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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Enhancing strontium clock atom interferometry using quantum optimal control

Strontium clock atom interferometry is a promising new technology, with multiple experiments under development around the world to explore its potential for dark matter and gravitational wave detection. In these detectors, large momentum transfer using sequences of many laser pulses is necessary, and thus high-fidelity pulses are important since small errors become magnified. Quantum optimal control (QOC) is a framework for developing control pulse waveforms that achieve high fidelity and are robust against experimental imperfections. Resonant single-photon transitions using the narrow clock transition of strontium involve significantly different quantum dynamics than more established atom interferometry methods based on far-detuned two-photon Raman or Bragg transitions, which leads to new opportunities and challenges when applying QOC. Here, we study in simulation QOC pulses for strontium clock interferometry and demonstrate their advantage over basic square pulses (primitive pulses) and composite pulses in terms of robustness against multiple noise channels. In conclusion, this could improve the scale of large momentum transfer in Sr clock interferometers, paving the way to achieving these scientific goals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Relation between sampling, sensitivity and precision in strain mapping using the Geometric Phase Analysis method in Scanning Transmission Electron Microscopy

The sensitivity and the precision of the Geometric Phase Analysis (GPA) method for strain characterization is a topic widely discussed in the literature and is usually difficult to quantify. Indeed, the GPA precision is intricately linked to the resolution of the strain maps defined when masking the periodic reflections in Fourier space. In this study an additional parameter, sampling, is proposed to be analyzed regarding the precision of GPA by developing the concept of a phase noise in the GPA equations. Both experimentally and theoretically, the following article demonstrates how the precision, and the sensitivity of the GPA method is improved when using a larger pixel spacing to record an electron micrograph in Scanning Transmission Electron Microscopy (STEM). In conclusion, the counterintuitive concept of increasing the field of view to improve the GPA precision results in an extension of the application of strain characterization methods in STEM towards low deformation levels.

47 OTHER INSTRUMENTATION↗
DOE OSTI2014

Design and Integrate Improved Systems for Nuclear Facility Ventilation and Exhaust Operations

Objective: The objective of this R&D project would complete the development of three new systems and integrate them into a single experimental effort. However, each of the three systems has stand-alone applicability across the DOE complex. At US DOE nuclear facilities, indoor air is filtered and ventilated for human occupancy, and exhaust air to the outdoor environment must be regulated and monitored. At least three technical standards address these functions, and the Los Alamos National Laboratory would complete an experimental facility to answer at least three questions: (1) Can the drag coefficient of a new Los Alamos air mixer be reduced for better operation in nuclear facility exhaust stacks? (2) Is it possible to verify the accuracy of a new dilution method for HEPA filter test facilities? (3) Is there a performance-based air flow metric (volumetric flow or mass flow) for operating HEPA filters? In summary, the three new systems are: a mixer, a diluter and a performance-based metric, respectively. The results of this project would be applicable to at least four technical standards: ANSI N13.1 Sampling and Monitoring Releases of Airborne Radioactive Substances from the Stacks and Ducts of Nuclear Facilities; ASTM F1471 Standard Test Method for Air Cleaning Performance of a High-Efficiency Particulate Air Filter System, ASME N511: In-Service Testing of Nuclear Air Treatment, Heating, Ventilating, and Air-Conditioning Systems, and ASME AG-1: Code On Nuclear Air And Gas Treatment. All of the three proposed new systems must be combined into a single experimental device (i.e. to develop a new function of the Los Alamos aerosol wind tunnel). Technical Approach: The Radiation Protection RP-SVS group at Los Alamos has an aerosol wind tunnel that was originally (2006) designed to evaluate small air samplers (cf. US EPA 40 CFR 53.42). In 2009, the tunnel was modified for exhaust stack verifications per the ANSI N13.1 standard. In 2010, modifications were started on the wind tunnel for testing HEPA filters (cf. ASTM F1471 and ASME N511). This project involves three systems that were developed for testing the 24*24*11 (inch) HEPA filters (i.e. the already mentioned mixer, diluter and metric). Prototypes of the mixer and the diluter have been built and individually tested on a preliminary basis. However, the third system (the HEPA metric method) has not been tested, since that requires complete operability of the aerosol wind tunnel device. (The experimental wind tunnel has test aerosol injection, control and measurement capabilities, and can be heated for temperature dependent measurements.) Benefits: US DOE facilities that use HEPA filters and/or require exhaust stacks from their nuclear facility buildings will benefit from access to the new hardware (mixer and diluter) and performance-based metric (for HEPA filter air flow).

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2013

Evaluation of experimentally measured and model-calculated pH for rock-brine-CO2 systems under geologic CO2 sequestration conditions

pH is an essential parameter for understanding the geochemical reactions that occur in rock-brine-CO2 systems when CO2 is injected into deep geologic formations for long-term storage. Due to a lack of reliable experimental methods, most laboratory studies conducted under geological CO2 sequestration (GCS) conditions have relied on thermodynamic modeling to estimate pH. The accuracy of these model predictions is typically uncertain. In our previous work, we have developed a method for pH determination by in-situ spectrophotometry. In the present work, we expanded the applicable pH range for this method and measured the pH of several rock-brine-CO2 systems at GCS conditions for five rock samples collected from ongoing GCS demonstration projects. Experimental measurements were compared with pH values calculated using several geochemical modeling approaches. The effect of different thermodynamic databases on the accuracy of model prediction was evaluated. Results indicate that the accuracy of model calculations is rock-dependent. For rocks comprised of carbonate and sandstone, model results generally agreed well with experimentally measured pH; however, for basalt, significant differences were observed. These discrepancies may be due to the models’ failure to fully account for certain reaction occurring between the basalt minerals the CO2-saturated brine solutions.

pH, carbon sequestration↗
DOE OSTI2012

Final Report on Reliability and Lifetime Prediction

This document highlights the important results obtained from the subtask of the Goodyear CRADA devoted to better understanding reliability of tires and to developing better lifetime prediction methods. The overall objective was to establish the chemical and physical basis for the degradation of tires using standard as well as unique models and experimental techniques. Of particular interest was the potential application of our unique modulus profiling apparatus for assessing tire properties and for following tire degradation. During the course of this complex investigation, extensive relevant information was generated, including experimental results, data analyses and development of models and instruments. Detailed descriptions of the findings are included in this report.

Gillen, Kenneth T.↗
DOE OSTI2021

Burning velocities of R-32/O 2 /N 2 mixtures: Experimental measurements and development of a validated detailed chemical kinetic model

This work entails characterizing the flammability of the refrigerant R-32 (CH 2 F 2 ) by both experimental measurements and modeling. Burning velocities S u were measured using a constant-volume spherical-flame method for R-32/O2/N 2 mixtures with O 2 /N 2 ratios ranging from 21% (synthetic air) to 40%, pressures of (1 to 3) bar, and equivalence ratios $\phi$ of (0.8 to 1.3). Based on a critical assessment of available data, and extended by our own calculations, a detailed chemical kinetic model was developed and key reactions determined using reaction path and sensitivity analyses. Initiation and combustion were identified as distinct kinetic regimes and burning velocities were found to be controlled by two primary reactions: unimolecular decomposition of CH 2 F 2 → CHF + HF and the subsequent reaction, CHF + O 2 → CHFO + O, the latter reaction initiating the radical chain propagating and branching by producing O atoms. Sensitive rate constants in the kinetic model were critically adjusted within their uncertainties and current knowledge bounds to best fit the experimental burning velocities. We found that rate constants in the model could be adjusted to match a given experimental S u for specific conditions (O 2 loading, P, T, $\phi$). This, however, then fixes predicted burning velocities for other all conditions within (3 to 4)% if physically realistic rate parameters are maintained. Thus, the entire set of experimental data is fit, not just to particular conditions. Relative random uncertainties in the experimental Su measurements were (4 to 6)%, but assumptions made for thermal radiation lost by the burned gas in the spherical-flame experiments add an additional systematic uncertainty. Systematic differences between the limiting cases of adiabatic (no thermal radiation lost) and optically-thin (all thermal radiation lost) varied significantly with conditions and ranged from (4 to 30)% at high to low velocities, respectively, translating into uncertainties of (2 to 15)% considering the average of two limiting cases. Comparison of experimental and kinetically modeled Su values suggests that the burned gas tends towards the optically-thin limit at the lowest pressures and fuel loadings and toward the adiabatic limit at the highest pressures and loadings. We tested and found support for this conclusion with a detailed analysis as a function of all the conditions (T, P, % O 2 , $\phi$). This behavior appears to transition from optically-thin to adiabatic as the density of the initial fuel increases, which results in increased CO 2 in the burned gas and thus increased absorption of the thermal radiation (consistent with the Beer-Lambert Law). The validated detailed model based on evaluated kinetics is shown to accurately predict burning velocities for R-32 O 2 /N 2 mixtures over a wide range of conditions and provides a reliable basis for extrapolation to other conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

SU-E-T-50: Automatic Validation of Megavoltage Beams Modeled for Clinical Use in Radiation Therapy

Purpose: To automatically validate megavoltage beams modeled in XiO™ 4.50 (Elekta, Stockholm, Sweden) and Varian Eclipse™ Treatment Planning Systems (TPS) (Varian Associates, Palo Alto, CA, USA), reducing validation time before beam-on for clinical use. Methods: A software application that can automatically read and analyze DICOM RT Dose and W2CAD files was developed using MatLab integrated development environment.TPS calculated dose distributions, in DICOM RT Dose format, and dose values measured in different Varian Clinac beams, in W2CAD format, were compared. Experimental beam data used were those acquired for beam commissioning, collected on a water phantom with a 2D automatic beam scanning system.Two methods were chosen to evaluate dose distributions fitting: gamma analysis and point tests described in Appendix E of IAEA TECDOC-1583. Depth dose curves and beam profiles were evaluated for both open and wedged beams. Tolerance parameters chosen for gamma analysis are 3% and 3 mm dose and distance, respectively.Absolute dose was measured independently at points proposed in Appendix E of TECDOC-1583 to validate software results. Results: TPS calculated depth dose distributions agree with measured beam data under fixed precision values at all depths analyzed. Measured beam dose profiles match TPS calculated doses with high accuracy in both open and wedged beams. Depth and profile dose distributions fitting analysis show gamma values < 1. Relative errors at points proposed in Appendix E of TECDOC-1583 meet therein recommended tolerances.Independent absolute dose measurements at points proposed in Appendix E of TECDOC-1583 confirm software results. Conclusion: Automatic validation of megavoltage beams modeled for their use in the clinic was accomplished. The software tool developed proved efficient, giving users a convenient and reliable environment to decide whether to accept or not a beam model for clinical use. Validation time before beam-on for clinical use was reduced to a few hours.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Transfer learning nonlinear plasma dynamic transitions in low dimensional embeddings via deep neural networks

Deep learning algorithms provide a new paradigm to study high-dimensional dynamical behaviors, such as those in fusion plasma systems. Development of novel, data-driven model reduction methods, coupled with detection of abnormal modes with plasma physics, opens a unique opportunity to identify plasma instabilities through automated construction of parsimonious models that can be tuned to balance accuracy and cost. Our fusion transfer learning (FTL) model demonstrates success in rapidly reconstructing nonlinear kink mode structures by learning from a limited amount of nonlinear simulation data. The knowledge transfer process leverages a pre-trained neural encoder–decoder network, initially trained on linear simulations, to effectively capture nonlinear dynamics. The low-dimensional embeddings extract the coherent structures of interest, while preserving the inherent dynamics of the complex system. Experimental results highlight FTL’s capacity to capture transitional behaviors and dynamical features in plasma dynamics—a task often challenging for conventional methods. The model developed in this study is generalizable and can be extended broadly through transfer learning to address various magnetohydrodynamics modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Motion as perturbation. II. Development of the method for dosimetric analysis of motion effects with fixed-gantry IMRT

Purpose: In this work, the feasibility of implementing a motion-perturbation approach to accurately estimate volumetric dose in the presence of organ motion—previously demonstrated for VMAT-–is studied for static gantry IMRT. The method's accuracy is improved for the voxels that have very low planned dose but acquire appreciable dose due to motion. The study describes the modified algorithm and its experimental validation and provides an example of a clinical application. Methods: A contoured region-of-interest is propagated according to the predefined motion kernel throughout time-resolved 4D phantom dose grids. This timed series of 3D dose grids is produced by the measurement-guided dose reconstruction algorithm, based on an irradiation of a staticARCCHECK (AC) helical dosimeter array (Sun Nuclear Corp., Melbourne, FL). Each moving voxel collects dose over the dynamic simulation. The difference in dose-to-moving voxel vs dose-to-static voxel in-phantom forms the basis of a motion perturbation correction that is applied to the corresponding voxel in the patient dataset. A new method to synchronize the accelerator and dosimeter clocks, applicable to fixed-gantry IMRT, was developed. Refinements to the algorithm account for the excursion of low dose voxels into high dose regions, causing appreciable dose increase due to motion (LDVE correction). For experimental validation, four plans using TG-119 structure sets and objectives were produced using segmented IMRT direct machine parameters optimization in Pinnacle treatment planning system (v. 9.6, Philips Radiation Oncology Systems, Fitchburg, WI). All beams were delivered with the gantry angle of 0°. Each beam was delivered three times: (1) to the static AC centered on the room lasers; (2) to a static phantom containing a MAPCHECK2 (MC2) planar diode array dosimeter (Sun Nuclear); and (3) to the moving MC2 phantom. The motion trajectory was an ellipse in the IEC XY plane, with 3 and 1.5 cm axes. The period was 5 s, with the resulting average motion speed of 1.45 cm/s. The motion-perturbed high resolution (2 mm voxel) volumetric dose grids on the MC2 phantom were generated for each beam. From each grid, a coronal dose plane at the detector level was extracted and compared to the corresponding moving MC2 measurement, using gamma analysis with both global (G) and local (L) dose-error normalization. Results: Using the TG-119 criteria of (3%G/3 mm), per beam average gamma analysis passing rates exceeded 95% in all cases. No individual beam had a passing rate below 91%. LDVE correction eliminated systematic disagreement patterns at the beams’ aperture edges. In a representative example, application of LDVE correction improved (2%L/2 mm) gamma analysis passing rate for an IMRT beam from 74% to 98%. Conclusions: The effect of motion on the moving region-of-interest IMRT dose can be estimated with a standard, static phantom QA measurement, provided the motion characteristics are independently known from 4D CT or otherwise. The motion-perturbed absolute dose estimates were validated by the direct planar diode array measurements, and were found to reliably agree with them in a homogeneous phantom.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Connection between asymptotic normalization coefficients and resonance widths of mirror states

Resonance widths are important characteristics of unstable nuclear states playing a crucial role in nuclear structure, nuclear reactions, and nuclear astrophysics. However, often it is difficult or impossible to determine the resonance widths from experiments, especially when required nuclei are unstable or the resonance widths are too small. In this paper, I suggest an indirect method of determination of resonance widths using transfer reactions populating bound states. From this reaction, one can extract the amplitudes of the tails of the bound-state wave functions. These amplitudes are called the asymptotic normalization coefficients (ANCs). The ANC method became one of the benchmarks of the Cyclotron Institute. Once the ANC is experimentally determined, one can find the resonance width of the mirror nuclei using the technique developed in this paper. Mirror nuclei are the ones in which the total number of nucleons is the same but the number of the protons of one of the nuclei is equal to the number of the neutrons of another nucleus. In this paper, 5 different examples of the application of the developed method are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Characterization of Gramicidin A in Triblock and Diblock Polymersomes and Hybrid Vesicles via Continuous Wave Electron Paramagnetic Resonance Spectroscopy

Studying membrane proteins in a native environment is crucial to understanding their structural and/or functional studies. Often, widely accepted mimetic systems have limitations that prevent the study of some membrane proteins. Micelles, bicelles, and liposomes are common biomimetic systems but have problems with membrane compatibility, limited lipid composition, and heterogeneity. To overcome these limitations, polymersomes and hybrid vesicles have become popular alternatives. Polymersomes form from amphiphilic triblock or diblock copolymers and are considered more robust than liposomes. Hybrid vesicles are a combination of lipids and block copolymers that form vesicles composed of a mixture of the two. These hybrid vesicles are appealing because they have the native lipid environment of bilayers but also the stability and customizability of polymersomes. Gramicidin A was incorporated into these polymersomes and characterized using continuous wave electron paramagnetic resonance (CW-EPR) and transmission electron microscopy (TEM). EPR spectroscopy is a powerful biophysical technique used to study the structure and dynamic properties of membrane proteins in their native environment. Spectroscopic studies of gramicidin A have been limited to liposomes; in this study, the membrane peptide is studied in both polymersomes and hybrid vesicles using CW-EPR spectroscopy. Lineshape analysis of spin-labeled gramicidin A revealed linewidth broadening, suggesting that the thicker polymersome membranes restrict the motion of the spin label more when compared to liposome membranes. Statement of Significance: Understanding membrane proteins’ structures and functions is critical in the study of many diseases. In order to study them in a native environment, membrane mimetics must be developed that can be suitable for obtaining superior biophysical data quality to characterize structural dynamics while maintaining their native functions and structures. Many currently widely accepted methods have limitations, such as a loss of native structure and function, heterogeneous vesicle formation, restricted lipid types for the vesicle formation for many proteins, and experimental artifacts, which leaves rooms for the development of new biomembrane mimetics. The triblock and diblock polymersomes and hybrid versicles utilized in this study may overcome these limitations and provide the stability and customizability of polymersomes, keeping the biocompatibility and functionality of liposomes for EPR studies of membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of soot formation from aviation fuels in laminar counterflow flames

Combustion emissions from aviation contribute to the formation of condensation trail (contrail) that can lead to the formation of anthropogenic cirrus clouds. Ice particles that form contrails are observed to have a linear correlation with soot particle number density. Synthetic aviation fuels (SAFs) offer a promising route to mitigate the production of soot particles while also increasing energy security. Although studies have focused on combustion and spray behavior, the detailed investigation of soot formation processes for different jet fuels and their impact on models for computational fluid dynamics (CFD) applications is not well understood. Moreover, experimental measurements of soot for canonical flames using Synthetic aviation fuels (SAF) for model validation remain scarce. To address this, we use employed the Lawrence Livermore National Laboratory (LLNL) detailed soot model based on the discrete sectional method. Additionally, we develop two reduced chemical mechanisms for Jet-A and Alcohol-to-Jet (C1) that are suitable for turbulent flame simulations and couple them with the Hybrid Method of Moments (HMOM). The detailed and reduced model frameworks are validated against experimental measurements of soot volume fraction (ƒ ν ) from a counterflow burner experiment previously reported in the literature. Given the good agreement between modeling results and experimental measurements for the (1) spatial distribution of ƒ ν and (2) the non-linear variation of peak ƒ ν with strain rate, we further investigate the modeled sub-processes (nucleation, condensation, surface growth, and oxidation) using the LLNL model to analyze the assumptions in the reduced model framework. Furthermore, the results indicate a significant contribution from resonant radicals to the surface growth of soot particles, which are not accounted for in the current implementation of HMOM and could help reconcile soot predictions by the reduced model with observations.

Counterflow↗
DOE OSTI2022

Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous ‘replacer’ gene rescues lethality caused by inactivation of a ‘target’ gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5’-phosphate (the active form of Vitamin B 6 ), which we validate experimentally via multicopy suppression. Here, we perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗
DOE OSTI2016

Epitaxial exchange-bias systems: From fundamentals to future spin-orbitronics

Exchange bias has been investigated for more than half a century and several insightful reviews, published around the year 2000, have already summarized many key experimental and theoretical aspects related to this phenomenon. Since then, due to developments in thin-film fabrication and sophisticated characterization methods, exchange bias continues to show substantial advances; in particular, recent studies on epitaxial systems, which is the focus of this review, allow many long-standing mysteries of exchange bias to be unambiguously resolved. The advantage of epitaxial samples lies in the well-defined interface structures, larger coherence lengths, and competing magnetic anisotropies, which are often negligible in polycrystalline samples. Beginning with a discussion of the microscopic spin properties at the ferromagnetic/antiferromagnetic interface, we correlate the details of spin lattices with phenomenological anisotropies, and finally connect the two by introducing realistic measurement approaches and models. We conclude by providing a brief perspective on the future of exchange bias and related studies in the context of the rapidly evolving interest in antiferromagnetic spintronics.

36 MATERIALS SCIENCE↗