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At least 883 records · Page 49

All sources NASA NTRS DOE OSTI

DOE OSTI2026

Mott vs Kondo: Influence of various density functional based methods on the Ce isostructural phase transition mechanism

The cerium iso-structural phase transition (γ–α) is dominated by f-electron localization changes that results in a magnetic ordering change and a volume collapse. Generally, these physics are difficult to capture with ab initio and first principles methods. However, previous works have shown various methods to be successful in predicting at least some of the physics of the γ to α phase transition. Therefore, here, we perform a broad survey of density functional based methods across three levels of theory and types of functions [GGA (generalized gradient approximation), MetaGGA, and hybrid functionals] and compare the results, focusing on hydrostatic compression across the phase boundary at zero kelvin. For the methods that best reproduce experimental results, we directly probe the predicted mechanisms and frame the results in the Mott/Kondo debate, assessing how the underlying methods and assumptions of different functionals can assess the physical drivers in the phase transition, providing insight into the governing processes of this unique phase transition.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Maximizing efficiency of dataset compression for machine learning potentials with information theory

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Hyperspectral radiance mapping and chromatic correction for temperature measurement in laser-heated diamond anvil cells

In laser-heated diamond anvil cell (DAC) experiments, the effective heated region typically decreases in size with increasing pressure, leading to steeper thermal gradients. Under these conditions, chromatic aberration in the optical path from sample to detector can significantly create bias in spectro-radiometric temperature measurement. We present a radiance-mapping approach using a hyperspectral camera that records 25 spectral channels spanning 605–875 nm at each pixel in a single exposure, providing spatially and spectrally resolved radiance in each frame. This enables chromatic effects to be recorded and corrected in data processing. We developed a procedure for hyperspectral mapping, involving per-camera calibration, crosstalk removal, measured spectral throughput functions, and optional sub-pixel co-registration to minimize chromatic distortion. The calibrated radiance maps are then used to derive temperature maps of the laser-heated hotspots. For smaller heating spots, the radiance mapping approach reveals chromatic shifts that conventional spectro-radiometric methods cannot quantify. Ambient-pressure heating experiments confirm accurate temperature retrieval. At high pressure, application of the hyperspectral system to a platinum-heating experiment at 12 GPa demonstrates stable temperature reconstruction under steep thermal gradients. Beyond mitigating chromatic aberrations, the ability to diagnose optical artifacts separately from emissivity variations during controlled test experiments or in situ suggests a path toward more rigorous spectral emissivity analysis and improved modeling of thermal transport in laser-heated DAC experiments.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

QR-code optical encryption in the scheme with spatially incoherent illumination based on two micromirror light modulators

An optical encryption scheme with spatially incoherent illumination based on two micromirror light modulators has been experimentally implemented for the first time. Currently, such modulators are the fastest tools for spatio-temporal light modulation; their high frame rates provide possibilities for developing optical encryption systems with a bandwidth of several gigabites per second. (optical encryption)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function

The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3 xm/xm mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Further, biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3 xm displayed a large compensatory alteration in switch I, which adopted a β-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I–interswitch–switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3 xm , strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) in Gpr89 phenocopied Rabl3 xm .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Ultrafast two-photon fluorescence imaging of cerebral blood circulation in the mouse brain in vivo

Characterizing blood flow dynamics in vivo is critical to understanding the function of the vascular network under physiological and pathological conditions. Existing methods for hemodynamic imaging have insufficient spatial and temporal resolution to monitor blood flow at the cellular level in large blood vessels. By using an ultrafast line-scanning module based on free-space angular chirped enhanced delay, we achieved two-photon fluorescence imaging of cortical blood flow at 1,000 two-dimensional (2D) frames and 1,000,000 one-dimensional line scans per second in the awake mouse. This orders-of-magnitude increase in temporal resolution allowed us to measure cerebral blood flow at up to 49 mm/s and observe pulsatile blood flow at harmonics of heart rate. Directly visualizing red blood cell (RBC) flow through vessels down to >800 µm in depth, we characterized cortical layer–dependent flow velocity distributions of capillaries, obtained radial velocity profiles and kilohertz 2D velocity mapping of multifile blood flow, and performed RBC flux measurements from penetrating blood vessels.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

CRISPR-based engineering of phages for in situ bacterial base editing

Investigation of microbial gene function is essential to the elucidation of ecological roles and complex genetic interactions that take place in microbial communities. While microbiome studies have increased in prevalence, the lack of viable in situ editing strategies impedes experimental progress, rendering genetic knowledge and manipulation of microbial communities largely inaccessible. Here, we demonstrate the utility of phage-delivered CRISPR-Cas payloads to perform targeted genetic manipulation within a community context, deploying a fabricated ecosystem (EcoFAB) as an analog for the soil microbiome. First, we detail the engineering of two classical phages for community editing using recombination to replace nonessential genes through Cas9-based selection. We show efficient engineering of T7, then demonstrate the expression of antibiotic resistance and fluorescent genes from an engineered λ prophage within an Escherichia coli host. Next, we modify λ to express an APOBEC-1-based cytosine base editor (CBE), which we leverage to perform C-to-T point mutations guided by a modified Cas9 containing only a single active nucleolytic domain (nCas9). We strategically introduce these base substitutions to create premature stop codons in-frame, inactivating both chromosomal ( lacZ ) and plasmid-encoded genes (mCherry and ampicillin resistance) without perturbation of the surrounding genomic regions. Furthermore, using a multigenera synthetic soil community, we employ phage-assisted base editing to induce host-specific phenotypic alterations in a community context both in vitro and within the EcoFAB, observing editing efficiencies from 10 to 28% across the bacterial population. The concurrent use of a synthetic microbial community, soil matrix, and EcoFAB device provides a controlled and reproducible model to more closely approximate in situ editing of the soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Video-rate Raman-based metabolic imaging by Airy light-sheet illumination and photon-sparse detection

Despite its massive potential, Raman imaging represents just a modest fraction of all research and clinical microscopy to date. This is due to the ultralow Raman scattering cross-sections of most biomolecules that impose low-light or photon-sparse conditions. Bioimaging under such conditions is suboptimal, as it either results in ultralow frame rates or requires increased levels of irradiance. Here, we overcome this tradeoff by introducing Raman imaging that operates at both video rates and 1,000-fold lower irradiance than state-of-the-art methods. To accomplish this, we deployed a judicially designed Airy light-sheet microscope to efficiently image large specimen regions. Further, we implemented subphoton per pixel image acquisition and reconstruction to confront issues arising from photon sparsity at just millisecond integrations. We demonstrate the versatility of our approach by imaging a variety of samples, including the three-dimensional (3D) metabolic activity of single microbial cells and the underlying cell-to-cell variability. To image such small-scale targets, we again harnessed photon sparsity to increase magnification without a field-of-view penalty, thus, overcoming another key limitation in modern light-sheet microscopy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Drying of tundra landscapes will limit subsidence-induced acceleration of permafrost thaw

We used a model for permafrost hydrology informed by detailed measurements of soil ice content to better understand the potential risk of abrupt permafrost thaw triggered by melting ground ice, a key open question associated with permafrost response to a warming Arctic. Our spatially resolved simulations of a well-characterized site in polygonal tundra near Utqiaġvik, Alaska, agree well with multiple types of observations in the current climate. Projections indicate 63 cm of bulk subsidence from 2006 to 2100 in the strong-warming Representative Concentration Pathway 8.5 climate. Permafrost thaw as measured by the increase in active layer thickness (ALT)—the thickness of the soil layer that thaws each summer—is accelerated by subsidence, but the effect is relatively small. The ALT increases from the current-day value of approximately 50 cm to approximately 180 cm by 2100 when subsidence is included compared to about 160 cm when it is neglected. In these simulations, previously identified positive feedbacks between subsidence and thaw are self-limiting on decadal time frames because landscape runoff and increasing evapotranspiration result in drier tundra with weaker surface/atmosphere coupling. These results for a tundra site that is representative of large swathes of the Alaska North Slope suggest that subsidence is unlikely to lead to abrupt thaw over large areas. However, subsidence does have significant effects on the hydrology of polygonal tundra. Specifically, subsidence increases landscape runoff, which helps maintain streamflow in the face of increased evapotranspiration but also causes drier tundra conditions that could have deleterious effects on sensitive Arctic wetland ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Scientific machine learning for modeling and simulating complex fluids

The formulation of rheological constitutive equations—models that relate internal stresses and deformations in complex fluids—is a critical step in the engineering of systems involving soft materials. While data-driven models provide accessible alternatives to expensive first-principles models and less accurate empirical models in many engineering disciplines, the development of similar models for complex fluids has lagged. The diversity of techniques for characterizing non-Newtonian fluid dynamics creates a challenge for classical machine learning approaches, which require uniformly structured training data. Consequently, early machine-learning based constitutive equations have not been portable between different deformation protocols or mechanical observables. Here, we present a data-driven framework that resolves such issues, allowing rheologists to construct learnable models that incorporate essential physical information, while remaining agnostic to details regarding particular experimental protocols or flow kinematics. These scientific machine learning models incorporate a universal approximator within a materially objective tensorial constitutive framework. By construction, these models respect physical constraints, such as frame-invariance and tensor symmetry, required by continuum mechanics. We demonstrate that this framework facilitates the rapid discovery of accurate constitutive equations from limited data and that the learned models may be used to describe more kinematically complex flows. This inherent flexibility admits the application of these “digital fluid twins” to a range of material systems and engineering problems. We illustrate this flexibility by deploying a trained model within a multidimensional computational fluid dynamics simulation—a task that is not achievable using any previously developed data-driven rheological equation of state.

Science & Technology - Other Topics↗

DOE OSTI2025

Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for translation of bicistronic mRNAs in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed a preference for weak Kozak-like sequences for ORF 1 and an underrepresentation of potential initiation codons before the ORF 2 start codon, which are suitable conditions for leaky ribosome scanning to allow ORF 2 translation. We used mutational analysis in A. protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames (uORFs) found across eukaryotic genomes and for transgene expression in synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗

DOE OSTI2026

Connecting collisional and photofragmentation resonances in the ungerade symmetry states of H 2

A recently developed energy-dependent frame transformation theory that incorporates both ionisation and dissociation channels of the H 2 molecule, is extended to treat the ungerade states that occur both in dissociative recombination and as the final state in ground state photoabsorption. The theoretical treatment includes the rotational degrees of freedom and is benchmarked against a two-dimensional model that can be solved with high accuracy and also compared with photoabsorption experiments. Analysis of the resulting spectra demonstrates how the same resonances appear in very different observables, often with quite different line shapes.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Two-Phase Turbulent Kinetic Energy Budget Computation in Co-Current Taylor Bubble Flow

Simulation of two-phase flows is relevant for reactor design and safety at normal operation or during accident scenarios. Often, the two-phase flow is in a regime in which slugs are formed or where the flow stratifies. Modeling such situations using standard single-phase Reynolds-averaged Navier-Stokes (RANS) turbulence models fails due to an overestimation of the eddy viscosity at the resolved two-phase interface. To solve this, an ad hoc turbulence damping term has been proposed in the literature that reduces the turbulence production locally at a two-phase interface, analogously to turbulence wall functions. However, this approach must be tailored to the specific setting and does not consider physical contributions such as surface tension or flow topology. Therefore, the problem of two-phase interfacial turbulence must be studied more in-depth. In this work, we consider co-current turbulent Taylor bubble flow using high-fidelity numerical simulation. The Basilisk code is used to simulate a Taylor bubble rising in a vertical pipe. By simulating the bubble in a moving frame of reference, we may study the turbulent kinetic energy (TKE) budgets ahead of the bubble, in its wake, and across the interface. The implementation of the TKE budget computation and the underlying averaging techniques are validated for the single-phase region ahead of the Taylor bubble using reference direct numerical simulation data. The analysis of the TKE budgets in the setting of Taylor bubble flow allows for the study of how turbulence behaves due to the presence of a two-phase interface and, in turn, supports the improvement of two-phase RANS models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Measurement of crack length in width tapered beam experiments

The width tapered beam method for measuring fracture toughness has been contemplated for use in measuring the adhesion of photovoltaic materials, is promoted by it being a viable method for use directly on modules rather than to engineered test specimens. However, precise determination of crack length is often difficult as failure often involves tendril formation, cavitation voids, and other plastic deformation at the crack front in addition to obfuscation by opaque materials. Because fracture energy varies as the square of crack length, imprecise crack tip length results in large measurement uncertainties. In this work, we develop a method to estimate the crack tip length using the relationship between the applied force and the displacement of the load frame. The crack tip is determined for every data point and can be defined from a calibration curve related to the amount of energy put into the beam, or from a theoretically idealized estimation. Once a calibration curve is set up and the equations programmed, the fracture energy as a function of position on the newly formed crack interface can be accurately estimated. The test additionally provides much easier analysis and insight into the joint failure through more precise knowledge of fracture toughness at each de-bonded area.

42 ENGINEERING↗

DOE OSTI2024

Explicit simulation of the Brownian rotation of arbitrary shaped aerosol particles using quaternions

The shape of an aerosol particle strongly influences its mass and momentum transfer cross-sections, charging properties, and other physical properties. Here, we present an explicit time-stepping procedure to simulate the rotational Brownian motion of arbitrary shaped aerosol particles by solving Euler’s equation of rotation. A Langevin formulation of the rotation equations is used, wherein Brownian motion due to thermal collisions between a particle and background gas molecules is represented using a stochastic fluctuating torque and fluid resistance is included as a drag torque. To avoid singularities associated with describing the orientation of a shape with Euler angles, we employ a quaternion formulation that leads to first-order stochastic differential equations to describe the evolution of the angular position and angular velocity of a rigid body. We perform all the rotational dynamics calculations in the body-fixed frame of reference attached to the rotating shape whose basis vectors are the normalized eigenvectors of the inertia tensor of the particle. Numerical solutions to rotation under torque-free conditions, damped rotation without Brownian motion, and stochastic rotation for arbitrary shapes are presented and discussed. The presented method enables time-resolved simulation of Brownian rotation for direct comparison with experimentally measured trajectories or statistical measures. The second order accuracy of the used time-stepping procedure places a severe restriction on the timestep that can be used for obtaining accurate results. Animations of presented simulations are included for visualizing rotational motion at various gas pressures. To aid implementation, MATLAB ® codes are also provided. Extension to include translation Brownian motion is straightforward.

Roy, Mrittika↗

DOE OSTI2021

Design and Analysis of an Advanced Three-Point Bend Test Approach for Miniature Irradiated Disk Specimens

Candidate tungsten armor materials in a magnetic confinement fusion device must be able to withstand thermal variation that leads to internal stresses caused by the impinging heat load. In addition, the thermomechanical properties of these materials are degraded by irradiation-induced defect accumulation. Fission reactor–based irradiation data are used to predict the fusion neutron damage and property change. This study examines the motivation and design of a custom-designed three-point bend test for neutron-irradiated disk specimens that are 3 mm in diameter to be able to define the flexural strength of advanced tungsten materials, alloys, and composites—and to the extent that embrittlement occurs after neutron irradiation. The theory provided shows a calculation for the flexural deflection and shear deflection due to the small-geometry constraints. A finite element deformation analysis is performed to evaluate the mechanical stress field of disk bend specimens. The stress values above 80% of the maximum stress are concentrated in 2.4 mm of the 3.0-mm length of the centerline across the tungsten disk diameter. A bend test fixture has been designed and fabricated to enable testing of these specimens with precisely engineered tolerance and minimal machine compliance. This fixture will be able to be placed inside a universal testing frame at elevated temperatures for the mechanical property evaluation of future neutron-irradiated disk specimens.

36 MATERIALS SCIENCE↗