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At least 865 records · Page 48

Predicting Hugoniot equation of state in erythritol with ab initio and reactive molecular dynamics

Erythritol has been proposed as an inert surrogate for developing theoretical and computational models to study aging in energetic materials. In this work, we present a comparison of mechanical and shock properties of erythritol computed using the ReaxFF reactive force field and from ab initio calculations employing density functional theory (DFT). We screened eight different ReaxFF parameterizations, of which the CHO parameters developed for hydrocarbon oxidation provide the most accurate predictions of mechanical properties and the crystal structure of erythritol. Further validation of the applicability of this ReaxFF parameterization for modeling erythritol is demonstrated by comparing predictions of the elastic constants, crystal structure, vibrational density of states, and Hugoniot curves against DFT calculations. The ReaxFF predictions are in close agreement with the DFT simulations for the elastic constants and shock Hugoniot when the crystal is loaded along its c axis but show as much as 30% disagreement in the elastic constants in the ab plane and 12% difference in shock pressures when shocked along the a or b crystal axes. Last, we compare thermomechanical properties predicted from classical molecular dynamics with those calculated using the quasi-harmonic approximation and show that quantum mechanical effects produce large discrepancies in the computed values of heat capacity and thermal expansion coefficients compared with classical assumptions. Combining classical molecular dynamics predictions of mechanical behavior with phonon-based calculations of thermal behaviors, we show that predicted shock-induced temperatures for pressures up to 6.5 GPa do not exceed the pressure-dependent melting point of erythritol.

Hu, Jing↗

Reactive burn model calibration using high-throughput initiation experiments at sub-millimeter length scales

We report a first-of-its-kind model calibration was performed using Sandia National Laboratories’ high-throughput initiation (HTI) experiment for two types of vapor-deposited explosive films consisting of hexanitrostilbene (HNS) or pentaerythritol tetranitrate (PETN). These films exhibit prompt initiation, and they reach steady detonation at sub-millimeter length scales. Following prior work on HNS, we test the hypothesis of approximating these explosive films as fine-grained homogeneous solids with simple Arrhenius kinetics burn models. The model calibration process is described herein using a single-step as well as a two-step Arrhenius rate law, and it consists of systematic parameter sampling leading to a reduction in the model degrees of freedom. Multiple local minima are observed; results are given for seven different optimized parameter sets. Each model set is further evaluated in a two-dimensional simulation of the critical failure thickness for a sustained detonation. Overall, the two-step Arrhenius kinetics model captures the observed behavior for HNS; however, neither model produces a good fit to the PETN data. We hypothesize that the HTI results for PETN correspond to a heterogeneous response, owing to the smaller reaction zone of PETN compared to HNS (i.e., it does not homogenize the fine-grained hot spots as well). Future work should consider using the ignition and growth model for PETN, as well as other reactive burn models such as xHVRB, AWSD, PiSURF, and CREST.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reactive co-sputtering of ternary Au–Ta–O films with tunable electrical resistivity

Heavy-metal-based films with high electrical resistivity are needed for hohlraums for magnetically-assisted inertial confinement fusion. Here, we study ternary Au-Ta-O films deposited by reactive direct-current magnetron co-sputtering from elemental Au and Ta targets in an oxygen containing atmosphere. By varying O content, the electrical resistivity of films can be tuned in a wide range of ~ 100 - 40,000 μΩ cm. With increasing O content, a drastic increase in resistivity occurs at ~ 45 at.% of O, separating regimes with two different dominant conduction mechanisms attributed to metallic conduction through the Au-Ta alloy matrix (for ≲ 45 at.% of O) and tunneling across insulating Ta 2 O 5 layers separating conducting islands (for ≳ 45 at.% of O). Post-deposition annealing at 300 °C leads to the segregation of Au into ~ 50-nm islands, sharply decreasing the resistivity for films with ≳ 45 at.% of O but not for the metal-like films with lower O content.

36 MATERIALS SCIENCE↗

Effects of diffusion barriers on reaction wave stability in Co/Al reactive multilayers

Bimetallic, reactive multilayers are uniformly structured materials composed of alternating sputter-deposited layers that may be ignited to produce self-propagating mixing and formation reactions. These nanolaminates are most commonly used as rapid-release heat sources. The specific chemical composition at each metal/metal interface determines the rate of mass transport in a mixing and formation reaction. The inclusion of engineered diffusion barriers at each interface will not only inhibit solid-state mixing but also may impede the self-propagating reactions by introducing instabilities to wavefront morphology. Here, this work examines the effect of adding diffusion barriers on the propagation of reaction waves in Co/Al multilayers. The Co/Al system has been shown to exhibit a reaction propagation instability that is dependent on the bilayer thickness, which allows for the occurrence of unstable modes in otherwise stable designs from the inclusion of diffusion barriers. Based on the known stability criteria in the Co/Al multilayer system, the way in which the inclusion of diffusion barriers changes a multilayer's heat of reaction, thermal conductivity, and material mixing mechanisms can be determined. These factors, in aggregate, lead to changes in the wavefront velocity and stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures

It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas mixtures undergoing reversible reactions described by the chemical Langevin equations, we show that thermodynamic consistency in reaction rates and the use of instantaneous temperatures for the evaluation of reaction rates is required for fluctuations for the overall system to be correct. We then formulate the required properties of a thermodynamically consistent reaction (TCR) model. As noted in the literature, while reactions are often discussed in terms of forward and reverse rates, these rates should not be modeled independently because they must be compatible with thermodynamic equilibrium for the system. Using a simple TCR model where each chemical species has constant heat capacity, we derive the explicit condition that the forward and reverse reaction rate constants must satisfy in order for the system to be thermodynamically consistent. We perform equilibrium and non-equilibrium simulations of ideal gas mixtures undergoing a reversible dimerization reaction to measure the fluctuational behavior of the system numerically. We confirm that FHD simulations with the TCR model give the correct static structure factor of equilibrium fluctuations. For the statistically steady simulation of a gas mixture between two isothermal walls with different temperatures, we show using the TCR model that the temperature variance agrees with the corresponding thermodynamic-equilibrium temperature variance in the interior of the system, whereas noticeable deviations are present in regions near walls, where chemistry is far from equilibrium.

Polimeno, Matteo [University of California, Merced↗

Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes

Hydrogen bonded electrolytes that exhibit accelerated proton transport via sequential reactive hops have drawn interest for their promise in clean energy applications. Molecular dynamics simulations of these electrolytes offer the opportunity to uncover microscopic mechanistic details that could be used to design and tune the properties of candidate electrolyte technologies. However, accurately modeling the proton transfer reactions and transport properties that give rise to high charge conductivites in these electrolytes proves computationally challenging because of the need to perform lengthy condensed phase simulations, treating both the electronic and nuclear degrees of freedom quantum mechanically. In this paper, we demonstrate that such a modeling task can be efficiently achieved with the use of density functional theory (DFT)-trained machine learning potentials (MLP) to accelerate path integral molecular dynamics (PIMD) simulations. We highlight the practical utility of this approach by using it to benchmark how closely PIMD simulations employing different DFT exchange–correlation functionals reproduce the composition-dependent densities, diffusion coefficients, and electrical conductivities of mixtures consisting of imidazole and levulinic acid. Even with the speedup afforded by our MLPs, PIMD simulations remain quite expensive. Furthermore, in order to render PIMD more computationally tractable, we introduce and benchmark the accuracy of a ring polymer contraction approach that leverages a computationally efficient short-range MLP to accelerate our PIMD simulations by an additional factor of four.

Chemical bonding↗

Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12

Cobalamin is a complex organometallic cofactor that is processed and targeted via a network of chaperones to its dependent enzymes. AdoCbl (5'-deoxyadenosylcobalamin) is synthesized from cob(II)alamin in a reductive adenosylation reaction catalyzed by adenosyltransferase (ATR), which also serves as an escort, delivering AdoCbl to methylmalonyl-CoA mutase (MCM). The mechanism by which ATR signals that its cofactor cargo is ready (AdoCbl) or not [cob(II)alamin] for transfer to MCM, is not known. In this study, we have obtained crystallographic snapshots that reveal ligand-induced ordering of the N terminus of Mycobacterium tuberculosis ATR, which organizes a dynamic cobalamin binding site and exerts exquisite control over coordination geometry, reactivity, and solvent accessibility. Cob(II)alamin binds with its dimethylbenzimidazole tail splayed into a side pocket and its corrin ring buried. The cosubstrate, ATP, enforces a four-coordinate cob(II)alamin geometry, facilitating the unfavorable reduction to cob(I)alamin. The binding mode for AdoCbl is notably different from that of cob(II)alamin, with the dimethylbenzimidazole tail tucked under the corrin ring, displacing the N terminus of ATR, which is disordered. In this solvent-exposed conformation, AdoCbl undergoes facile transfer to MCM. The importance of the tail in cofactor handover from ATR to MCM is revealed by the failure of 5'-deoxyadenosylcobinamide, lacking the tail, to transfer. In the absence of MCM, ATR induces a sacrificial cobalt–carbon bond homolysis reaction in an unusual reversal of the heterolytic chemistry that was deployed to make the same bond. Finally, the data support an important role for the dimethylbenzimidazole tail in moving the cobalamin cofactor between active sites.

59 BASIC BIOLOGICAL SCIENCES↗

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↗