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At least 631 records · Page 35

Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families

Broadly reactive antibodies that target sequence-diverse antigens are of interest for vaccine design and monoclonal antibody therapeutic development because they can protect against multiple strains of a virus and provide a barrier to evolution of escape mutants. Using LIBRA-seq (linking B cell receptor to antigen specificity through sequencing) data for the B cell repertoire of an individual chronically infected with human immunodeficiency virus type 1 (HIV-1), we identified a lineage of IgG3 antibodies predicted to bind to HIV-1 Envelope (Env) and influenza A Hemagglutinin (HA). Two lineage members, antibodies 2526 and 546, were confirmed to bind to a large panel of diverse antigens, including several strains of HIV-1 Env, influenza HA, coronavirus (CoV) spike, hepatitis C virus (HCV) E protein, Nipah virus (NiV) F protein, and Langya virus (LayV) F protein. We found that both antibodies bind to complex glycans on the antigenic surfaces. Antibody 2526 targets the stem region of influenza HA and the N-terminal domain (NTD) region of SARS-CoV-2 spike. A crystal structure of 2526 Fab bound to mannose revealed the presence of a glycan-binding pocket on the light chain. Antibody 2526 cross-reacted with antigens from multiple pathogens and displayed no signs of autoreactivity. These features distinguish antibody 2526 from previously described glycan-reactive antibodies. Further study of this antibody class may aid in the selection and engineering of broadly reactive antibody therapeutics and can inform the development of effective vaccines with exceptional breadth of pathogen coverage.

Microbiology↗

Dependable classical-quantum computing systems engineering

Increasing evidence suggests quantum computing (QC) complements traditional High-Performance Computing (HPC) by leveraging its unique capabilities, leading to the emergence of a new, hybrid paradigm, QHPC. However, this integration introduces new challenges, with dependability–defined by reproducibility, resiliency, and security and privacy–emerging as a central concern for building trustworthy systems that provide an advantage to the users. This paper proposes a framework for dependable QHPC system design, organized around these three pillars. We identify integration challenges, anticipate roadblocks, and highlight productive synergies across QC, HPC, cloud platforms, and network security. Drawing from both classical computing principles and quantum-specific insights, we present a roadmap for co-design that supports robust hybrid architectures. Our approach offers concrete metrics for assessing dependability, provides design guidance for engineers working at the QC-HPC interface, and surfaces new engineering questions around complexity, scale, and fault tolerance. Ultimately, designing for dependability is key to realizing practical, scalable QHPC systems and accelerating the broader quantum ecosystem capable of translating quantum promises into actual application delivery.

HPC↗

A permafrost implementation in the simple carbon–climate model Hector v.2.3pf

Abstract. Permafrost currently stores more than a fourth of global soil carbon. A warming climate makes this carbon increasingly vulnerable to decomposition and release into the atmosphere in the form of greenhouse gases. The resulting climate feedback can be estimated using land surface models, but the high complexity and computational cost of these models make it challenging to use them for estimating uncertainty, exploring novel scenarios, and coupling with other models. We have added a representation of permafrost to the simple, open-source global carbon–climate model Hector, calibrated to be consistent with both historical data and 21st century Earth system model projections of permafrost thaw. We include permafrost as a separate land carbon pool that becomes available for decomposition into both methane (CH4) and carbon dioxide (CO2) once thawed; the thaw rate is controlled by region-specific air temperature increases from a preindustrial baseline. We found that by 2100 thawed permafrost carbon emissions increased Hector’s atmospheric CO2 concentration by 5 %–7 % and the atmospheric CH4 concentration by 7 %–12 %, depending on the future scenario, resulting in 0.2–0.25 ∘C of additional warming over the 21st century. The fraction of thawed permafrost carbon available for decomposition was the most significant parameter controlling the end-of-century temperature change in the model, explaining around 70 % of the temperature variance, and was distantly followed by the initial stock of permafrost carbon, which contributed to about 10 % of the temperature variance. The addition of permafrost in Hector provides a basis for the exploration of a suite of science questions, as Hector can be cheaply run over a wide range of parameter values to explore uncertainty and can be easily coupled with integrated assessment and other human system models to explore the economic consequences of warming from this feedback.

54 ENVIRONMENTAL SCIENCES↗

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Deep-UV Trigger for Ground-State Ring-Opening Dynamics of 1,3-Cyclohexadiene

While the ring-opening reaction of 1,3-cyclohexadiene upon excitation to the 1B state has been extensively studied, little is known about the reaction dynamics when exciting higher-lying states. The complexity of the potential energy surfaces found in computational studies suggests that the reaction outcome may depend sensitively on the excitation wavelength and the initially prepared electronic state. We explore the photo-induced kinetics of 1,3-cyclohexadiene upon excitation at 200 nm to the 3p state by ultrafast time-resolved, gas-phase X-ray scattering using the Linac Coherent Light Source (LCLS). Analysis of the experimental scattering data, particularly with respect to the anisotropy, and comparison to ab-initio calculations reveals that the excitation leads dominantly to the 3px and 3py Rydberg electronic states, which relax to the ground state with a time constant of 208 ±11 fs. Unlike in the conventional photochemically induced conrotatory electrocyclic reaction observed at lower excitation energies, at 200 nm the majority of the molecules (76 ± 3%) relax to vibrationally hot cyclohexadiene in the ground electronic state. Furthermore, the photoexcitation activates the reaction on the ground electronic state surface. An equilibrium between the hot cyclohexadiene and 1,3,5-hexatriene is reached by a thermal reaction, giving rates for the forward and backward reaction of 174 ±13 ps and 355 ±45 ps, respectively. The scattering pattern of the final hexatriene product reveals a thermal distribution of rotamers about the carbon-carbon single bonds. The rapid decay of the initially excited state back into the ring-closed form allows us to observe a ground state chemical reaction using ultrafast X-ray scattering.

74 ATOMIC AND MOLECULAR PHYSICS↗

Channel Rank Improvement in Urban Drone Corridors Using Passive Intelligent Reflectors

Multiple-input multiple-output (MIMO) techniques can help in scaling the achievable air-to-ground (A2G) channel capacity while communicating with drones. However, spatial multiplexing with drones suffers from rank deficient channels due to the unobstructed line-of-sight (LoS), especially in millimeter wave (mmWave) frequencies that use narrow beams. One possible solution is utilizing low-cost and low-complexity metamaterial based intelligent reflecting surfaces (IRS) to enrich the multipath environment, taking into account that the drones are restricted to fly only within well-defined drone corridors. A hurdle with this solution is placing the IRSs optimally. In this study, we propose an approach for IRS placement with a goal to improve the spatial multiplexing gains, and hence to maximize the average channel capacity in a predefined drone corridor. Our results at 6 GHz, 28 GHz and 60 GHz show that the proposed approach increases the average rates for all frequency bands for a given drone corridor, when compared with the environment where there are no IRSs present, and IRS-aided channels perform close to each other at sub-6 and mmWave bands.

99 GENERAL AND MISCELLANEOUS↗

Learning heterogeneous reaction kinetics from X-ray movies pixel-by-pixel

Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries 1 and electrocatalysts 2. Experimental characterizations of such materials by operando microscopy produce rich image datasets 3–6, but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation 7. Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces.

Chueh, William↗

Distinct Surface and Bulk Thermal Behaviors of LiNi 0.6 Mn 0.2 Co 0.2 O 2 Cathode Materials as a Function of State of Charge

Understanding how structural and chemical transformations take place in particles under thermal conditions can inform designing thermally robust electrode materials. Such a study necessitates the use of diagnostic techniques that are capable of probing the transformations at multiple length scales and at different states of charge (SOC). In this study, the thermal behavior ofLiNi 0.6 Mn 0.2 Co 0.2 O 2 (NMC-622) was examined as a function of SOC, using an array of bulk and surface-sensitive techniques. In general, thermal stability decreases as lithium content is lowered and conversion in the bulk to progressively reduced metal oxides (spinels, rock salt) occurs as the temperature is raised. Hard X-ray absorption spectroscopy (XAS) and X-ray Raman spectroscopy (XRS) experiments, which probe the bulk, reveal that Ni and Co are eventually reduced when partially delithiated samples (regardless of the SOC) are heated, although Mn is not. Surface-sensitive synchrotron techniques, such as soft XAS and transmission X-ray microscopy (TXM), however, reveal that for 50% delithiated samples, apparent oxidation of nickel occurs at particle surfaces under some circumstances. This is partially compensated by reduction of cobalt but may also be a consequence of redistribution of lithium ions upon heating. TXM results indicate the movement of reduced nickel ions into particle interiors or oxidized nickel ions to the surface or both. These experiments illustrate the complexity of the thermal behavior of NMC cathode materials. The study also informs the importance of investigating the surface and bulk difference as a function of SOC when studying the thermal behaviors of battery materials.

25 ENERGY STORAGE↗

Evaluation of global teleconnections in CMIP6 climate projections using complex networks

In climatological research, the evaluation of climate models is one of the central research subjects. As an expression of large-scale dynamical processes, global teleconnections play a major role in interannual to decadal climate variability. Their realistic representation is an indispensable requirement for the simulation of climate change, both natural and anthropogenic. Therefore, the evaluation of global teleconnections is of utmost importance when assessing the physical plausibility of climate projections. We present an application of the graph-theoretical analysis tool δ-MAPS, which constructs complex networks on the basis of spatio-temporal gridded data sets, here sea surface temperature and geopotential height at 500 hPa. Complex networks complement more traditional methods in the analysis of climate variability, like the classification of circulation regimes or empirical orthogonal functions, assuming a new non-linear perspective. While doing so, a number of technical tools and metrics, borrowed from different fields of data science, are implemented into the δ-MAPS framework in order to overcome specific challenges posed by our target problem. Those are trend empirical orthogonal functions (EOFs), distance correlation and distance multicorrelation, and the structural similarity index. δ-MAPS is a two-stage algorithm. In the first place, it assembles grid cells with highly coherent temporal evolution into so-called domains. In a second step, the teleconnections between the domains are inferred by means of the non-linear distance correlation. We construct 2 unipartite and 1 bipartite network for 22 historical CMIP6 climate projections and 2 century-long coupled reanalyses (CERA-20C and 20CRv3). Potential non-stationarity is taken into account by the use of moving time windows. The networks derived from projection data are compared to those from reanalyses. Our results indicate that no single climate projection outperforms all others in every aspect of the evaluation. But there are indeed models which tend to perform better/worse in many aspects. Differences in model performance are generally low within the geopotential height unipartite networks but higher in sea surface temperature and most pronounced in the bipartite network representing the interaction between ocean and atmosphere.

58 GEOSCIENCES↗

Characterization of a Molecule Partially Confined at the Pore Mouth of a Zeotype

Abstract We investigate the interaction between a molecule and a pore mouth—a critical step in adsorption processes—by characterizing the conformation of a macrocyclic calix[4]arene‐Ti IV complex, which is grafted on the external surface of a zeotype (*‐SVY). X‐ray absorption and 13 C{ 1 H} CPMAS NMR spectroscopies independently detect a unique conformation of this complex when it is grafted at crystallographically equivalent locations that lie at the interface of 7 Å hemispherical microporous cavities and the external surface. Electronic structure calculations support the presence of this unique conformation, and suggest that it is brought about by a specific orientation of the macrocycle that maximizes non‐covalent interactions between calix[4]arene upper‐rim tert ‐butyl substituents and the microporous‐cavity walls. Our comparative study provides a rare “snapshot” of a molecule partially confined at a pore mouth, an essential intermediate for adsorption into micropores, and demonstrates how surrounding environment controls this confinement in a sensitive fashion.

Grosso‐Giordano, Nicolás A.↗

Site heterogeneity and broad surface-binding isotherms in modern catalysis: Building intuition beyond the Sabatier principle

Learning the science of heterogeneous catalysis and electrocatalysis always starts with the simple case of a flat, uniform surface with an ideal adsorbate. It has of course been recognized for a century that real catalysts are more complicated. For the increasingly complex catalysts of the 21st century, this Perspective argues that surface heterogeneity and non-ideal binding isotherms are central features, and their implications need to be incorporated in current thinking. A variety of systems are described herein where catalyst complexity leads to broad, non-Langmuirian surface isotherms for the binding of hydrogen atoms – and this occurs even for ideal, flat Pt(111) surfaces. Modern catalysis employs nanoscale materials whose surfaces have substantial step, edge, corner, impurity, and other defect sites, and they increasingly have both metallic and non-metallic elements M n X m , including metal oxides, chalcogenides, pnictides, carbides, doped carbons, etc. The surfaces of such catalysts are often not crystal facets of the bulk phase underneath, and they typically have a variety of potential active sites. Catalytic surfaces in operando are often non-stoichiometric, amorphous, dynamic, and impure, and often vary from one part of the surface to another. Understanding of the issues that arise at such nanoscale, multi-element catalysts is just beginning to emerge. Yet these catalysts are widely discussed using Brønsted/Bell-Evans-Polanyi (BEP) relations, volcano plots, Tafel slopes, the Butler-Volmer equation, and other linear free energy relations (LFERs), which all depend on the implicit assumption that the active sites are “similar” and that surface adsorption is close to ideal. These assumptions underly the ubiquitous intuition based on the Sabatier Principle, that the fastest catalysis will occur when key intermediates have free energies of adsorption that are not too strong nor too weak. Current catalysis research often aims to minimize the complexity of non-ideal isotherms through experimental and computational design (e.g., the use of single crystal surfaces), and these studies are the foundation of the field. In contrast, this Perspective argues that the heterogeneity of binding sites and binding energies is an inherent strength of these catalysts. Here, this diversity makes many nanoscale catalysts inherently a high-throughput screen wrapped in a tiny package. Only by making the heterogeneity part of the foundation of catalysis models, sorting the types of active sites and dissecting non-ideal binding isotherms, will modern catalysis learn to harness the inherent diversity of real catalysts. Controlling and exploiting diversity rather than avoiding it will help to optimize complex modern catalysts and catalytic conditions.

Mayer, James M.↗

Methane Chemisorption on Oxide‐Supported Pt Single Atom

Abstract Methane chemisorption has been recently demonstrated on the rutile IrO 2 (110) surface. However, it remains unclear how the general requirements are for methane chemisorption or complexation with a single atom on an oxide surface. By exploring methane adsorption on Pt 1 substitutionally doped on many rutile‐type oxides using hybrid density functional theory, we show that the occupancy of the Pt d z 2 orbital is the key to methane chemisorption. Pt single atom on the semiconducting or wide‐gap oxides such as TiO 2 and GeO 2 strongly chemisorbs methane, because the empty Pt d z 2 orbital is located in the gap and can effectively accept σ‐electron donation from the methane C−H bond. In contrast, Pt single atom on metallic oxides such as IrO 2 and RuO 2 does not chemisorb methane, because the Pt d z 2 orbital strongly mixes with the support‐oxide electronic states and become more occupied, losing its ability to chemisorb methane. This study sheds further light on the impact of the interaction between a Pt single atom and the oxide support on methane adsorption.

Fung, Victor↗

Hydrogen Bonds and H 3 O + Formation at the Water Interface with Formic Acid Covered Anatase TiO 2

Carboxylic acid-modified TiO 2 surfaces in aqueous environment are of widespread interest, yet atomic-scale understanding of their structure is limited. In this work, we investigate formic acid (FA) on anatase TiO 2 (101) (A-101) in contact with water using density functional theory (DFT) and ab-initio molecular dynamics (AIMD). Isolated FA molecules adsorbed in a deprotonated bridging bidentate (BD) form on A-101 are found to remain stable at the interface with water, with the acid proton transferred to a surface oxygen to form a surface bridging hydroxyl (O br H). With increasing FA coverage, adsorbed monolayers of only BD and successively of alternating monodentate (MD) and BD species give rise to a higher concentration of surface O br H’s. Simulations of these adsorbed monolayers in water environment show that some protons are released from the surface O br H’s to water resulting in a negatively charged surface with nearby solvated H 3 O + ions. These results provide insight into the complex acid-base equilibrium between an oxide surface, adsorbates and water and can also help obtain a better understanding of the wetting properties of chemically modified TiO 2 surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strengthening of Calcite Assemblages Through Chemical Complexation Reactions

Abstract Utilization of subsurface reservoirs, including fluid extraction/injection, can induce stress changes and modify in‐situ chemical equilibrium causing subcritical fracturing and deformation. Here, we show that chemical complexation reactions at the newly created fracture surfaces within the crack tip limit fracturing during consolidation of granular calcite assemblages. Previously, we showed that analogous chemical complexation reactions can increase in‐situ fracture toughness in pre‐fractured single crystal calcite. To test the chemical complexation effect under subsurface conditions, we consolidated samples under increasing hydrostatic pressure to induce widespread intergranular fracturing in the presence of fluid containing common anions. Measured consolidation, acoustic emissions, and microfracturing demonstrate that deformation correlates with complexation affinity for calcium in calcite and aqueous anions. We observed that deformation is lowest in the presence of strongly complexing anions (e.g., sulphate), provided sufficient anion diffusion rates. This understanding is important for predicting reservoir effective strength in the presence of complex aqueous fluids.

Choens, R. C.↗

Development of a Method for Shape Optimization for a Gas Turbine Fuel Injector Design Using Metal-Additive Manufacturing

Adjoint shape optimization has enabled physics-based optimal designs for aerodynamic surfaces. Additive manufacturing (AM) makes it possible to manufacture complex shapes. However, there has been a gap between optimal and manufacturable surfaces due to the inherent limitations of commercial computational fluid dynamics (CFD) codes to implement geometric constraints during adjoint computation. In such cases, the design sensitivities are exported and used to perform constrained shape modifications using parametric information stored in computer aided design (CAD) files to satisfy manufacturability constraints. However, modifying the design using adjoint methods in CFD solvers and performing constrained shape modification in CAD can lead to inconsistencies due to different shape parameterization schemes. This paper describes a method to enable the simultaneous optimization of the fluid domain and impose AM manufacturability constraints, resolving one of the key issues of geometry definition for isogeometric analysis. Similar to a grid convergence study, the proposed method verifies the consistencies between shape parameterization techniques present within commercial CAD and CFD software during mesh movement as a part of the adjoint shape optimization routine. By identifying the appropriate parameters essential to a shape optimization study, the error metric between the different parameterization techniques converges to demonstrate sufficient consistencies for justifiable exchange of data between CAD and CFD. For the identified shape optimization parameters, the error metric to measure the deviation between the two parameterization schemes lies within the AM laser-powder bed fusion (L-PBF) process tolerance. Additionally, comparison for subsequent objective function calculations between iterations of the optimization loop showed acceptable differences within 1% variation between the modified geometries obtained using the two parameterization schemes. This method provides justification for the use of multiphysics guided adjoint design sensitivities computed in CFD software to perform shape modifications in CAD to incorporate AM manufacturability constraints during the shape optimization loop such that optimal designs are also additively manufacturable.

33 ADVANCED PROPULSION SYSTEMS↗

Structural chemistry of penta- and hexanitrato thorium($\tiny{IV}$) complexes isolated using N–H donors

In this study, a series of fifteen tetravalent thorium phases were prepared. The compounds were isolated from acidic aqueous nitrate solutions using protonated nitrogen heterocycles of varying hydrogen-bond donation strength. Structural analysis via single crystal X-ray diffraction showed that the structures are built from pentanitrato, [Th(NO 3 ) 5 (H 2 O) 2 ] 1- , and hexanitrato, [Th(NO 3 ) 6 ] 2- , molecular units, with the latter being far more prevalent in the solid state. The vibrational properties of the compounds were examined using Raman and IR spectroscopy; the spectra are dominated by stretches characteristic of nitrate and the organic ions. The relative energetics of nitrate complexation was examined using electronic structure theory. These results confirmed that there are clear thermodynamic sinks for the penta- and hexanitrato structural units that were observed experimentally. Additionally, electrostatic surface potentials (ESPs) were calculated in an effort to better understand the counterion stabilization of the complexes. The ESP surfaces showed that the position of the water and nitrate molecules and the coordination geometry of the metal complex had a clear effect on the polarizability of the two structural motifs. Despite limited speciation of the Th–nitrate structural units, the compounds exhibit rich supramolecular chemistry resulting from hydrogen bonding of the Th complexes with the organic N–H donors and π–π stacking interactions from the protonated N-heterocycles.

36 MATERIALS SCIENCE↗

Microstructure and corrosion of CrFeMnV multi-principal element alloy

In this study, a multi-principal element alloy consisting of equiatomic concentrations of Cr, Fe, Mn, and V was produced by arc melting. The combination of X-ray diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy indicated that the CrFeMnV MPEA was comprised of a BCC matrix with a dispersion of a secondary phase. Cyclic potentiodynamic polarization tests in 0.6M NaCl revealed high corrosion resistance – superior to that of stainless steel 304L, as evident from high breakdown and repassivation potentials. X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry provided insight into the formed multi-layer surface film after constant immersion and potentiostatic conditioning.

36 MATERIALS SCIENCE↗