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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Flow Z-pinch plasma production on the FuZE experiment

The Fusion Z Pinch Experiment (FuZE) investigates sheared-flow stabilization of classic m = 0 and m = 1 instabilities in Z pinches with an embedded axial flow. FuZE consists of a 100 cm coaxial plasma accelerator, where neutral gas is ionized and accelerated in a pulsed electrical discharge, followed by a 50 cm assembly region, where pinches are formed. Maintaining the pinch requires continuous plasma injection provided by a deflagration mode in the coaxial accelerator. Two discharge modes, with and without deflagration, are investigated on FuZE. Pinch formation is observed with deflagration only. Plasma velocities in the assembly region are found to match the E × B velocity estimated in the accelerator based on a 1D circuit model, indicating that a 1D MHD approximation may offer a valid description of the plasma in the accelerator channel. The velocity of magnetic field propagation is found to agree with the snowplow model based on momentum conservation, and the lifetime of the pinch is shown to be in agreement with constraints imposed by mass conservation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Possible mitigation of tokamak plasma–surface interactions using thermionic divertor plates with inverse sheaths

Recent studies demonstrate that when a plasma-facing surface emits a sufficient flux of electrons, it will form an inverse sheath. In this work, we consider a possibility of using thermionic target plates with inverse sheaths as an innovative divertor operating scenario. We derive an electron heat flux boundary condition for inverse sheaths and show that for given power exhaust into a tokamak scrape-off-layer, an inverse sheath leads to a much lower target plasma electron temperature than a conventional sheath. Low enough target plasma temperatures for radiative divertor detachment could therefore be achieved using inverse sheaths instead of the usual need to inject neutral atoms that compromise the core plasma. Other advantages of inverse sheath detachment over conventional sheath operating scenarios include (a) ion impact energies are as low as possible, minimizing sputtering and tritium implantation, (b) surface recombination heat flux is reduced due to ion flux reduction, and (c) arcs are inhibited due to the sign of the surface electric field. This paper outlines the basic properties of inverse sheath detachment and considers the feasibility of implementation. We offer recommendations for future modeling efforts needed to better understand the effects of thermionic emission in tokamaks and whether inverse sheaths present a viable divertor solution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Simulation of divertor heat flux width on EAST by BOUT++ transport code

The BOUT++ edge plasma transport code is applied to study the effects of neutral recycling, drifts and heating scheme on edge plasma profiles and the divertor heat flux width of two discharges of the experimental advanced superconducting tokamak (EAST) steady-state H-mode plasmas heated by low hybrid wave (LHW) and neutral beam (NB), respectively. Neutral recycling seems to have played an important role in the plasma density profile. The edge plasma density drops dramatically for the case w/o neutral recycling, while it can be sustained for the case w/ neutral recycling. Drifts are found to have significant influences on edge plasma profiles. Both the amplitude and width of the divertor heat flux are found to have increased a lot due to drifts. The simulated heat flux width w/ drifts for the two discharges shows reasonable agreement with the experiments. However, the width from the simulation and experiment for the LHW heated discharge is much larger than that of the NB heated discharge. Comparison with Goldston's drift-based model and more detailed analysis on the heat flux contributions from drifts versus turbulence show that drifts are the dominant factor in edge plasma transport for both LHW and NB heated discharges, while turbulence may have played a more important role in determining the heat flux width in LHW heated discharges than that in NB heated discharges. This may account for the larger heat flux width in the LHW heated discharge. The magnetic topology and the equilibrium change by the LHW power may also be a potential reason for the larger heat flux width in the LHW heated discharges, which still needs more evidence and studies to support it. Finally, additional SOLPS simulation w/o drifts for the two discharges show reasonable agreement with the counterpart from the BOUT++ simulation, suggesting the two are both suitable codes for EAST edge plasma simulation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Keck/NIRSPEC Studies of He ι in the Atmospheres of Two Inflated Hot Gas Giants Orbiting K Dwarfs: WASP-52b and WASP-177b

We present the detection of neutral helium at 10833 Å in the atmosphere of WASP-52b and tentative evidence of helium in the atmosphere of the grazing WASP-177b, using high-resolution observations acquired with the NIRSPEC instrument on the Keck II telescope. We detect excess absorption by helium in WASP-52b's atmosphere of 3.44% ± 0.31% (11σ), or equivalently 66 ± 5 atmospheric scale heights. This absorption is centered on the planet's rest frame (Δv = 0.00 ± 1.19 km s –1 ). We model the planet's escape using a 1D Parker wind model and calculate its mass-loss rate to be ~1.4 × 10 11 g s –1 , or equivalently 0.5% of its mass per gigayear. For WASP-177b, we see evidence for redshifted (Δv = 6.02 ± 1.88 km s –1 ) helium-like absorption of 1.28% ± 0.29% (equal to 23 ± 5 atmospheric scale heights). However, due to residual systematics in the transmission spectrum of similar amplitude, we do not interpret this as significant evidence for He absorption in the planet's atmosphere. Using a 1D Parker wind model, we set a 3σ upper limit on WASP-177b's escape rate of 7.9 × 10 10 g s –1 . Our results, taken together with recent literature detections, suggest the tentative relation between XUV irradiation and He ι absorption amplitude may be shallower than previously suggested. Our results highlight how metastable helium can advance our understanding of atmospheric loss and its role in shaping the exoplanet population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Q2 Report for FY25 Theory and Simulation Performance Target: Development of an integrated modeling framework for fusion reactor design and assessment

This report describes the work and activities carried out towards the completion of each of the following milestones in FY25 Q2: 1. Demonstrate workflow for generating self-consistent CESOL plasma profiles + first wall and divertor loading prediction and generate the CAT plasma and neutron loading needed for further engineering analysis: $\circ$ Run CESOL with BOUT++/Hermes-3 and immersed boundary condition to directly map to wall: • Run BOUT++/Hermes-3 through the IPS workflow to find radial particle and energy diffusivities to match either the Eich or the physics-based scaling of the SOL heat flux width, and • Expand source of first wall heat flux to include charged particles, neutrals, and radiation from the core+edge. 2. Generate medium fidelity parametrized CAD: $\circ$ Develop the TRACER tool to read an existing CAD, regenerate the geometry based on vertex location and connectivity information, define vertex translation and parameters needed for scaling the CAD, and $\circ$ Utilize the FreeGS code to determine CAT PF coil placement, including minimizing the number of coils, coil current, and electromechanical stresses. 3. Utilize plasma loading for engineering analysis: $\circ$ Couple the plasma loading to input for OpenFOAM and demonstrate initial test of thermal analysis of CAT first wall loading with typical DCLL blanket component cooling boundary conditions. 4. Demonstrate nuclear analysis: $\circ$ Apply initial analysis of tritium transport in DCLL blanket by evaluating spatially resolved tritium generation rates, tritium diffusion and convection.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Role of deep levels and barrier height lowering in current-flow mechanism in 150 μ m thick epitaxial n-type 4H–SiC Schottky barrier radiation detectors

Schottky barrier detectors (SBDs) require larger surface areas than conventional electronics to increase the detection efficiency although such SBDs manifest large diode ideality factors due to inhomogeneous areal distribution of surface barrier height (SBH). Inhomogeneous SBH distributions lead to various current flow mechanisms in SBDs, which need to be identified to optimize detector performance. In this Letter, we identify the current flow mechanism in large area Schottky barrier diodes for radiation detection fabricated on 150 μm thick n-4H–SiC epitaxial layers. The analysis of temperature-dependent forward current–voltage (I–V–T) characteristics of SBDs revealed two linear regions in current–voltage curves up to 450 K, one corresponding to the current flow through a low barrier patch, while the other corresponds to that of average barrier distribution. Applying a SBH distribution model to the reverse I–V–T characteristics, an activation energy of 0.76 eV for the current flow over the Schottky barrier was calculated. Additionally, the activation energy did not directly correspond to any of the defect levels observed from the deep level transient spectroscopy (DLTS). Above 450 K, a Schottky type barrier lowering suggested a current flow through a low barrier patch of ≈ 0.8 eV. The absence of any SBH lowering below 450 K indicated that the current corresponded to a neutrally charged trap level at ≈ 0.6 eV below the conduction band edge, which was consistent with DLTS measurements revealing the presence of an electron trap level Z1/2 at 0.59 eV below the conduction band edge.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Verification of neoclassical toroidal viscosity induced by energetic particles

The thermal particles contributed neoclassical toroidal viscosity (NTV) have been successfully developed and explored by many impressive works such as the study by Shaing et al. [Phys. Plasmas 10, 1443 (2003)] and Zhu et al. [Phys. Rev. Lett. 96, 225002 (2006)]. In this work, the scope of the NTV study is extended to explore the contribution of energetic particles (EPs) through both theory and experiments. In theory, the existence of the NTV torque due to the precessional drift resonance of trapped EPs is identified based on the equivalence between the NTV torque and the perturbed drift kinetic energy [J. Park, Phys. Plasmas 18, 110702 (2011)]. Toroidal modeling with the Magneto Resistive Spectrum - drift Kinetic code [Y. Liu, Phys. Plasmas 15, 112503 (2008)], based on this equivalence, indicates that trapped EPs can contribute a significant amount of the NTV torque. Meanwhile, this work also focuses on developing the dedicated DIII-D experiments in the presence of the n = 2 external magnetic perturbation to verify the EP induced NTV (EP-NTV) by measuring the change of the NTV torque while varying the angle and the voltage of the neutral beam injection. However, the developed experiments have been unable to create conditions necessary to clearly demonstrate the presence of EP-NTV. The main challenge is separating the resonant and non-resonant momentum transport responses in the plasma. Finally, the experience, gained from this study, can help the further exploration of EP-NTV in the future experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Economics of Crop Rotations With and Without Carinata for Sustainable Aviation Fuel Production in the SE United States

In 2019, the aviation sector in the United States emitted 255 million metric tons of carbon dioxide (CO 2 ) emissions, i.e., about five percent of the total domestic CO 2 emissions from the energy sector. The sustainable aviation fuel (SAF) derived from carinata (Brassica carinata) could reduce CO 2 emissions of the aviation sector in the United States. Therefore, it is important to estimate changes in farm economics with and without carinata for ascertaining its production feasibility. In this context, the current study first assesses a combination of 12 popular rotations of corn, cotton, peanut, and soybean with winter crops of winter wheat and carinata in South Georgia over 4 years. Then, the net present values (NPVs) of 292 feasible cropping systems over 4 years are calculated. Finally, this study develops a risk model for ascertaining the probability distributions of NPVs for selected cropping systems subject to uncertainties related to prices and yields of summer and winter crops. Carinata in the corn-corn-soybean rotation has the highest NPV ($\$$2,996/ha). The least risky rotation is cotton-cotton-peanut, with a 58.9% probability of a positive NPV. Carinata can decrease the risk level of crop rotations by 8.1%, only if a contract price of $\$$440.9/t is offered. Therefore, a risk averse, risk neutral, or risk acceptant farmer can potentially include carinata in the rotation. Overall, carinata would increase the profitability of farm operations and decrease risk in the SE United States, and therefore, a high likelihood exists, that farmers would adopt it for meeting the growing demand for SAF in the United States.

09 BIOMASS FUELS↗
DOE OSTI2022

Towards a neutron multiplicity measurement with the Accelerator Neutrino Neutron Interaction Experiment

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a 26 ton Gadolinium (Gd)-loaded water Cherenkov detector located on the Booster Neutrino Beam line at Fermilab. Its main goals are the measurement of the neutron multiplicity in neutrino-nucleus interactions as well as the cross-section of Charged Current Quasi-Elastic (CCQE) neutrino interactions on water. Besides the physics goals, the experiment also aims to be a testbed for new technologies such as Large Area Picosecond Photodetectors (LAPPDs) and Water-based Liquid Scintillators (WbLS). This thesis presents a preliminary measurement of the neutron multiplicity with {ANNIE}, using an analysis conducted on a fraction of the 2021 beam year. As preparatory measures, the efficiency of ANNIE's Front Muon Veto (FMV) was determined to be {$\bar{\varepsilon}_{\mathrm{FMV}} = (95.6 \pm 1.6)\%$} while the average efficiency for active scintillator paddles in the Muon Range Detector (MRD) was found to be {$\bar{\varepsilon}_ {\mathrm{MRD}} = (92.1 \pm 7.9)\%$}. Furthermore, the simulation framework used for ANNIE was validated and adapted to reproduce the experimental data by comparing the detector response for samples of Michel electrons, Americium Beryllium neutrons, and through-going muons. The analysis finds average neutron yields of {$\bar{n}_{\mathrm{data}} (\mathrm{beam}) = (0.272 \pm 0.010_{\mathrm{stat}})$} for an inclusive set of all identified muon neutrino candidates and {$\bar{n}_{\mathrm{data}} (\mathrm{beam,FV}) = (0.287 \pm 0.044_{\mathrm{stat}})$ for interactions which happened inside of the Fiducial Volume of ANNIE, which was optimized to increase the neutron detection acceptance. The presented neutron multiplicity values represent the number of detected neutrons after all event selection cuts and are not yet corrected for the neutron detection efficiency. An equivalent analysis on a simulated beam sample predicts neutron yields of $\bar{n}_{\mathrm{MC}}(\mathrm{beam}) = (0.515 \pm 0.0 07_{\mathrm{stat}})$ and $\bar{n}_{\mathrm{MC}}(\mathrm{beam,FV}) = (0.627 \pm 0.031_{\mathrm{stat}})$, indicating that the models tend to overpredict the number of neutrons produced in such interactions. Systematic errors have been briefly considered to contribute {$\sigma_{\mathrm{sys,FMV}} \sim 0.01\,$neutrons/$\nu$-interaction} due to the slight FMV inefficiency and {$\sigma_{\mathrm{sys,n}} \sim 0.05\,$neutrons/$\nu$-interaction} due to the neutron detection efficiency. Simulation studies further highlighted the importance of neutron detection in Diffuse Supernova Background (DSNB) searches. A combination of neutron tagging and Convolutional Neural Networks was found to reduce the most relevant Neutral Current Quasi-Elastic (NCQE) interaction background below the signal level, achieving a Signal-to-Background ratio of 4:1. In a further study, we investigated the positive impact of a deployment of a WbLS target on the energy reconstruction in ANNIE. WbLS provides a scintillation signal from hadronic recoils in addition to the charged lepton that can be included in neutrino energy reconstruction. It was found that a deployed WbLS volume in ANNIE improves the neutrino energy reconstruction from 14\% to 12\%, with the potential of going beyond this if more sophisticated reconstruction algorithms are developed in the future.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Modulating Ce 3+ Sites in Ce-Zr Oxide Nanocatalysts through Protamine Biomineralization for Organophosphate Dephosphorylation

Catalytic is a crucial reaction for environmental detoxication of pesticides and neutralization of various molecules classified as chemical warfare agents. Herein, we report on a series of tunable Ce-Zr-based metal oxides, (Zr a Ce 1–a O x ) prepared using a facile biomineralization technique, as catalysts for organophosphates dephosphorylation. Synchrotron scattering and spectroscopy methods showcase that Zr a Ce 1–a O x catalysts are highly defective and exhibit an abundance of Ce 3+ sites that promote oxygen vacancies needed for enhanced dephosphorylation reactions. The catalytic performance was assessed using a model para-nitrophenyl phosphate reaction and showcases a strong dependence on Zr dopant concentration and subsequent tuning of the Ce 3+ /Ce 4+ ratio. Analysis of synchrotron datasets allowed structure-performance correlations between the Ce 3+ concentration and associated oxygen vacancies, the dephosphorylation rate constant, and Zr concentration to be established, confirming that Ce 3+ as active sites is positively correlated with the rate constant. We envision that similar biomineralization approaches can be used to fabricate Ce 3+ -rich Ce-Zr oxide for environmental application in dephosphorylation and other hydrolysis reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Resistive contributions to the stability of DIII-D ITER baseline demonstration discharges

Here, measurements of the plasma response to applied n = 1 perturbations from DIII-D ITER baseline scenario (IBS) demonstration discharges exhibit increasing amplitude prior to disruption inducing mode locking events. Simulations reveal that changes in ideal and resistive stability impact the response in the DIII-D IBS regime, well below the pressure limit of the external kink mode. The dependencies of the response measurements on the plasma normalized internal inductance ℓ i and beta β N are qualitatively consistent with ideal MHD, although in most cases the amplitude of the measurements exceeds predictions, indicating that the experimental discharges are less stable than expected. Resistive MHD simulations of the response show improved compatibility with the measurements, and the closest agreement is obtained by including the experimental plasma rotation in the simulations. Although the input neutral beam torque is near zero, the simulations show that the corresponding level of rotation can lead to nearly complete screening of the pitch-resonant field component at the q = 2 surface. However, the simulation results exhibit a significant weakening of this screening effect at the lowest rotation levels in the data set, concurrent with predictions of elevated response amplitudes that are consistent with measurements. These comparisons with DIII-D data provide a qualitative validation of a linear, resistive MHD response model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Twisted bilayer graphene. V. Exact analytic many-body excitations in Coulomb Hamiltonians: Charge gap, Goldstone modes, and absence of Cooper pairing

We find exact analytic expressions for the energies and wave functions of the charged and neutral excitations above the exact ground states (at rational filling per unit cell) of projected Coulomb Hamiltonians in twisted bilayer graphene. Our exact expressions are valid for any form of the Coulomb interaction and any form of A A and A B / B A tunneling. The single charge excitation energy is a convolution of the Coulomb potential with a quantum geometric tensor of the TBG bands. The neutral excitations are (high-symmetry group) magnons, and their dispersion is analytically calculated in terms of the form factors of the active bands in TBG. The two-charge excitation energy and wave functions are also obtained, and a sufficient condition on the graphene eigenstates for obtaining a Cooper pair from Coulomb interactions is obtained. For the actual TBG bands at the first magic angle, we can analytically show that the Cooper pair binding energy is zero in all such projected Coulomb models, implying that either phonons and/or nonzero kinetic energy are needed for superconductivity. Since Vafek and Kang [Phys. Rev. Lett. 125, 257602 (2020)] showed that the kinetic energy bounds on the superexchange energy are less 10 -3 in Coulomb units, the phonon mechanism becomes then very likely. If nonetheless the superconductivity is due to kinetic terms which render the bands nonflat, one prediction of our theory is that the highest T c would not occur at the highest DOS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

A generalized platform for artificial intelligence-powered autonomous enzyme engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Divertor plasma detachment: roles of plasma momentum, energy, and particle balances

Abstract Contrary to statements from some recent papers, the bifurcation of the scrape-off layer and divertor plasma parameters, as described within a 1D model, does exist. The analysis of both numerical simulations and experimental data shows that the real physical reasons that can cause a strong reduction of the plasma particle flux to the target j d are impurity radiation loss and volumetric plasma recombination. Fitting the parameter describing the ‘plasma momentum removal’, based on the results of 2D numerical simulations, then using this fit in subsequent analytic expressions for j d , and finally interpreting the evolution of j d as the result of elastic plasma-neutral interactions break the causality principle and lead to a wrong physical picture of divertor plasma detachment.

Physics↗
DOE OSTI2025

Search for events with one displaced vertex from long-lived neutral particles decaying into hadronic jets in the ATLAS muon spectrometer in 𝑝⁢𝑝 collisions at $\sqrt{𝑠}$ = 13 TeV

A search for events with one displaced vertex from long-lived particles using data collected by the ATLAS detector at the Large Hadron Collider is presented, using 140 fb −1 of proton-proton collision data at $\sqrt{𝑠}$ =13 TeV recorded in 2015–2018. The search employs techniques for reconstructing vertices of long-lived particles decaying into hadronic jets in the muon spectrometer displaced between 3 m and 14 m from the primary interaction vertex. The observed number of events is consistent with the expected background and limits for several benchmark signals are determined. A scalar-portal model and a Higgs-boson-portal baryogenesis model are considered. A dedicated analysis channel is employed to target Z-boson associated long-lived particle production, including an axionlike particle and a dark photon model. For the Higgs boson model, branching fractions above 1% are excluded at 95% confidence level for long-lived particle proper decay lengths ranging from 5 cm to 40 m. For the photophobic axionlike particle model considered, this search produces the strongest limits to date for proper decay lengths greater than 𝒪⁡(10) cm.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Task 2.1: Adsorption-Based ISPR for BETO-Relevant Bioproducts

This task focuses on the development of adsorption-based in situ product recovery (ISPR) integrated with simulated moving bed chromatography for the recovery and purification of carboxylate products that are relevant to BETO. ISPR has been pursued previously in the Separations Consortium to recover carboxylic acids near or below their pKa values with liquid-liquid extraction coupled to downstream distillation. However, there are many acid products in the BETO portfolio that require neutralization well above their pKa values wherein ISPR could still be a major benefit to the bioprocess performance, including muconic acid, beta-ketoadipic acid, 3-hydroxypropionic acid, itaconic acid, butyric acid, and others. In this task, we are combining dynamic filtration with a rotating ceramic disk, resin capacity measurements, tailored resin synthesis, and simulated moving bed chromatography into an ISPR system that can be used to recover BETO-relevant carboxylates from bioreactor cultivations. We are working across process scales and using computational modeling where applicable alongside techno-economic analysis and life cycle assessment to understand major cost, energy, and GHG emissions drivers. The impact of this project will be a bench-scale integrated approach to recover carboxylate products in situ, which will reduce the waste generation from biological carboxylate production processes and improve the productivities of biological systems.

bio-based acid↗
DOE OSTI2020

Crossover from Rouse to Reptation Dynamics in Salt-Free Polyelectrolyte Complex Coacervates

Considerable interest in the dynamics and rheology of polyelectrolyte complex coacervates has been motivated by their industrial application as viscosity modifiers. A central question is the extent to which classical Rouse and reptation models can be applied to systems where electrostatic interactions play a critical role on the thermodynamics. By relying on molecular simulations, we present a direct analysis of the crossover from Rouse to reptation dynamics in salt-free complex coacervates as a function of chain length. This crossover shifts to shorter chain lengths as electrostatic interactions become stronger, which corresponds to the formation of denser coacervates. To distinguish the roles of Coulomb interactions and density, here we compare the dynamics of coacervates to those of neutral, semidilute solutions at the same density. Both systems exhibit a universal dynamical behavior in the connectivity-dominated (subdiffusion and normal diffusion) regimes, but the monomer relaxation time in coacervates is much longer and increases with increasing Bjerrum length. This is similar to the cage effect observed in glass-forming polymers, but the local dynamical slowdown is caused here by strong Coulomb attractions (ion pairing) between oppositely charged monomers. Our findings provide a microscopic framework for the quantitative understanding of coacervate dynamics and rheology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗