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All sources NASA NTRS DOE OSTI

DOE OSTI2024

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗

DOE OSTI2025

Local order, disorder, and everything in between: using 91 Zr solid-state NMR spectroscopy to probe zirconium-based metal–organic frameworks

Characterization of metal centers in metal–organic frameworks (MOFs) is critical for rational design and further understanding of structure–property relationships. The short-range structure about Zr atoms is challenging to properly elucidate in many Zr MOFs, particularly when local disorder is present. Static 91 Zr solid-state NMR spectra of the seven zirconium MOFs UiO-66, UiO-66-NH 2 , UiO-67, MOF-801, MOF-808, DUT-68 and DUT-69 have been acquired at high magnetic fields of 35.2 T and 19.6 T, yielding valuable information on the local structure, site symmetry and order about Zr. 91 Zr NMR is very sensitive to differences in MOF short-range structure caused by guest molecules, linker substitution and post-synthetic treatment. Complementary density functional theory (DFT) calculations assist in the interpretation and assignment of 91 Zr solid-state NMR spectra, lend insight into structural origins of 91 Zr NMR parameters and enable determination of local Zr coordination environments. This approach can be extended to many other materials containing zirconium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Thermal and structural analysis of a new WEST reciprocating probe head with Titanium-Zirconium-Molybdenum armour material

The Tore Supra tokamak was transformed into an X-point divertor fusion device in the frame of the WEST (W-for tungsten-Environment in Steady-state Tokamak) project, launched in support of the ITER tungsten divertor strategy. WEST began operation in 2017. A new reciprocating probe head, equipped with a Titanium-Zirconium-Molybdenum (TZM) heat shield, was recently built and operated on WEST during the C9 Campaign in early 2024. TZM was chosen as armour material for its very good mechanical properties between 700 °C and 1400 °C. This material was already extensively used for probe heads and other plasma facing components on the Alcator C-Mod tokamak. Here, this paper presents the design of the new WEST probe head. It is equipped with tungsten filaments that can be heated to emit electrons and provide a direct measurement of the plasma potential in the scrape-off layer, and it is also equipped with a pair of Langmuir probes. The probe plunges vertically into the plasma, reaches its maximum dive depth, then returns to its protected resting position in about 0.25 s. Thermal loads are calculated using as input the thermal properties of TZM and radial profiles of the heat flux measured in the past by other reciprocating probes, and scaled upwards to the expected heat loads in the WEST scrape-off layer. An analytical estimation of Electromagnetic (EM) loads will also be presented, as well as a thermal and structural analysis of the probe for 15 cycles at maximum plunge depth. The probe is observed by an infrared camera. Comparisons between the heat flux deduced by the Langmuir probe and the infrared radiance of the probe housing during plasma exposure are finally presented.

Diagnostic↗

DOE OSTI2026

The Interplay of Pauli Repulsion, Electrostatics, and Field Inhomogeneity for Blueshifting and Redshifting Vibrational Probe Molecules

Many molecules' vibrational frequencies are sensitive to intermolecular electric fields, enabling them to probe the field in complex molecular environments. However, it is often unclear whether the probe is responding to the local electric field or other types of intermolecular interactions, inhibiting interpretation of the frequency and effectiveness as probes. This is especially true for molecules whose vibrational frequencies blueshift instead of the more typical redshift in hydrogen bonding configurations. In this work, we computationally investigate the causes of redshifting versus blueshifting over a range of vibrational reporters. First, we apply adiabatic energy decomposition analysis to a paradigmatic set of probes, finding that redshifting only occurs when electrostatic interactions are strong enough to overcome the dominant and large blueshifting contribution of Pauli repulsion. Furthermore, we demonstrate that field inhomogeneity can further shift the frequency of many probes substantially to either reinforce or counteract the shift expected from a homogeneous field. We find that redshifting is reinforced by electric field inhomogeneity, otherwise field inhomogeneity further weakens the electrostatic contribution relative to Pauli repulsion, leading to blueshifting. Further calculations indicate that the probe's response to field inhomogeneity can be understood by considering the mass of the atoms involved in the stretching mode and sign of the electric field. In explaining the interplay of different intermolecular interactions and field inhomogeneity for many probes, our results should enable the use and interpretation of spectroscopic probes and their connection to electric fields in more complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

New model for the ion collection by cylindrical probes over a wide range of collisionality

Langmuir probes remain one of the most important diagnostic tools for plasma processing applications. Modern probe analysis usually relies on the electron current part of the Langmuir probe characteristic using the Druyvesteyn method. However, for electronegative plasmas or for discharges containing dust the analysis of the ion current attracted by the probe can be desirable to determine the ion density. But, even at low pressures of a few Pa, the ion current is affected by collisions due to the large cross section for charge exchange. Available theories for collisional or collision-enhanced ion currents onto probes are complex and not well validated. Thus, in this contribution, we compare available collisional probe theories for the ion current to results of particle-in-cell (PIC) simulations. To this end, the probe surrounded by a semi-infinite plasma is simulated using a modified version of the open-source code EDIPIC. A dataset of currents for different neutral gas pressures is obtained and compared to the different theories from the literature. Based on these results, we propose a simpler and more intuitive model for the ion current collected by the probe, based on the model of Gatti and Kortshagen (Phys. Rev. E 78, 046402, 2008), developed for the charging of dust particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Multi-modal dynamic radiography using short-pulse laser-generated probe beams

Radiography is an important tool for the interrogation of dynamic experiments in the fields of dynamic properties of materials, and in condensed matter, high explosive, and high-energy-density physics. Multi-modal radiography advances the hypothesis that combining the information delivered by multiple radiographic modalities can lead to more constrained (improved) “reconstruction” of the scene than can be obtained from a single probe. We identify four modalities: multi-probe, time sequence, multi-view, and multi-messenger. Multi-probe radiography is a promising candidate for a next-generation dynamic radiographic facility. High-energy X-rays are the most frequently used probe for dynamic radiography, although recent developments show the utility of proton (pRad), electron (eRad), and neutron probe beams. Because each probing species interacts with material in the radiographic scene through quantitatively different mechanisms, each returns independent information about the scene, which can add extra constraints to the reconstruction process. How to conduct detailed, quantitative “co-analysis” of multiple data streams remains an area of active research. Multi-beam, short-pulse, laser-generated probes offer sufficient dose, an appropriate spectrum, and appropriate spatio-temporal resolution to produce high-quality dynamic radiographs. This paper reports on technology development to advance the state of the art of multi-modal/multi-probe radiography and the pursuit of both deterministic and inferential (AI/ML assisted) co-analysis methodologies to produce more constrained reconstructions from multi-modal data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Test of Harmonic Coil Accuracy Using a Multi Vertex Probe

Magnets are integral components of particle accelerators, with different multipoles used to perform various beam conditioning functions, like steering and focusing. Testing accelerator magnets to ensure compliance with specification is a crucial step of fabrication. One of the most popular techniques for verifying magnetic field strength and integrity is the harmonic coil probe. Harmonic coil probes are comprised of passive loops that are rotated around the aperture of a magnet and are used to measure magnetic flux. Oftentimes the measurements of the harmonic coil probe are affected by transverse vibrations along the axis of rotation and torsional vibrations of the position closure sensor, both causing spurious harmonics. To make matters challenging, it is difficult to distinguish between the real harmonics of the magnet and the spurious harmonics during analysis. This research explores the use of a novel configuration of harmonic coil probe, Multi-Vertex Probe (MVP), to address multiple factors that affect the accuracy and repeatability of harmonic coil probe measurement. Most of the results are based on simulation data, in which artificial torsional distortions are introduced and removed with the proposed processing method. In addition to implementing torsional vibration removal in simulation, laboratory analysis regarding the source of vibrations was performed using a pre-fabricated MVP. More specifically, various mechanical conditions were used to explore the standard deviation of main harmonic’s flux amplitude. The conditions included: coupling type (rigid or soft), rotation speed, probe starting position within magnetic field, and cabling location inside the magnetic field. Along with this, the MVP’s measured noise floor in and outside a magnetic field was quantified.

Lofquist, Claire [Northern Illinois U.]↗

DOE OSTI2026

Fingerprinting fractons with pump-probe spectroscopy

We demonstrate how pump-probe techniques enable specific spectroscopic diagnostics of fracton phases of matter by studying lineon-planon braiding in the paradigmatic X-cube model. Our discussion builds on previous works probing anyonic exchange statistics in conventional spin liquids, but the extension to fracton phases reveals qualitatively different phenomena due to the restricted mobility of fractionalized excitations. A key feature is that nearby planons can form an emergent bound state by accessing different planes via alternative pairing configurations. We show that this bound state qualitatively modifies the long-time linear and nonlinear responses, leading to an asymptotic linear-in-𝑡 behavior for the pump-probe signal 𝜒 𝑍𝑍𝑋 . By contrast, swapping the pump and probe polarizations produces a nonlinear response 𝜒 𝑋𝑋𝑍 that is asymptotically 𝑡 independent. This asymmetry reflects the fact that the two species of fractionalized excitations live in different spatial dimensions. Thus the pump-probe signals studied here are sensitive to (i) nontrivial braiding statistics in three dimensions, (ii) the existence of bound states among fractionalized excitations, and (iii) the one-dimensional mobility of lineons. Furthermore, our results therefore provide spectroscopic signatures that distinguish fracton phases from conventional topologically ordered spin liquids.

braiding↗

DOE OSTI2025

Driven probe particle dynamics in a bubble and pattern forming system

We numerically examine the dynamics of a probe particle driven at a constant force through an assembly of particles with competing long-range repulsion and short-range attraction that forms a bubble or stripe state. In the bubble regime, we identify several distinct types of motion, including an elastic or pinned regime where the probe particle remains inside a bubble and drags all other bubbles with it. There is also a plastic bubble phase where the bubble in which the probe particle is trapped is able to move past the adjacent bubbles. At larger drives, there is a breakthrough regime where the probe particle jumps from bubble to bubble and, in some cases, can induce correlated rotations or plastic rearrangements of the particles within the bubbles. At the highest drives, the probe particle moves sufficiently rapidly that the background particles undergo only small distortions. The distinctive dynamic flow states and the transitions between them are accompanied by signatures in the effective drag on the driven particle, jumps in the velocity–force curves, and changes in the time-dependent velocity fluctuations. We map the dynamic phase diagram for this system for varied interaction lengths, bubble sizes, and densities.

36 MATERIALS SCIENCE↗

DOE OSTI2026

A tetrahedral probe constellation approach for measuring canonical momentum in self-organized laboratory plasma

To examine momentum redistribution processes and study generalized helicities during plasma relaxation in Madison Symmetric Torus, MST, reversed field pinch plasma, a new probe is being tested to measure the full 3D plasma ion flow and magnetic field vectors at four spatial locations arranged in a tetrahedral shape reminiscent of a satellite measurement constellation. These measurements permit calculation of ∇ x $\vec{u}$ and canonical momentum, where $\vec{u}$ is the plasma ion flow vector. The probe consists of four probe heads arranged in a tetrahedral pattern, with an overall probe diameter of ∼31.75 mm. The probe head diameter is ∼1.0 cm, which is of the order of the ion Larmor radius. Each head has four molybdenum electrodes, also arranged in tetrahedral geometry, which are biased relative to a common return electrode, using four power supplies (one for each head), to measure the local ion flow. Additionally, each head has three orthogonal magnetic pickup coils within it to measure equilibrium and fluctuating magnetic fields.

Physics - Plasma physics↗

DOE OSTI2025

Magneto-optical spectroscopy based on pump-probe strobe light

Here, we demonstrate a pump-probe strobe light spectroscopy for sensitive detection of magneto-optical dynamics in the context of hybrid magnonics. The technique uses a combinatorial microwave-optical pump-probe scheme, leveraging both the high-energy resolution of microwaves and high-efficiency detection using optical photons. In contrast with conventional stroboscopy using continuous-wave light, we apply microwave and optical pulses with varying pulse widths, and demonstrate magneto-optical detection of magnetization dynamics in Y 3 Fe 5 O 12 films. The detected magneto-optical signals depend strongly on the characteristics of both the microwave and the optical pulses, as well as their relative time delays. We show that good magneto-optical sensitivity and coherent stroboscopic character are maintained, even at a microwave pump pulse of 1.5 ns and an optical probe pulse of 80 ps, under a 7 MHz clock rate, corresponding to a pump-probe footprint of approximately 1% in one detection cycle. Our results show that time-dependent strobe light measurement of magnetization dynamics can be achieved in the gigahertz frequency range under a pump-probe detection scheme.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Impacts of Focused Ion Beam Processing on the Fabrication of Nanoscale Functionalized Probes

Herein, we examine the impact of Ga + ion kinetic energy and the target material type on the extent of ion implantation and structural damage in atomic force microscopy probes made of Al 2 O 3 and ZnO manufactured by focused ion beam (FIB) using scanning transmission electron microscopy and energy-dispersive X-ray mapping. Penetration of Ga into the Al 2 O 3 lattice induced structural distortions and amorphization. For ZnO probes, Ga is uniformly dispersed across the surface, resulting in the formation of distinct clusters. Atom probe tomography further validates the Ga distributions in Al 2 O 3 and ZnO nanoprobes. Complementary Monte Carlo simulations with the transport of ions in the matter program indicated that the introduction of Ga + prompts the generation of cation and anion vacancies, an occurrence more pronounced in Al 2 O 3 compared to ZnO. In conclusion, this study not only enriches the knowledge of ion-matter interactions, but also serves as a practical guide for the fabrication of nanoscale functionalized AFM probes.

Al2O3↗

DOE OSTI2025

Probing the Solvation Shells of Lithium Ions in Glyme-Based Electrolytes

Glymes have been extensively studied as solvents for Li-battery electrolytes, most recently in equimolar mixtures with lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), due to their ability to form stable solvates. However, directly quantifying free and coordinated glyme molecules in the liquid state has been challenging due to several experimental limitations. Here, in this work, new vibrational probes are demonstrated for studying the solvation structures of diglyme and triglyme in LiTFSI electrolytes. These IR probes make use of an amine group to report the solvation state of glymes at salt-to-solvent molar ratios ranging from 1:5 to 1:10. Characterization of the thermodynamic properties of the solvent exchange occurring in the first solvation shell of lithium ions (Li + ) showed an equilibrium constant for these probes close to unity at room temperature. This result demonstrates that the probes exhibit a similar solvation behavior to their glyme analogue. Concentration dependence studies also revealed a lack of significant amounts of contact ion pairs at the studied concentrations. Moreover, the first solvation shell of Li + appears to be formed by two partially chelating glyme molecules, establishing that even triglyme with multiple chelation sites does not fully coordinate the cation. Complementary molecular dynamics (MD) simulations agree with the experimental results and suggest that at these concentrations, TFSI – predominantly forms solvent-separated ion pairs. However, the simulations do not properly capture the partial solvation structure of the glyme molecules in the solvation shell of Li + as derived from the experiments.

electrolytes↗

DOE OSTI2025

Estimating Soil Thermal Inertia Profiles From the Passive Equilibration of a Temperature Probe

Knowledge of the distribution of soil thermal properties is important for understanding subsurface hydrological and biogeochemical processes. This study describes and evaluates quick thermal profiling (QTP), a new measurement technique aimed at providing rapid, depth-resolved measurements of soil thermal inertia at numerous locations across the landscape. A cylindrical probe with temperature sensors at multiple depths is quickly inserted into the ground, and soil thermal inertia is estimated from how quickly the probe temperature equilibrates with the soil. To this end, a finite volume heat transfer model is used to generate temperature equilibration time series across combinations of controlling factors, and a gridded search inversion approach is applied to infer soil thermal inertia. Field tests in the Arctic indicate that QTP measurements have a minimum uncertainty of 0.14 J m −2 K −1 s −1/2 and covary with dual-probe heat pulse thermal analyzer measurements (concordance correlation coefficient = 0.56) with a root-mean-square error of 0.40 J m −2 K −1 s −1/2 . Besides demonstrating the value of QTP for estimating thermal inertia, this study identifies various sources of measurement uncertainty, particularly probe-soil contact resistance and frictional heating. Further, analysis of soil samples indicates that thermal inertia can be used to estimate thermal conductivity and dry bulk density in the studied area, although such inferences are highly site-specific. Overall, the QTP method holds promise to generate thermal inertia data products and to complement other characterization approaches for advancing understanding of soil properties across far more locations than is currently possible.

Lamb, J. R. [Lawrence Berkeley National Laboratory↗

DOE OSTI2024

Probing plexciton emission from 2D materials on gold nanotrenches

Probing strongly coupled quasiparticle excitations at their intrinsic length scales offers unique insights into their properties and facilitates the design of devices with novel functionalities. In this work, we investigate the formation and emission characteristics of plexcitons, arising from the interaction between surface plasmons in narrow gold nanotrenches and excitons in monolayer WSe 2 . We study this strong plasmon–exciton coupling in both the far-field and the near-field. Specifically, we observe a Rabi splitting in the far-field reflection spectra of about 80 meV under ambient conditions, consistent with our theoretical modeling. Using a custom-designed near-field probe, we find that plexciton emission originates predominantly from the lower-frequency branch, which we can directly probe and map its local field distribution. We precisely determine the plexciton's spatial extension, similar to the trench width, with nanometric precision by collecting spectra at controlled probe locations. Our work opens exciting prospects for nanoscale mapping and engineering of plexcitons in complex nanostructures with potential applications in nanophotonic devices, optoelectronics, and quantum electrodynamics in nanoscale cavities.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Learning neural representations for X-ray ptychography reconstruction with unknown probes

X-ray ptychography provides exceptional nanoscale resolution and is widely applied in materials science, biology, and nanotechnology. However, its full potential is constrained by the critical challenge of accurately reconstructing images when the illuminating probe is unknown. Conventional iterative methods and deep learning approaches are often suboptimal, particularly under the low-signal conditions inherent to low-dose and high-speed experiments. These limitations compromise reconstruction fidelity and restrict the broader adoption of the technique. In this work, we introduce the Ptychographic Implicit Neural Representation (PtyINR), a self-supervised framework that simultaneously addresses the object- and probe-recovery problem. By parameterizing both as continuous neural representations, PtyINR performs end-to-end reconstruction directly from raw diffraction patterns without requiring any pre-characterization of the probe. Extensive evaluations demonstrate that PtyINR achieves superior reconstruction quality on both simulated and experimental data, with remarkable robustness under challenging low-signal conditions. Furthermore, PtyINR offers a generalizable, physics-informed framework for addressing probe-dependent inverse problems, making it applicable to a wide range of computational microscopy problems.

36 MATERIALS SCIENCE↗

DOE OSTI2024

X-ray nano-holotomography reconstruction with simultaneous probe retrieval

In conventional tomographic reconstruction, the pre-processing step includes flat-field correction, where each sample projection on the detector is divided by a reference image taken without the sample. When using coherent X-rays as a probe, this approach overlooks the phase component of the illumination field (probe), leading to artifacts in phase-retrieved projection images, which are then propagated to the reconstructed 3D sample representation. The problem intensifies in nano-holotomography with focusing optics, which, due to various imperfections creates high-frequency components in the probe function. Here, we present a new iterative reconstruction scheme for holotomography, simultaneously retrieving the complex-valued probe function. Implemented on GPUs, this algorithm results in 3D reconstruction resolving twice thinner layers in a 3D ALD standard sample measured using nano-holotomography.

Nikitin, Viktor↗

DOE OSTI2026

Constraints on Dynamical Dark Energy from Multiple Probes in the Full Dark Energy Survey

We present results on dark energy evolution, assuming a time-dependent equation of state $w(a)=w_0+w_a(1-a)$, from growth and geometric probes using the full six-year Dark Energy Survey dataset: type Ia supernovae, baryon acoustic oscillations, and weak gravitational lensing and galaxy clustering (3$\times$2pt). The combination yields $w_0=-0.84^{+0.10}_{-0.10}$ and $w_a=-0.44^{+0.60}_{-0.55}$, the tightest constraints ever obtained from a single survey, with $2.2σ$ deviation from a cosmological constant. Adding the DESI DR2 BAO data yields $w_0=-0.84^{+0.06}_{-0.07}$ and $w_a=-0.53^{+0.33}_{-0.28}$, representing the most stringent low-redshift-only test of dynamical dark energy to date, with a $2.3σ$ deviation. In this combination, adding 3$\times$2pt doubles the constraining power. Finally, when combined with primary CMB information, we obtain $w_0=-0.82^{+0.05}_{-0.05}$, $w_a=-0.63^{+0.21}_{-0.18}$, with a $3.0σ$ deviation. We find that including 3$\times$2pt in the previously studied SN + DESI BAO + CMB combination leaves the significance essentially unchanged ($3.2 σ$ to $3.0σ$) while improving the figure of merit by $\sim$10%. We systematically investigate the impact of leaving out each one of the probes and find that the significance of the deviation from a cosmological constant ranges from 2.3 to 3.2$σ$, with best-fit parameters consistently in the region $w_0 >-1$ and $w_a <0$. Excluding SN from the all data combination yields a $2.6σ$ departure from $Λ$CDM, providing a cross-check independent of supernova photometric calibration. These results support the weak preference for evolving dark energy reported by several recent cosmological analyses. By combining growth and geometric probes from a single survey, this work realizes the multi-probe dark energy program envisioned at the inception of DES.

Abbott, T. M.C. [Cerro-Tololo InterAmerican Obs.] ↗