations were used to complete the following objectives: 1) Determine the controlling elementary reaction pathways and intrinsic kinetics involved in ORR and their potential dependent behavior; 2) Establish the influence of the extrinsic reaction environment including surface structure, alloy composition and spatial arrangement and the humidity on ORR kinetics; 3) Elucidate the effects of particle size and morphology as well as the atomic structure and composition of nanoparticles of Pt, Pt 3 Co, Pt 3 Ni, Pt 3 Fe and other Pt-alloys on the electrocatalytic activity and reaction selectivity; 5) Construct surface Pourbaix phase diagrams for different Pt and Pt-alloys in order to map out the most stable surface phases for different material compositions and reaction conditions; 6) Elucidate the mechanisms that control dissolution and re-deposition of Pt.

08 HYDROGEN↗
DOE OSTI2015

Simultaneous dynamic electrical and structural measurements of functional materials

A new materials characterization system developed at the XMaS beamline, located at the European Synchrotron Radiation Facility in France, is presented. We show that this new capability allows to measure the atomic structural evolution (crystallography) of piezoelectric materials whilst simultaneously measuring the overall strain characteristics and electrical response to dynamically (ac) applied external stimuli.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Decoding Active Sites for Highly Efficient Semihydrogenation of Acetylene in Palladium–Copper Nanoalloys

Accurately decoding the three-dimensional atomic structure of surface active sites is essential yet challenging for a rational catalyst design. Here, we used comprehensive techniques combining the pair distribution function and reverse Monte Carlo simulation to reveal the surficial distribution of Pd active sites and adjacent coordination environment in palladium-copper nanoalloys. After the fine-tuning of the atomic arrangement, excellent catalytic performance with 98% ethylene selectivity at complete acetylene conversion was obtained in the Pd 34 Cu 66 nanocatalysts, outperforming most of the reported advanced catalysts. Further, t he quantitative deciphering shows a large number of active sites with a Pd-Pd coordination number of 3 distributed on the surface of Pd 34 Cu 66 nanoalloys, which play a decisive role in highly efficient semihydrogenation. This finding not only opens the way for guiding the precise design of bimetal nanocatalysts from atomic-level insight but also provides a method to resolve the spatial structure of active sites.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Accelerating Quantum Materials Development with Advances in Transmission Electron Microscopy

Quantum materials are driving a technology revolution in sensing, communication, and computing, while simultaneously testing many core theories of the past century. Materials such as topological insulators, complex oxides, superconductors, quantum dots, color center-hosting semiconductors, and other types of strongly correlated materials can exhibit exotic properties such as edge conductivity, multiferroicity, magnetoresistance, superconductivity, single photon emission, and optical-spin locking. These emergent properties arise and depend strongly on the material’s detailed atomic-scale structure, including atomic defects, dopants, and lattice stacking. In this review, we describe how progress in the field of electron microscopy (EM), including in situ and in operando EM, can accelerate advances in quantum materials and quantum excitations. We begin by describing fundamental EM principles and operation modes. We then discuss various EM methods such as (i) EM spectroscopies, including electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and electron energy gain spectroscopy (EEGS); (ii) four-dimensional scanning transmission electron microscopy (4D-STEM); (iii) dynamic and ultrafast EM (UEM); (iv) complementary ultrafast spectroscopies (UED, XFEL); and (v) atomic electron tomography (AET). We describe how these methods could inform structure–function relations in quantum materials down to the picometer scale and femtosecond time resolution, and how they enable precision positioning of atomic defects and high-resolution manipulation of quantum materials. For each method, we also describe existing limitations to solve open quantum mechanical questions, and how they might be addressed to accelerate progress. Among numerous notable results, our review highlights how EM is enabling identification of the 3D structure of quantum defects; measuring reversible and metastable dynamics of quantum excitations; mapping exciton states and single photon emission; measuring nanoscale thermal transport and coupled excitation dynamics; and measuring the internal electric field and charge density distribution of quantum heterointerfaces- all at the quantum materials’ intrinsic atomic and near atomic-length scale. Finally, we conclude by describing open challenges for the future, including achieving stable sample holders for ultralow temperature (below 10K) atomic-scale spatial resolution, stable spectrometers that enable meV energy resolution, and high-resolution, dynamic mapping of magnetic and spin fields. With atomic manipulation and ultrafast characterization enabled by EM, quantum materials will be poised to integrate into many of the sustainable and energy-efficient technologies needed for the 21st century.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Mössbauer study of conductive oxide glass

Heat treatment of barium iron vanadate glass, BaO‐Fe{sub 2}O{sub 3}‐V{sub 2}O{sub 5}, at temperatures higher than crystallization temperature causes a marked decrease in resistivity (ρ) from several MΩcm to several Ωcm. {sup 57}Fe Mössbauer spectrum of heat-treated vanadate glass shows a marked decrease in quadrupole splitting (Δ) of Fe{sup III}, reflecting a structural relaxation, i.e., an increased symmetry of 'distorted' FeO{sub 4} and VO{sub 4} tetrahedra which are connected to each other by sharing corner oxygen atoms. Structural relaxation of 3D-network of vanadate glass accompanies a decrease in the activation energy for the conduction, reflecting a decreased energy gap between the donor level and conduction band. A marked increase in the conductivity was observed in CuO- or Cu{sub 2}O-containing barium iron vanadate glass after heat treatment at 450 °C for 30 min or more. 'n-type semiconductor model combined with small polaron hopping theory' was proposed in order to explain the high conductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Anti-phase boundaries at the SrTiO{sub 3}/Si(001) interface studied using aberration-corrected scanning transmission electron microscopy

In this work, the atomic structure of anti-phase boundary defects at the SrTiO{sub 3}/Si (001) interface is investigated by aberration-corrected scanning transmission electron microscopy. Atomic-resolution images reveal an abrupt SrTiO{sub 3}/Si interface with no intermediate oxide layer. Both single and double Si atomic columns (“dumbbells”) from different terraces of the Si(001) surface are visible at the interface. Anti-phase boundaries (APB) consisting of two adjacent TiO{sub 2} planes in the SrTiO{sub 3} (STO) film resulting either from Si surface steps or from the merging of crystalline domains from different surface nucleation sites are identified. These APBs occur on either {110} or {010} planes and both types have displacement vectors of a{sub STO}/2〈110〉.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1995

Resistance to Rolling in the Adhesive Contact of Two Elastic Spheres

For the stability of agglomerates of micron sized particles it is of considerable importance to study the effects of tangential forces on the contact of two particles. If the particles can slide or roll easily over each other, fractal structures of these agglomerates will not be stable. We use the description of contact forces by Johnson, Kendall and Roberts, along with arguments based on the atomic structure of the surfaces in contact, in order to calculate the resistance to rolling in such a contact. It is shown that the contact reacts elastically to torque forces up to a critical bending angle. Beyond that, irreversible rolling occurs. In the elastic regime, the moment opposing the attempt to roll is proportional to the bending angle and to the pull-off force P(sub c). Young's modulus of the involved materials has hardly any influence on the results. We show that agglomerates of sub-micron sized particles will in general be quite rigid and even long chains of particles cannot be bent easily. For very small particles, the contact will rather break than allow for rolling. We further discuss dynamic properties such as the possibility of vibrations in this degree of freedom and the typical amount of rolling during a collision of two particles.

Dominik, C.↗
NASA NTRS1995

Resistance to Rolling in the Adhesive Contact of Two Elastic Spheres

For the stability of agglomerates of micron sized particles it is of considerable importance to study the effects of tangential forces on the contact of two particles. If the particles can slide or roll easily over each other, fractal structures of these agglomerates will not be stable. We use the description of contact forces by Johnson, Kendall and Roberts, along with arguments based on the atomic structure of the surfaces in contact, in order to calculate the resistance to rolling in such a contact. It is shown that the contact reacts elastically to torque forces up to a critical bending angle. Beyond that, irreversible rolling occurs. In the elastic regime, the moment opposing the attempt to roll is proportional to the bending angle and to the pull-off force P(sub c). Young's modulus of the involved materials has hardly any influence on the results. We show that agglomerates of sub-micron sized particles will in general be quite rigid and even long chains of particles cannot be bent easily. For very small particles, the contact will rather break than allow for rolling. We further discuss dynamic properties such as the possibility of vibrations in this degree of freedom and the typical amount of rolling during a collision of two particles.

Dominik, C.↗
DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Crystal structure of monobasic sodium tartrate monohydrate

Crystals of a new polymorphic modification of monobasic sodium tartrate monohydrate NaHC{sub 4}H{sub 4}O{sub 6} · H{sub 2}O have been grown in a metasilicate gel. Their atomic structure is solved by X-ray diffraction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Integrating Machine Learning Potential and X-ray Absorption Spectroscopy for Predicting the Chemical Speciation of Disordered Carbon Nitrides

Precise determination of atomic structural information in functional materials holds transformative potential and broad implications for emerging technologies. Spectroscopic techniques, such as X-ray absorption near-edge structure (XANES), have been widely used for material characterization; however, extracting chemical information from experimental probes remains a significant challenge, particularly for disordered materials. We present an integrated approach that combines atomic simulations, data-driven techniques, and experimental measurements to investigate chemical speciation of amorphous carbon nitride systems as a case study. Here, we discuss the development of machine learning potentials that can efficiently explore the vast configuration space of amorphous carbon nitrides. By employing statistical methods, this structural database enables the elucidation of the most representative local structures and how they evolve with chemical compositions and density. Density functional theory simulations are used to establish a correlation between the local structure and spectroscopic signatures, which then serve as the basis for interpreting and extracting chemical content from experimental data. Although our framework is specifically demonstrated for XANES and carbon nitrides, the approach described herein is readily adaptable as applied to other experimental characterization probes and materials classes.

36 MATERIALS SCIENCE↗
NASA NTRS1998

Cross Sections for Electron Impact Excitation of Ions Relevant to Planetary Atmospheres Observation

The goal of this research grant was to calculate accurate oscillator strengths and electron collisional excitation strengths for inelastic transitions in atomic species of relevance to Planetary Atmospheres. Large scale configuration-interaction atomic structure calculations have been performed to obtain oscillator strengths and transition probabilities for transitions among the fine-structure levels and R-matrix method has been used in the calculations of electron-ion collision cross sections of C II, S I, S II, S III, and Ar II. A number of strong features due to ions of sulfur have been detected in the spectra of Jupiter satellite Io. The electron excitation cross sections for the C II and S II transitions are studied in collaboration with the experimental atomic physics group at the Jet Propulsion Laboratory. There is excellent agreement between experiment and theory which provide an accurate and broad-base test of the ability of theoretical methods used in the calculation of atomic processes. Specifically, research problems have been investigated for: electron impact excitation cross sections of C II: electron impact excitation cross sections of S III; energy levels and oscillator strengths for transitions in S III; collision strengths for electron collisional excitation of S II; electron impact excitation of inelastic transitions in Ar II; oscillator strengths of fine-structure transitions in neutral sulfur; cross sections for inelastic scattering of electrons from atomic nitrogen; and excitation of atomic ions by electron impact.

Tayal, Swaraj S.↗
DOE OSTI2022

Atomically thin interlayer phase from first principles enables defect-free incommensurate SnO2/CdTe interface

Advancing optoelectronic and emerging technologies increasingly requires control and design of interfaces between dissimilar materials. However, incommensurate interfaces are notoriously defective and rarely benefit from first-principles predictions, because no explicit atomic-structure models exist. Here, we adopt a bulk crystal structure prediction method to the interface geometry and apply it to SnO2/CdTe heterojunctions without and with the addition of CdCl2, a ubiquitous and beneficial, but abstruse processing step in CdTe photovoltaics. Whereas the direct SnO2/CdTe interface is highly defective, we discover a unique two-dimensional CdCl2 interphase, unrelated to the respective bulk structure. It facilitates a seamless transition from the rutile to zincblende lattices and removes defect-states from the interface bandgap. Implementing the predicted interface electronic structure in device simulations, we demonstrate the theoretical feasibility of bufferless oxide-CdTe heterojunction solar cells approaching the Shockley–Queisser limit. Our results highlight the broader potential of designing atomically thin interlayers to enable defect-free incommensurate interfaces.

14 SOLAR ENERGY↗