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At least 199 records · Page 11

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy

T cell states are prognostic in different cancer types. Recent technologies enable joint profiling of T cell RNA and T cell receptor (TCR) sequences at single-cell resolution. Here we present the TCR-RNA Integrating Model (TRIM), a multi-modal variational autoencoder framework that integrates RNA-TCR data and predicts T cell clonality and transcriptional states. TRIM learns a shared representation of the data conditioned on patient, tissue source, and treatment timepoint. We applied TRIM to three independent datasets that included T cells collected before and after checkpoint inhibitor treatment, sourced either from blood and tumor biopsies in patients with head and neck squamous cell carcinoma and colorectal cancer, or from tumor and adjacent tissue in a pan-cancer dataset. In all settings, TRIM accurately predicted intra-tumor T cell clonal expansion and transcriptional status based on T cells from blood or normal tissue before treatment, demonstrating its utility in modeling multimodal T cell data and predicting T cell response to treatment and disease progression.

60 APPLIED LIFE SCIENCES↗

A Representation Fusion Framework for Decoupling Diagnostic Information in Multimodal Learning

Modern medicine increasingly relies on multimodal data, ranging from clinical notes to imaging and genomics, to guide diagnosis and treatment. However, integrating these heterogeneous data sources in a principled and interpretable manner remains a major challenge. We present MODES (Multi-mOdal Disentangled Embedding Space), a representation fusion framework that explicitly separates shared and modality-specific factors of variation, offering a structured latent space for multimodal information that improves both prediction and interpretability. By leveraging pre-trained unimodal foundation models, MODES mitigates the dependency on extensive paired datasets, crucial in data-scarce clinical settings. We introduce a masking strategy that optimizes representation dimensionality by eliminating low-information dimensions, to achieve compact, information-rich representations. Our framework demonstrates superior performance in predicting diagnoses and phenotypes compared to unimodal and conventional fusion models. MODES also enables robust diagnostic inference in missing data scenarios, offering an opportunity toward interpretable and efficient multimodal diagnostics in personalized healthcare.

60 APPLIED LIFE SCIENCES↗

GA-NIFS and EIGER: A merging quasar host at z = 7 with an overmassive black hole

The James Webb Space Telescope is revolutionising our ability to understand the host galaxies and local environments of high-z quasars. Here we obtain a comprehensive understanding of the host galaxy of the z = 7.08 quasar J1120+0641 by combining NIRSpec integral field spectroscopy with NIRCam photometry of the host continuum emission. Our emission-line maps reveal that this quasar host is undergoing a merger with a bright companion galaxy. The quasar host and the companion have similar dynamical masses of ∼10 10 M ⊙ , suggesting that this is a major galaxy interaction. Through detailed quasar subtraction and SED fitting using the NIRCam data, we obtained an estimate of the host stellar mass of M ∗ = (3.0 −1.4 +2.5 ) × 10 9 M ⊙ , with M ∗ = (2.7 −0.5 +0.5 ) × 10 9 M ⊙ for the companion galaxy. Using the Hβ Balmer line, we estimated a virial black hole mass of M BH = (1.9 −1.1 +2.9 ) × 109 M ⊙ . Thus, J1120+0641 has an extreme black hole–stellar mass ratio of M BH /M ∗ = 0.63 −0.31 +0.54 , which is ∼3 dex larger than expected by the local scaling relations between black hole and stellar mass. J1120+0641 is powered by an overmassive black hole with the highest reported black hole–stellar mass ratio in a quasar host that is currently undergoing a major merger. These new insights highlight the power of JWST for measuring and understanding these extreme first quasars.

79 ASTRONOMY AND ASTROPHYSICS↗

Accelerating plasma and radiation surface science using transient grating spectroscopy

A facility for the investigation of in situ radiation-materials and plasma-materials interaction is demonstrated with tungsten, using transient grating spectroscopy as a probe of thermal diffusivity and surface acoustic wave speed. Helium plasma exposure at 645 °C to 1.18 × 10 18 cm −2 helium, until the growth of tungsten fuzz, showed an increase in surface acoustic wave speed at the near-surface from 2542 ± 1 m s −1 up to 2565 ± 1 m s −1 , followed by a greater drop to 2499 ± 7 m s −1 . No observable change in thermal diffusivity was present for plasma exposure alone. A separate 10.26 MeV self-ion-irradiation of tungsten to a dose of 7.92 dpa showed a reduction in both thermal diffusivity from 61.4 ± 1.4 mm 2 s −1 to 36.0 ± 0.7 mm 2 s −1 , following trends seen in existing studies, and surface acoustic wave speed from 2647.8 ± 0.6 m s −1 to 2640.0 ± 0.4 m s −1 . Facilities like these are poised to rapidly close critical knowledge gaps regarding the coupled effects of plasma and radiation damage for materials in fusion systems.

Accelerated plasmas↗

A novel method for thermal noise reduction, enabling measurements of broadband, low-amplitude electron temperature fluctuations using individual radiometer channels

A new analysis method has been developed for measurements of broadband, low-amplitude turbulent electron temperature fluctuations in fusion plasmas using individual radiometer channels of a correlation electron cyclotron emission diagnostic. This method takes advantage of differences in the correlation time of thermal noise compared to the correlation time of plasma fluctuations in fusion reactors. The validation of this single-channel method is demonstrated using comparisons with the standard dual-channel radiometer spectral decorrelation method for measurements of turbulent electron temperature fluctuations in the core and edge of low confinement (L), improved confinement (I), and high confinement (H)-mode plasmas at the ASDEX Upgrade tokamak.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The next-generation particle x-ray temporal diagnostic for simultaneous time-resolved measurements of nuclear-burn and x-ray emission histories in support of basic-science and inertial confinement fusion experiments at OMEGA

The next-generation Particle X-ray Temporal Diagnostic (PXTD) has been implemented for simultaneous measurements of x-ray, charged particle, and neutron emission histories from a wide range of inertial confinement fusion and high energy density plasma experiments, demonstrating excellent timing accuracy and greatly improved experimental flexibility. The key changes to the previously fielded system are a redesigned set of thin foil filters in front of the scintillators and individual neutral density filters for each region of the detector. The fully implemented PXTD system can provide unique information about the evolution of ion and electron temperatures in multi-ion and kinetic-physics experiments, proton radiography experiments, and DT experiments executed at the OMEGA facility. The system has 35 ps time resolution and negligible relative timing uncertainty between measured emission history signals. The first use of the upgraded four-channel PXTD system during a set of D 3 He-filled silica-glass implosions on OMEGA captured electron temperatures with a minimum uncertainty of 0.5 keV and resolved both the relative timings and widths of neutron, proton, and x-ray peaks within a single recorded image.

Evans, T. E. [Massachusetts Inst. of Technology (M↗

The low frequency edge oscillation in alcator C-Mod and ASDEX upgrade I-mode

The low frequency edge oscillation (LFEO) is a low frequency fluctuation in many plasma quantities in the pedestal region of the I-Mode confinement regime. It is observed on Alcator C-Mod between 10–30 kHz and on ASDEX Upgrade between 5–10 kHz. On both tokamaks it has been previously identified as a geodesic acoustic mode (GAM), however the recent discovery of the edge temperature ring oscillation (ETRO) in a similar frequency and spatial location as the LFEO in I-Modes on EAST has called this identification into question. In this paper we investigate the LFEO on C-Mod and AUG using a variety of different experimental techniques including spectral analysis, magnetic mode number analysis, localization, and direct measurement of the LFEO zonal structure and propagation using a mirror Langmuir probe. This investigation has reconfirmed the identification of the LFEO as a GAM and determined that it has several key differences from the ETRO.

AUG↗

Gyrokinetic profile prediction and validation of a negative triangularity plasma in ASDEX Upgrade

In this work, gyrokinetic simulations are performed with the CGYRO code (Candy et al 2016 J. Comput. Phys. 324 73–93) for a negative triangularity H-mode plasma in ASDEX Upgrade, and compared with experimental measurements. The PORTALS framework (Rodriguez-Fernandez et al 2024 Nucl. Fusion 64 076034) is used to accelerate the prediction of kinetic profiles for this plasma, using surrogate modeling and Bayesian optimization. Ion heat flux, electron heat flux, and electron particle flux are simultaneously matched across the simulated radial regime of the plasma (normalized radius $r/a = 0.35-0.90$), and the resulting ion temperature, electron temperature, and electron density profiles match well with the experimental profile data within this radial range. A synthetic Correlation Electron Cyclotron Emission diagnostic is applied to find well-matched electron temperature fluctuation properties between simulation and experiment. The flux-matched profiles provide a basis for investigation of the turbulence nature across the plasma radius, revealing the dominance of Trapped Electron Mode turbulence at $r/a = 0.35$, the dominance of Ion Temperature Gradient turbulence at $r/a = 0.55$, 0.75, and 0.83, and an instability boundary at $r/a = 0.90$.

gyrokinetic simulation↗

Mode Multiplexing for Scalable Cavity-Enhanced Operations in Neutral-Atom Arrays

Neutral-atom arrays provide a versatile platform for quantum information processing. However, in large-scale arrays, efficient photon collection remains a bottleneck for key tasks such as fast, nondestructive qubit readout and remote entanglement distribution. We propose a cavity-based approach that enables fast, parallel operations over many atoms using multiple modes of a single optical cavity. By selectively shifting the relevant atomic transitions, each atom can be coupled to a distinct cavity mode, allowing independent simultaneous processing. We present practical system designs that support cavity-mode multiplexing with up to 50 modes, enabling rapid mid-circuit syndrome extraction and significantly enhancing entanglement distribution rates between remote atom arrays. This approach offers a scalable solution to core challenges in neutral-atom arrays, advancing the development of practical quantum technologies.

Aqua, Ziv [Massachusetts Institute of Technology (↗

Spin-Forbidden Excitations in the Magneto-optical Spectra of CrI 3 Tuned by Covalency

Spin-forbidden (Δ⁢𝑆 ≠0) multiplet excitations and their coupling to magnetic properties are of increasing importance for magneto-optical studies of correlated materials. Nonetheless, the mechanisms for optically brightening these transitions and their generality remain poorly understood. Here, we report magnetic circular dichroism (MCD) spectroscopy on the van der Waals ferromagnet (FM) CrI 3 . Previously unreported spin-forbidden (Δ⁢𝑆 =1) 4 𝐴 2⁢g → 2 𝐸 g / 2 𝑇 1⁢g Cr 3+ 𝑑⁢𝑑 excitations are observed near the ligand-to-metal charge-transfer excitation threshold. The assignment of these excitations and their Cr 3+ multiplet character is established through complementary Cr 𝐿 3 -edge resonant inelastic x-ray scattering measurements along with charge-transfer multiplet calculations and chemical trends in the chromium trihalide series (Cr⁢𝑋 3 , 𝑋 = Cl, Br, I). We utilize the high sensitivity of MCD spectroscopy to study the thickness-dependent optical response. The spin-forbidden excitations remain robust down to the monolayer limit, and we observe a significant magnetic-field dependence of the MCD spectrum across the antiferromagnetic-to-FM transition in few-layer samples. We preliminarily attribute this behavior to changes in the metal-ligand covalency with magnetic state. Our results clarify the magneto-optical response of CrI 3 and identify covalency as a central mechanism for the brightening and field tunability of spin-forbidden multiplet excitations.

36 MATERIALS SCIENCE↗

Efficiently Measuring 𝑑-Wave Pairing and Beyond in Quantum Gas Microscopes

Understanding the mechanism of high-temperature superconductivity is among the most important problems in physics, one for which quantum simulation can provide new insights. However, it remains challenging to characterize superconductivity in existing cold-atom quantum simulation platforms. Here, in this work, we introduce a protocol for measuring a broad class of observables in fermionic quantum gas microscopes, including long-range superconducting pairing correlations (after a repulsive-to-attractive mapping). The protocol only requires global controls followed by site-resolved particle number measurements—capabilities that have been already demonstrated in multiple experiments—and is designed by analyzing the Hilbert space of fermions on two sites. The protocol is sample-efficient and we further optimize our pulses for robustness to experimental imperfections such as lattice inhomogeneity. Our Letter introduces a general tool for manipulating quantum states on optical lattices, enhancing their ability to tackle problems such as high-temperature superconductivity.

Hubbard model↗

Atacama Cosmology Telescope: Multiprobe cosmology with unWISE galaxies and ACT DR6 CMB lensing

We present a joint analysis of the cosmic microwave background (CMB) lensing power spectra measured from the Data Release 6 of the Atacama Cosmology Telescope (ACT) and Planck PR4, cross-correlations between the ACT and Planck lensing reconstruction and galaxy clustering from unWISE, and the unWISE clustering auto-spectrum. We obtain 1.5% constraints on the matter density fluctuations at late times parametrized by the best constrained parameter combination 𝑆$^{3⁢x⁢2⁢pt}_{8}$ ≡ 𝜎 8 ⁢(Ω 𝑚 /0.3) 0.4 = 0.815 ± 0.012. The commonly used 𝑆 8 ≡ 𝜎 8⁢ (Ω 𝑚 /0.3) 0.5 parameter is constrained to 𝑆 8 = 0.816 ± 0.015. In combination with baryon acoustic oscillation (BAO) measurements we find 𝜎 8 = 0.815 ± 0.012. We also present sound-horizon-independent estimates of the present day Hubble rate of 𝐻 0 = 66.4$^{+3.2}_{−3.7}$ km s −1 Mpc −1 from our large scale structure data alone and 𝐻 0 = 64.3$^{+2.1}_{−2.4}$ km s −1 Mpc −1 in combination with uncalibrated supernovae from Pantheon+. Using parametric estimates of the evolution of matter density fluctuations, we place constraints on cosmic structure in a range of high redshifts typically inaccessible with cross-correlation analyses. Combining lensing cross- and autocorrelations, we derive a 3.3% constraint on the integrated matter density fluctuations above 𝑧 = 2.4, one of the tightest constraints in this redshift range and fully consistent with a Λ cold dark matter (Λ⁢CDM) model fit to the primary CMB from Planck. Finally, combining with primary CMB observations and using the extended low redshift coverage of these combined datasets we derive constraints on a variety of extensions to the Λ⁢CDM model including massive neutrinos, spatial curvature, and dark energy. We find in flat Λ⁢CDM⁢ ∑𝑚 𝜈 < 0.12 eV at 95% confidence using the large scale structure data, BAO measurements from Sloan Digital Sky Survey, and primary CMB observations.

79 ASTRONOMY AND ASTROPHYSICS↗

Atacama Cosmology Telescope DR6 and DESI: Structure growth measurements from the cross-correlation of DESI legacy imaging galaxies and CMB lensing from ACT DR6 and 𝑃⁢𝑙⁢𝑎⁢𝑛⁢𝑐⁢𝑘 PR4

We measure the growth of cosmic density fluctuations on large scales and across the redshift range 0.3 < 𝑧 < 0.8 through galaxy clustering and the cross-correlation of the ACT data release 6 cosmic microwave background (CMB) lensing map and galaxies from the Dark Energy Spectroscopic Instrument Legacy Survey, using three galaxy samples spanning the redshifts of 0.3 ≲ 𝑧 ≲ 0.45, 0.45 ≲ 𝑧 ≲ 0.6, 0.6 ≲ 𝑧 ≲ 0.8. We adopt a scale cut where nonlinear effects are negligible, so that the cosmological constraints are derived from the linear regime. We determine the amplitude of matter fluctuations over all three redshift bins using Atacama Cosmology Telescope (ACT) data alone to be 𝑆 8 ≡ 𝜎 8 ⁢(Ω 𝑚 /0.3) 0.5 =0.772 ± 0.040 in a joint analysis combining the three redshift bins and ACT lensing alone. Using a combination of ACT and Planck data we obtain 𝑆 8 = 0.765 ± 0.032. The lowest redshift bin used is the least constraining and exhibits a ∼2⁢𝜎 tension with the other redshift bins; thus we also report constraints excluding the first redshift bin, giving 𝑆 8 = 0.785 ± 0.033 for the combination of ACT and Planck. This result is in excellent agreement at the 0.3⁢𝜎 level with measurements from galaxy lensing, but is 1.8⁢𝜎 lower than predictions based on Planck primary CMB data. Understanding whether this hint of discrepancy in the growth of structure at low redshifts arises from a fluctuation, from systematics in data, or from new physics is a high priority for forthcoming CMB lensing and galaxy cross-correlation analyses.

cosmic microwave background↗

Spin Squeezing with Itinerant Magnetic Dipoles

Entanglement can improve the measurement precision of quantum sensors beyond the shot noise limit. Neutral atoms, the basis of some of the most precise and accurate optical clocks and interferometers, do not naturally exhibit the all-to-all interactions traditionally used to generate such entangled states. On the other hand, these systems exhibit exceedingly high degrees of experimental control over parameters such as temperature, spatial entropy, and itinerancy. In this work, we investigate spin squeezing in a highly coherent itinerant system of neutral atoms with magnetic dipole-dipole interactions. We achieve 7.1 dB of metrologically useful squeezing using finite-range spin-exchange interactions in an erbium quantum gas microscope, and we demonstrate that introducing atomic motion, realizing a dipolar 𝑡−𝐽 model, protects the spin sector coherence at low fillings, significantly improving the achievable spin squeezing in a 2D dipolar system. This work’s protocol can be implemented with most neutral atoms, opening the door to quantum-enhanced metrology in other itinerant dipolar systems, such as molecules or optical lattice clocks, and serves as a novel method for studying itinerant quantum magnetism with long-range interactions.

Atomic, optical & lattice clocks↗

Theory of quasiparticle generation by microwave drives in superconducting qubits

Microwave drives play a central role in the control of superconducting quantum circuits, enabling qubit gates, readout, and parametric interactions. As the drive frequencies are typically an order of magnitude smaller than (twice) the superconducting gap, it is generally assumed that such drives do not disturb the BCS ground state. However, sufficiently strong drives can activate multiphoton pair-breaking processes that generate quasiparticles (QPs) and result in qubit errors. In this work, we present a theoretical framework for calculating the rates of multiphoton-assisted pair-breaking transitions induced by charge- or flux-coupled microwave drives. Through illustrative examples, we show that photon-assisted QP generation may affect novel high-frequency dispersive readout architectures, as well as Floquet-engineered superconducting circuits operating under strong driving.

circuit quantum electrodynamics↗

Non-Neutron Transmutation of Used Nuclear Fuel (Final Report)

The primary goal of this study is to develop a national facility concept for transmuting long-lived fission products (LLFP) to substantially reduce the disposal impact by minimizing the need for a geologic-timescale repository. As a charter for this study, the national transmutation facility was required to reduce the radiotoxicity and decay heat of LLFP isotopes by at least 90% relative to their values at discharge from a commercial LWR, while consuming less than 10% of the reactor's energy. The identified LLFP isotopes are Se-79, Zr-93, Tc-99, I-129, Sn-126, and Cs-135, whose radiotoxicity is about 99% of the total radiotoxicity of all fission products at 1,000 years. Approximately ~72 kg of LLFPs is discharged every year from a 1,000 MWe commercial or advanced nuclear reactor. First, LLFP transmutation options with non-neutron beams (photons and protons) were explored. The study concluded that LLFP transmutation is feasible with high-energy, high-intensity photons or protons, but impractical on an engineering scale due to low transmutation rates and the high energy requirements to produce the desired photon or proton beams. As alternatives, LLFP transmutation options with neutrons from fission, fusion, and spallation reactions were additionally explored. The transmutation options using advanced critical reactors are attractive only for selective LLFP isotopes because the production rates of several LLFP isotopes (Zr-93, Sn-126, and Cs-135) from fission reactions are larger than the transmutation rates. The transmutation options with only spallation neutrons are favorable to transmute all LLFP isotopes, but as a tradeoff, the net transmutation rates are reduced. The national transmutation facility concept was developed following an exploration of transmutation options using various incident particles. The proposed national LLFP transmutation comprises a dedicated molten-salt reactor (MSR), a proton accelerator, and a spallation neutron-based transmuter. The MSR power was set at 300 MWt and 120 MWe, with the thermal power approximately 10% of that of a commercial 1,000 MWe PWR. The electricity generated by the MSR powers the accelerator and transmuter. The accelerator produces 1 GeV, 30 mA protons, which are introduced into the spallation neutron-based transmuter. The spallation neutron-based transmuter consists of a central spallation target and LLFP target pins merged in a heavy water tank. The six LLFP isotopes are separated into two groups. Tc-99, I-129, and Se-79, having larger neutron cross sections, belong to group A, while Zr-93, Sn126, and Cs-135, having smaller neutron cross sections, belong to group B. Then, for effective transmutation, LLFPs in groups A and B are transmuted in the dedicated MSR and in a spallation neutron-based transmuter, respectively. The estimated capital cost of the national transmutation facility is approximately $\$$3.1B, and its annual O&M cost is expected to be ~$\$$182M. Radiotoxicity and decay heat of LLFPs were calculated and compared with those of the original LLFPs. It was assumed that the targets were made with elementwise LLFP rather than isotopic LLFP, owing to the potentially high cost of isotopic separation from used nuclear fuels. The decay heat of LLFPs can be reduced by more than 90% using a single national transmutation facility. However, radiotoxicity decreases by 79–84%, which does not meet the transmutation performance requirement, primarily because Cs-135 is produced rather than depleted. Thus, to meet the design requirement, Cs-135 should be separated from other Cs isotopes and irradiated in a spallation neutron-based transmuter. Then, radiotoxicity decreases by ~92%.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Multizone Modeling of Black Hole Accretion and Feedback in 3D GRMHD: Bridging Vast Spatial and Temporal Scales

Simulating accretion and feedback from the horizon scale of supermassive black holes (SMBHs) out to galactic scales is challenging because of the vast range of scales involved. Elaborating on H. Cho et al., we describe and test a "multizone" technique, which is designed to tackle this difficult problem in three-dimensional general relativistic magnetohydrodynamic (GRMHD) simulations. While short-timescale variability should be interpreted with caution, the method is demonstrated to be well-suited for finding dynamical steady states over a wide dynamic range. We simulate accretion on a nonspinning SMBH ($a\ast$ = 0) using initial conditions and the external galactic potential from a large-scale galaxy simulation and achieve a steady state over eight decades in radius. As found in H. Cho et al., the density scales with radius as ρ ∝ r –1 inside the Bondi radius R B , which is located at R B = 2 × 10 5 r g (≈60 pc for M87), where r g is the gravitational radius of the SMBH; the plasma-β is ~ unity, indicating an extended magnetically arrested state; the mass accretion rate $\dot{M}$ is ≈1% of the analytical Bondi accretion rate ${\dot{M}}_{{\rm{B}}};$ and there is continuous energy feedback out to ≈100R B (or beyond > kpc) at a rate $\approx 0.02\dot{M}{c}^{2}$. Surprisingly, no ordered rotation in the external medium survives as the magnetized gas flows to smaller radii, and the final steady solution is very similar to when the exterior has no rotation. Using the multizone method, we simulate GRMHD accretion over a wide range of Bondi radii, R B ~ 10 2 –10 7 r g , and find that $\dot{M}/{\dot{M}}_{{B}}\approx {({R}_{{B}}/6\,{r}_{g})}^{-0.5}$.

79 ASTRONOMY AND ASTROPHYSICS↗