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DOE OSTI2025

Super-Resolution Ptychography with Small Segmented Detectors

To overcome the spatial resolution limit set by aperture-limited diffraction in traditional scanning transmission electron microscopy, microscopists have developed ptychography enabled by iterative phase retrieval algorithms and high-dynamic-range pixel array detectors. Current detector designs are limited by the data rate off chip, so a high-pixel-count detector has a proportionally lower frame rate than the few-segment detectors used for differential phase contrast (DPC) imaging. This slower acquisition speed leads to heightened vulnerability to scan noise, drift, and potential sample damage. This creates opportunities for repurposing fast segmented detectors for ptychography by trading a reduction in reciprocal space pixels for an increase in real space pixels. Here, we explore a strategy of oversampling in real space and instead apply detector pixel upsampling during the reconstruction process. Further, we demonstrate the viability of achieving super-resolution ptychography on thin objects using only 2 × 2 detector pixels, surpassing the resolution of integrated DPC (iDPC) imaging. With optimization using simulated datasets and experiments on MoTe 2 /WSe 2 bilayer moiré superlattices, we achieved super-resolution ptychography reconstructions under rapid acquisition conditions (37.5 pA, 1 μs dwell time), yielding over 50% improvements in contrast and information limit compared to annular dark field and iDPC imaging on the same detectors.

2D materials↗

DOE OSTI2025

Precision Local Burnup Assessment Through Dynamic Peak Fitting in Atom Probe Tomography for Depleted, Enriched, and Irradiated Metallic and Ceramic Fuels

Abstract Burnup estimation in nuclear fuels is vital for evaluating fuel performance, transportation, and safe fuel storage. Accurate assessments of burnup from service period and spent fuels involve tracking the consumption of fissile isotopes of uranium (U) offering a direct insight into energy changes within the fuels especially for thermal spectrum reactors. In current approach, mass spectroscopic technique in atom probe tomography (APT) is utilized for accurate quantification of U isotopes. Quantification of U peaks in mass spectrum is performed on asymmetric shapes due to delayed signals, known as thermal tails, particularly for poorly conducting samples analyzed in laser mode. In this study, we introduce a novel quantification tool for isotopic analysis from APT datasets by developing a fitting algorithm based on shapes of the peaks. A MATLAB-based dynamic peak fitting toolbox is developed and designed to adapt to various peak shapes, ensuring accurate quantification of U isotopes. The effectiveness of this approach is demonstrated in standard Ni-Cr sample, depleted and enriched U samples, and U-based fuels with different burnup levels. The viability of this approach for isotopic quantification is demonstrated on both metallic and ceramic fuels.

Burnup↗

DOE OSTI2023

Critical magnetic Reynolds number of the turbulent dynamo in collisionless plasmas

The intracluster medium of galaxy clusters is an extremely hot and diffuse, nearly collisionless plasma, which hosts dynamically important magnetic fields of ~μG strength. Seed magnetic fields of much weaker strength of astrophysical or primordial origin can be present in the intracluster medium. In collisional plasmas, which can be approximated in the magnetohydrodynamical (MHD) limit, the turbulent dynamo mechanism can amplify weak seed fields to strong dynamical levels efficiently by converting turbulent kinetic energy into magnetic energy. However, the viability of this mechanism in weakly collisional or completely collisionless plasma is much less understood. In this study, we explore the properties of the collisionless turbulent dynamo using three-dimensional hybrid-kinetic particle-in-cell simulations. We explore the properties of the collisionless turbulent dynamo in the kinematic regime for different values of the magnetic Reynolds number, Rm, initial magnetic-to-kinetic energy ratio, (E mag /E kin ) i , and initial Larmor ratio, (r Larmor /L box ) i , i.e. the ratio of the Larmor radius to the size of the turbulent system. We find that in the ‘un-magnetized’ regime, (r Larmor /L box ) i > 1, the critical magnetic Reynolds number for the dynamo action Rm crit ≈ 107 ± 3. In the ‘magnetized’ regime, (r Larmor /L box ) i ≲ 1, we find a marginally higher Rm crit = 124 ± 8. We find that the growth rate of the magnetic energy does not depend on the strength of the seed magnetic field when the initial magnetization is fixed. We also study the distribution and evolution of the pressure anisotropy in the collisionless plasma and compare our results with the MHD turbulent dynamo.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Exploring modified gravity: constraints on the μ and Σ parametrization with WMAP , ACT, and SPT

ABSTRACT The cosmic acceleration problem remains one of the most significant challenges in cosmology. One of the proposed solutions to this problem is the modification of gravity on large scales. In this paper, we explore the well-known μ–Σ parametrization scenarios and confront them with observational data, including the cosmic microwave background (CMB) radiation from the Wilkinson Microwave Anisotropy Probe (WMAP), Atacama Cosmology Telescope (ACT), and South Pole Telescope (SPT), as well as large-scale structure data from the Sloan Digital Sky Survey (SDSS; baryon acoustic oscillation + redshift-space distortion) and Pantheon supernova (SN) catalogue. We employ a Bayesian framework to constrain the model parameters and discuss the implications of our results on the viability of modified gravity theories. Our analysis reveals the strengths and limitations of the μ–Σ parametrization and provides valuable insights into the nature of gravity on cosmological scales. From the joint analysis of the ACT + WMAP + SDSS + SN, we find μ0 − 1 = 0.02 ± 0.19 and Σ0 − 1 = 0.021 ± 0.068 at 68 per cent confidence level (CL). In light of the SPT + WMAP + SDSS + SN, we find μ0 − 1 = 0.07 ± 0.18 and $\Sigma _0 -1 = -0.009^{+0.078}_{-0.11}$ at 68 per cent CL. In all the analyses carried out, we do not find any deviations from the theory of general relativity. Our results represent an observational update on the well-known μ–Σ parametrization in view of current CMB data, independent of and competitive with the constraints obtained with the Planck data.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast

Abstract Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Polα-primase complex to telomeres via Tpz1, thus promoting lagging-strand DNA synthesis at stalled replication forks.

Carvalho Borges, Pâmela C. (ORCID:0000000244919874↗

DOE OSTI2025

Genomic insights into local adaptation and migration success in reintroduced Coho Salmon of the Wenatchee River basin

ABSTRACT Objective Reintroduction of salmonids into regions where they have been extirpated is a common conservation strategy that is often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focused on the mid-Columbia River Coho Salmon reintroduction program managed by Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon into the Wenatchee and Methow River basins, Washington. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15-km, high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Methods Low-coverage whole-genome resequencing data were used to screen for genomic regions associated with the phenotypes of interest. Results A weak polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions occurring across eight chromosomes. Conclusions These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.

Horn, Rebekah L.↗

DOE OSTI2021

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Simple, low-cost and accurate data-driven geophysical forecasting with learned kernels

Modelling geophysical processes as low-dimensional dynamical systems and regressing their vector field from data is a promising approach for learning emulators of such systems. We show that when the kernel of these emulators is also learned from data (using kernel flows, a variant of cross-validation), then the resulting data-driven models are not only faster than equation-based models but are easier to train than neural networks such as the long short-term memory neural network. In addition, they are also more accurate and predictive than the latter. When trained on geophysical observational data, for example the weekly averaged global sea-surface temperature, considerable gains are also observed by the proposed technique in comparison with classical partial differential equation-based models in terms of forecast computational cost and accuracy. When trained on publicly available re-analysis data for the daily temperature of the North American continent, we observe significant improvements over classical baselines such as climatology and persistence-based forecast techniques. Although our experiments concern specific examples, the proposed approach is general, and our results support the viability of kernel methods (with learned kernels) for interpretable and computationally efficient geophysical forecasting for a large diversity of processes.

58 GEOSCIENCES↗

DOE OSTI2022

Simulations of frustrated Ising Hamiltonians using quantum approximate optimization

Novel magnetic materials are important for future technological advances. Theoretical and numerical calculations of ground-state properties are essential in understanding these materials, however, computational complexity limits conventional methods for studying these states. Here we investigate an alternative approach to preparing materials ground states using the quantum approximate optimization algorithm (QAOA) on near-term quantum computers. We study classical Ising spin models on unit cells of square, Shastry-Sutherland and triangular lattices, with varying field amplitudes and couplings in the material Hamiltonian. We find relationships between the theoretical QAOA success probability and the structure of the ground state, indicating that only a modest number of measurements (≲100) are needed to find the ground state of our nine-spin Hamiltonians, even for parameters leading to frustrated magnetism. We further demonstrate the approach in calculations on a trapped-ion quantum computer and succeed in recovering each ground state of the Shastry-Sutherland unit cell with probabilities close to ideal theoretical values. The results demonstrate the viability of QAOA for materials ground state preparation in the frustrated Ising limit, giving important first steps towards larger sizes and more complex Hamiltonians where quantum computational advantage may prove essential in developing a systematic understanding of novel materials.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

ABSTRACT The Shox2 homeodomain transcriptional regulator is known for its critical functions during mouse embryogenesis, enabling accurate development of limbs, craniofacial structures, neural populations and the cardiac conduction system. At the genomic level, the Shox2 gene is flanked by an extensive gene desert, a continuous non-coding genomic region spanning over 500 kilobases that contains a multitude of evolutionarily conserved elements with predicted cis -regulatory activities. However, the transcriptional enhancer potential of the vast majority of these elements in combination with the biological necessity of the gene desert have not yet been explored. Using transgenic reporter assays in mouse embryos to validate an extensive set of stringent epigenomic enhancer predictions, we identify several novel gene desert enhancers with distinct tissue-specific activities in Shox2 expressing tissues. 4C-seq chromatin conformation capture further uncovers a repertoire of gene desert enhancers with overlapping activities in the proximal limb, in a compartment essential for Shox2 -mediated stylopod formation. Leveraging CRISPR/Cas9 to delete the gene desert region contained in the Shox2 topologically associated domain (TAD), we demonstrate that this complex cis -regulatory platform is essential for embryonic survival and required for control of region-specific Shox2 expression in multiple developing tissues. While transcription of Shox2 in the embryonic limb is only moderately affected by gene desert loss, Shox2 expression in craniofacial and cardiac domains is nearly abolished. In particular, Shox2 transcripts in the sinus venosus (SV) encompassing the sinoatrial node (SAN) were depleted in embryos lacking the gene desert, likely accounting for the embryonic lethality due to Shox2 -dependency of the SAN pacemaker. Finally, we discover a 1.5kb SV enhancer within the deleted gene desert region, which may act as a genomic module controlling the development of the cardiac conduction system. In summary, our results identify a gene desert indispensable for pleiotropic patterning and highlight the importance of these extensive regulatory landscapes for embryonic development and viability.

Abassah-Oppong, Samuel↗

DOE OSTI2021

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

Topologically associating domain (TAD) boundaries are thought to partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotype, but the overall extent to which this occurs remains unknown. Here we show that TAD boundary deletions commonly disrupt normal genome function in vivo . We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80kb in size) from the genome in mice. All deletions examined resulted in at least one detectable molecular or organismal phenotype, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. For 5 of 8 (62%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and suggest that noncoding deletions affecting TAD boundaries should be carefully considered for potential pathogenicity in clinical genetics screening.

Rajderkar, Sudha↗

DOE OSTI2026

Investigation of low-energy particle remnants in high-energy collisions at the LHC with a skipper-CCD detector

We deployed the Mobile Skipper Testing Apparatus ∼33 m away from the Compact Muon Solenoid collision point, the first skipper-CCD detector probing low-energy particles produced in high-energy collisions at the Large Hadron Collider. In this work, we search for beam-related events using data collected in 2024 during beam-on and beam-off periods. The dataset corresponds to integrated luminosities of 113.3 fb −1 and 1.54 nb −1 for the proton-proton and Pb-Pb collision periods, respectively. We report observed event rates in a model-independent framework across two ionization regions: ≤ 20⁢𝑒 − and > 20⁢𝑒 − . For the low-energy region, we perform a likelihood analysis to test the null hypothesis of no beam-correlated signal. We found no significant correlation during proton-proton and Pb-Pb collisions. For the high-energy region, we present the energy spectra for both collision periods and compare event rates for images with and without luminosity. We observe a slight increase in the event rate following the Pb-Pb collisions, coinciding with a rise in the single-electron rate, which will be investigated in future work. Using the low-energy proton-proton results, we place 95% confidence level constraints on the mass-millicharge parameter space of millicharged particles. Overall, the results in this work demonstrate the viability of skipper-CCD technology to explore new physics at high-energy colliders and motivate future searches with more massive detectors.

Cervantes-Vergara, Brenda A. [Fermi National Accel↗

DOE OSTI2020

Quantum state reduction: Generalized bipartitions from algebras of observables

Reduced density matrices are a powerful tool in the analysis of entanglement structure, approximate or coarse-grained dynamics, decoherence, and the emergence of classicality. It is straightforward to produce a reduced density matrix with the partial-trace map by tracing out part of the quantum state, but in many natural situations this reduction may not be achievable. We investigate the general problem of identifying how the quantum state is reduced given a restriction on the observables. For example, in an experimental setting, the set of observables that can actually be measured is usually modest (compared to the set of all possible observables) and their resolution is limited. In such situations, the appropriate state-reduction map can be defined via a generalized bipartition, which is associated with the structure of irreducible representations of the algebra generated by the restricted set of observables. One of our main technical results is a general, not inherently numeric, algorithm for finding irreducible representations of matrix algebras. In our work, we demonstrate the viability of this approach with two examples of limited-resolution observables. The definition of quantum state reductions can also be extended beyond algebras of observables. To accomplish this task we introduce a more flexible notion of bipartition, the partial bipartition, which describes coarse grainings preserving information about a limited set (not necessarily algebra) of observables. We describe a variational method to choose the coarse grainings most compatible with a specified Hamiltonian, which exhibit emergent classicality in the reduced state space. We apply this construction to the concrete example of the one-dimensional Ising model. Our results have relevance for quantum information, bulk reconstruction in holography, and quantum gravity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Experimental generation of polarization entanglement from spontaneous parametric down-conversion pumped by spatiotemporally highly incoherent light

Here, we investigate the cross influence of the pump coherence on the entanglement produced from spontaneous parametric down-conversion (SPDC) in different degrees of freedom (DOFs). We experimentally demonstrate the generation of polarization entanglement from SPDC pumped by a spatiotemporally highly incoherent (STHI) light-emitting diode. Our quantum state tomography measurements using multimode collection fibers to avoid postselection yield a two-qubit state with the concurrence of 0.531 ± 0.006 and purity of 0.647 ± 0.005, in excellent agreement with our theoretically predicted concurrence of 0.552 and purity of 0.652. We find that using an STHI pump reduces the entanglement and purity of the output polarization two-qubit state due to a coupling between the spatiotemporal and polarization DOFs introduced by the birefringence and dispersion of the nonlinear crystal. The viability of SPDC with STHI pumps is important for two reasons: (i) STHI sources are ubiquitous and available at a wider range of wavelengths than lasers, and (ii) the generated STHI polarization-entangled two-photon states could potentially be useful in long-distance quantum communication schemes due to their robustness to scattering.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Deviation from Debye-Waller behavior in single crystalline freestanding Ni⁢ O membranes studied via ultrafast electron diffraction

Here, we realize single-crystal freestanding Ni⁢O films on Si⁢N membranes, enabling thin-film scattering experiments with little or no substrate background signal. These membrane samples provide a critical platform for performing ultrafast electron diffraction (UED) to probe the response of the lattice to laser excitation. We show that epitaxial Ni⁢O films on a water-soluble Sr 2 ⁢Ca⁢Al 2⁢ O 6 buffer layer on Sr⁢Ti⁢O 3 substrates can be transferred as freestanding films to the Si⁢N membranes while maintaining the epitaxial character of the films. An above-gap photoexcitation (𝜆 =266 nm) incident on the sample stimulates an initial lattice response of the order of 1.1 ps, followed by the persistence of this state for more than 20 ps. We observe typical Debye-Waller behavior in peaks with 𝑞 above the (220) family, but a distinct deviation from this behavior is seen in low-𝑞 peaks. We relate this behavior to a dynamic decrease in sample mosaicity in response to the optical pump of the order of 3% that endures for approximately 4 ps. We suspect that this dynamic mosaicity is due to laser-induced strain propagation. This work demonstrates the viability of the thin-film transfer method for UED and paves the way for the study of the dynamic response of antiferromagnetic thin-film oxides.

Wisser, Jacob J. [Stanford Univ., CA (United State↗

DOE OSTI2022

Pairwise connected tensor network representation of path integrals

It has been recently shown how the tensorial nature of real-time path integrals (PIs) involving the Feynman-Vernon influence functional can be utilized with matrix product states, taking advantage of the finite length of the bath-induced memory. Tensor networks (TNs) promise to provide a unified language to express the structure of a PI. A generalized TN specifically incorporating the pairwise interaction structure of the influence functional and its invariance with respect to the average forward-backward position or the sojourn value in the form of the blip representation is derived and implemented. This pairwise connected TNPI (PC-TNPI) is illustrated through applications to typical spin-boson problems and explorations of the differences caused by the exact form of the spectral density. The storage and performance scalings are reported, showing the compactness of the representation and the efficiency of the contraction process. Finally, taking advantage of the compressed representation, the viability of using PC-TNPI for simulating multistate problems is demonstrated. The PC-TNPI structure can be shown to yield other TN algorithms currently in use. Consequently, it should be possible to use it as a starting point for deriving other optimized procedures.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Uncovering extreme nonlinear dynamics in solids through time-domain field analysis

Time-domain analysis of harmonic fields with sub-cycle resolution is now experimentally viable due to the emergence of sensitive, on-chip techniques for petahertz-scale optical-field sampling. We demonstrate how such a time-domain, field-resolved analysis uncovers the extreme nonlinear electron dynamics responsible for high-harmonic generation within solids. Time-dependent density functional theory was used to simulate harmonic generation from a solid-state band-gap system driven by near- to mid-infrared waveforms. Particular attention was paid to regimes where both intraband and interband emission mechanisms play a critical role in shaping the nonlinear response. We show that a time-domain analysis of the harmonic radiation fields identifies the interplay between intra- and interband dynamical processes underlying the nonlinear light generation. With further analysis, we show that changes to the dominant emission regime can occur after only slight changes to the peak driving intensity and central driving wavelength. Furthermore, time-domain analysis of harmonic fields also reveals, for the first time, the possibility of rapid changes in the dominant emission mechanism within the temporal window of the driving pulse envelope. Finally, we examine the experimental viability of performing time-domain analysis of harmonic fields with sub-cycle resolution using realistic parameters.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Calculating n-point charge correlations in evolving systems

Background: In dynamic systems such as heavy-ion collisions, charge susceptibilities and local charge correlations change with time. These changes are accompanied by nonlocal correlations, which spread diffusively with time and are constrained by local charge conservation. Such correlations have been measured at the Relativistic Heavy-Ion Collider (RHIC) and have been linked to the chemical evolution of the matter and possible phase separation or critical phenomena. The evolution of such correlations has been modeled for two-point correlators superimposed onto hydrodynamics, but not for three- or four-point correlators. These higher-order correlators represent an essential basis for calculating the kurtosis and skewness of charge distributions measured at RHIC. For short-range correlations, such as those between charges on the same particle, and the associated charge-balance correlations a theoretical formalism was lacking for handling higher-order correlations. In particular, one needed to understand how higher-order charge fluctuations was split onto lower numbers of particles. For example, correlations of order three have contributions with charge all on one particle, split onto two particle, or split onto three. By assuming local chemical equilibrium of short-range correlations, the sources of the various correlators were found to be uniquely determined. The relevant theoretical foundation is presented here, including a diagrammatic technique to correctly account for all the possible terms to higher-order correlations. Here, we found a consistent theoretical treatment and its applicability, viability, and tractability are discussed. The formalism derived here enables realistic and quantitative modeling of the three- and four-point charge correlations necessary for understanding measurements of the kurtosis and skewness of charge distributions at RHIC. These observables have been promoted as signals of phase transitions or measures of chemical evolution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗