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DOE OSTI2021

Laser blow-off with photodiode detection system at the helically symmetric experiment

Abstract A laser blow-off (LBO) system has been installed in the HSX stellarator to investigate impurity transport. A Nd:YAG laser is used to ablate a target area on a glass slide that has been coated with a thin film of aluminum and rapidly deposits a small, controlled quantity of aluminum atoms into HSX plasma. To study the radial propagation and confinement of the injected aluminum impurities, time-resolved emission measurements are made using a 20 channel AXUV photodiode detection system. The LBO system has achieved its design purpose, most notably the ability to make controlled impurity injection without significant perturbation to the background plasma. A detailed description of the setup as well as initial results of operation are presented.

Instruments & Instrumentation↗

DOE OSTI2023

DeepAstroUDA: semi-supervised universal domain adaptation for cross-survey galaxy morphology classification and anomaly detection

Abstract Artificial intelligence methods show great promise in increasing the quality and speed of work with large astronomical datasets, but the high complexity of these methods leads to the extraction of dataset-specific, non-robust features. Therefore, such methods do not generalize well across multiple datasets. We present a universal domain adaptation method, DeepAstroUDA , as an approach to overcome this challenge. This algorithm performs semi-supervised domain adaptation (DA) and can be applied to datasets with different data distributions and class overlaps. Non-overlapping classes can be present in any of the two datasets (the labeled source domain, or the unlabeled target domain), and the method can even be used in the presence of unknown classes. We apply our method to three examples of galaxy morphology classification tasks of different complexities (three-class and ten-class problems), with anomaly detection: (1) datasets created after different numbers of observing years from a single survey (Legacy Survey of Space and Time mock data of one and ten years of observations); (2) data from different surveys (Sloan Digital Sky Survey (SDSS) and DECaLS); and (3) data from observing fields with different depths within one survey (wide field and Stripe 82 deep field of SDSS). For the first time, we demonstrate the successful use of DA between very discrepant observational datasets. DeepAstroUDA is capable of bridging the gap between two astronomical surveys, increasing classification accuracy in both domains (up to 40 % on the unlabeled data), and making model performance consistent across datasets. Furthermore, our method also performs well as an anomaly detection algorithm and successfully clusters unknown class samples even in the unlabeled target dataset.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Multi-View Convolutional Neural Network for Data Spoofing Cyber-Attack Detection in Distribution Synchrophasors

Security of Distribution Synchrophasors Data (DSD) is of paramount importance as the data is used for critical smart grid applications including situational awareness, advanced protection, and dynamic control. Unfortunately, the DSD are attractive targets for malicious attackers aiming to damage grid. Data spoofing is a new class of deceiving attack, where the DSD of one Phasor Measurement Units (PMUs) is tampered by other PMUs thereby spoiling measurement based applications. In order to address this issue, a source authentication based data spoofing attack detection method is proposed using Multi-view Convolutional Neural Network (MCNN). First, common components embedded in raw frequency measurements from DSD are removed by Savitzky-Golay (SG) filter. Second, fast S transform (FST) is utilized to extract representative spatial fingerprints via time frequency analysis. Third, the spatial fingerprint is fed to MCNN, which combines dilated and standard convolutions for automatic feather extraction and source identification. Finally, according to the output of MCNN, spoofing attack detection is performed via threshold criterion. Extensive experiments with actual DSD from multiple locations in FNET/Grideye are conducted to verify the effectiveness of the proposed method.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Detection and Aggregation of Listeria Monocytogenes Using Polyclonal Antibody Gold-Coated Magnetic Nanoshells Surface-Enhanced Raman Spectroscopy Substrates

Magnetic nanoshells with tailored surface chemistry can enhance bacterial detection and separation technologies. This work demonstrated a simple technique to detect, capture, and aggregate bacteria with the aid of end-functionalized polyclonal antibody gold-coated magnetic nanoshells (pAb-Lis-AuMNs) as surface-enhanced Raman spectroscopy (SERS) probes. Listeria monocytogenes were used as the pathogenic bacteria and the pAb-LisAuMNs, 300 nm diameter, were used as probes allowing facile magnetic separation and aggregation. An optimized covalent bioconjugation procedure between the magnetic nanoshells and the polyclonal antibody was performed at pH six via a carbodiimide crosslinking reaction. Spectroscopic and morphological characterization techniques confirmed the fabrication of stable pAb-Lis-AuMNs. The resulting pAb-Lis-AuMNs acted as a SERS probe for L. monocytogenes based on the targeted capture via surface binding interactions and magnetically induced aggregation. Label-free SERS measurements were recorded for the minimum detectable amount of L. monocytogenes based on the SERS intensity at the 1388 cm -1 Raman shift. L. monocytogenes concentrations exhibited detection limits in the range of 10 4 –10 7 CFU ml -1 , before and after aggregation. By fitting these concentrations, the limit of detection of this method was ~10 3 CFU ml -1 . Using a low-intensity magnetic field of 35 G, pAb-LisAuMNs aggregated L. monocytogenes as demonstrated with microscopy techniques, including SEM and optical microscopy. Overall, this work presents a label-free SERS probe method comprised of a surface-modified polyclonal antibody sub-micron magnetic nanoshell structures with high sensitivity and magnetic induced separation that could lead to the fabrication of multiple single-step sensors.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2026

Photon temporal-mode readout for inference of neutron star merger remnant gravitational waves

Gravitational waves emitted after neutron star binary coalescences and the information they carry about dense matter are a high-priority target for next-generation detectors. Even though such detectors are expected to observe millions of signals, detectable postmerger emission will remain rare. Here, in this work, we explore postmerger detectability and inference through an alternative detector readout scheme for data dominated by quantum-noise, which is the case above 1 kHz; photon-counting. In such a readout, signals and noise become quantized into discrete distributions corresponding to the detection of single photons measured in a chosen basis of modes. Through simulated data, we demonstrate that photon counting can be efficient even for weak signals. We find ∼1 in 100 signals with a postmerger signal-to-noise ratio of 0.2 can result in a single photon and thus be detected. Furthermore, after 2 ×10 4 signals—equivalent to 10 −2 to 1.5 years of observation—photon counting results in a twofold improvement in the measurement of the radius of a 1.6⁢𝑀 ⊙ neutron star. Constraints can be further tightened if the detector classical noise is reduced. Photon counting offers a promising alternative to traditional homodyne readout techniques for extracting information from low signal-to-noise ratio postmerger signals.

gravitational wave detection↗

DOE OSTI2020

Search for elements 119 and 120

In this work, a search for production of the superheavy elements with atomic numbers 119 and 120 was performed in the 50 Ti + 249 Bk and 50 Ti + 249 Cf fusion-evaporation reactions, respectively, at the gas-filled recoil separator TASCA at GSI Darmstadt, Germany. Over four months of irradiation, the 249 Bk target partially decayed into 249 Cf, which allowed for a simultaneous search for both elements. Neither was detected at cross-section sensitivity levels of 65 and 200 fb for the 50 Ti + 249 Bk and 50 Ti + 249 Cf reactions, respectively, at a midtarget beam energy of E lab = 281.5 MeV. The nonobservation of elements 119 and 120 is discussed within the concept of fusion-evaporation reactions including various theoretical predictions on the fission-barrier heights of superheavy nuclei in the region of the island of stability.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2024

First Simultaneous Measurement of Differential Muon-Neutrino Charged-Current Cross Sections on Argon for Final States with and without Protons Using MicroBooNE Data

We report the first double-differential neutrino-argon cross section measurement made simultaneously for final states with and without protons for the inclusive muon neutrino charged-current interaction channel. The proton kinematics of this channel are further explored with a differential cross section measurement as a function of the leading proton’s kinetic energy that extends across the detection threshold. These measurements use data collected with the MicroBooNE detector from 6.4 × 10 20 protons on target from the Fermilab booster neutrino beam with a mean neutrino energy of ∼ 0.8 GeV . Extensive data-driven model validation utilizing the conditional constraint formalism is employed. This motivates enlarging the uncertainties with an empirical reweighting approach to minimize the possibility of extracting biased cross section results. The extracted nominal flux-averaged cross sections are compared to widely used event generator predictions revealing severe mismodeling of final states without protons for muon neutrino charged-current interactions, possibly from insufficient treatment of final state interactions. These measurements provide a wealth of new information useful for improving event generators which will enhance the sensitivity of precision measurements in neutrino experiments. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Dynamic STEM-EELS for single-atom and defect measurement during electron beam transformations

This study introduces the integration of dynamic computer vision–enabled imaging with electron energy loss spectroscopy (EELS) in scanning transmission electron microscopy (STEM). This approach involves real-time discovery and analysis of atomic structures as they form, allowing us to observe the evolution of material properties at the atomic level, capturing transient states traditional techniques often miss. Rapid object detection and action system enhances the efficiency and accuracy of STEM-EELS by autonomously identifying and targeting only areas of interest. This machine learning (ML)–based approach differs from classical ML in that it must be executed on the fly, not using static data. We apply this technology to V-doped MoS 2 , uncovering insights into defect formation and evolution under electron beam exposure. This approach opens uncharted avenues for exploring and characterizing materials in dynamic states, offering a pathway to increase our understanding of dynamic phenomena in materials under thermal, chemical, and beam stimuli.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

First Measurement of Differential Charged Current Quasielastic-like $\nu_\mu$–Argon Scattering Cross Sections In Kinematic Imbalance Variables With The MicroBooNE Detector

We report the first measurement of flux-integrated multi-differential cross sections for charged-current events with muon neutrinos scattering on argon with solely a muon and a single proton in the final state as a function of kinematic imbalance variables. The measurement was carried out using the Booster Neutrino Beam at Fermi National Accelerator Laboratory within the MicroBooNE Liquid Argon Time Projection Chamber detector with an exposure of 6.79 × 10 20 protons on target. Events were selected to enhance the contribution of charged-current mesonless interactions with one proton detected in the final state. The data discussed here are reported in terms of multidifferential cross sections in kinematic imbalance variables, which are generally sensitive to nuclear effects. The double-differential results in these variables can provide an excellent handle to disentagle specific nuclear aspects not easily isolated via single differential cross sections. Our results pave a path towards identifying regions of the phase-space where future interaction modeling development and Monte Carlo neutrino generator tuning efforts should concentrate. EVENT SELECTION Neutrino oscillation measurements aim to extract neutrino mixing angles, mass differences, the value of the chargeparity violating phase in the lepton sector, and to search for new physics beyond the Standard Model [1, 2]. For that to be achieved, an unprecedented understanding of neutrino-argon interactions is of utmost importance since a growing number of neutrino oscillation experiments employ Liquid Argon Time Projector Chamber (LArTPC) neutrino detectors [3–6]. The accuracy to which these experiments can extract neutrino oscillation parameters requires a good understanding of the neutrino energy. Experimentally, this energy is deduced from the measured kinetic energies of particles that are emitted following the neutrino interaction in the detector. The kinematic properties of such finalstate particles reflect complex dynamics due to nuclear and initial-state effects of the interaction [7]. However, certain categories of nuclear effects can be isolated by variables built specifically to characterize the degeneracy between such effects [8–10]. This note reports cross sections in kinematic variables sensitive to nuclear effects using events with one detected muon with momentum 0.1 < pµ < 1.2 GeV/c, and exactly one proton with 0.3 < pp < 1 GeV/c. This signal definition includes events with any number of protons below 300 MeV/c, neutrons at any momenta, and charged pions with momentum lower than 70 MeV/c. This choice is guided by the fact that their experimental signature of correlated muon-proton pairs is fairly straightforward to reconstruct [11–22]. Such events primarily originate from chargedcurrent (CC) neutrino-nucleon quasielastic (QE) scattering interactions where the neutrino removes a single intact nucleon from the nucleus without producing any additional particles. This definition can also include contributions from interactions that lead to the production of additional particles that are absent from the final state due to nuclear effects, such as pion absorption, or have momenta that are below the experimental detection threshold.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

First Measurement of Differential Charged Current Quasielastic-like $\nu_\mu$–Argon Scattering Cross Sections in Kinematic Imbalance Variables with the MicroBooNE Detector

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

A Search for Pulsars around Sgr A* in the First Event Horizon Telescope Data Set

In 2017 the Event Horizon Telescope (EHT) observed the supermassive black hole at the center of the Milky Way, Sagittarius A* (Sgr A*), at a frequency of 228.1 GHz (λ = 1.3 mm). The fundamental physics tests that even a single pulsar orbiting Sgr A* would enable motivate searching for pulsars in EHT data sets. The high observing frequency means that pulsars—which typically exhibit steep emission spectra—are expected to be very faint. However, it also negates pulse scattering, an effect that could hinder pulsar detections in the Galactic center. Additionally, magnetars or a secondary inverse Compton emission could be stronger at millimeter wavelengths than at lower frequencies. We present a search for pulsars close to Sgr A* using the data from the three most sensitive stations in the EHT 2017 campaign: the Atacama Large Millimeter/submillimeter Array, the Large Millimeter Telescope, and the IRAM 30 m Telescope. We apply three detection methods based on Fourier-domain analysis, the fast folding algorithm, and single-pulse searches targeting both pulsars and burst-like transient emission. We use the simultaneity of the observations to confirm potential candidates. No new pulsars or significant bursts were found. Being the first pulsar search ever carried out at such high radio frequencies, we detail our analysis methods and give a detailed estimation of the sensitivity of the search. We conclude that the EHT 2017 observations are only sensitive to a small fraction (≲2.2%) of the pulsars that may exist close to Sgr A*, motivating further searches for fainter pulsars in the region.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

A Search for Faint Resolved Galaxies Beyond the Milky Way in DES Year 6: A New Faint, Diffuse Dwarf Satellite of NGC 55

We report results from a systematic wide-area search for faint dwarf galaxies at heliocentric distances from 0.3 to 2 Mpc using the full 6 yr of data from the Dark Energy Survey (DES). Unlike previous searches over the DES data, this search specifically targeted a field population of faint galaxies located beyond the Milky Way virial radius. We derive our detection efficiency for faint, resolved dwarf galaxies in the Local Volume with a set of synthetic galaxies and expect our search to be complete to M$_{V}$ ∼ (−7, −10) mag for galaxies at D = (0.3, 2.0) Mpc. We find no new field dwarfs in the DES footprint, but we report the discovery of one high-significance candidate dwarf galaxy at a distance of , a potential satellite of the Local Volume galaxy NGC 55, separated by 47′ (physical separation as small as 30 kpc). We estimate this dwarf galaxy to have an absolute V-band magnitude of and an azimuthally averaged physical half-light radius of , making this one of the lowest surface brightness galaxies ever found with . This is the largest, most diffuse galaxy known at this luminosity, suggesting possible tidal interactions with its host.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

The Dark Energy Camera Plane Survey 2 (DECaPS2): More Sky, Less Bias, and Better Uncertainties

Abstract Deep optical and near-infrared imaging of the entire Galactic plane is essential for understanding our Galaxy’s stars, gas, and dust. The second data release of the Dark Energy Camera (DECam) Plane Survey extends the five-band optical and near-infrared survey of the southern Galactic plane to cover 6.5% of the sky, ∣ b ∣ ≤ 10°, and 6° > ℓ > −124°, complementary to coverage by Pan-STARRS1. Typical single-exposure effective depths, including crowding effects and other complications, are 23.5, 22.6, 22.1, 21.6, and 20.8 mag in g , r , i , z , and Y bands, respectively, with around 1″ seeing. The survey comprises 3.32 billion objects built from 34 billion detections in 21,400 exposures, totaling 260 hr open shutter time on the DECam at Cerro Tololo. The data reduction pipeline features several improvements, including the addition of synthetic source injection tests to validate photometric solutions across the entire survey footprint. A convenient functional form for the detection bias in the faint limit was derived and leveraged to characterize the photometric pipeline performance. A new postprocessing technique was applied to every detection to debias and improve uncertainty estimates of the flux in the presence of structured backgrounds, specifically targeting nebulosity. The images and source catalogs are publicly available at http://decaps.skymaps.info/ .

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Search for the NΔ resonance in the 𝛾𝑑 → 𝑑𝜋 +𝜋 − reaction

A dibaryon which is an object with baryon number B = 2 has been studied for a long time. Dyson and Xuong classified non-strangeness dibaryon states based on SU(6) symmetries in 1960?s. In the framework, the deuteron is classified as one of the sextet states of dibaryons. Although dibaryon have been an interesting subject of research for a long time, most of the experimental studies up to the early 2000?s were unsuccessful. The CELCIUS/WASA collaboration reported this state via the double-pionic fusion reaction (?= ! 3c0c0) in 2009. Thereafter, the WASA-at-COSY collaboration revealed properties of the isoscaler resonance state via the ?= ! 3c0c0 reaction in 2011. The dibaryon resonance state with isospin ? = 0 and spin ( = 3 thought to be a ?03 which was predicted by Dyson and Xuong at 2.35 GeV?22 with a configuration of ??. The reported mass and width of that state were 2?37 GeV?22 and 0?07 GeV?22, espectively. The mass was ?0?08 GeV?22 smaller than that of 2?, the width was narrower than that of single ?. This surprising result made dibaryon study come back into the limelight. ?12 is one of the dibaryon states classified by Dyson and Xuong with isospin ? = 1, spin ( = 2. This state can be regarded as an s-wave #? resonance. ?12 is an interesting state from the point of view of the possibilities of existence as an internal structure of ?03 and contribution to many-body effects in nuclei. Though there were some experimental clues and theoretical studies of this state, it was unclear whether the obtained experimental results represented a real resonance or not due to the difficulty of separation from kinematical effects. Very recently, the FOREST group at Tohoku University reported a photoproduced isovector dibaryon state at mass of 2.14 GeV?22 in the 3c0 invariant mass spectra of the W3 ! 3c0c0 reaction. The most probable ?% configuration was 2¸ although they didn?t exclude the possibility of ?% = 1¸ or 3?. They separated the dibaryon production process from conventional pion production process for the first time using angular distribution of deuteron. We investigated the W3 ! 3c¸c? reaction for study of a possible #? dibaryon state using a deuterium target at the Research Center for Electron Photon Science, Tohoku University, Japan. In the experiment, ?3 ? 1012 tagged photon beam at energies ranging from 0.8 to 1.1 GeV was impinged to the liquid deuterium target (?520 mg?cm2) and the charged particles in the final state: deuteron, c¸, and c?, were detected by a magnetic spectrometer with a large solid angle named NKS2. NKS2 had capabilities of reconstructing momentum of charged particles, multi-track analysis, and ??c separation. We performed two different analyses named 2-track analysis and 3-track analysis. The 2-track (3-track) analysis was for events in which two (three) particles of 3c¸c? in the final state, including deuteron, were detected by NKS2. In the 3-track and 2-track analysis, ?2000? ?15000 events were identified as the W3 ! 3c¸c? reaction events, respectively. The 2-track analysis with higher statistics was mainly used to derive the cross sections, and the 3-track analysis was used to check the consistency of the 2-track analysis. In this thesis, we have shown the total cross section, the differential cross sections of the W3 ! 3c¸c? reaction in the region of jC j ¡ 0?15 GeV2. This is the world?s first measurement of this reaction in this energy region. Dibaryon resonance structures were observed below the #? threshold in the differential cross section of the invariant mass of 3c?. The mass and width of the structure were consistent with these of ?12 measured by the W3 ! 3c0c0 reaction. The mechanism of the production process was discussed based on the angular distribution of emitted deuteron.

Toyama, Yuichi↗

DOE OSTI2024

Diamond surface functionalization via visible light–driven C–H activation for nanoscale quantum sensing

Nitrogen-vacancy (NV) centers in diamond are a promising platform for nanoscale NMR sensing. Despite significant progress toward using NV centers to detect and localize nuclear spins down to the single spin level, NV-based spectroscopy of individual, intact, arbitrary target molecules remains elusive. Such sensing requires that target molecules are immobilized within nanometers of NV centers with long spin coherence. The inert nature of diamond typically requires harsh functionalization techniques such as thermal annealing or plasma processing, limiting the scope of functional groups that can be attached to the surface. Solution-phase chemical methods can be readily generalized to install diverse functional groups, but they have not been widely explored for single-crystal diamond surfaces. Moreover, realizing shallow NV centers with long spin coherence times requires highly ordered single-crystal surfaces, and solution-phase functionalization has not yet been shown with such demanding conditions. In this work, we report a versatile strategy to directly functionalize C–H bonds on single-crystal diamond surfaces under ambient conditions using visible light, forming C–F, C–Cl, C–S, and C–N bonds at the surface. This method is compatible with NV centers within 10 nm of the surface with spin coherence times comparable to the state of the art. As a proof-of-principle demonstration, we use shallow ensembles of NV centers to detect nuclear spins from surface-bound functional groups. Our approach to surface functionalization opens the door to deploying NV centers as a tool for chemical sensing and single-molecule spectroscopy.

Science & Technology - Other Topics↗

DOE OSTI2023

Anomaly detection search for new resonances decaying into a Higgs boson and a generic new particle $X$ in hadronic final states using $\sqrt{s}$ = 13 TeV $pp$ collisions with the ATLAS detector

A search is presented for a heavy resonance $Y$ decaying into a Standard Model Higgs boson $H$ and a new particle $X$ in a fully hadronic final state. The full Large Hadron Collider run 2 dataset of proton-proton collisions at $\sqrt{s}$ = 13 TeV collected by the ATLAS detector from 2015 to 2018 is used and corresponds to an integrated luminosity of 139 fb –1 . The search targets the high $Y$-mass region, where the $H$ and $X$ have a significant Lorentz boost in the laboratory frame. A novel application of anomaly detection is used to define a general signal region, where events are selected solely because of their incompatibility with a learned background-only model. It is constructed using a jet-level tagger for signal-model-independent selection of the boosted $X$ particle, representing the first application of fully unsupervised machine learning to an ATLAS analysis. Two additional signal regions are implemented to target a benchmark $X$ decay into two quarks, covering topologies where the $X$ is reconstructed as either a single large-radius jet or two smallradius jets. The analysis selects Higgs boson decays into $b$$\overline{b}$, and a dedicated neural-network-based tagger provides sensitivity to the boosted heavy-flavor topology. No significant excess of data over the expected background is observed, and the results are presented as upper limits on the production cross section $σ$ ($pp$ → $Y$ → $XH$ → $q$$\overline{q}$$b$$\overline{b}$) for signals with $m_Y$ between 1.5 and 6 TeV and $m_X$ between 65 and 3000 GeV

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

A distributed voltage inference framework for cyber-physical attacks detection and localization in active distribution grids

The transition to active distribution grids with real-time monitoring and control depends on the proliferation of advanced communication networks and devices. This paradigm shift towards a cyber-physical architecture also introduces new vulnerabilities for adversaries to exploit and launch sophisticated cyber-physical attacks targeting grid observability. Current research highlights the challenges in distinguishing attacks on voltage phasor or nodal injection measurements and isolating multi-source attack locations in a multiphase distribution grid. The attack detection and localization methods in literature face accuracy issues, applications across diverse attack scenarios, or scalability limits. Here, to bridge these gaps, this paper proposes a distributed Voltage Inference framework for real-time detection and localization of cyber-physical attacks, addressing scalability, adaptability, and accuracy challenges in state-of-the-art methods. The proposed methodology leverages the distributed nature of the Voltage Inference framework through a two-step process of prediction and correction, together with a tractable graph partitioning approach, providing a reliable solution to identify compromised measurement sources and facilitate isolation. Extensive testing on IEEE 13 and 123-node distribution feeders underscores the algorithm’s efficacy, enhancing the security and resilience of active distribution grids against evolving cyber threats. Additionally, Hardware-in-the-Loop (HIL) implementation validates the proposed strategy’s practical applicability in real-world scenarios.

active distribution grids↗

DOE OSTI2023

Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways

Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)—also known as multiple reaction monitoring (MRM)—and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.

mathematical modeling↗