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At least 703 records · Page 39

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Science & Technology - Other Topics↗

Mathematical Models and Numerical Methods for High-Fidelity Simulation of Ignition of Reactive Mixtures by Nanosecond Plasma Discharges in Realistic Configurations

We present a newly developed framework for the numerical simulation of ignition of reactive mixtures using single or repeated nanosecond discharge pulses. The framework builds upon the AMReX library, using the existing compressible solver PeleC and low-Mach solver PeleLMeX and allowing for adaptive mesh refinement, complex geometries, and execution on next-generation high-performance computing (HPC) systems. High-fidelity elementary models are adopted for weakly-ionised plasma discharges with significant energy deposition, consistent with nanosecond discharge pulses, and then implemented in the solver. The treatment of non-thermal electrons and charged species, thermodynamics of non-equilbrium species, plasma kinetics, limiting time scales, and boundary conditions for charged species are discussed and addressed for computational efficiency. The framework is demonstrated for three relevant applications: single and multi-pulse discharges in air, single pulse ignition of an ethylene/air mixture, and a three-dimensional plasma discharge in air with temperature stratification. The successful application of the framework demonstrates the feasibility of high-fidelity simulation of ignition of air/hydrocarbon mixtures in three-dimensions with multiple discharge pulses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Generation of reactive species in water film dielectric barrier discharges sustained in argon, helium, air, oxygen and nitrogen

Activation of liquids with atmospheric pressure plasmas is being investigated for environmental and biomedical applications. When activating the liquid using gas plasma produced species (as opposed to plasmas sustained in the liquid), a rate limiting step is transport of these species into the liquid. To first order, the efficiency of activating the liquid is improved by increasing the ratio of the surface area of the water in contact with the plasma compared to its volume—often called the surface-to-volume ratio (SVR). Maximizing the SVR then motivates the plasma treatment of thin films of liquids. In this paper, results are discussed from a computational investigation using a global model of atmospheric pressure plasma treatment of thin water films by a dielectric barrier discharge (DBD) sustained in different gases (Ar, He, air, N 2 , O 2 ). The densities of reactive species in the plasma activated water (PAW) are evaluated. The residence time of the water in contact with the plasma is increased by recirculating the PAW in plasma reactor. Longer lived species such as H 2 O 2aq and NO 3 - aq accumulate over time (aq denotes an aqueous species). DBDs sustained in Ar and He are the most efficient at producing H 2 O 2aq , DBDs sustained in argon produces the largest density of NO 3 - aq with the lowest pH, and discharges sustained in O 2 and air produce the highest densities of O 3aq . Finally, comparisons to experiments by others show agreement in the trends in densities in PAW including O 3aq , OH aq , H 2 O 2aq and NO 3 - aq , and highlight the importance of controlling desolvation of species from the activated water.

42 ENGINEERING↗

Blue phosphorene reactivity on the Au(111) surface

Abstract The synthesis of blue phosphorene by molecular beam epitaxy (MBE) has recently come under the spotlight due to its potential applications in electronic and optoelectronic devices. However, this synthesis remains a significant challenge. The surface reactivity between the P atoms and the Au atoms should be considered for the P/Au(111) system. In the MBE process, the temperature of the substrate is a key parameter for the growth of blue phosphorene. During the initial growth stage, irregularly shaped Phosphorus clusters grow on top of Au(111) surface at room temperature. When the substrate temperature is increased, these clusters transform into a phosphorene-like structure with a honeycomb lattice. An atom exchange reaction is observed between the P and first layer Au atoms under thermal activation at higher temperature, where the P atoms replace Au atoms to form a blue phosphorene structure within the top Au layer and at the step edges.

Materials Science↗

En echelon faults reactivated by wastewater disposal near Musreau Lake, Alberta

We use machine-learning and cross-correlation techniques to enhance earthquake detectability by two magnitude units for the earthquake sequence near Musreau Lake, Alberta, which is induced by wastewater disposal. This deep catalogue reveals a series of en echelon ~N–S oriented strike-slip faults that are favourably oriented for reactivation. These faults require only ~0.6 MPa overpressure for triggering to occur. Earthquake activity occurs in bursts, or episodes; episodes restricted to the largest fault tend to have earthquakes starting near the southern end (distant from injectors) and progressing northwards (towards the injectors). While most events are concentrated along these ~N–S oriented faults, we also delineate smaller faults. Together, these findings suggest pore pressure as the triggering mechanism, where a time-dependent increase in pore pressure likely caused these faults to progressively reawaken. Analysis of the ‘next record-breaking event’, a statistical model that forecasts the sequencing of earthquake magnitudes, suggests that the next largest event would be M L ~4.3. The seismically illuminated length of the largest fault indicates potential magnitudes as large as M w 5.3.

58 GEOSCIENCES↗

Induced microseismicity and tremor signatures illuminate different slip behaviours in a natural shale fault reactivated by a fluid pressure stimulation (Mont Terri)

SUMMARY Fault slip induced by fluid perturbation in shale formations may only lead to a sparse seismicity. However, fault slip may strongly impact the integrity of shale formations that serve as caprocks for geological reservoirs holding buoyant fluids such as CO2, natural gas or hydrogen. A better understanding of the fluid reactivation processes of fault and the seismic triggering process is therefore critical for reservoir monitoring and fault stability. Here we analyse the seismic responses of a shale fault exposed to fluid pressurization during an in situ field-scale injection experiment at ∼340 m depth in the Mont Terri underground research laboratory (Switzerland). Two main types of seismic signals are observed as the fault was activated and started to slowly slip. After an aseismic phase, we observed tremor signatures and an increase in noise amplitude, which were directly associated with the slowly propagating fault slip in response to fluid injection. These signatures were later followed by micro-earthquakes that seem to occur further away from the fluid-pressurized area. We interpret these micro-earthquakes to be triggered by stress perturbations from the main slip growth. These two classes of seismic responses therefore highlight two different processes. Tremors seem to be a more direct observation for the fluid-induced slip propagation than micro-earthquakes. Even hidden in the noise, they precede earthquake failures, thus providing a useful tool for monitoring fluid leakage activated by slow deformation on low permeable shale faults, with applications for sealing integrity of caprocks.

De Barros, Louis (ORCID:0000000255419162)↗

Revisiting the reactivity between HCO and CH 3 on interstellar grain surfaces

The formation of interstellar complex organic molecules is currently thought to be dominated by the barrierless coupling between radicals on the interstellar icy grain surfaces. Previous standard density functional theory (DFT) results on the reactivity between CH 3 and HCO on amorphous water surfaces showed that the formation of CH 4 + CO by H transfer from HCO to CH 3 assisted by water molecules of the ice was the dominant channel. In contrast, the adopted description of the electronic structure of the biradical (i.e. CH 3 /HCO) system was inadequate [without the broken-symmetry (BS) approach]. In this work, we revisit the original results by means of BS-DFT both in gas phase and with one water molecule simulating the role of the ice. Results indicate that the adoption of BS-DFT is mandatory to describe properly biradical systems. In the presence of the single water molecule, the water-assisted H transfer exhibits a high energy barrier. In contrast, CH 3 CHO formation is found to be barrierless. Yet, direct H transfer from HCO to CH 3 to give CO and CH 4 presents a very low energy barrier, hence being a potential competitive channel to the radical coupling and indicating, moreover, that the physical insights of the original work remain valid.

79 ASTRONOMY AND ASTROPHYSICS↗

Inelastic, exchange, and reactive processes in rovibrationally excited collisions of HD with H

ABSTRACT The HD molecule is an important coolant in early universe chemistry models and a tracer of H2 in star-forming regions. Rate coefficients for collisional excitation and de-excitation of HD rotational and vibrational levels form important ingredients in astrophysical models. While collisions with He, H2, and H are the most important, available data for H + HD collisions are largely limited to temperatures less than 1000 K for the vibrational ground state, low-lying rotational levels of the v = 1 HD vibrational level, or computed without reactive contributions. Here, through explicit quantum scattering calculations, we report extensive data for rovibrational transitions in HD induced by H atoms for a range of rotational levels in v = 1 and some v = 0 levels for temperatures up to 1000 K. The significance of the computed results for astrophysical modeling is discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chlamydomonas as a model for reactive oxygen species signaling and thiol redox regulation in the green lineage

While the maintenance of redox balance is important for all organisms, the energy balance in the chloroplast is particularly tightly linked to the overall cellular redox status in photosynthetic organisms. Excess light can cause overreduction of the photosynthetic electron transport chain, which, when unchecked, results in the generation of reactive oxygen species (ROS) that can oxidize cellular components including nucleic acids, proteins, and lipids (Li et al., 2009). A photosynthetic cell possesses multiple layers of defense against oxidative stress, such as antioxidant enzymes (Foyer and Noctor, 2005) and alternative electron transfer pathways (Alric and Johnson, 2017). At the same time, ROS can function as important signals that mediate responses to biotic and abiotic stresses (Apel and Hirt, 2004). Reversibly oxidizable small molecules and proteins can serve as ROS sinks and signals and are re-reduced by multiple mechanisms. For example, the ascorbate–glutathione (GSH) cycle is central in controlling ROS levels and regenerating/reducing oxidized cellular redox agents (Figure 1A; reviewed by Foyer and Noctor, 2011). The functions of many proteins can be regulated by the redox state of cysteine residues, such as the formation or reduction of disulfides by thioredoxins (TRX) (Buchanan, 1991) and glutaredoxins (Michelet et al., 2013b; Figure 1, B and C).

59 BASIC BIOLOGICAL SCIENCES↗

Complexion dictated thermal resistance with interface density in reactive metal multilayers

Multilayers composed of aluminum (A1) and platinum (Pt) exhibit a non-monotonic trend in thermal resistance with bilayer thickness as measured by time domain thermoreflectance. The thermal resistance initially increases with reduced bilayer thickness only to reach a maximum and then decrease with further shrinking of the multilayer period. These observations are attributed to the evolving impact of an intermixed amorphous complexion approximately 10 nm in thickness, which forms at each boundary between Al- and Pt-rich layers. Scanning transmission electron microscopy combined with energy dispersive X-ray spectroscopy find that the elemental composition of the complexion varies based on bilayer periodicity as does the fraction of the multilayer composed of this interlayer. These variations in complexion mitigate boundary scattering within the multilayers as shown by electronic transport calculations employing density functional theory and non-equilibrium Green's functions on amorphous structures obtained via finite temperature molecular dynamics. The lessening of boundary scattering reduces the total resistance to thermal transport leading to the observed non-monotonic trend thereby highlighting the central role of complexion on thermal transport within reactive metal multilayers.

36 MATERIALS SCIENCE↗

Distributed Neural Representation for Reactive In Situ Visualization

Implicit neural representations (INRs) have emerged as a powerful tool for compressing large-scale volume data. This opens up new possibilities for in situ visualization. However, the efficient application of INRs to distributed data remains an underexplored area. Here, in this work, we develop a distributed volumetric neural representation and optimize it for in situ visualization. Our technique eliminates data exchanges between processes, achieving state-of-the-art compression speed, quality and ratios. Our technique also enables the implementation of an efficient strategy for caching large-scale simulation data in high temporal frequencies, further facilitating the use of reactive in situ visualization in a wider range of scientific problems. We integrate this system with the Ascent infrastructure and evaluate its performance and usability using real-world simulations.

Wu, Qi↗

Phase evolution during conventional and reactive flash sintering of (Mg,Ni,Co,Cu,Zn)O via in situ X-ray diffraction

Reactive flash sintering (RFS) enables the simultaneous synthesis and sintering of ceramics and has been shown to affect the reaction pathway of different materials. Herein, in situ synchrotron X-ray diffraction (XRD) is used to investigate the (Mg,Ni,Co,Cu,Zn)O entropy-stabilized oxide formation during: (i) conventional heating and (ii) RFS under current rate-controlled mode. The same reaction pathway is verified in both instances: the starting rock-salt (RS), spinel (Co 3 O 4 ), tenorite (CuO), and wurtzite (ZnO) phases transform into a single RS phase with a (1 1 1) to (2 0 0) intensity ratio of 0.67, consistent with a random distribution of the cations into the structure. Pt lattice peak shift from the XRD patterns is used as standard to monitor the sample surface temperature, revealing a strong endothermic reaction during the RS single-phase formation (Pt peaks shift toward higher angles while increasing sample temperature/current density). Furthermore, in RFS, the single-phase RS structure is formed in just 60 s at a furnace temperature of 600°C and a current rate of 220 mA mm -2 /min. Therefore, RFS greatly accelerates the synthesis of (Mg,Ni,Co,Cu,Zn)O, however, it does not play a role in the reaction pathway for this material formation.

36 MATERIALS SCIENCE↗

Plastoquinone redox status influences carboxysome integrity via a RpaA ‐ and reactive oxygen species‐dependent regulatory network

SUMMARY Carboxysomes are bacterial microcompartments that encapsulate Rubisco and are a core component of the cyanobacterial carbon concentration mechanism (CCM). While carboxysome number, size, and spatial organization vary in different environmental conditions (CO 2 , light availability, redox state, temperature, and light quality), the molecular mechanisms underlying this potentially adaptive process remain elusive. Herein, we observe that mutants of the circadian rhythm/metabolism factor, Regulator of Phycobilisome Association A (RpaA), exhibit a striking breakdown of carboxysomes under certain environmental conditions. We find that conditions leading to overreduction of the plastoquinone (PQ) pool (mixotrophic growth, high irradiance, or chemical inhibition of electron transfer from PQ to the cytochromeb 6 fcomplex) are accompanied by an elevated generation of reactive oxygen species (ROS) and correlate with the loss of carboxysome integrity. Carboxysome breakdown is reversed by environmental conditions or chemical inhibitors that prevent PQ overreduction and accompanying ROS generation. Taken together, our data support a novel link between the redox status of the PQ pool and carboxysome integrity. Our results have implications for the fundamental understanding of cyanobacterial energy‐balancing pathways and may indicate new research directions for understanding how the carboxysome is remodeled in response to changing environments.

Plant Sciences↗

Gasoline Compression Ignition on a Light-Duty Multi-Cylinder Engine Using a Wide Range of Fuel Reactivities and Heavy Fuel Stratification

Many research studies have focused on utilizing gasoline in modern compression ignition engines to reduce emissions and improve efficiency. Collectively, this combustion mode has become kn+own as gasoline compression ignition (GCI). One of the biggest challenges with GCI operation is maintaining control over the combustion process through the fuel injection strategy, such that the engine can be controlled on a cycle-by-cycle basis. Research studies have investigated a wide variety of GCI injection strategies (i.e., fuel stratification levels) to maintain control over the heat release rate while achieving low-temperature combustion (LTC). This work shows that at loads relevant to light-duty engines, partial fuel stratification (PFS) with gasoline provides very little controllability over the timing of combustion. On the contrary, heavy fuel stratification (HFS) provides very linear and pronounced control over the timing of combustion. However, the HFS strategy has challenges achieving LTC operation due to the air handling burdens associated with the high exhaust gas recirculation (EGR) rates that are required to reduce NOx emissions to near zero levels. In this work, a wide variety of gasoline fuel reactivities (octane numbers ranging from <40 to 87) were investigated to understand the engine performance and emissions of HFS-GCI operation on a multi-cylinder light-duty engine. Overall, the results indicate that over an EGR sweep at 4 bar brake mean effective pressure (BMEP), the gasoline fuels can achieve LTC operation with ultra-low NO x and soot emissions, while conventional diesel combustion (CDC) is unable to simultaneously achieve low NO x and soot. At 10 bar BMEP, all the gasoline fuels were compared to diesel, but using mixing controlled combustion and not LTC.

33 ADVANCED PROPULSION SYSTEMS↗

A Double-Wiebe Function for Reactivity Controlled Compression Ignition Combustion Using Reformate Diesel

Abstract Reactivity controlled compression ignition (RCCI) combustion has previously been proposed as a method to achieve high fuel conversion efficiency and reduce engine emissions. A single-fuel RCCI combustion strategy can have decreased fuel system complexity by using a reformate fuel for port fuel injection and the parent fuel (diesel) for direct injection. This paper presents a one-dimensional computational model of a compression ignition engine with single-fuel RCCI. A Wiebe function is used to predict the combustion process by representing the mass fraction burned (MFB) on a crank angle resolved basis. One single-Wiebe function (SWF) and two double-Wiebe functions(DWFs) were fitted to experimentally derive MFB data using the least-square method. The fitted results were compared with MFBs calculated from experimental data to verify the accuracy. The SWF did not fully capture the MFB curve with high fidelity while the detailed DWF captured the MFB curve within a root mean square error of 1.4%. The reduced double-Wiebe function (RDWF) also resulted in a predicted combustion profile with similar accuracy. Hence, the RDWF was used in a GT-power thermodynamic study to understand the effects of the low-temperature heat release (LTHR) fraction and combustion phasing on combustion characteristics. At optimum phasing of 5–10 crank angle degree after the top dead center, increasing the LTHR fraction from 20% to 60% resulted in the fuel conversion efficiency increasing from 39.5% to 41.1%, thus suggesting that the reformate fuel-based RCCI strategy is viable to unlock improved combustion performance.

Energy & Fuels↗

Gasoline Compression Ignition (GCI) on a Light-Duty Multi-Cylinder Engine Using a Wide Range of Fuel Reactivities and Heavy Fuel Stratification

Many research studies have focused on utilizing gasoline in modern compression ignition engines to reduce emissions and improve efficiency. Collectively, this combustion mode has become known as gasoline compression ignition (GCI). One of the biggest challenges with GCI operation is maintaining control over the combustion process through the fuel injection strategy, such that the engine can be controlled on a cycle-by-cycle basis. Research studies have investigated a wide variety of GCI injection strategies (i.e., fuel stratification levels) to maintain control over the heat release rate while achieving low temperature combustion (LTC). This work shows that at loads relevant to light-duty engines, partial fuel stratification (PFS) with gasoline provides very little controllability over the timing of combustion. On the contrary, heavy fuel stratification (HFS) provides very linear and pronounced control over the timing of combustion. However, the HFS strategy has challenges achieving LTC operation due to the air handling burdens associated with the high EGR rates that are required to reduce NOx emissions to near zero levels. In this work, a wide variety of gasoline fuel reactivities (octane numbers ranging from < 40 to 87) were investigated to understand the engine performance and emissions of HFS-GCI operation on a multi-cylinder light-duty engine. The results indicate that over an EGR sweep at 4 bar BMEP, the gasoline fuels can achieve LTC operation with ultra-low NOx and soot emissions, while conventional diesel combustion (CDC) is unable to simultaneously achieve low NOx and soot. At 10 bar BMEP, all the gasoline fuels were compared to diesel, but using mixing controlled combustion and not LTC.

Dempsey, Adam↗

Electron beam injection from a hollow cathode plasma into a downstream reactive environment: Characterization of secondary plasma production and Si 3 N 4 and Si etching

A material etching system was developed by combining beam electron injection from a direct current (DC) hollow-cathode (HC) electron source with the downstream reactive environment of a remote CF 4 /O 2 low temperature plasma. The energy of the injected beam electrons is controlled using an acceleration electrode biased positively relative to the HC Argon discharge. For an acceleration voltage greater than the ionization potential of Ar, the extracted primary electrons can produce a secondary plasma in the process chamber. We characterized the properties of the secondary plasma by performing Langmuir probe measurements of the electron energy probability function (EEPF) 2.5 cm below the extraction ring. The data indicate the existence of two major groups of electrons, including electrons with a primary beam electron energy which varies as the acceleration voltage is varied, along with low energy electrons produced by ionization of the Ar gas atoms in the process chamber by the injected beam electrons. When combining the HC Ar beam electron with a remote CF 4 /O 2 electron cyclotron wave resonance (ECWR) plasma, the EEPF of both the low energy plasma electron and beam electron components decreases. Additionally, we studied surface etching of Si3N4 and poly-crystalline Si (poly-Si) thin films as a function of process parameters, including the acceleration voltage (0-70 V), discharge current of the HC discharge (1-2 A), pressure (2- 100 mTorr), source to substrate distance (2.5 to 5 cm), and feed gas composition (with or without CF 4 /O 2 ). The direction of the incident beam electrons was perpendicular to the surface. Si 3 N 4 and poly-crystalline silicon etching are seen and indicate an electronneutral synergy effect. No/little remote plasma spontaneous etching was observed for the conditions used in this study, and the etching is confined to the substrate area irradiated by the injected beam electrons. The electron etched Si 3 N 4 surface etching rate profile distribution is confined within a ~30 mm diameter circle, which is slightly broader than the area for which poly-Si etching is seen, and coincides closely with the spatial profile of beam electrons as determined by the Langmuir probe measurements. The magnitude of poly-Si etching rate is by a factor of two times smaller than the Si 3 N 4 etching rate. In this paper, we discuss possible explanations of the data and the role of surface charging.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Shape tuning of large area silicon nanotip arrays through reactive ion etching

Nanostructures formed in silicon form an important class of structures that span a broad spectrum of application areas. Of these, columnar structures of silicon featuring tiplike apexes have their own niche applications. Here, the ability to afford shape tunability for these structures further enhances their application potential. In this paper, we present our findings on the large area fabrication of silicon nanotips defined through microsphere lithography and shape tuned through a combination of different reactive ion etching (RIE) techniques. The self-sharpening mechanism of the tips when using nonplanar etch masks (microspheres) under anisotropic etching conditions is elucidated. We further show that depending on the manner of etching (continuous versus discrete multistep etch), identical anisotropic etching recipes produce vastly different tip morphologies. Hourglass-shaped silicon tips were obtained when silicon was subjected to anisotropic followed by isotropic etching conditions. Sharp silicon tips with tip apex radii on the order of 2 nm have been successfully realized when the RIE shape tuned tips were subjected to a series of oxidative sharpening steps.

74 ATOMIC AND MOLECULAR PHYSICS↗