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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 OSTI2024

Analysis of static Wilson line correlators from lattice QCD at finite temperature with T -matrix approach

The thermodynamic T-matrix approach is used to study Wilson line correlators (WLCs) for a static quark-antiquark pair in the quark-gluon plasma (QGP). Selfconsistent results that incorporate constraints from the QGP equation of state can approximately reproduce WLCs computed in 2+1-flavor lattice-QCD (lQCD), provided the input potential exhibits less screening than in previous studies. Utilizing the updated potential to calculate pertinent heavylight T-matrices we evaluate thermal relaxation rates of heavy quarks in the QGP. We find a more pronounced temperature dependence for low-momentum quarks than in our previous results (with larger screening), which turns into a weaker temperature dependence of the (temperature-scaled) spatial diffusion coefficient, in fair agreement with the most recent lQCD data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

General balance functions of identified charged hadron pairs of (π, Κ, ρ) in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 2.76 TeV

First measurements of balance functions (BFs) of all combinations of identified charged hadron (π, Κ, ρ) pairs in Pb–Pb collisions at $\sqrt{s_{NN}}$ = 2.76 TeV recorded by the ALICE detector are presented. The BF measurements are carried out as two-dimensional differential correlators versus the relative rapidity (Δy) and azimuthal angle (Δφ) of hadron pairs, and studied as a function of collision centrality. The Δφ dependence of BFs is expected to be sensitive to the light quark diffusivity in the quark–gluon plasma. While the BF azimuthal widths of all pairs substantially decrease from peripheral to central collisions, the longitudinal widths exhibit mixed behaviors: BFs of ππ and cross-species pairs narrow significantly in more central collisions, whereas those of KK and pp are found to be independent of collision centrality. This dichotomy is qualitatively consistent with the presence of strong radial flow effects and the existence of two stages of quark production in relativistic heavy-ion collisions. Finally, the first measurements of the collision centrality evolution of BF integrals are presented, with the observation that charge balancing fractions are nearly independent of collision centrality in Pb–Pb collisions. Overall, the results presented provide new and challenging constraints for theoretical models of hadron production and transport in relativistic heavy-ion collisions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Plasma physics in strong-field regimes: Theories and simulations

In strong electromagnetic fields, unique plasma phenomena and applications emerge whose description requires recently developed theories and simulations [Y. Shi, Ph.D. thesis, Princeton University (2018)]. In the classical regime, to quantify effects of strong magnetic fields on three-wave interactions, a convenient formula is derived by solving the fluid model to the second order in general geometry. As an application, magnetic resonances are exploited to mediate laser pulse compression, whereby higher intensity pulses can be produced in wider frequency ranges, as confirmed by particle-in-cell simulations. In even stronger fields, relativistic-quantum effects become important, and a plasma model based on scalar quantum electrodynamics (QED) is developed which unveils observable corrections to Faraday rotation and cyclotron absorption in strongly magnetized plasmas. Beyond the perturbative regime, lattice QED is extended as a numerical tool for plasma physics, using which the transition from wakefield acceleration to electron-positron pair production is captured when laser intensity exceeds the Schwinger threshold.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Dynamic load balancing with enhanced shared-memory parallelism for particle-in-cell codes

Furthering our understanding of many of today’s interesting problems in plasma physics – including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects – requires large-scale kinetic simulations using particle-in-cell (PIC) codes. However, these simulations are extremely demanding, requiring that contemporary PIC codes be designed to efficiently use a new fleet of exascale computing architectures. To this end, the key issue of parallel load balance across computational nodes must be addressed. We discuss the implementation of dynamic load balancing by dividing the simulation space into many small, self-contained regions or ‘‘tiles,’’ along with shared-memory (e.g., OpenMP) parallelism both over many tiles and within single tiles. The load balancing algorithm can be used with three different topologies, including two space-filling curves. Here, we tested this implementation in the code Osiris and show low overhead and improved scalability with OpenMP thread number on simulations with both uniform load and severe load imbalance. Compared to other load-balancing techniques, our algorithm gives order-of-magnitude improvement in parallel scalability for simulations with severe load imbalance issues.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

System and method for alfvenic reconnecting plasmoid plasma acceleration

According to various embodiments, a system for using magnetic reconnection to accelerate plasma is disclosed. The system includes a pair of electrodes including two concentric rings separated by an electrode gap and held at different electrostatic potential by applying a voltage to generate an inter-electrode electric field. The system further includes a plurality of magnetic coils configured to produce magnetic field lines that connect the pair of electrodes. The system additionally includes a gas injector configured to inject gas into the electrode gap, the injected gas being partially ionized by the inter-electrode electric field to generate a poloidal current that flows along open magnetic field lines across the electrode gap. A total Lorentz force causes oppositely directed magnetic field lines to be expanded around a region of the gas injector to further create an azimuthal current in the form of an axially elongated current sheet that is unstable such that the axially elongated current sheet reconnects and breaks into plasmoids.

Ebrahimi, Fatima Arezu↗

DOE OSTI2023

Effects of surface vacancy-adatom pair formation on PFC tungsten surface morphological response

Abstract We report a simulation study of the effect of He-irradiation-induced surface vacancy-adatom pair formation on the surface morphological evolution of plasma-facing component (PFC) tungsten and examine a number of factors that impact such evolution. Our analysis is based on self-consistent dynamical simulations according to an atomistically-informed, continuum-scale surface evolution model that has been developed following a hierarchical multiscale modeling strategy and can access the spatiotemporal scales of relevance to fuzz formation. The model accounts for the flux of surface adatoms generated as a result of the surface vacancy-adatom pair formation effect upon He implantation, which contributes to the anisotropic growth of surface nanostructural features due to the different rates of adatom diffusion along and across step edges of islands on the tungsten surface. We have carried out atomic-scale computations of optimal diffusion pathways along and across island step edges on the W(110) surface and calculated Ehrlich–Schwoebel (ES) barriers in adatom diffusion along and across such step edges. This aspect of surface adatom diffusion contributes to anisotropic surface atomic fluxes, terrace and step diffusive currents, and has been incorporated into our PFC surface evolution model, which predicts the formation of preferentially aligned nanoridge stripe patterns on the PFC surface. We establish that these anisotropic diffusive currents accelerate nanotendril growth on the PFC surface and the onset of surface nanostructure pattern formation. We also explore systematically the dependence of the PFC surface morphological response on the surface temperature and He ion incident flux, characterize in detail the resulting surface topographies and growth kinetics, and compare the predicted surface morphologies with experimental observations. Our simulation predictions for the emerging surface nanostructure patterns under certain plasma exposure conditions are consistent with experimental findings in the literature.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Bottomonium suppression in an open quantum system using the quantum trajectories method

We solve the Lindblad equation describing the Brownian motion of a Coulombic heavy quark-antiquark pair in a strongly coupled quark-gluon plasma using the highly efficient Monte Carlo wave-function method. The Lindblad equation has been derived in the framework of pNRQCD and fully accounts for the quantum and non-Abelian nature of the system. The hydrodynamics of the plasma is realistically implemented through a 3+1D dissipative hydrodynamics code. We compute the bottomonium nuclear modification factor and compare with the most recent LHC data. The computation does not rely on any free parameter, as it depends on two transport coefficients that have been evaluated independently in lattice QCD. Our final results, which include late-time feed down of excited states, agree well with the available data from LHC 5.02 TeV PbPb collisions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Observation of Forward Neutron Multiplicity Dependence of Dimuon Acoplanarity in Ultraperipheral Pb-Pb Collisions at $\sqrt{s_{NN}}$ = 5.02 TeV

The first measurement of the dependence of $γγ → μ^+μ^–$ production on the multiplicity of neutrons emitted very close to the beam direction in ultraperipheral heavy ion collisions is reported. Data for lead-lead interactions at $\sqrt{s_{NN}}$ = 5.02 TeV, with an integrated luminosity of approximately 1.5 nb –1 , are collected using the CMS detector at the LHC. The azimuthal correlations between the two muons in the invariant mass region 8 < $m_{μμ}$ < 60 GeV are extracted for events including 0, 1, or at least 2 neutrons detected in the forward pseudorapidity range |η| > 8.3. The back-to-back correlation structure from leading-order photon-photon scattering is found to be significantly broader for events with a larger number of emitted neutrons from each nucleus, corresponding to interactions with a smaller impact parameter. This observation provides a data-driven demonstration that the average transverse momentum of photons emitted from relativistic heavy ions has an impact parameter dependence. These results provide new constraints on models of photon-induced interactions in ultraperipheral collisions. They also provide a baseline to search for possible final-state effects on lepton pairs caused by traversing a quark-gluon plasma produced in hadronic heavy ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Quantile-specific heritability of plasma fibrinogen concentrations

Fibrinogen is a moderately heritable blood protein showing different genetic effects by sex, race, smoking status, pollution exposure, and disease status. These interactions may be explained in part by “quantile-dependent expressivity”, where the effect size of a genetic variant depends upon whether the phenotype (e.g. plasma fibrinogen concentration) is high or low relative to its distribution. Determine whether fibrinogen heritability (h 2 ) is quantile-specific, and whether quantile-specific h 2 could account for fibrinogen gene-environment interactions. Plasma fibrinogen concentrations from 5689 offspring-parent pairs and 1932 sibships from the Framingham Heart Study were analyzed. Quantile-specific heritability from offspring-parent (β OP , h 2 = 2β OP /(1+r spouse )) and full-sib regression slopes (β FS , h 2 = {(1+8r spouse β FS ) 0.05 –1}/(2r spouse )) were robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples. Quantile-specific h 2 (±SE) increased with increasing percentiles of the offspring’s age- and sex-adjusted fibrinogen distribution when estimated from β OP (P trend = 5.5x10 -6 ): 0.30±0.05 at the 10 th , 0.37±0.04 at the 25 th , 0.48±0.05 at the 50 th , 0.61±0.06 at the 75 th , and 0.65±0.08 at the 90 th percentile, and when estimated from β FS (P trend = 0.008): 0.28±0.04 at the 10 th , 0.31±0.04 at the 25 th , 0.36±0.03 at the 50 th , 0.41±0.05 at the 75 th , and 0.50±0.06 at the 90 th percentile. The larger genetic effect at higher average fibrinogen concentrations may contribute to fibrinogen’s greater heritability in women than men and in Blacks than Whites, and greater increase from smoking and air pollution for the FGB -455G>A A-allele. It may also explain greater fibrinogen differences between: 1) FGB -455G>A genotypes during acute phase reactions than usual conditions, 2) GTSM1 and IL-6 -572C>G genotypes in smokers than nonsmokers, 3) FGB -148C>T genotypes in untreated than treated diabetics, and LPL PvuII genotypes in macroalbuminuric than normoalbuminuric patients. Fibrinogen heritability is quantile specific, which may explain or contribute to its gene-environment interactions. The analyses do not disprove the traditional gene-environment interpretations of these examples, rather quantile-dependent expressivity provides an alternative explanation that warrants consideration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Evaluation of ITER divertor shunts as a synthetic diagnostic for detachment control

Reliable diagnostics that measure the detached state of the ITER divertor plasma will be necessary to control heat flux to the divertor targets during steady state, burning plasma operation. This paper conducts an initial exploration into the feasibility of the divertor shunt diagnostic as a lightweight, robust, and real-time detachment sensor. This diagnostic is a set of shunt lead pairs that measure the voltage drop along the divertor cassette body, from which the plasma scrape-off layer (SOL) current is calculated. Using SOLPS-ITER simulations for control-relevant ITER plasma scenarios, the thermoelectric current magnitude along the SOL is shown to decrease significantly with the onset of partial detachment at the outer divertor target. Electromagnetic modelling of a simplified divertor cassette is used to develop a control-oriented inductance-resistance circuit model, from which SOL currents can be calculated from shunt pair voltage measurements. The sensitivity and frequency-response of the resulting system indicates that the diagnostic will accurately measure SOL thermoelectric currents during ITER operation. These currents will be a good measure of the detached state of the divertor plasma, making the divertor shunt diagnostic a potentially extremely valuable and physically robust sensor for real-time detachment control.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Additive Molar Volumes in Amorphous Ca/Sr Carbonate Solid Solutions

The development of predictive models of minor element incorporation in crystalline carbonate end products requires an understanding of the fundamental controls on metastable intermediate phase composition. In this study, we used small-angle X-ray scattering (SAXS), X-ray pair distribution function (PDF), thermogravimetric analysis (TGA), inductively coupled plasma mass spectrometry (ICP-MS), and transmission electron microscopy (TEM) to determine the composition-dependent density of an amorphous calcium–strontium carbonate (ACSC) solid solution. The amorphous calcium carbonate (ACC) and strontium carbonate (ASC) measured densities were ρ ACC = 2.19 ± 0.04 g/cm 3 and ρ ASC = 2.97 ± 0.05 g/cm 3 . Throughout our work, the experiments showed a dependence of the water content of the amorphous solid solution on the Sr mole fraction. An equation that relates the molar volume to the average cation radius, the carbonate ion radius, and the water volume was parameterized for hydrated crystalline carbonates and predicted well the molar volume of the ACSC solid solution. This finding indicates that, as for hydrated crystalline carbonates, the molar volumes of amorphous carbonates are additive and that water is a structural component of ACSC. Ab initio molecular dynamics (AIMD) simulations of the ACSC solid solutions showed strong linear correlations between calculated molar volumes and Sr and H 2 O contents, thus supporting the experimental results. In conclusion, our findings highlight the need to consider the full CaCO 3 –MeCO 3 –H 2 O ternary when quantifying metal cation incorporation in ACC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Quantile-dependent expressivity of plasma adiponectin concentrations may explain its sex-specific heritability, gene-environment interactions, and genotype-specific response to postprandial lipemia

“Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g. adiponectin) is high or low relative to its distribution. We have previously shown that the heritability ( h 2 ) of adiposity, lipoproteins, postprandial lipemia, pulmonary function, and coffee and alcohol consumption are quantile-specific. Whether adiponectin heritability is quantile specific remains to be determined. Plasma adiponectin concentrations from 4,182 offspring-parent pairs and 1,662 sibships from the Framingham Heart Study were analyzed. Quantile-specific heritability from offspring-parent (β OP , h 2 = 2 β OP /(1 + r spouse )) and full-sib regression slopes ( β FS , h 2 = {(1 + 8r spouse β FS ) 0.05 -1}/(2r spouse )) were robustly estimated by quantile regression with nonparametric significance assigned from 1,000 bootstrap samples. Quantile-specific h 2 (± SE) increased with increasing percentiles of the offspring’s age- and sex-adjusted adiponectin distribution when estimated from β OP ( P trend = 2.2 × 10 -6 ): 0.30 ± 0.03 at the 10th, 0.33 ± 0.04 at the 25th, 0.43 ± 0.04 at the 50th, 0.55 ± 0.05 at the 75th, and 0.57 ± 0.08 at the 90th percentile, and when estimated from β FS (P trend = 7.6 × 10 -7 ): 0.42 ± 0.03 at the 10th, 0.44 ± 0.04 at the 25th, 0.56 ± 0.05 at the 50th, 0.73 ± 0.08 at the 75th, and 0.79 ± 0.11 at the 90th percentile. Consistent with quantile-dependent expressivity, adiponectin’s: (1) heritability was greater in women in accordance with their higher adiponection concentrations; (2) relationships to ADIPOQ polymorphisms were modified by adiposity in accordance with its adiponectin-lowering effect; (3) response to rosiglitazone was predicted by the 45T> G ADIPOQ polymorphism; (4) difference by ADIPOQ haplotypes increased linearly with increasing postprandial adiponectin concentrations. Adiponectin heritability is quantile dependent, which may explain sex-specific heritability, gene-environment and gene-drug interactions, and postprandial response by haplotypes.

Postprandial↗

DOE OSTI2021

Magnetically collimated relativistic charge-neutral electron–positron beams from high-power lasers

In this work, we report the observation of charge-neutral MeV electron-positron beams from magnetically collimated laser-driven pair-production experiments. Relativistic pairs of electrons were generated from laser-solid interactions in an external 13-T mirror field. The pairs were subsequently confined, deflected or collimated depending on the particle energy and field strength, and measured by a magnetic particle spectrometer. Equal quantities of positrons and electrons were measured in the collimated beams with an energy around 13 MeV along the magnetic mirror axis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Active Aerodynamic Load Control for Wind Turbines

The goal of this project was to develop and demonstrate an advanced dielectric barrier discharge (DBD) plasma actuator technology. We set out to demonstrate the efficacy and impact of the new actuator technology as a key component of an active load control system for wind turbines. A DBD plasma actuator consists of a thin layer of dielectric material separating a pair of offset electrodes. One of those electrodes is embedded between the dielectric layer and a non-conductive substrate, while the other is exposed to air. When driven by an appropriate high voltage waveform, the device ionizes the air near the surface of the dielectric and adjacent to the exposed electrode. Collisions between the ions in the plasma and neutral air molecules result in a wall-jet – a region of induced air velocity that can be used to modify the flow around a lifting body. Use of the device near the trailing edge of a wind turbine blade, designed in such a way as to amplify the effects of the flow-modifying device, can result in large changes to the global forces experienced by the blade. Because of the fast response time of the device, it can allow the turbine to react in real time to changes in the wind associated with turbulence, wind shear, gusts, and the like, when paired with appropriate sensors and control algorithms. The goal of this project was to increase the capacity of the device to induce velocity on its surface at the levels required by large, utility-scale wind turbines. The first technical goal was to increase the induced velocity from the current industry-best of about 4 m/s to 10 m/s by modifying the electrical waveform used to drive the device and by introducing a semi-conductive surface coating to control electrostatic charge build-up on the surface. The second goal was to use the device to modify the lift on a representative airfoil in a wind tunnel, demonstrating a reduction in lift coefficient of 0.2 or better. The third goal was to produce an actuator-induced velocity of 20 m/s. Alongside our partners at the University of Texas at Dallas, we also applied modern, advanced design methods to optimize the impact of the technology on the design of wind turbines. We also had planned to install a segmented, active load control system on a test turbine to demonstrate the ability to reduce unsteady aerodynamic forces on the turbine associated with changes in the wind. The highest induced velocity achieved during this research was 11 m/s. However, practical design constraints limited the change in lift coefficient to about 0.12 for a representative airfoil in the wind tunnel at a Reynolds number of 400,000. The primary conclusion is that the plasma actuator control authority remains insufficient for practical purposes when extrapolated to Reynolds numbers over 1 million. The potential impact of the active lift control concept was evaluated through detailed simulations for three wind turbine sizes: a 3.4MW onshore turbine, a 10MW offshore turbine, and a 15MW offshore turbine. A feedback control system was designed for each turbine within two scenarios: one where the active lift control is used as a retrofit capability on the baseline design, and the other where the designers were permitted to “upscale” the turbines in order increase annual energy production. The levelized cost of energy was then evaluated for the range of turbine sizes and design configuration. It was found that the LCOE reduction associated with active lift control fell in the range of 0.7% to 7.2%, with the highest reduction associated with upscaling the 3.4MW turbine.

17 WIND ENERGY↗

DOE OSTI2020

Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence

Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A Discrete Hankel Transform Approach to Nuclear Data Processing for Fusion Applications

This study introduces advancements to the numerical solutions employed in the processing of nuclear data for fusion applications. It leverages the convolution theorem and Fourier transform techniques to enhance computational efficiency and broaden applicability. Building upon a previously reported discrete Hankel transform approach for Doppler broadening, this work refines the solution of convolution integrals central to these applications. The methodology provides a general and unified framework for evaluating any convolution operation, regardless of whether the underlying problem involves temperature effects in nuclear reactions. The applicability to the nuclear data processing for fusion is demonstrated by deriving the convolution integrals for some of the fusion-related quantities. As before, the convolution operation utilizes a Gaussian-based kernel; however, the discrete Hankel transform of order $𝛼$ = $\frac{1}{2}$ is now applied to the forward Fourier transform of the nonkernel argument, rather than the inverse Fourier transform. This modification eliminates the need for the integration of the nonkernel, cross section–based function, which is a step that posed challenges for certain pointwise cross-section representations. It also removes the requirement for cross-section linearization. Optimized for graphics processing unit architectures, the approach significantly improves computational performance. These advancements are currently under evaluation as the foundation for the next-generation thermonuclear data file processing codes being developed at Lawrence Livermore National Laboratory.

Nuclear science and engineering↗

DOE OSTI2026

A Multiplexed Quantitative Analysis of Germline Single Amino Acid Variants by Targeted Proteomics in Nondepleted Human Plasma

Single amino acid variants (SAAVs) in protein sequences are often a direct result of single-nucleotide polymorphisms (SNPs). Certain germline SAAVs have shown biological relevance in different disease conditions but lack precise quantification in circulation, which could hinder functional investigations and progress in biomarker development. Here, we have developed a multiplexed liquid chromatography-selected reaction monitoring (LC-SRM) assay that monitors 5 wild-type and variant peptide pairs (Complement Factor B: CFB-R32Q/R32W, Clusterin: CLU-N317H, Fetuin B: FETUB-K360R, and Kininogen: KNG1-L212P) in nondepleted human plasma. The assay was optimized for imprecision, linearity, stability, and calibration assessments with CVs of under 20%. The wild-type and variant peptide pairs were characterized in a set of healthy individual plasma samples. These target identifications were also validated by SNP genotyping with more than 99% accuracy. For all protein targets, we observed significantly lower concentrations of WT species in the presence variant peptides. In CFB, the concentration of R32Q was significantly lower than its counterpart R32W variant and WT species. Furthermore, our results distinguished phenotypes of homozygosity and heterozygosity of the SAAV presence through direct concentration level characterization. These findings provide some insights into how SAAVs affect quantitative assessments of target peptides. The assay demonstrates a platform for proteogenomic analyses with potential applications in both research and clinical settings.

genetics↗