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DOE OSTI2017

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer’s J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. We develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded ”flexible hinges” to assist in loop formation. We also combine the Czapla-Swigon-Olson structural model of DNA with our extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Furthermore, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Discovery and characterization of two Neptune-mass planets orbiting HD 212729 with TESS

ABSTRACT We report the discovery of two exoplanets orbiting around HD 212729 (TOI 1052, TIC 317060587), a Teff = 6146 K star with V = 9.51 observed by TESS in Sectors 1 and 13. One exoplanet, TOI-1052b, is Neptune-mass and transits the star, and an additional planet TOI-1052c is observed in radial velocities but not seen to transit. We confirm the planetary nature of TOI-1052b using precise radial velocity observations from HARPS and determined its parameters in a joint RV and photometry analysis. TOI-1052b has a radius of $2.87^{+0.29}_{-0.24}$ R⊕, a mass of 16.9 ± 1.7 M⊕, and an orbital period of 9.14 d. TOI-1052c does not show any transits in the TESS data, and has a minimum mass of $34.3^{+4.1}_{-3.7}$ M⊕ and an orbital period of 35.8 d, placing it just interior to the 4:1 mean-motion resonance. Both planets are best fit by relatively high but only marginally significant eccentricities of $0.18^{+0.09}_{-0.07}$ for planet b and $0.24^{+0.09}_{-0.08}$ for planet c. We perform a dynamical analysis and internal structure model of the planets as well as deriving stellar parameters and chemical abundances. The mean density of TOI-1052b is $3.9^{+1.7}_{-1.3}$ g cm−3 consistent with an internal structure similar to Neptune. A nearby star is observed in Gaia DR3 with the same distance and proper motion as TOI-1052, at a sky projected separation of $\scriptstyle \sim$1500 au, making this a potential wide binary star system.

Armstrong, David J. (ORCID:0000000250804117)↗

DOE OSTI2019

NMR spin diffusion measurements in disordered polymers: Insights and limitations

Nuclear magnetic resonance (NMR) spin diffusion measurements have been widely used to estimate domain sizes in a variety of polymer materials. In cases where the domains are well-described as regular, repeating structures (e.g., lamellar, cylindrical channels, monodispersed spherical domains), the domain sizes estimated from NMR spin diffusion experiments agree with the characteristic length scales obtained from small-angle x-ray scattering and microscopy. In our laboratory, recent NMR spin diffusion experiments for hydrated sulfonated Diels Alder poly(phenylene) (SDAPP) polymer membranes have revealed that assuming a simple structural model can often misrepresent or overestimate the domain size in situations where more complex and disordered morphologies exist. Molecular dynamics simulations of the SDAPP membranes predict a complex heterogeneous hydrophilic domain structure that varies with the degree of sulfonation and hydration and is not readily represented by a simple repeating domain structure. This heterogeneous morphology results in NMR-measured domain sizes that disagree with length scales estimated from the ionomer peak in scattering experiments. Here we present numerical NMR spin diffusion simulations that show how structural disorder in the form of domain size distributions or domain clustering can significantly impact the spin diffusion analysis and estimated domain sizes. As a result, simulations of NMR spin diffusion with differing domain size distributions and domain clustering are used to identify the impact of the heterogeneous domain structure and highlight the limitations of using NMR spin diffusion techniques for irregular structures.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Probing the Atomic-Scale Structure of Amorphous Aluminum Oxide Grown by Atomic Layer Deposition

Atomic layer deposition (ALD) is a well-established technique for depositing nanoscale coatings with pristine control of film thickness and composition. The trimethylaluminum (TMA) and water (H 2 O) ALD chemistry is inarguably the most widely used and yet to date, we have little information about the atomic-scale structure of the amorphous aluminum oxide (AlO x ) formed by this chemistry. This lack of understanding hinders our ability to establish process-structure-property relationships and ultimately limits technological advancements employing AlOx made via ALD. In this work, we employ synchrotron high-energy X-ray diffraction (HE-XRD) coupled with pair distribution function (PDF) analysis to characterize the atomic structure of amorphous AlO x ALD coatings. We combine ex situ and in operando HE-XRD measurements on ALD AlO x and fit these experimental data using stochastic structural modeling to reveal variations in the Al-O bond length, Al and O coordination environment, and extent of Al vacancies as a function of growth conditions. In particular, the local atomic structure of ALD AlO x is found to change with the substrate and number of ALD cycles. The observed trends are consistent with the formation of bulk Al 2 O 3 surrounded by an O-rich surface layer. We deconvolute these data to reveal atomic-scale structural information for both the bulk and surface phases. Overall, this work demonstrates the usefulness of HE-XRD and PDF analysis in improving our understanding of the structure of amorphous ALD thin films and provides a pathway to evaluate how process changes impact the structure and properties of ALD films.

36 MATERIALS SCIENCE↗

DOE OSTI2012

Unique Structural and Nucleotide Exchange Features of the Rho1 GTPase of Entamoeba histolytica

The single-celled human parasite Entamoeba histolytica possesses a dynamic actin cytoskeleton vital for its intestinal and systemic pathogenicity. The E. histolytica genome encodes several Rho family GTPases known to regulate cytoskeletal dynamics. EhRho1, the first family member identified, was reported to be insensitive to the Rho GTPase-specific Clostridium botulinum C3 exoenzyme, raising the possibility that it may be a misclassified Ras family member. Here, we report the crystal structures of EhRho1 in both active and inactive states. EhRho1 is activated by a conserved switch mechanism, but diverges from mammalian Rho GTPases in lacking a signature Rho insert helix. EhRho1 engages a homolog of mDia, EhFormin1, suggesting a role in mediating serum-stimulated actin reorganization and microtubule formation during mitosis. EhRho1, but not a constitutively active mutant, interacts with a newly identified EhRhoGDI in a prenylation-dependent manner. Furthermore, constitutively active EhRho1 induces actin stress fiber formation in mammalian fibroblasts, thereby identifying it as a functional Rho family GTPase. EhRho1 exhibits a fast rate of nucleotide exchange relative to mammalian Rho GTPases due to a distinctive switch one isoleucine residue reminiscent of the constitutively active F28L mutation in human Cdc42, which for the latter protein, is sufficient for cellular transformation. Nonconserved, nucleotide-interacting residues within EhRho1, revealed by the crystal structure models, were observed to contribute a moderating influence on fast spontaneous nucleotide exchange. Collectively, these observations indicate that EhRho1 is a bona fide member of the Rho GTPase family, albeit with unique structural and functional aspects compared with mammalian Rho GTPases.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Temperature Uncertainty Modeling with Proxy Structural Data as Geostatistical Constraints for Well Siting: An Example Applied to Granite Springs Valley, NV, USA

Utilizing existing temperature and structural information around Granite Springs Valley, Nevada, we build 3D stochastic temperature models with the aim of evaluating the 3D uncertainty of temperature and choosing between candidate exploration well locations . The data used to support the modeling are measured temperatures and structural proxies from 3D geologic modeling, the latter considered "secondary" data. Two stochastic geostatistical techniques are explored for incorporating the structural proxies: cosimulation and local varying mean. With both the cosimulation and local varying mean methods, many equally likely temperature models (i.e., realizations) are produced, from which temperature probability profiles are calculated at candidate well locations. To aid in choosing between the candidate locations, two quantities summarize the temperature probabilities: Vprior and entropy. Vprior quantifies the likelihood for economic temperatures at each candidate location, whereas entropy identifies where new information has the most potential to reduce uncertainty. In general, the cosimulation realizations have smoother spatial structure, and extrapolate high temperatures at candidate locations that are located along the direction of the longest spatial correlation, which are down dip from existing temperature logs. The smooth realizations result in tight temperature probability profiles that are easier to interpret, but they have unrealistic temperature reversals in some locations because the cosimulation technique does not enforce a conductive geothermal gradient as a baseline (i.e., linearly increasing temperature with depth). The local varying mean results produce realizations with more realistic geothermal gradients, with temperatures increasing downward since a depth-temperature relationship is included. However, because they have much noisier spatial nature compared to cosimulation, it is harder to interpret the temperature probability profiles. The different local varying mean results allow the geologist to determine which proxy (e.g., dilation versus distance to fault termination) should be used given the specific geothermal system. In general, Vprior from local varying mean results identify locations that are close to high values for the structural proxies: areas with highe r probabilities for higher temperatures. The entropy results identify where uncertainty is greatest and therefore new drilling information could be most useful. Though these techniques provide useful information, even when applied to areas of sparse data, our comp arison of these two techniques demonstrates the need for new geothermal geostatistics techniques that combine the advantages of these two methods and that are tailored to the spatial uncertainty issues inherent in geothermal exploration.

3D temperature modeling↗

DOE OSTI2016

Electron Transport Modeling of Molecular Nanoscale Bridges Used in Energy Conversion Schemes

The goal of the research program is to reliably describe electron transport and transfer processes at the molecular level. Such insight is essential for improving molecular applications of solar and thermal energy conversion. We develop electronic structure models to study (1) photoinduced electron transfer and transport processes in organic semiconducting materials, and (2) charge and heat transport through molecular bridges. We seek fundamental understanding of key processes, which lead to design new experiments and ultimately to achieve systems with improved properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Electron Transport Modeling of Molecular Nanoscale Bridges Used in Energy Conversion Schemes

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Predicted Structure, Thermo-Mechanical Properties and Li Ion Transport in LiAlF4 Glass

Materials with the LiAlF{sub 4} composition are of interest as protective electrode coatings in Li ion battery applications due to their high cationic conductivity. Here classical molecular dynamics calculations are used to produce amorphous model structures by simulating a quench from the molten state. These are analysed in terms of their individual pair correlation functions and atomic coordination environments. This indicates that amorphous LiAlF{sub 4} is formed of a network of corner sharing AlF{sub 6} octahedra. Li ions are distributed within this network, primarily associated with non-bridging fluorine atoms. The nature of the octahedral network is further analysed through intra- and interpolyhedral bond angle distributions and the relative populations of bridging and non-bridging fluorine ions are calculated. Network topology is considered through the use of ring statistics, which indicates that, although topologically well connected, LiAlF{sub 4} contains an appreciable number of corner-linked branch-like AlF{sub 6} chains. Thermal expansion values are determined above and below the predicted glass transition temperature of 1340 K. Finally, movement of Li ions within the network is examined with predictions of the mean squared displacements, diffusion coefficients and Li ion activation energy. Different regimes for lithium ion movement are identified, with both diffusive and sessile Li ions observed. For migrating ions, a typical trajectory is illustrated and discussed in terms of a hopping mechanism for Li transport.

25 ENERGY STORAGE↗

DOE OSTI2017

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1 H– 29 Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1 H– 29 Si HETCOR and dipolar 2D 1 H– 1 H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Instead the 2D NMR spectra illustrate that there is large distribution of 1 H and 29 Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1 H– 29 Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29 Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3 ), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1 H and 29 Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.

29Si NMR↗

DOE OSTI2016

Conformational landscape of an amyloid intra-cellular domain and Landau-Ginzburg-Wilson paradigm in protein dynamics

The Landau-Ginzburg-Wilson paradigm is proposed as a framework, to investigate the conformational landscape of intrinsically unstructured proteins. A universal Cα-trace Landau free energy is deduced from general symmetry considerations, with the ensuing all-atom structure modeled using publicly available reconstruction programs Pulchra and Scwrl. As an example, the conformational stability of an amyloid precursor protein intra-cellular domain (AICD) is inspected; the reference conformation is the crystallographic structure with code 3DXC in Protein Data Bank (PDB) that describes a heterodimer of AICD and a nuclear multi-domain adaptor protein Fe65. Those conformations of AICD that correspond to local or near-local minima of the Landau free energy are identified. For this, the response of the original 3DXC conformation to variations in the ambient temperature is investigated, using the Glauber algorithm. The conclusion is that in isolation the AICD conformation in 3DXC must be unstable. A family of degenerate conformations that minimise the Landau free energy is identified, and it is proposed that the native state of an isolated AICD is a superposition of these conformations. The results are fully in line with the presumed intrinsically unstructured character of isolated AICD and should provide a basis for a systematic analysis of AICD structure in future NMR experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Thermodynamic Modeling of Intrinsic Defects in MnBi₂Te₄

This repository contains the computational data supporting the manuscript titled “The critical role of intrinsic defects and many-body interactions on the stability of MnBi₂Te₄.” It includes: 1. DFT data generated using VASP, used for training and benchmarking electronic structure models. 2. Quantum Monte Carlo (QMC) data produced with QMCPACK, used to apply many-body corrections and validate the electronic and magnetic properties of MnBi₂Te₄. 3. Relevant scripts used to run, analyze, and process the calculations, enabling reproducibility and transparency of the workflows.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Sound velocity of Fe-S liquids at high pressure: Implications for the Moon's molten outer core

Sound velocities of Fe and Fe–S liquids were determined by combining the ultrasonic measurements and synchrotron X-ray techniques under high pressure–temperature conditions from 1 to 8 GPa and 1573 K to 1973 K. Four different liquid compositions were studied including Fe, Fe–10 wt% S, Fe–20 wt% S, and Fe–27 wt% S. Our data show that the velocity of Fe-rich liquids increases upon compression and decreases with increasing sulfur content, whereas temperature has negligible effect on the velocity of Fe–S liquids. The sound velocity data were combined with ambient-pressure densities to fit the Murnaghan equation of state (EOS). Compared to the lunar seismic model, our velocity data constrain the sulfur content at 4±3 wt%, indicating a significantly denser (6.5±0.5 g/cm 3 ) and hotter (1870-70+100 K) outer core than previously estimated. A new lunar structure model incorporating available geophysical observations points to a smaller core radius. Our model suggests a top–down solidification scenario for the evolution of the lunar core. Such “iron snow” process may have been an important mechanism for the growth of the inner core.

Jing, Zhicheng↗

DOE OSTI2020

Consequences of long-term water exposure for bulk crystal structure and surface composition/chemistry of nickel-rich layered oxide materials for Li-ion batteries

Water exposure of layered nickel-rich transition metal oxide electrodes, widely used in high-energy lithium-ion batteries, has detrimental effects on the electrochemical performance, which complicates electrode handling and prevents implementation of environmentally benign aqueous processing procedures. Elucidating the degradation mechanisms in play may help rationally mitigate/circumvent key challenges. Here, the bulk structural consequences of long-term (>2.5 years) deuterated water (D2O) exposure of intercalation materials with compositions Li x Ni 0.5 Co 0.2 Mn 0.3 O 2 (NCM523) and Li x Ni 0.8 Co 0.1 Mn 0.1 O 2 (NCM811) are studied by neutron powder diffraction (NPD). Detailed inspection of the NPD data reveals gradual formation of a secondary crystalline phase in all exposed samples, not previously reported for this system. This unknown phase forms faster in liquid- compared to vapor-exposed compounds. Structural modelling of the NPD data shows a stable level of Li/Ni anti-site defects and does not indicate any significant changes in lattice parameters or hydrogen-lithium (D + /Li + ) exchange in the structure. Consequently, the secondary phase formation must take place via transformation rather than modification of the parent material. X-ray photoelectron spectroscopy data indicate formation of LiHCO 3 /Li 2 CO 3 at the surface and a Li-deficient oxide in the sub-surface region of the pristine compounds, and the presence of adsorbed water and transition metal hydroxides at the exposed sample surfaces.

25 ENERGY STORAGE↗

DOE OSTI2018

Exciton photoluminescence and benign defect complex formation in zinc tin nitride

Emerging photovoltaic materials need to prove their viability by demonstrating excellent electronic properties. In ternary and multinary semiconductors, disorder and off-stoichiometry often cause defects that limit the potential for high-efficiency solar cells. We report on Zn-rich ZnSnN 2 (Zn/(Zn + Sn) = 0.67) photoluminescence, high-resolution X-ray diffraction, and electronic structure calculations based on Monte-Carlo structural models. The mutual compensation of Zn excess and O incorporation affords a desirable reduction of the otherwise degenerate n-type doping, but also leads to a strongly off-stoichiometric and disordered atomic structure. It is therefore remarkable that we observe only near-edge photoluminescence from well-resolved excitons and shallow donors and acceptors. Based on first principles calculations, this result is explained by the mutual passivation of Zn Sn and O N defects that renders both electronically benign. The calculated bandgaps range between 1.4 and 1.8 eV, depending on the degree of non-equilibrium disorder. The experimentally determined value of 1.5 eV in post-deposition annealed samples falls within this interval, indicating that further bandgap engineering by disorder control should be feasible via appropriate annealing protocols.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Structural transformation in Ge x S 100–x (10 ≤ x ≤ 40) network glasses: Structural varieties in short-range, medium-range, and nanoscopic scale

Precise x-ray diffraction measurements using high-energy x rays of synchrotron radiation and systematic Raman scattering measurements were carried out for Ge x S 100–x (10 ≤ x ≤ 40) network glasses. The structural models of the network glasses were proposed based on the results. In the stoichiometric composition Ge 33 S 67 , GeS 4 tetrahedral units are connected forming either corner-sharing or edge-sharing structures. In the S-rich glasses, S atoms are inserted between two neighboring GeS 4 tetrahedra, resulting in a flexible floppy network. In a much more S-rich region, some S 8 ring molecules are isolated from the network, and assemble to form a crystal in nanoscopic scale. In this respect, Ge 10 S 90 samples are regarded as crystallized glasses. In the Ge-rich region, the GeS 4 tetrahedra are connected with bridging Ge atoms. The connection makes a new rigid network. Furthermore, the bridging Ge-S bond is weaker than the intratetrahedron bond, and this leads to drastic changes in the optical properties.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Evaluation of Leading Modes of Climate Variability in the CMIP Archives

The adequate simulation of internal climate variability is key for our understanding of climate as it underpins efforts to attribute historical events, predict on seasonal and decadal time scales, and isolate the effects of climate change. Here the skill of models in reproducing observed modes of climate variability is assessed, both across and within the CMIP3, CMIP5, and CMIP6 archives, in order to document model capabilities, progress across ensembles, and persisting biases. A focus is given to the well-observed tropical and extratropical modes that exhibit small intrinsic variability relative to model structural uncertainty. These include El Niño–Southern Oscillation (ENSO), the Pacific decadal oscillation (PDO), the North Atlantic Oscillation (NAO), and the northern and southern annular modes (NAM and SAM). Significant improvements are identified in models’ representation of many modes. Canonical biases, which involve both amplitudes and patterns, are generally reduced across model generations. For example, biases in ENSO-related equatorial Pacific sea surface temperature, which extend too far westward, and associated atmospheric teleconnections, which are too weak, are reduced. Stronger tropical expression of the PDO in successive CMIP generations has characterized their improvement, with some CMIP6 models generating patterns that lie within the range of observed estimates. For the NAO, NAM, and SAM, pattern correlations with observations are generally higher than for other modes and slight improvements are identified across successive model generations. Finally, for ENSO and PDO spectra and extratropical modes, changes are small compared to internal variability, precluding definitive statements regarding improvement.

54 ENVIRONMENTAL SCIENCES↗