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DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗

DOE OSTI2026

Spatiotemporal control of laser intensity using differentiable programming

Optical techniques for spatiotemporal control can produce laser pulses with custom amplitude, phase, or polarization structure. In nonlinear optics and plasma physics, the use of structured pulses typically follows a forward design approach, in which the efficacy of a known structure is analyzed for a particular application. Inverse approaches, in contrast, enable the discovery of new structures with the potential for superior performance. Here, an implementation of the unidirectional pulse propagation equation that supports automatic differentiation is combined with gradient-based optimization to design structured pulses with features that are advantageous for a range of nonlinear optical and plasma-based applications: (1) a longitudinally uniform intensity over an extended region, (2) a superluminal intensity peak that travels many Rayleigh ranges with constant duration, spot size, and amplitude, and (3) a laser pulse that ionizes a gas to form a uniform column of plasma. In the final case, optimizing the full spatiotemporal structure improves the performance by a factor of 15 compared to optimizing only spatial or only temporal structure, highlighting the advantage of spatiotemporal control.

automatic differentiation↗

DOE OSTI2024

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Noninteracting electrons in a prototypical one-dimensional sinusoidal potential

A prototypical model of a one-dimensional metallic monatomic solid containing noninteracting electrons is studied, where the argument of the cosine potential energy, periodic with the lattice, contains the first reciprocal lattice vector G 1 =2π/a, where a is the lattice constant. The time-independent Schrödinger equation can be written in reduced variables as a Mathieu equation for which numerically exact solutions for the band structure and wave functions are obtained. The band structure has band gaps that increase with increasing amplitude q of the cosine potential. In the extended-zone scheme, the energy gaps decrease with increasing index n of the Brillouin-zone boundary ka=nπ, where k is the crystal momentum of the electron. The wave functions of the band electron are derived for various combinations of k and q as complex combinations of the real Mathieu functions with even and odd parity, and the normalization factor is discussed. The wave functions at the bottoms and tops of the bands are found to be real or imaginary, respectively, corresponding to standing waves at these energies. Irrespective of the wave vector k within the first Brillouin zone, the electron probability density is found to be periodic with the lattice. The Fourier components of the wave functions are derived versus q, which reveal multiple reciprocal-lattice-vector components with variable amplitudes in the wave functions unless q = 0. The magnitudes of the Fourier components are found to decrease exponentially as a power of n for n~3 to 45 for ka = π/2 and q = 2, and a precise fit is obtained to the data. The probability densities and probability currents obtained from the wave functions are also discussed. The probability currents are found to be zero for crystal momenta at the tops and bottoms of the energy bands, because the wave functions for these crystal momenta are standing waves. To conlcude, the band structure is calculated from the central equation and compared to the numerically exact band structure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Enhanced electron amplifier structure and method of fabricating the enhanced electron amplifier structure

An enhanced electron amplifier structure includes a microporous substrate having a front surface and a rear surface, the microporous substrate including at least one channel extending substantially through the substrate between the front surface and the rear surface, an ion diffusion layer formed on a surface of the channel, the ion diffusion layer comprising a metal oxide, a resistive coating layer formed on the first ion diffusion layer, an emissive coating layer formed on the resistive coating layer, and an optional ion feedback layer formed on the front surface of the structure. The emissive coating produces a secondary electron emission responsive to an interaction with a particle received by the channel. The ion diffusion layer, the resistive coating layer, the emissive coating layer, and the ion feedback layer are independently deposited via chemical vapor deposition or atomic layer deposition.

Mane, Anil U.↗

DOE OSTI2026

Manipulating Na/TM Ratio‐Driven Structural Heterogeneity of O3‐NaNi 1/3 Fe 1/3 Mn 1/3 O 2 Cathode for High‐Voltage Sodium‐Ion Batteries

The stability of O3-type NaNi 1/3 Fe 1/3 Mn 1/3 O 2 under high-voltage cycling is dictated by how synthesis encodes lattice strain and redox heterogeneity. Here, in this study, the role of Na:TM stoichiometry is systematically resolved by tuning the NaOH:precursor ratio during solid-state synthesis. The stoichiometric condition (Na:TM = 1.00) yields minimized microstrain, enabling uniform O3–P3 phase evolution and homogeneous multi-metal redox with preserved octahedral symmetry. In contrast, Na-excess compositions inherit disordered intermediates and heterogeneous distortion fields that trigger abrupt multiphase transitions and promote localized charge redistribution. In situ XRD captures the divergence in phase-transition pathways, TXM resolves particle-level redox heterogeneity, and XANES corroborates a stronger and more reversible Fe redox contribution at stoichiometry, shifting to diminished Fe participation and spatially inhomogeneous redox at higher Na content. These results establish Na:TM stoichiometry as a critical synthesis parameter controlling both structural coherence and redox stability. Electrochemically, the stoichiometric composition exhibits smooth voltage profiles with minimal polarization growth and retains nearly 80% of its initial capacity after 100 cycles even at an extended 4.2 V cutoff, whereas Na-excess compositions show significantly reduced initial coulombic efficiency and rapid voltage fade. Precise stoichiometric tuning provides a scalable route to defect-suppressed O3 frameworks, enabling structurally resilient, high-voltage sodium-layered cathodes.

36 MATERIALS SCIENCE↗

DOE OSTI2024

High–Energy Earth–Abundant Cathodes with Enhanced Cationic/Anionic Redox for Sustainable and Long–Lasting Na–Ion Batteries

Layered iron/manganese-based oxides are a class of promising cathode materials for sustainable batteries due to their high energy densities and earth abundance. However, the stabilization of cationic and anionic redox reactions in these cathodes during cycling at high voltage remain elusive. Here, an electrochemically/thermally stable P2-Na 0.67 Fe 0.3 Mn 0.5 Mg 0.1 Ti 0.1 O 2 cathode material with zero critical elements is designed for sodium-ion batteries (NIBs) to realize a highly reversible capacity of ≈210 mAh g –1 at 20 mA g –1 and good cycling stability with a capacity retention of 74% after 300 cycles at 200 mA g –1 , even when operated with a high charge cut-off voltage of 4.5 V versus sodium metal. Combining a suite of cutting-edge characterizations and computational modeling, it is shown that Mg/Ti co-doping leads to stabilized surface/bulk structure at high voltage and high temperature, and more importantly, enhances cationic/anionic redox reaction reversibility over extended cycles with the suppression of other undesired oxygen activities. This work fundamentally deepens the failure mechanism of Fe/Mn-based layered cathodes and highlights the importance of dopant engineering to achieve high-energy and earth-abundant cathode material for sustainable and long-lasting NIBs.

25 ENERGY STORAGE↗

DOE OSTI2023

Multistage robust optimization for the day-ahead scheduling of hybrid thermal-hydro-wind-solar systems

The integration of large-scale uncertain and uncontrollable wind and solar power generation has brought new challenges to the operations of modern power systems. In a power system with abundant water resources, hydroelectric generation with high operational flexibility is a powerful tool to promote a higher penetration of wind and solar power generation. In this paper, we study the day-ahead scheduling of a thermal-hydro-wind-solar power system. The uncertainties of renewable energy generation, including uncertain natural water inflow and wind/solar power output, are taken into consideration. We explore how the operational flexibility of hydroelectric generation and the coordination of thermal-hydro power can be utilized to hedge against uncertain wind/solar power under a multistage robust optimization (MRO) framework. To address the computational issue, mixed decision rules are employed to reformulate the original MRO model with a multi-level structure into a bi-level one. Column-and-constraint generation (C &CG) algorithm is extended into the MRO case to solve the bi-level model. The proposed optimization approach is tested in three real-world cases. Furthermore, the computational results demonstrate the capability of hydroelectric generation to promote the accommodation of uncertain wind and solar power.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Dielectric relaxation of neodymium chloride in water and in methanol

In this work, an open-ended coaxial probe was used to study the dielectric relaxation of neodymium chloride (NdCl 3 ) in water and in methanol at room temperature over the frequency range 0.2–40.0 GHz. An equivalent circuit model based on the antenna model was used to obtain the dielectric spectra with the effective removal of spurious effects. This extends the use of the open-ended coaxial probe technique for highly conductive substances. The structural and thermodynamic parameters obtained from the dielectric spectra of aqueous NdCl 3 solutions suggest that solvent-separated ion pairs and solvent-shared ion pairs dominate the low-frequency behavior at low concentrations. In methanol, solvent-shared ion pair relaxation modes were detected. No contact pair relaxation was observed in either solvent. Under all conditions, Nd 3+ was strongly solvated, as reflected by its high effective hydration number. The estimated association constant of NdCl 3 in water at infinite dilution was within the literature values and was lower than that observed in methanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Theory-Based Mechanism for Fluoromethane Combustion I: Thermochemistry and Abstraction Reactions

A new detailed chemical kinetic mechanism is presented for small fluorinated hydrocarbons. Ab initio electronic structure theory is used to provide heats of formation with subchemical accuracy. The ANL0 method is extended to include fluorine. The resulting heats of formation at 0 K are in excellent agreement with 36 benchmark species in the Active Thermochemical Tables, with a mean error of μ = –0.02 kJ/mol and a standard deviation of σ = 0.91 kJ/mol. The thermophysical properties for 92 small-molecule H/C/O/F species are computed. The rate coefficients for 40+ H-abstraction reactions involving H, O, F, OH, OF, HO 2 , and various methyl radicals with CH 4 , CH 3 F, CH 2 F 2 , CHF 3 , CH 2 O, and CHFO are discussed. Here, the computed rate constants are in excellent agreement with the available literature. Additionally, 30+ rate constants are provided for F abstraction, which are several orders of magnitude smaller than H abstraction. The thermophysical properties and rate constants are provided in a mechanism. This mechanism is the first in a series of theory-based investigations into the thermal destruction of per- and polyfluorinated species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Utilizing Single-Crystalline Transformations for Precise Atom Placement in Multicomponent Cluster-Based Coordination Networks

The assembly of cluster or superatom building-blocks into extended solids has revolutionized materials design, enabling the synthesis of modular semiconductors with well-defined structures and tunable electronic, magnetic or optical properties. This strategy has recently advanced the synthesis of complex metal oxides with multifunctional or emergent behaviors, but precise atom placement of multiple elements with similar chemistries or preferred coordination environments remains a significant challenge. Here, in this study, we present a strategy for synthesizing polyoxometalate (POM)-based coordination networks with up to three different cations in precisely defined positions. Our approach leverages a single-crystal-to-single-crystal (SCSC) transformation in which the spatial placement of cations is governed by their availability at distinct stages of crystallization and transformation. Specifically, [ZP 5 W 30 O 110 ] (15-n)- (Z = Na + , K + , Ca 2+ , Ag + , Bi 3+ , Y 3+ , any Ln 3+ , Th 4+ ) is coordinatively assembled with various bridging metal cations (Y 3+ , any Ln 3+ , Th 4+ ). By using the encapsulated cation (Z) to "label" the POM, we track the phase-transformation and confirm the retention of single crystallinity. The integrated use of POM labeling and SCSC transformation enables rational control over cation distribution and establishes a versatile strategy for constructing multicomponent materials with high compositional and spatial precision.

Chen, Linfeng [Univ. of California, San Diego, CA ↗

DOE OSTI2023

Traces of electron-phonon coupling in one-dimensional cuprates

Abstract The appearance of certain spectral features in one-dimensional (1D) cuprate materials has been attributed to a strong, extended attractive coupling between electrons. Here, using time-dependent density matrix renormalization group methods on a Hubbard-extended Holstein model, we show that extended electron-phonon ( e–ph ) coupling presents an obvious choice to produce such an attractive interaction that reproduces the observed spectral features and doping dependence seen in angle-resolved photoemission experiments: diminished 3 k F spectral weight, prominent spectral intensity of a holon-folding branch, and the correct holon band width. While extended e–ph coupling does not qualitatively alter the ground state of the 1D system compared to the Hubbard model, it quantitatively enhances the long-range superconducting correlations and suppresses spin correlations. Such an extended e–ph interaction may be an important missing ingredient in describing the physics of the structurally similar two-dimensional high-temperature superconducting layered cuprates, which may tip the balance between intertwined orders in favor of uniform d -wave superconductivity.

36 MATERIALS SCIENCE↗

DOE OSTI2023

A first-principles machine-learning force field for heterogeneous ice nucleation on microcline feldspar

The formation of ice in the atmosphere affects precipitation and cloud properties, and plays a key role in the climate of our planet. Although ice can form directly from liquid water at deeply supercooled conditions, the presence of foreign particles can aid ice formation at much warmer temperatures. Over the past decade, experiments have highlighted the remarkable efficiency of feldspar minerals as ice nuclei compared to other particles present in the atmosphere. However, the exact mechanism of ice formation on feldspar surfaces has yet to be fully understood. Here, we develop a first-principles machine-learning model for the potential energy surface aimed at studying ice nucleation at microcline feldspar surfaces. The model is able to reproduce with high-fidelity the energies and forces derived from density-functional theory (DFT) based on the SCAN exchange and correlation functional. Our training set includes configurations of bulk supercooled water, hexagonal and cubic ice, microcline, and fully-hydroxylated feldspar surfaces exposed to vacuum, liquid water, and ice. In this work, we apply the machine-learning force field to study different fully-hydroxylated terminations of the (100), (010), and (001) surfaces of microcline exposed to vacuum. Our calculations suggest that terminations that do not minimize the number of broken bonds are preferred in vacuum. We also study the structure of supercooled liquid water in contact with microcline surfaces, and find that water density correlations extend up to around 10 Å from the surfaces. Finally, we show that the force field maintains a high accuracy during the simulation of ice formation at microcline surfaces, even for large systems of around 30,000 atoms. Future work will be directed towards the calculation of nucleation free energy barriers and rates using the force field developed herein, and understanding the role of different microcline surfaces on ice nucleation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Generalized kinetic equation for tokamak plasma equilibrium distribution function

A generalised kinetic equation for the equilibrium distribution function in a finite beta, arbitrary tokamak plasma is derived. The equation is correct to second order in ρ/L (ρ is the particle Larmor radius and L is the system size). Resolving finite Larmor radius length scales with no restriction on the ratio of poloidal to total equilibrium magnetic field, B $\vartheta$ /B, it generalises the drift kinetic theory of [Hazeltine Phys. Plasmas 15 (1973) 77] to the limit of B $\vartheta$ /B ~ 1 (e.g. to ensure validity for spherical tokamaks). Two cases are considered. The first provides the equilibrium distribution function, consistent with the generalised gyrokinetic formalism of [Dudkovskaia et al. Plasma Phys. Control. Fusion 65 (2023) 045010], derived specifically to capture neoclassical equilibrium currents in gyrokinetic stability analyses in strong gradient regions. The second assumes short length scales in the direction perpendicular to the magnetic field, which can occur as a result of small coherent magnetic structures in the plasma, such as neoclassical tearing mode magnetic islands close to threshold. This then extends the drift island equations of [Dudkovskaia et al. Nucl. Fusion 63 (2023) 016020] for the plasma response to magnetic islands to a spherical tokamak plasma configuration. In conclusion, resolving ρ ~ ρ $\vartheta$ (or B $\vartheta$ ~ B), where ρ $\vartheta$ is the particle poloidal Larmor radius, is also expected to influence calculations of the magnetic island propagation frequency and the associated contributions to the island onset conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: a catalogue of strong galaxy–galaxy lens candidates

ABSTRACT We spectroscopically detected 838 likely, 448 probable, and 265 possible strong lens candidates within ≈2 million galaxy spectra contained within the extended Baryon Oscillation Spectroscopic Survey (eBOSS) from the sixteenth data release (DR16) of the Sloan Digital Sky Survey (SDSS). We apply the spectroscopic detection method of the Baryon Oscillation Spectroscopic Survey (BOSS) Emission-Line Lens Survey (BELLS) and add Gaussian fit information, grading, additional inspection observables, and additional inspection methods to improve our selection method. We observed 477 candidates with lensing evidence within low-resolution images from both the Legacy survey of SDSS-I/II and the DESI Legacy survey, which is $12{{\ \rm per\ cent}}$ higher than the percentage of BELLS candidates observed with similar lensing evidence. Our search within the latest and improved reductions of the BOSS survey yielded a $20{{\ \rm per\ cent}}$ increase in the number of lens candidates expected from searching all BOSS and eBOSS galaxies. The distribution of target and background redshifts of our candidates is similar to the candidates and confirmed lenses within the BELLS observations. We present our Spectroscopic Identification of Lensing Object candidates in a value-added catalogue in SDSS DR16. The examination of these lens candidates in follow-up high-resolution imaging may yield more than twice the lenses found in previous spectroscopic detection surveys within SDSS, which would extend the results of previous lens surveys within SDSS to higher redshifts, constrain models of mass structures in spiral galaxies, and test if including the identification of possible lensing features within low-resolution images has merit to spectroscopic detection programmes.

Talbot, Michael S.↗

DOE OSTI2021

On the degeneracy of spin ice graphs, and its estimate via the Bethe permanent

The concept of spin ice can be extended to a general graph. We study the degeneracy of spin ice graph on arbitrary interaction structures via graph theory. We map spin ice graphs to the Ising model on a graph and clarify whether the inverse mapping is possible via a modified Krausz construction. From the gauge freedom of frustrated Ising systems, we derive exact, general results about frustration and degeneracy. We demonstrate for the first time that every spin ice graph, with the exception of the one-dimensional Ising model, is degenerate. We then study how degeneracy scales in size, using the mapping between Eulerian trails and spin ice manifolds, and a permanental identity for the number of Eulerian orientations. Furthermore, we show that the Bethe permanent technique provides both an estimate and a lower bound to the frustration of spin ices on arbitrary graphs of even degree. While such a technique can also be used to obtain an upper bound, we find that in all finite degree examples we studied, another upper bound based on Schrijver inequality is tighter.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Experimental study of the nature of the 1 – and 2 – excited states in 10 Be using the 11 Be (p,d) reaction in inverse kinematics

In this paper, we investigated the structure of two excited states in the nucleus 10 Be, which were suspected to have spatially extended wave functions (or "haloes"). This was done by performing a transfer reaction that removed a neutron from the core of the 11 Be nucleus, a well-known one-neutron halo nucleus. By doing so, we specifically produced configurations, whereas the halo neutron in 11 Be remained when populating excited states in 10 Be. If the two excited states in 10 Be had a strong overlap with those configurations, one would have expected them to be strongly populated in the reaction. We find that this was not quite the case and we postulated that the reason why was because those states had a mixed configuration that not only displayed halo-like, but also cluster-like, properties. The overlap was therefore not as strong as expected (and suggested by previous experiments).

6 ≤ A ≤ 19↗

DOE OSTI2020

Exotic silicon phases synthesized through ultrashort laser-induced microexplosion: Characterization with Raman microspectroscopy

Exotic metastable phases of silicon formed under high pressure are expected to have attractive semiconducting properties including narrow band gaps that open up novel technological applications. Confined microexplosions induced by powerful ultrashort laser pulses have been demonstrated as an advanced tool for the creation of new high-pressure phases that cannot be synthesized by other means. Tightly focused laser pulses are used to generate localized modifications inside the material structure, providing the possibility for precise controlled band-gap engineering. In this study, noninvasive Raman spectroscopy was used for analysis of laser-modified zones in silicon and to determine the metastable high-pressure phases contained. Low laser energies induced the formation of amorphous-only silicon, while higher energies led to crystalline silicon polymorphs within the modifications, albeit under considerable residual stress up to 4.5 GPa. The presence of the structurally similar r8-Si, bc8-Si, and bt8-Si phases is revealed, as well as other yet to be identified phases, and the stacking-related 9R Si polytype is evidenced, presumably stress-induced by the highly compressed laser-modified zone. The ab initio random structure searching approach is used to calculate the Raman signatures and to help identify different Si polymorphs. The findings of this study by Raman spectroscopy from ultrashort laser-induced microexplosion sites may yield insights into the local structure and properties of new silicon metastable phases and the prospect of utilizing exotic phases for extending current applications.

36 MATERIALS SCIENCE↗