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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

Disordering and H-embrittlement of Pb(110) surface using embedded atom method and molecular dynamics

The dynamics and structure of the crystal melt interface are of great importance in crystal growth, melting, and other properties of the solid-liquid interface. The Embedded Atom Method (EAM), a semiempirical method developed by Daw and Baskes for determining the energetics of atoms in a bulk environment, is a useful method in the computer simulation. The EAM functions of PB in conjunction with the MD code are employed to study melting and disordering of the Pb(100) surface. The EAM functions are fitted to the bulk experimental data at zero temperature, and it is not clear if it will behave correctly at higher temperatures. In fact, it is shown that use of a similar type of potential at higher temperatures might result in a negative coefficient of thermal expansion. The primary purpose here is to perform MD simulation combined with the EAM functions of PB to study melting of the Pb(100) surface. This provides an accurate test of the EAM functions at higher temperatures. In particular, we calculate the two dimensional structure factor, the two dimensional distribution function, and density profile as a function of temperature up to the melting point of lead.

Karimi, Majid↗
DOE OSTI2022

Molecular beam homoepitaxy of N-polar AlN on bulk AlN substrates

N-polar AlN epilayers were grown on the N-face of single-crystal bulk AlN substrates by plasma-assisted molecular beam epitaxy. A combination of in situ thermal deoxidation and Al-assisted thermal desorption at high temperature aided in removing native surface oxides and impurities from the N-polar surface of the substrate enabling successful homoepitaxy. Subsequent epitaxial growth of the AlN layer on the in situ cleaned substrates, grown in a sufficiently high Al droplet regime, exhibited smooth surface morphologies with clean and wide atomic steps. KOH etch studies confirmed the N-polarity of the homoepitaxial films. Secondary ion mass spectrometry profiles show Si and H impurity concentrations below the noise levels, whereas O and C impurity concentrations of [Formula: see text] and [Formula: see text] atoms/cm 3 are observed, respectively. Although the structural defect densities are low, they interestingly appear as inversion domains of different dimensionalities.

Singhal, Jashan↗
DOE OSTI2023

Lithium crystallization at solid interfaces

Understanding the electrochemical deposition of metal anodes is critical for high-energy rechargeable batteries, among which solid-state lithium metal batteries have attracted extensive interest. A long-standing open question is how electrochemically deposited lithium-ions at the interfaces with the solid-electrolytes crystalize into lithium metal. Here, using large-scale molecular dynamics simulations, we study and reveal the atomistic pathways and energy barriers of lithium crystallization at the solid interfaces. In contrast to the conventional understanding, lithium crystallization takes multi-step pathways mediated by interfacial lithium atoms with disordered and random-closed-packed configurations as intermediate steps, which give rise to the energy barrier of crystallization. This understanding of multi-step crystallization pathways extends the applicability of Ostwald’s step rule to interfacial atom states, and enables a rational strategy for lower-barrier crystallization by promoting favorable interfacial atom states as intermediate steps through interfacial engineering. Our findings open rationally guided avenues of interfacial engineering for facilitating the crystallization in metal electrodes for solid-state batteries and can be generally applicable for fast crystal growth.

25 ENERGY STORAGE↗
NASA NTRS1994

Preliminary crystallographic studies of four crystal forms of serum albumin

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Serum Albumin/chemistry↗
DOE OSTI2024

Understanding Strain and Failure of a Knot in Polyethylene Using Molecular Dynamics with Machine-Learned Potentials

A neural network potential (NNP) has been developed by fitting to ab initio electronic structure data on hydrocarbons and is used to study failure of linear and knotted polyethylene (PE) chains. A linear PE chain must be highly strained before breaking as the stress is equally distributed across the chain. In contrast, the stress in a PE chain with a 31 or overhand knot, accumulates at the knot’s entrance/exit. We find the strain energy is greatest when the bond length and angle are strained simultaneously, and that the knot weakens the chain by increasing the variance of the C–C–C angle, thereby allowing rupture at lower bond strains. Here, we extend our analysis to both 51 and 52 knots and find that both break at the entrance/exit of a loop. Notably, molecular scale PE knots exhibit many of the same characteristics as knots in a macroscopic rope, with stick–slip phenomena upon tightening and similar points of failure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1982

Dipole-field sums and Lorentz factors for orthorhombic lattices, and implications for polarizable molecules

A method for computing the Lorentz tensor components in single crystals via rapidly convergent sums of Bessels functions is developed using the relationship between dipole-field sums and the tensor components. The Lorentz factors for simple, body-centered, and base-centered orthorhombic lattices are computed using this method, and the derivative Lorentz factors for simple orthorhombic lattices are also determined. Both the Lorentz factors and their derivatives are shown to be very sensitive to a lattice structure. The equivalent of the Clausius-Mossotti relation for general orthorhombic lattices is derived using the Lorentz-factor formalism, and the permanent molecular dipole moment is related to crystal polarization for the case of a ferroelectric of polarizable point dipoles. It is concluded that the polarization enhancement due to self-polarization familiar from classical theory may actually be a reduction in consequences of negative Lorentz factors in one or two lattice directions for noncubic crystals.

Purvis, C. K.↗
DOE OSTI2024

Predicted Fracture Tendency of Naturally Occurring Aluminum Surface Coatings under Tensile Loading

Naturally occurring coatings on aluminum metal, such as its oxide or hydroxide, serve to protect the material from corrosion. Understanding the conditions under which these coatings mechanically fail is therefore expected to be an important aspect of predictive models for aluminum component lifetimes. To this end, we develop and apply a molecular dynamics (MD) modeling framework for conducting tension tests that is capable of isolating factors governing the mechanical strength as a function of coating chemistry, defect morphology, and variables associated with the loading path. We consider two representative materials, including γ-Al 2 O 3 and γ-Al(OH) 3 (i.e., oxide and hydroxide), both of which form readily as aluminum surface coatings. Our results indicate that defects have a significant bearing on the strength of aluminum oxide, with grain boundaries serving to reduce the strain at failure from ε zz = 0.300 to 0.219, relative to perfect single crystal. Our simulations also predict that porosity lowers the elastic stiffness and yield strength of the oxide. Relative to perfect crystal, we find porosity factors of 5%, 10% and 20% decrease the yield stress by 26%, 36% and 53%, respectively. MD predicts that perfect hydroxide and oxide single crystal have respective strains at failure of 0.08 and 0.31 under tensile uniaxial strain loading, and that the corresponding yield stresses are respectively 1.6 and 11.1 GPa. These data indicate that the hydroxide is substantially more susceptible to mechanical failure than the oxide. Our results, coupled with literature findings that indicate hot and humid conditions favor formation of hydroxide and defective oxide coatings, indicate the potential for a complicated dependence of aluminum corrosion susceptibility and stress corrosion cracking on aging history.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2021

Comparing plasma conditions in short-pulse-heated foils via fine-structure x-ray emission

Fine-structure x-ray spectra have been measured from foils with embedded tracer layers at two laser facilities. In this work, a suite of layered foils with thin Ti tracers under varied tamper layers was studied at both the Titan and the ALEPH 400 nm laser facilities, where Ti Heα emission was recorded using a high-resolution Bragg crystal spectrometer. Several indicators of plasma parameters are examined in the spectra, including temperature- and density-dependent line ratios and line broadening from Stark and opacity effects. Spectra indicate that (1) the plasma density at ALEPH is significantly higher than at Titan and (2) the electron temperature is high for near-surface layers at both facilities but drops more quickly with depth at ALEPH. These inferences of plasma conditions are consistent with differing levels of temporal contrast at each laser facility.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

A Revisited Mechanism of the Graphite-to-Diamond Transition at High Temperature

The graphite-diamond transition, under high-pressure and high-temperature conditions, has been a central subject in physical science. However, its atomistic mechanism remains under debate. Employing large-scale molecular dynamics (MD) simulations, we report a mechanism whereby the diamond nuclei in the graphite matrix propagate in two preferred directions, among which the graphite [120] is about 2.5 times faster than [001]. Consequently, cubic diamond (CD) is the kinetically favorable product, while only a few hexagonal diamonds (HDs) can exist as the twins of CDs. The coherent interface of t-(100)gr//(11-1)cd + [010]gr//[1-10]cd observed in MD simulation was confirmed by our high-resolution transmission electron microscopy experiment. This proposed mechanism not only clarifies the role of HD in graphite-diamond transition but also yields atomistic insight into strengthening synthetic diamond via microstructure engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2025

High dopant activation in arsenic doped single-crystal CdTe thin films: Insights from MBE growth and rapid thermal processing

Single-crystal model systems are valuable tools to investigate fundamental material properties. In this work, we use molecular beam epitaxy to deposit in situ arsenic (As) doped single-crystal CdTe films on large area Si substrates to better understand As doping for photovoltaic applications. We found that As incorporation is highly temperature dependent: a substrate temperature difference of 50 °C can lead to several orders of magnitude difference in As concentration. Cd overpressure during in situ doping may limit out-diffusion of As but decrease As incorporation, especially at lower growth temperatures. Carrier concentrations greater than 10 16 cm −3 can be achieved with or without Cd overpressure when annealed at temperatures above 500 °C. However, unlike the low (∼1% to 5%) dopant activation commonly observed in polycrystalline CdTe, our films achieve significantly higher activation ratios—exceeding 50%, and in some cases approaching 80%. These values are consistent with or exceed prior reports in single-crystal CdTe systems. In addition to as-deposited arsenic concentrations, we also consider arsenic distribution after different rapid thermal processing temperatures. We propose a detailed definition and description of how arsenic incorporation is considered and calculated. Due to carrier concentration saturation, As incorporation also needs to be controlled to average levels of 10 17 cm −3 to achieve high activation. These findings suggest that higher annealing temperature regimes may be beneficial to polycrystalline CdTe based PV devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Molecular-Resolution Electron Imaging of Defects and Dynamics at the Ice-Water Interface

Water crystallization into hexagonal ice (type I h ) is one of the most critical processes relevant to the Earth’s environment and human activities. However, despite recent breakthroughs in imaging non-equilibrium condensed ice structures, the ice-water interface has never been imaged at a molecular resolution. This is primarily due to the low stability of the hydrogen bonds in ice under high-resolution microscopy conditions and a lack of methods to prepare compatible samples. Here, this presentation describes the first molecular-resolution imaging of ice crystallized from liquid water and the ice-water interface using high-resolution transmission electron microscopy (HRTEM). By encapsulating deionized (DI) water between two amorphous carbon (a-C) TEM grids and subsequently freezing it with liquid N 2 on a cryo sample stage, we generated two types of ice: non-equilibrium, condensed ice from the atmosphere and encapsulated ice from the DI water (Fig. 1A). Condensed ice usually shows irregular, spherulitic shapes (Fig. 1B). Selected area electron diffraction (SAED) shows that they are a mixture of cubic and hexagonal crystals (Fig. 1C). On the contrary, encapsulated ice forms thin films that contain large-area single-crystalline regions of hexagonal ice oriented along the [0001] zone axis (Fig. 1D). Differential electron energy-loss spectroscopy (EELS) confirmed the high purity of the encapsulated ice free from organic contaminations that are common in other encapsulation methods for HRTEM such as graphene liquid cells. These single-crystalline areas are robust under the electron beam up to ~100 e/Å 2 s. Aberration-corrected HRTEM imaging in these areas achieved a line resolution of ~1.3 Å (Fig. 1E and F). This platform allows us to study near-equilibrium ice structures and dynamics at an unprecedented spatial resolution (Fig. 2). For example, we discovered subdomain-rich regions near the defective crystal edges despite the structure appearing single-crystalline according to diffraction criteria. These subdomains connect via low-angle grain boundaries with flat energy landscapes as a function of tilt angles (according to simulations), showing the high tolerance of ice to defect structures. When we tuned the sample temperature and electron flux rate, we observed radiolysis-controlled bubble generation and dissolution in ice single crystals near a steady state of bubble dynamics. Furthermore, rich beam-induced melting and recrystallization dynamics were observed at the ice-water interface with lattice resolution. These data represent the first observation of the ice-water phase transformation at the sub-nanometer level. In summary, the methods developed in this work enabled molecular-resolution observations of ice and the ice-water interface and shed light on the microstructures and phase transformation pathways. Finer control on the temperature, electron irradiation profile, and imaging detector could eventually lead to real-time observation of ice nucleation in water and address long-standing questions in the nucleation pathways.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Interfacial intermixing and anti-phase boundaries in GaP/Si(0 0 1) heterostructures

Epitaxial GaP/Si heterostructures grown by molecular beam epitaxy (MBE) and migration-enhanced epitaxy (MEE) have been studied, primarily using aberration-corrected scanning transmission electron microscopy (AC-STEM). Atomically-resolved structure images, which are sensitive to atomic-column intensity revealed the detailed geometry of antiphase boundaries that were both parallel and also inclined to the growth direction. The polar/non-polar GaP/Si interfaces were neither atomically flat laterally nor abrupt vertically. Measurements of intensity profiles using both bright-field and dark-field AC-STEM images, as well as chemically-sensitive g 002 dark-field imaging, indicated substantial interfacial intermixing, which increased significantly from ~1.3 nm (MEE growth at 440 °C) to ~2.1 nm (MBE growth at 600 °C). The finite interface width will impact theoretical predictions of charge imbalance and strong electric fields across the heterointerface.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Interzeolite Transformation through Cross-Nucleation: A Molecular Mechanism for Seed-Assisted Synthesis

Polymorph selection and efficient crystallization are central goals in zeolite synthesis. Crystalline seeds are used for both purposes. While it has been proposed that zeolite seeds induce interzeolite transformation by dissolving into structural units that promote nucleation of the daughter crystal, the seed’s structural elements do not always match those of the target zeolite. This discrepancy raises the question of how the seed promotes the daughter phase. Here, we present the first molecularly resolved investigation of seed-assisted zeolite synthesis. Using molecular simulations, we reproduce the experimental finding that a parent zeolite can promote the nucleation of a daughter zeolite even when it lacks common composite building units (CBUs) or crystal planes. Modeling the seed-assisted synthesis of an AFI-type zeolite using zeolite CHA, our simulations indicate that stand-alone CBUs from the parent seed do not facilitate daughter crystal formation. However, introducing the intact seed significantly reduces the synthesis time, supporting that seed integrity is key to increased efficiency. This reduction arises from the cross-nucleation of the AFI-type zeolite on the CHA (001) face. We find that parent and daughter zeolites are connected by an interfacial transition layer with an order distinct from that of both zeolites. Simulations reveal that cross-nucleation occurs over a broad range of synthesis conditions. We argue that cross-nucleation would be most favorable for zeolite pairs that share crystalline planes such as those forming intergrowths. In conclusion, our findings suggest that the prevalence of intergrowths with a common lattice plane in zeolite synthesis is likely a kinetic effect of accelerated cross-nucleation.

Crystallization↗
NASA NTRS1980

Theoretical model applicable to the experimental determination of surface anchoring energies of nematic liquid crystals

For a cell configuration consisting of a thin nematic layer bounded by two parallel plane surfaces, with opposing surfaces suitably treated to produce dissimilar molecular orientations, the elastic continuum theory for nematic liquid crystals was applied to derive an expression relating surface anchoring energies to elastic constants, director orientations at the substrate surfaces, and cell thickness. A numerical comparison with the elastically isotropic result over a range K sub 3 = 1.5 K sub 1 to K sub 3 = 10 K sub 1 showed the effect of elastic anisotropy could be quite significant. Surface anchoring energies calculated for anisotropic of K sub 3 = 2 K sub 1 and K sub 3 + 10 K sub 1 were approximately 50% and 500%, respectively, than the isotropic values.

Wintucky, E. G.↗