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At least 505 records · Page 28

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

The design of protein–protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein–protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning–based methods to unlock the widespread application of designed protein–protein interfaces and self-assembling protein nanomaterials in biotechnology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Supramolecular assembly of polycation/mRNA nanoparticles and in vivo monocyte programming

Size-dependent phagocytosis is a well-characterized phenomenon in monocytes and macrophages. However, this size effect for preferential gene delivery to these important cell targets has not been fully exploited because commonly adopted stabilization methods for electrostatically complexed nucleic acid nanoparticles, such as PEGylation and charge repulsion, typically arrest the vehicle size below 200 nm. Here, we bridge the technical gap in scalable synthesis of larger submicron gene delivery vehicles by electrostatic self-assembly of charged nanoparticles, facilitated by a polymer structurally designed to modulate internanoparticle Coulombic and van der Waals forces. Specifically, our strategy permits controlled assembly of small poly(β-amino ester)/messenger ribonucleic acid (mRNA) nanoparticles into particles with a size that is kinetically tunable between 200 and 1,000 nm with high colloidal stability in physiological media. We found that assembled particles with an average size of 400 nm safely and most efficiently transfect monocytes following intravenous administration and mediate their differentiation into macrophages in the periphery. When a CpG adjuvant is co-loaded into the particles with an antigen mRNA, the monocytes differentiate into inflammatory dendritic cells and prime adaptive anticancer immunity in the tumor-draining lymph node. This platform technology offers a unique ligand-independent, particle-size-mediated strategy for preferential mRNA delivery and enables therapeutic paradigmsviamonocyte programming.

Science & Technology - Other Topics↗

Polarons are probes of the dynamic nanoscale environments found in electrochemically doped π-conjugated polymers

Charge carriers (i.e., polarons) in electrochemically doped organic (semi)conductors are proposed to be regulated by several physicochemical features, including the chemical compositions and structures of the π-conjugated frameworks of the semiconductor building blocks, the chemistry of the electrolyte (considering both the salt and solvent), multiscale and time-dependent morphology variations across the material as a function of electrochemical processes, and assorted permutations of these and other factors. To address these hypotheses, we investigate the energetic, optoelectronic, chemical, and local structural properties of negative polarons (radical anions) as a function of electrochemical doping in the donor–acceptor, π-conjugated redox copolymer P(NDI2OD-T2), also referred to as N2200. A critical finding is that there is not just “one type” of polaron in electrochemically doped P(NDI2OD-T2). Rather, an ensemble of polarons exists, with the polarons having optoelectronic signatures that are defined by their nanoscale environments. Importantly, the polaron optical signatures serve as local probes for how the operando electrochemical environments are dynamically working in concert to facilitate charge transport. Collectively, the distinctive and extensive integration of theory and measurement science presented here establishes a baseline for the roles that semiconductor and electrolyte chemistries and dynamic structural features have on polarons in electrochemically doped organic semiconductors and how these factors influence the energetics and rates of polaron transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analysis of overlapping count data

Counts of a specific characteristic were obtained within regions defined on an object that was manufactured in a proprietary setting. The count regions were altered during production and resulted in misaligned or overlapping count data. A closed-formula maximum likelihood estimator (MLE) of the new region means is derived using all of the available count data and an independent Poisson model. The MLE is shown to be preferable to estimators constructed using generalized linear models for the overlapping data setting. This closed-form estimator extends to over-dispersed overlapping count data as the quasi-MLE and also performs well with correlated overlapping count data. Standard errors for the estimator are approximated and are validated with a simulation study. Additionally, the methods are extended to overlapping multinomial data. Illustrative examples of the methods are provided throughout the paper and are reproducible with the supplemental R code. Additionally, proofs of the paper’s results are also included in the supplemental material.

97 MATHEMATICS AND COMPUTING↗

Electrochemistry of PUREX: R is for Reduction and Ion Transfer

The PUREX (Plutonium, Uranium, Reduction, EXtraction) process is the foundation of all industrial activities that involve the recycling of plutonium and uranium from used nuclear fuel. With over 70 years of research, engineering, and operations, it can be argued that little opportunity is left for further discovery and new fundamental understandings regarding PUREX, in general, and tri-n-butyl phosphate (TBP), in particular. Through use of an advanced electroanalytical approach, molecular-level insights regarding the back-extraction of Pu(IV) by reductive separation is reported. Studies of model PUREX systems, with lanthanide ions extracted into 20 % TBP in n-dodecane, are used to demonstrate the approach. These studies reveal knowledge pertinent to mass transfer aspects of the biphasic reductive stripping reaction central to the separation of U and Pu in PUREX. Two lanthanide ions—Ce(IV) and Yb(III)—were extracted from their concentrated solutions in aqueous 3 M HNO 3 to expressly provide electrically conducting third phases to facilitate electrochemical data acquisition. To simplify the diabolically-complicated reductive separation aspects of PUREX, the controlled polarization of electrode surfaces was used to reduce Ce(IV) and Yb(III) in place of chemical reductants. Electroanalyses of the biphasic systems with Ce(IV) and Yb(III) using three-phase electrode differential pulse voltammetry demonstrate the effects of mass transfer across water-oil interfaces on the electrode potentials for the reduction to Ce(III) and Yb(II). These reductions trigger nitrate transfer out of the oil phase for Ce and proton transfer into the organic phase for Yb. This is in correlation with the transfer of the charge-neutral ion pairs Ce·3NO 3 and Yb·2NO 3 out of the oil phases. Here, the differences in ion transfer steps reflect significant variations in the equilibrium speciation of multinuclear Ce(IV) and mononuclear Yb(III) solvates of TBP in the oil phases and the loading of the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Functionally graded magnetic materials: a perspective to advance charged particle optics through compositional engineering

Additive manufacturing has ushered in a new paradigm of bottom-up materials-by-design of spatially non-uniform materials. Functionally graded materials have locally tailored compositions to provide optimized global properties and performance. In this letter, we propose an opportunity for the application of graded magnetic materials as lens elements for charged particle optics. A Hiperco50/Hymu80 (FeCo-2 V/Fe-80Ni-5Mo) graded magnetic alloy was successfully additively manufactured via Laser Directed Energy Deposition with spatially varying magnetic properties. The compositional gradient is then applied using computational simulations to demonstrate how a tailored material can enhance the magnetic performance of a critical, image-forming component of a transmission electron microscope.

36 MATERIALS SCIENCE↗

Chiral soft algebras for $\mathcal{N}$ = $2$ gauge theory

Some time ago, Seiberg and Witten solved for moduli spaces of vacua parameterized by scalar vacuum expectation values in $\mathcal{N}$ = $2$ gauge theories. More recently, new vacua associated to soft theorems and asymptotic symmetries have been found. Furthermore, this paper takes some first steps towards a complete picture of the infrared geometry of $\mathcal{N}$ = $2$ gauge theory incorporating both of these infrared structures.

N = 2 gauge theory↗

Velocity-dependent J-factors for annihilation radiation from cosmological simulations

Abstract We determine the dark matter pair-wise relative velocity distribution in a set of Milky Way-like halos in the Auriga and APOSTLE simulations. Focusing on the smooth halo component, the relative velocity distribution is well-described by a Maxwell-Boltzmann distribution over nearly all radii in the halo. We explore the implications for velocity-dependent dark matter annihilation, focusing on four models which scale as different powers of the relative velocity: Sommerfeld, s-wave, p-wave, and d-wave models. We show that the J-factors scale as the moments of the relative velocity distribution, and that the halo-to-halo scatter is largest for d-wave, and smallest for Sommerfeld models. The J-factor is strongly correlated with the dark matter density in the halo, and is very weakly correlated with the velocity dispersion. This implies that if the dark matter density in the Milky Way can be robustly determined, one can accurately predict the dark matter annihilation signal, without the need to identify the dark matter velocity distribution in the Galaxy.

Astronomy & Astrophysics↗

Velocity-dependent annihilation radiation from dark matter subhalos in cosmological simulations

Here, we use the suite of Milky Way-like galaxies in the Auriga simulations to determine the contribution to annihilation radiation from dark matter subhalos in three velocity-dependent dark matter annihilation models: Sommerfeld, p-wave, and d-wave models. We compare these to the corresponding distribution in the velocity-independent s-wave annihilation model. For both the hydrodynamical and dark-matter-only simulations, only in the case of the Sommerfeld-enhanced annihilation does the total annihilation flux from subhalos exceed the total annihilation flux from the smooth halo component within the virial radius of the halo. Progressing from Sommerfeld to the s, p, and d-wave models, the contribution from the smooth component of the halo becomes more dominant, implying that for the p-wave and d-wave models the smooth component is by far the dominant contribution to the radiation. Comparing to the Galactic center excess observed by Fermi-LAT, for all simulated halos the emission is dominated by the smooth halo contribution. However, it is possible that for Sommerfeld models, extrapolation down to mass scales below the current resolution limit of the simulation would imply a non-negligible contribution to the gamma-ray emission from the Galactic Center region.

79 ASTRONOMY AND ASTROPHYSICS↗

Velocity-dependent J-factors for Milky Way dwarf spheroidal analogues in cosmological simulations

We study the impact of the dark matter velocity distribution modelling on signals from velocity-dependent dark matter annihilation in Milky Way dwarf spheroidal galaxies. Using the high resolution APOSTLE simulations, we identify analogues corresponding to Milky Way dwarf spheroidal galaxies, and from these directly determine the dark matter pair-wise relative velocity distribution, and compare to best-fitting Maxwell-Boltzmann distribution models. For three velocity-dependent annihilation models, p-wave, d-wave, and the Sommerfeld model, we quantify the errors introduced when using the Maxwell-Boltzmann parameterization. We extract a simple power-law relation between the maximum circular velocity of the dwarf spheroidal analogue and the peak speed of the Maxwell-Boltzmann distribution. We show that this relation can be used to accurately calculate the dark matter relative velocity distribution, and find that it allows us to estimate the dark matter annihilation signal without the need to directly calculate the relative velocity distribution for each galaxy. The scatter in the J-factors calculated from the analogues dominates the uncertainty obtained when compared to the J-factor as determined from the observational data for each dwarf spheroidal, with the largest scatter from d-wave models and the smallest from Sommerfeld models.

79 ASTRONOMY AND ASTROPHYSICS↗

The Atacama Cosmology Telescope: DR6 maps

We present Atacama Cosmology Telescope (ACT) Data Release 6 (DR6) maps of the Cosmic Microwave Background temperature and polarization anisotropy at arcminute resolution over three frequency bands centered on 98, 150 and 220 GHz. The maps are based on data collected with the AdvancedACT camera over the period 2017–2022 and cover 19,000 square degrees with a median combined depth of 10 μK arcmin. We describe the instrument, mapmaking and map properties and illustrate them with a number of figures and tables.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The Atacama Cosmology Telescope: DR6 power spectra, likelihoods and ΛCDM parameters

We present power spectra of the cosmic microwave background (CMB) anisotropy in temperature and polarization, measured from the Data Release 6 maps made from Atacama Cosmology Telescope (ACT) data. These cover 19,000 deg 2 of sky in bands centered at 98, 150 and 220 GHz, with white noise levels three times lower than Planck in polarization. We find that the ACT angular power spectra estimated over 10,000 deg 2 , and measured to arcminute scales in TT, TE and EE, are well fit by the sum of CMB and foregrounds, where the CMB spectra are described by the ΛCDM model. Combining ACT with larger-scale Planck data, the joint P-ACT dataset provides tight limits on the ingredients, expansion rate, and initial conditions of the universe. We find similar constraining power, and consistent results, from either the Planck power spectra or from ACT combined with WMAP data, as well as from either temperature or polarization in the joint P-ACT dataset. When combined with CMB lensing from ACT and Planck, and baryon acoustic oscillation data from the Dark Energy Spectroscopic Instrument (DESI DR1), we measure a baryon density of Ω b h 2 = 0.0226 ± 0.0001, a cold dark matter density of Ω c h 2 = 0.118 ± 0.001, a Hubble constant of H 0 = 68.22 ± 0.36 km/s/Mpc, a spectral index of n s = 0.974 ± 0.003, and an amplitude of density fluctuations of σ 8 = 0.813 ± 0.005. Including the DESI DR2 data tightens the Hubble constant to H 0 = 68.43 ± 0.27 km/s/Mpc; ΛCDM parameters agree between the P-ACT and DESI DR2 data at the 1.6σ level. We find no evidence for excess lensing in the power spectrum, and no departure from spatial flatness. The contribution from Sunyaev-Zel'dovich (SZ) anisotropy is detected at high significance; we find evidence for a tilt with suppressed small-scale power compared to our baseline SZ template spectrum, consistent with hydrodynamical simulations with feedback.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Atacama Cosmology Telescope: DR6 constraints on extended cosmological models

We use new cosmic microwave background (CMB) primary temperature and polarization anisotropy measurements from the Atacama Cosmology Telescope (ACT) Data Release 6 (DR6) to test foundational assumptions of the standard cosmological model, ΛCDM, and set constraints on extensions to it. We derive constraints from the ACT DR6 power spectra alone, as well as in combination with legacy data from the Planck mission. To break geometric degeneracies, we include ACT and Planck CMB lensing data and baryon acoustic oscillation data from DESI Year-1. To test the dependence of our results on non-ACT data, we also explore combinations replacing Planck with WMAP and DESI with BOSS, and further add supernovae measurements from Pantheon+ for models that affect the late-time expansion history. We verify the near-scale-invariance (running of the spectral index dn s /d ln k = 0.0062 ± 0.0052) and adiabaticity of the primordial perturbations. Neutrino properties are consistent with Standard Model predictions: we find no evidence for new light, relativistic species that are free-streaming (N eff = 2.86 ± 0.13, which combined with astrophysical measurements of primordial helium and deuterium abundances becomes N eff = 2.89 ± 0.11), for non-zero neutrino masses (∑m ν < 0.089 eV at 95% CL), or for neutrino self-interactions. We also find no evidence for self-interacting dark radiation (N idr < 0.134), or for early-universe variation of fundamental constants, including the fine-structure constant (α EM /α EM,0 = 1.0043 ± 0.0017) and the electron mass (m e /m e,0 = 1.0063 ± 0.0056). Our data are consistent with standard big bang nucleosynthesis (we find Y p = 0.2312 ± 0.0092), the COBE/FIRAS-inferred CMB temperature (we find T CMB = 2.698 ± 0.016 K), a dark matter component that is collisionless and with only a small fraction allowed as axion-like particles, a cosmological constant (w = -0.986 ± 0.025), and the late-time growth rate predicted by general relativity (γ = 0.663 ± 0.052). We find no statistically significant preference for a departure from the baseline ΛCDM model. In fits to models invoking early dark energy, primordial magnetic fields, or an arbitrary modified recombination history, we find H 0 = 69.9 +0.8 -1.5 , 69.1 ± 0.5, or 69.6 ± 1.0 km/s/Mpc, respectively; using BOSS instead of DESI BAO data reduces the central values of these constraints by 1–1.5 km/s/Mpc while only slightly increasing the error bars. In general, models introduced to increase the Hubble constant or to decrease the amplitude of density fluctuations inferred from the primary CMB are not favored over ΛCDM by our data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Abatement of ionizing radiation for superconducting quantum devices

Ionizing radiation has been shown to reduce the performance of superconducting quantum circuits. In this report, we evaluate the expected contributions of different sources of ambient radioactivity for typical superconducting qubit experiment platforms. Our assessment of radioactivity inside a typical cryostat highlights the importance of selecting appropriate materials for the experiment components nearest to qubit devices, such as packaging and electrical interconnects. We present a shallow underground facility (30-meter water equivalent) to reduce the flux of cosmic rays and a lead shielded cryostat to abate the naturally occurring radiogenic gamma-ray flux in the laboratory environment. We predict that superconducting qubit devices operated in this facility could experience a reduced rate of correlated multi-qubit errors by a factor of approximately 20 relative to the rate in a typical above-ground, unshielded facility. Finally, we outline overall design improvements that would be required to further reduce the residual ionizing radiation rate, down to the limit of current generation direct detection dark matter experiments.

47 OTHER INSTRUMENTATION↗

Urban NO x emissions around the world declined faster than anticipated between 2005 and 2019

Emission inventory development for air pollutants, by compiling records from individual emission sources, takes many years and involves extensive multi-national effort. A complementary method to estimate air pollution emissions is in the use of satellite remote sensing. In this study, NO 2 observations from the Ozone Monitoring Instrument are combined with re-analysis meteorology to estimate urban nitrogen oxide (NO X ) emissions for 80 global cities between 2005 and 2019. The global average downward trend in satellite-derived urban NO X emissions was 3.1%–4.0% yr -1 between 2009 and 2018 while inventories show a 0%–2.2% yr -1 drop over the same timeframe. This difference is primarily driven by discrepancies between satellite-derived urban NO X emissions and inventories in Africa, China, India, Latin America, and the Middle East. In North America, Europe, Korea, Japan, and Australasia, NO X emissions dropped similarly as reported in the inventories. In Europe, Korea, and Japan only, the temporal trends match the inventories well, but the satellite estimate is consistently larger over time. While many of the discrepancies between satellite-based and inventory emissions estimates represent real differences, some of the discrepancies might be related to the assumptions made to compare the satellite-based estimates with inventory estimates, such as the spatial disaggregation of emissions inventories. Overall, our work identifies that the three largest uncertainties in the satellite estimate are the tropospheric column measurements, wind speed and direction, and spatial definition of each city.

54 ENVIRONMENTAL SCIENCES↗