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At least 685 records · Page 38

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DOE OSTI2023

Design of stimulus-responsive two-state hinge proteins

In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here, in this work, we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Excitons in two-dimensional metal-halide perovskites

Georgia Tech School of Chemistry and Biochemistry Special Summer Seminar Series, Prof Carlos Silva; While polarons --- charges bound to a lattice deformation induced by electron-phonon coupling --- are primary photoexcitations at room temperature in bulk metal-halide hybrid organic-inorganic perovskites (HOIP), excitons --- Coulomb-bound electron-hole pairs --- are the stable quasi-particles in their two-dimensional (2D) analogues. Here we address the fundamental question: are polaronic effects consequential for excitons in 2D-HIOPs? Based on our recent work, we argue that polaronic effects are manifested intrinsically in the exciton spectral structure, which is comprised of multiple non-degenerate resonances with constant inter-peak energy spacing. We highlight measurements of population and dephasing dynamics that point to the apparently deterministic role of polaronic effects in excitonic properties. We contend that an interplay of long-range and short-range exciton-lattice couplings give rise to exciton polarons, a character that fundamentally establishes their effective mass and radius, and consequently, their quantum dynamics. Given this complexity, a fundamentally far-reaching issue is how Coulomb-mediated many-body interactions---elastic scattering such as excitation-induced dephasing, inelastic exciton bimolecular scattering, and multi-exciton binding---depend upon the specific exciton-lattice coupling within the structured excitation lineshape. We measure the intrinsic and density-dependent exciton dephasing rates of the multiple excitons and their dependence on temperature by means of two-dimensional coherent excitation spectroscopy. We find that diverse excitons display distinct intrinsic dephasing rates mediated by phonon scattering involving different effective phonons, and contrasting rates of exciton-exciton elastic scattering. These findings establish specifically the consequence of distinct lattice dressing on exciton many-body quantum dynamics, which critically define fundamental optical properties that underpin photonics and quantum optoelectronics.

solar cells, metal-halide perovskites, excitons, p↗

NASA NTRS1991

Hydride structures in Ti-aluminides subjected to high temperature and hydrogen pressure charging conditions

The distribution and chemistry of hydrides produced in single and dual phase alloys with a composition near TiAl have been investigated by using a combination of TEM and X-ray diffraction techniques. The alloys were exposed at 650 C to 13.8 MPa of gaseous H2 for 100 h. In the single-phase gamma alloy, large hydrides preferentially nucleated on the grain boundaries and matrix dislocations and a population of small hydrides was distributed throughout the matrix. X-ray and electron diffraction patterns from these hydrides indicated that they have an fcc structure with a lattice parameter of 0.45 nm. EDAX analysis of the hydrides showed that they were enriched in Ti. The hydrides were mostly removed by vacuum annealing at 800 C for 24 h. On dissolution of the hydrides, the chemistry of hydride-free regions of the grain boundary returned to the matrix composition, suggesting that Ti segregation accompanied the hydride formation rather than Ti enrichment causing the formation of the hydride.

Legzdina, D.↗

DOE OSTI2021

Unveiling the mechanism of phase and morphology selections during the devitrification of Al-Sm amorphous ribbon

The complex interplay between energetic and kinetic factors that governs the phase and morphology selections can originate at the earliest stage of crystallization in the amorphous parent phases. Because of the extreme difficulties in capturing the microscopic nucleation process, a detailed picture of how initial disordered structures affect the transformation pathway remains unclear. Here, we report the experimental observation of widely varying phase selection and grain size evolution during the devitrification of a homogeneous melt-spun glassy ribbon. Two different crystalline phases, θ-Al 5 Sm and ε-Al 60 Sm 11 , are found to form in the different regions of the same metallic glass ribbon during the devitrification. The grain size of ε-Al 60 Sm 11 phase shows a strong spatial heterogeneity. Coarse-grained ε-Al 60 Sm 11 phase coupled with the small volume fraction of θ-Al 5 Sm phase is preferably formed close to wheel side of the melt-spun ribbon. Combining experimental characterization and computational simulations, we show that phase selection and microstructure evolution can be traced back to different types and populations of atomic clusters that serve as precursors for the nucleation of different crystalline phases. Inhomogeneous cooling rates cause different structure orders across the glass sample during the quenching process. Our findings provide direct insight into the effect of structural order on the crystallization pathways during the devitrification of metallic glass. It also opens an avenue to study the detailed nucleation process at the atomic level using the metallic glass as a platform and suggests the opportunity of microstructure and property design via controlling the cooling process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Excited electronic states of Na 2 and K 2 : The potential for long-lived “reservoir” states leading to collision induced population inversions

Potential energy curves (PECs) for the spin-free (ΛS) and spin–orbit (Ω) states associated with the four lowest-lying dissociation channels of Na 2 and K 2 were calculated at the SA-CASSCF/SO-CASPT2/aug-cc-pwCVQZ-DK level. The PECs of Na 2 were consistent with the experimental data and with the FS-CCSD (2,0) calculations, reproducing the double-well and the “shelf” character for some of the potentials of the excited states. For K 2 , the PECs behaved in a similar way and the spectroscopic parameters for the ground and the excited states are in good agreement with the available experimental values. The dissociation energy of K 2 was predicted to be D e = 4454 cm −1 , within an agreement of 5 cm −1 with the experiments. For Na 2 , D e = 5789 cm −1 compared to the experimental value of 6022 cm −1 . The inclusion of spin–orbit coupling effects resulted in avoided crossings, which affect the PECs. Spin–orbit changes the predicted curves for some excited Ω states arising from ΛS states that overlap each other, affecting their associated vibrational frequencies and bond distances. Here, the current studies of the low-lying states in K 2 reveal a similar structure to those of Na 2 , which suggests the accessibility of long-lived energy storing reservoir states and possible population inversions in K 2 following prior experimental work on the reaction of halogen atoms with Na 3 to produce excited states of Na 2 .

Ab-initio methods↗

NASA NTRS2004

Invariant Theory for Dispersed Transverse Isotropy: An Efficient Means for Modeling Fiber Splay

Most soft tissues possess an oriented architecture of collagen fiber bundles, conferring both anisotropy and nonlinearity to their elastic behavior. Transverse isotropy has often been assumed for a subset of these tissues that have a single macroscopically-identifiable preferred fiber direction. Micro-structural studies, however, suggest that, in some tissues, collagen fibers are approximately normally distributed about a mean preferred fiber direction. Structural constitutive equations that account for this dispersion of fibers have been shown to capture the mechanical complexity of these tissues quite well. Such descriptions, however, are computationally cumbersome for two-dimensional (2D) fiber distributions, let alone for fully three-dimensional (3D) fiber populations. In this paper, we develop a new constitutive law for such tissues, based on a novel invariant theory for dispersed transverse isotropy. The invariant theory is based on a novel closed-form splay invariant that can easily handle 3D fiber populations, and that only requires a single parameter in the 2D case. The model is polyconvex and fits biaxial data for aortic valve tissue as accurately as the standard structural model. Modification of the fiber stress-strain law requires no re-formulation of the constitutive tangent matrix, making the model flexible for different types of soft tissues. Most importantly, the model is computationally expedient in a finite-element analysis.

Freed, alan D.↗

DOE OSTI2023

The Origin of Anomalous Density Behavior of Silica Glass

The anomalous density–temperature relationship of vitreous silica with low hydroxyl content is explained by the formation of medium-range ordering structure in the glass transition process. The ordered medium-range structure has the shape of a “nanoflake” and consists of two layers of SiO 4 tetrahedra, bonded by O atoms located in the middle of the structure. The nanoflakes interact with their surrounding structures through both covalent chemical bonds and van der Waals bonds. In the formation of the van der Waals bonds, the orientation of SiO 4 tetrahedra can change, which results in an increase in distance between the nanoflakes and their surrounding structures. Thus, there is a slight volume enlargement associated with the formation of nanoflakes. Since the nanoflakes’ formation starts at a temperature near 1480 °C, and the population of the nanoflakes grows continuously as temperature decreases until about 950 °C, the bulk volume of silica glass increases in the temperature range from about 1480 °C to 950 °C. Therefore, the density anomaly of silica glass can be explained as a byproduct of forming of medium-range ordering structure in the silica glass transition.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases

Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.

crystal structures↗

DOE OSTI2022

Heterogeneous Ice Growth in Micron-Sized Water Droplets Due to Spontaneous Freezing

Understanding how ice nucleates and grows into larger crystals is of crucial importance for many research fields. The purpose of this study was to shed light on the phase and structure of ice once a nucleus is formed inside a metastable water droplet. Wide-angle X-ray scattering (WAXS) was performed on micron-sized droplets evaporatively cooled to temperatures where homogeneous nucleation occurs. We found that for our weak hits ice grows more cubic compared to the strong hits that are completely hexagonal. Due to efficient heat removal caused by evaporation, we propose that the cubicity of ice at the vicinity of the droplet’s surface is higher than for ice formed within the bulk of the droplet. Moreover, the Bragg peaks were classified based on their geometrical shapes and positions in reciprocal space, which showed that ice grows heterogeneously with a significant population of peaks indicative of truncation rods and crystal defects. Frequent occurrences of the (100) reflection with extended in-planar structure suggested that large planar ice crystals form at the droplet surface, then fracture into smaller domains to accommodate to the curvature of the droplets. Planar faulting due to misaligned domains would explain the increased cubicity close to the droplet surface.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1994

Microbial community structure at the U.S.-Joint Global Ocean Flux Study Station ALOHA: Inverse methods for estimating biochemical indicator ratios

Modeling biogeochemical fluxes in the marine plankton requires the application of factors for extrapolation of biomass indicators measured in the field (chlorophyll a, adenosine triphosphate, bacterial counts) to biomass carbon or nitrogen. These are often inferred from culture studies and are poorly constrained for natural populations. At least squares inverse method with a simple linear model constrains the values of several common indicator ratios, giving self-consistent solutions that provide useful information about the structure of the microbial community at our North Pacific Ocean study site (Station ALOHA (A Long-term Oligotrophic Habitat Assessment)). These results indicate that the fraction of the microbial biomass that is autotrophic (pigmented) is greater in the mixed layer than at the deep chlorophyll maximum layer and that heterotrophic bacteria are a significant but not necessarily predominant component of the microbial community in the euphotic zone.

Christian, James R.↗

DOE OSTI2024

The structural OFF and ON states of myosin can be decoupled from the biochemical super- and disordered-relaxed states

Abstract There is a growing awareness that both thick-filament and classical thin-filament regulations play central roles in modulating muscle contraction. Myosin ATPase assays have demonstrated that under relaxed conditions, myosin may reside either in a high-energy-consuming disordered-relaxed (DRX) state available for binding actin to generate force or in an energy-sparing super-relaxed (SRX) state unavailable for actin binding. X-ray diffraction studies have shown that the majority of myosin heads are in a quasi-helically ordered OFF state in a resting muscle and that this helical ordering is lost when myosin heads are turned ON for contraction. It has been assumed that myosin heads in SRX and DRX states are equivalent to the OFF and ON states, respectively, and the terms have been used interchangeably. In this study, we use X-ray diffraction and ATP turnover assays to track the structural and biochemical transitions of myosin heads, respectively, induced with either omecamtiv mecarbil (OM) or piperine in relaxed porcine myocardium. We find that while OM and piperine induce dramatic shifts of myosin heads from the OFF to the ON state, there are no appreciable changes in the population of myosin heads in the SRX and DRX states in both unloaded and loaded preparations. Our results show that biochemically defined SRX and DRX can be decoupled from structurally defined OFF and ON states. In summary, while SRX/DRX and OFF/ON transitions can be correlated in some cases, these two phenomena are measured using different approaches, reflect different properties of the thick filament, and should be investigated and interpreted separately.

Jani, Vivek P. (ORCID:0000000238114973)↗

DOE OSTI2021

Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions

The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.

Nielson, Felicity F.↗

DOE OSTI2020

Probing the electrical double layer by operando X‐ray photoelectron spectroscopy through a graphene‐carbon nanotube composite window

Abstract The electrical double layer is known to spontaneously form at the electrode‐electrolyte interface, impacting many important chemical and physical processes as well as applications including electrocatalysis, electroorganic synthesis, nanomaterial preparation, energy storage, and even emulsion stabilization. However, it has been challenging to study this fundamental phenomenon at the molecular level because the electrical double layer is deeply “buried” by the bulk electrolyte solution. Here, we report a quantitative probing of the electrical double layer of ionic liquids from the solid side of a photoelectron‐transparent graphene‐carbon nanotube hybrid membrane electrode using X‐ray photoelectron spectroscopy. The membrane window is ultrathin (1‐1.5 nm), large (~1 cm 2 ), and robust, enabling a tight seal of the electrolyte and quantitative measurement with excellent photoelectron signals. By operando monitoring the population changes of cations and anions in response to the applied electrical potentials, we experimentally resolve the chemical structure and dynamics of the electrical double layer, which corroborate results from molecular dynamics simulations. image

Wang, Peng↗

DOE OSTI2021

Enabling Magnesium Anodes by Tuning the Electrode/Electrolyte Interfacial Structure

Here, a new deposition mechanism is presented in this study to achieve highly reversible plating and stripping of magnesium (Mg) anodes for Mg-ion batteries. It is known that the reduction of electrolyte anions such as bi s (trifluoromethanesulfonyl) imide (TFSI - ) causes Mg surface passivation, resulting in poor electrochemical performance for Mg-ion batteries. We reveal that the addition of sodium cations (Na + ) in Mg-ion electrolytes can fundamentally alter the interfacial chemistry and structure at the Mg anode surface. The molecular dynamics simulation suggests that Na + cations contribute to a significant population in the interfacial double layer so that TFSI - anions are excluded from the immediate interface adjacent to the Mg anode. As a result, the TFSI - decomposition is largely suppressed so does the formation of passivation layers at the Mg surface. This mechanism is supported by our electrochemical, microscopic, and spectroscopic analyses. The resultant Mg deposition demonstrates smooth surface morphology and lowered overpotential compared to the pure Mg(TFSI) 2 electrolyte.

25 ENERGY STORAGE↗

DOE OSTI2021

Probabilistic Evaluation of Geoscientific Hypotheses with Geophysical Data: Application to Electrical Resistivity Imaging of a Fractured Bedrock Zone

As climate changes and populations grow, groundwater sustainability is becoming increasingly important. Groundwater models, based on a conceptual understanding of the subsurface structure, are crucial tools for making sustainable management decisions. Conceptual models of the subsurface are based on knowledge of geological processes, and, frequently, observations from geophysical data. A frequent problem in groundwater model development occurs when multiple geological phenomena could explain a single subsurface observation. Uncertainty in geophysical data makes it even more difficult to discern which explanations are consistent with the geophysics. Here, we present a framework for testing geological when a geological feature is observed in geophysical data, but its physical characteristics are uncertain. The framework builds on Popper-Bayes methods developed in previous work, and is applied to study a fractured bedrock zone in a mountainous watershed in southwest Colorado. First, we outline six hypotheses based on the geological history of the watershed. Then, using the proposed Popper-Bayes approach, we demonstrate that three of the six hypotheses are inconsistent with measured electrical resistivity data, even after accounting for uncertainty. Finally, we discuss the importance of the prior model, and how this framework for handling geophysical uncertainty can be applied in other settings.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Learning to concentrate: multi-tracer forecasts on local primordial non-Gaussianity with machine-learned bias

Local primordial non-Gaussianity (LPNG) is predicted by many non-minimal models of inflation, and creates a scale-dependent contribution to the power spectrum of large-scale structure (LSS) tracers, whose amplitude is characterized by b Φ . Knowledge of b Φ for the observed tracer population is therefore crucial for learning about inflation from LSS. Recently, it has been shown that the relationship between linear bias b 1 and b Φ for simulated halos exhibits significant secondary dependence on halo concentration. We leverage this fact to forecast multi-tracer constraints on ${f}^{loc}_{NL}$. We train a machine learning model on observable properties of simulated IllustrisTNG galaxies to predict b Φ for samples constructed to approximate DESI emission line galaxies (ELGs) and luminous red galaxies (LRGs). We find σ(${f}^{loc}_{NL}$) = 2.3, and σ(${f}^{loc}_{NL}$) = 3.7, respectively. These forecasted errors are roughly factors of 3, and 35% improvements over the single-tracer case for each sample, respectively. When considering both ELGs and LRGs in their overlap region, we forecast σ(${f}^{loc}_{NL}$) = 1.5 is attainable with our learned model, more than a factor of 3 improvement over the single-tracer case, while the ideal split by b Φ could reach σ(${f}^{loc}_{NL}$) < 1. In conclusion, we also perform multi-tracer forecasts for upcoming spectroscopic surveys targeting LPNG (MegaMapper, SPHEREx) and show that splitting tracer samples by b Φ can lead to an order-of-magnitude reduction in projected σ(${f}^{loc}_{NL}$) for these surveys.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1974

Long life neutron generator target using deuterium pass-through structure

Target structure permits all deuterons, except the one-in-a-million that interacts with tritium atom to produce a neutron, to pass completely through target structure and be returned to vacuum system. Since tritium atoms are not displaced as in conventional targets, tritium population will remain unchanged while under deuteron bombardment.

Alger, D. L.↗