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At least 559 records · Page 31

Interaction–Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions

The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG + G + TG + G + g – )-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as “preparation energy” or “reorganization energy”. We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme’s efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 310-polyglycine and H+GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction–deletion in 2-nitrobenzene-1,3-diol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Investigation of Dimethylmercury Formation Mediated by a Sulfide Mineral Surface

Mercury (Hg) pollution is a global environmental problem, but many key transformations among 29 various Hg species are not well understood. Although anaerobic microorganisms are the primary 30 producers of monomethylmercury (MMeHg), the abiotic formation of dimethylmercury (DMeHg) 31 from MMeHg have been suggested to account for a large portion of DMeHg in the ocean. It has 32 been shown that abiotic formation of DMeHg from MMeHg can be facilitated by reduced sulfur 33 groups on mineral surfaces. However, a detailed mechanistic understanding of this reaction is 34 lacking. Here we perform density functional theory (DFT) calculations to explore mechanisms of 35 DMeHg formation on the 110 surface of a CdS(s) (hawleyite) nanoparticle. We show that 36 coordination of MMeHg substituents to adjacent reduced sulfur groups protruding from the surface 37 facilitate DMeHg formation and that the reaction proceeds through direct transmethylation from 38 one MMeHg substituent to another. Solvation effects were found to play an important role in the 39 surface reconstruction of the nanoparticle and in decreasing the energetic barrier for DMeHg 40 formation. We also investigate DMeHg formation from MMeHg mediated by organic dithiols and 41 compare the results to those mediated by the mineral surface. In contrast to the surface reaction, 42 the calculations suggest that dithiol-mediated formation of DMeHg instead proceeds through a 43 mechanism in which Hg–Hg interactions activate a methyl group from one MMeHg substituent 44 for intramolecular transfer to the adjacent MMeHg substituent. These findings refine previously 45 proposed mechanisms of abiotic DMeHg formation and fill gaps in our understanding of global 46 Hg cycling in the environment.

Lian, Peng↗

Photophysical Properties and Electronic Structure of Hydroporphyrin Dyads Exhibiting Strong Through-Space and Through-Bond Electronic Interactions

Electronic interactions between tetrapyrroles are utilized in natural photosynthetic systems to tune the light-harvesting and energy/charge-transfer processes in these assemblies. Such interactions also can be employed to tailor the electronic properties of tetrapyrrolic dyads and larger arrays for use in materials science and biomedical research. Here we have utilized static and time-resolved optical spectroscopy to characterize the optical absorption and emission properties of a set of chlorin and bacteriochlorin dyads with varied degrees of through-bond (TB) and through-space (TS) interactions between the constituent macrocycles. The dyads consist of two chlorins or two bacteriochlorins joined by a linker that utilizes a triple-double-triple bond (enediyne) motif in which the double bond portion is a ester-substituted ethylene or o-phenylene unit. The photophysical studies are coupled with density functional theory (DFT) calculations to probe the ground-state molecular orbital (MO) characteristics of the dyads and time-dependent calculations (TDDFT) to elucidate excited-state properties. The latter include electronic characteristics of the singlet excited state manifold and the absorption transitions to these states from the electronic ground state. Comparison of the MO and calculated spectral properties of each dyad with the linker present versus disrupted (by eliminating the double-bond portion) gives insight into the relative contributions of TB versus TS interactions to the electronic properties of the dyads. The results show that the TB and TS contributions are additive (constructively interfere), which is not always the case for molecular dyads. Most of the dyads have shorter lifetimes of the lowest singlet excited state compared to the parent monomer, which derives from increased S 1 → S 0 internal conversion. The enhancement is greater for the dyads in benzonitrile than in toluene. Furthermore, the studies provide insights into the nature of the electronic interactions between the constituents in the tetrapyrrole arrays and how these interactions dictate the spectral properties and excited-state decay characteristics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanobubble Formation and Coverage during High Current Density Alkaline Water Electrolysis

Gas bubbles are a necessary byproduct of water electrolysis whereby hydrogen and oxygen are produced from water. These attached gases reduce the electrode’s active area, which necessitates a deep understanding of the bubble life cycle starting from nanobubbles. Synchronized with the electrochemistry, the time evolution of the surface nanobubble size and coverage is resolved using grazing incidence small-angle X-ray scattering (GISAXS) and correlated with optical microscopy and theoretical calculations to show that a significant portion of the surface is covered in nanobubbles after larger micron-sized bubbles are observed. Further, these nanobubbles increase in number and decrease in size, toward 2 nm diameter, with the charge passed. The trend in size and number is consistent with an increase in supersaturation, which reduces the nascent bubble size. Altogether, this study suggests a significant portion of the surface contains nanobubbles and that strategies to reduce the dissolved hydrogen would be effective at reducing the nanobubble surface coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Valence Electron Distributions from Sub-Angstrom Convergent Beam Electron Diffraction

Modern aberration-corrected scanning transmission electron microscopes can acquire four-dimensional data sets (“4D STEM”) by recording convergent beam electron diffraction (CBED) patterns, using precisely positioned, sub-angstrom probes. Here, we demonstrate that these patterns can probe the site symmetry, atomic displacements, and valence electron distributions at individual atomic columns. To this end, 4D STEM CBED patterns were acquired from SrTiO 3 single crystals and compared with patterns calculated using scattering potentials derived from density functional theory. Here, we show that an aspherical valence electron charge build-up at the oxygen sites causes intensity asymmetries in the low-angle scattering portion of the patterns. Using strained SrTiO 3 films containing subtle polar displacements within nanometer-sized domains, it is shown that the high-angle scattering portion in each pattern is sensitive to atomic displacements.

36 MATERIALS SCIENCE↗

Using Ambient Noise Seismic Interferometry and Local and Teleseismic Earthquakes to Determine Crustal Thickness and Moho Structure of the Northwestern Gulf of Mexico Margin

Abstract The northwestern part of the Gulf of Mexico has undergone two episodes of continental rifting and collision and produced structural artifacts that are now buried under many kilometers of sediments, complicating investigations of the region. The deep sedimentary package precludes outcrops and points to a need for the application of seismic techniques, but low rates of seismicity in the region and sparse seismic monitoring limit the utility of traditional seismic methods. We therefore use diverse data to perform two‐dimensional seismic tomography across the dry land portion of the margin. Data are gleaned from teleseismic and regional earthquakes, postcritical SsPmp arrivals, and direct P wave energy identified with seismic interferometry that were recorded by a broadband, three‐component array and partially overlapping short‐period, vertical‐component array. The Pn and postcritical SsPmp phase help constrain the Moho discontinuity, which a previous receiver function study suggested was absent beneath the seaward portion of this transect. A high‐velocity body is observed in the crust at the same location as the Houston Magnetic Anomaly, possibly marking rocks from the Alleghenian continental assembly. The crust thins from NW to SE, indicating that extension occurred mostly to the south of the Ouachita orogeny. Our model indicates that the margin's sediment package reaches a maximum thickness of ~15 km at the coast and becomes unresolvably thin near the Llano Uplift.

58 GEOSCIENCES↗

Strong Local Evaporative Cooling Over Land Due to Atmospheric Aerosols

Abstract Aerosols can enhance terrestrial productivity through increased absorption of solar radiation by the shaded portion of the plant canopy—the diffuse radiation fertilization effect. Although this process can, in principle, alter surface evaporation due to the coupling between plant water loss and carbon uptake, with the potential to change the surface temperature, aerosol‐climate interactions have been traditionally viewed in light of the radiative effects within the atmosphere. Here, we develop a modeling framework that combines global atmosphere and land model simulations with a conceptual diagnostic tool to investigate these interactions from a surface energy budget perspective. Aerosols increase the terrestrial evaporative fraction, or the portion of net incoming energy consumed by evaporation, by over 4% globally and as much as ∼40% regionally. The main mechanism for this is the increase in energy allocation from sensible to latent heat due to global dimming (reduction in global shortwave radiation) and slightly augmented by diffuse radiation fertilization. In regions with moderately dense vegetation (leaf area index >2), the local surface cooling response to aerosols is dominated by this evaporative pathway, not the reduction in incident radiation. Diffuse radiation fertilization alone has a stronger impact on gross primary productivity (+2.18 Pg C y −1 or +1.8%) than on land evaporation (+0.18 W m −2 or +0.48%) and surface temperature (−0.01 K). Our results suggest that it is important for land surface models to distinguish between quantity (change in total magnitude) and quality (change in diffuse fraction) of radiative forcing for properly simulating surface climate.

Chakraborty, TC↗

Predicting Characteristics of the Water Cycle From Scaling Relationships

Over multi-decadal time scales, assuming that changes in subsurface water storage are negligible, the continental precipitative water flux, P, can be divided into two principal components, Q (run-off, including soil infiltration and groundwater recharge) and ET (evapotranspiration). Taking into account a broadly applied Budyko's phenomenology to describe the relationship of ET/P as a function of PET/P, where PET is the potential evapotranspiration, we propose a theoretical framework for predicting characteristics of the water cycle from scaling relationships. In this framework, the ecosystem net primary productivity is expressed in terms of soil formation and vegetation growth, which is mathematically optimized with respect to the water partitioning, generating directly the value ET/P. Here, the mathematical optimization is based on the general ecological principle that dominant ecosystems tend to be those that, for any given conditions, maximize conversion of atmospheric carbon to biomass. It is shown that application of the results of mathematical optimization to water-limited ecosystems is possible by applying the optimization only to a vegetation covered portion of the surface. For energy-limited ecosystems, the optimization can be applied only to a portion of the precipitation equal to PET, assuming that the remaining P simply runs off. We use theoretical and actual values of plant root fractal dimensionalities, d f , to predict ranges of ET/P as a function of PET/P for 0 ≤ PET/P ≤ 1 and compare with annual and multi-decadal means of ET/P. By comparing the developed approach with a large amount of data collected from the literature, we demonstrate its successful applications to both water- and energy-limited systems.

54 ENVIRONMENTAL SCIENCES↗

Can Glacial Sea‐Level Drop‐Induced Gas Hydrate Dissociation Cause Submarine Landslides?

Abstract We conducted two‐dimensional numerical simulations to investigate the mechanisms underlying the strong spatiotemporal correlation observed between submarine landslides and gas hydrate dissociation due to glacial sea‐level drops. Our results suggest that potential plastic deformation or slip could occur at localized and small scales in the shallow‐water portion of the gas hydrate stability zone (GHSZ). This shallow‐water portion of the GHSZ typically lies within the area enclosed by three points: the BGHSZ–seafloor intersection, the seafloor at ∼600 m below sea level (mbsl), and the base of the GHSZ (BGHSZ) at ∼1,050 mbsl in low‐latitude regions. The deep BGHSZ (>1,050 mbsl) could not slip; therefore, the entire BGHSZ was not a complete slip surface. Glacial hydrate dissociation alone is unlikely to cause large‐scale submarine landslides. Observed deep‐water (much greater than 600 mbsl) turbidites containing geochemical evidence of glacial hydrate dissociation potentially formed from erosion or detachment in the GHSZ pinch‐out zone.

58 GEOSCIENCES↗

Atmospheric River Detection Under Changing Seasonality and Mean-State Climate: ARTMIP Tier 2 Paleoclimate Experiments

Atmospheric rivers (ARs) are filamentary structures within the atmosphere that account for a substantial portion of poleward moisture transport and play an important role in Earth's hydroclimate. However, there is no one quantitative definition for what constitutes an atmospheric river, leading to uncertainty in quantifying how these systems respond to global change. This study seeks to better understand how different AR detection tools (ARDTs) respond to changes in climate states utilizing single-forcing climate model experiments under the aegis of the Atmospheric River Tracking Method Intercomparison Project (ARTMIP). We compare a simulation with an early Holocene orbital configuration and another with CO2 levels of the Last Glacial Maximum to a preindustrial control simulation to test how the ARDTs respond to changes in seasonality and mean climate state, respectively. We find good agreement among the algorithms in the AR response to the changing orbital configuration, with a poleward shift in AR frequency that tracks seasonal poleward shifts in atmospheric water vapor and zonal winds. In the low CO2 simulation, the algorithms generally agree on the sign of AR changes, but there is substantial spread in their magnitude, indicating that mean-state changes lead to larger uncertainty. This disagreement likely arises primarily from differences between algorithms in their thresholds for water vapor and its transport used for identifying ARs. These findings warrant caution in ARDT selection for paleoclimate and climate change studies in which there is a change to the mean climate state, as ARDT selection contributes substantial uncertainty in such cases.

Atmospheric river, paleoclimate↗

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Hagen, Live↗

Predicting fault slip via transfer learning

Abstract Data-driven machine-learning for predicting instantaneous and future fault-slip in laboratory experiments has recently progressed markedly, primarily due to large training data sets. In Earth however, earthquake interevent times range from 10’s-100’s of years and geophysical data typically exist for only a portion of an earthquake cycle. Sparse data presents a serious challenge to training machine learning models for predicting fault slip in Earth. Here we describe a transfer learning approach using numerical simulations to train a convolutional encoder-decoder that predicts fault-slip behavior in laboratory experiments. The model learns a mapping between acoustic emission and fault friction histories from numerical simulations, and generalizes to produce accurate predictions of laboratory fault friction. Notably, the predictions improve by further training the model latent space using only a portion of data from a single laboratory earthquake-cycle. The transfer learning results elucidate the potential of using models trained on numerical simulations and fine-tuned with small geophysical data sets for potential applications to faults in Earth.

58 GEOSCIENCES↗

Remarkable heat conduction mediated by non-equilibrium phonon polaritons

Surface waves can lead to intriguing transport phenomena. In particular, surface phonon polaritons (SPhPs), which result from coupling between infrared light and optical phonons, have been predicted to contribute to heat conduction along polar thin films and nanowires. However, experimental efforts so far suggest only very limited SPhP contributions. Through systematic measurements of thermal transport along the same 3C-SiC nanowires with and without a gold coating on the end(s) that serves to launch SPhPs, here we show that thermally excited SPhPs can substantially enhance the thermal conductivity of the uncoated portion of these wires. The extracted pre-decay SPhP thermal conductance is more than two orders of magnitude higher than the Landauer limit predicted on the basis of equilibrium Bose–Einstein distributions. Here, we attribute the notable SPhP conductance to the efficient launching of non-equilibrium SPhPs from the gold-coated portion into the uncoated SiC nanowires, which is strongly supported by the observation that the SPhP-mediated thermal conductivity is proportional to the length of the gold coating(s). The reported discoveries open the door for modulating energy transport in solids by introducing SPhPs, which can effectively counteract the classical size effect in many technologically important films and improve the design of solid-state devices.

42 ENGINEERING↗

Evidence for the existence and ecological relevance of fast-cycling mineral-associated organic matter

Longstanding theories and models classify mineral-associated organic matter as the large ( ~ 60%) but slow-cycling and persistent portion of soil organic matter. Strong physico-chemical interactions and diffusion limitations restrict the turnover of mineral-associated organic matter, allowing carbon and nitrogen bound therein to persist in soil for as long as centuries to millennia. However, mineral-associated organic matter is a chemically and functionally diverse pool with a substantial portion cycling at relatively fast (i.e., minutes to years) timescales. Despite a growing body of evidence for the heterogenous and multi-pool nature of mineral-associated organic matter, we lack consensus on how to conceptualize and directly quantify fast-cycling mineral-associated organic matter and its ecological significance. We demonstrate that the dynamic qualities of fast-cycling mineral-associated organic matter vary based on 1) the chemistry of the mineral particles and organic matter, 2) the complex set of interactions between organic matter and the mineral matrix, and 3) the presence and strength of destabilizing forces that lead to decomposition or loss of mineral-associated organic matter (i.e., plant-microbe interactions, agricultural intensification, and climate change). Finally, we discuss potential implications and research opportunities for how we measure, manage, and model the dynamic subfraction of this otherwise persistent pool of soil organic matter.

Biological and medical sciences↗

A highly efficient uranium grabber derived from acrylic fiber for extracting uranium from seawater

Acrylic fiber can be chemically converted to an am- idoxime and carboxylate containing chelating adsorbent for extraction of uranium from seawater. At an optimized ratio of amidoxime:carboxylate, the chelating fiber in real seawater shows a higher uranium, shorter saturation time and lower vanadium adsorption capacity relative to similar high-surface area chelating fibers developed recently using a radiation-induced grafting method. This simple and low-cost synthesis method can be scaled up to mass produce the chelating fiber for recovering metals from aquatic environments including production of uranium from seawater.

Pan, H B.↗

Biobased chemical recycling: aminolysis of PET using renewable reagents and monomers to synthesize new semi-aromatic polyamides

Chemical recycling of PET is a method of depolymerizing polymer chains to monomeric components enabling the synthesis of second-generation materials with virgin-like quality. Commercial chemical recycling techniques rely upon high pressure methanolysis to create precursors capable of synthesizing a second-generation PET resin. However, despite the circular approach of methanolysis, a product with a very short lifespan and similar value is created. The approach of the current study is to utilize aminolysis as an ambient pressure technique to create precursors for higher value materials with longer lifespans to address the current crisis in plastic waste. Semi-aromatic polyamides (SAP) are desired in this circumstance because of their high melting point and heat resistance combined with good melt-processability similar to aliphatic polyamides. In this study SAPs were synthesized using precursors recovered from the aminolysis of PET employing biobased diamines and dicarboxylic acids. While aminolysis has been explored in previous studies, this work investigated the use of biobased components from castor oil: decamethylene diamine during recycling and sebacic acid during polymerization. Polymer synthesis resulted in the formation of SAPs similar to polyphthalamides (PPA) with novel structures given the aromatic portion from terephthalic acid (TPA) and aliphatic portion from the diamines and diacids. The synthesized materials exhibited excellent thermal stability with high glass transition temperatures. Novel polymers were created with varying aliphatic chain length to understand fundamental parameters needed to produce a valuable polymer from post-consumer waste.

High performance Applications↗

Vortex guidance and transport in channeled pinning arrays

Here, we numerically examine vortices interacting with pinning arrays where a portion of the pinning sites have been removed in order to create coexisting regions of strong and weak pinning. The region without pinning sites acts as an easy-flow channel. For driving in different directions with respect to the channel, we observe distinct types of vortex flow. When the drive is parallel to the channel, the flow first occurs in the pin free region followed by a secondary depinning transition in the pinned region. At high vortex densities there is also an intermediate plastic flow phase due to the coupling between the weak and strong pinning regions. For driving applied perpendicular to the channel, we observe a jammed phase in which vortices accumulate on the boundary of the pinned region due to the vortex-vortex repulsion, while at higher drives the vortices begin to flow through the pinning array. For driving at an angle to the channel, depending on the filling we observe a drive-induced reentrant pinning effect as well as negative differential mobility which occurs when vortices move from the unpinned to the pinned portion of the sample.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Investigation of theoretical scaling laws using large eddy simulations for airborne spreading of viral contagion from sneezing and coughing

Using a set of large eddy point-particle simulations, we explore the fluid dynamics of an ejected puff resulting from a cough/sneeze. The ejection contains over 61,000 potentially virus-laden droplets at an injection Reynolds number of about 46,000, comparable to an actual cough/ sneeze. We observe that global puff properties, such as centroid, puff volume, momentum, and buoyancy vary little across realizations. Other properties, such as maximum extent, shape, and edge velocity of the puff, may exhibit substantial variation. In many realizations, a portion of the puff splits off and advances along a random direction, while keeping airborne droplet nuclei afloat. This peeled-off portion provides a mechanism for virus-laden droplets to travel over large distances in a short amount of time. We also observe that the vast majority of droplets remain suspended within the puff after all liquid has evaporated. The main objectives of the study are to (i) evaluate assumptions of Balachandar’s et al. theory [Int. J. Multiphase Flow 132, 103439 (2020)], which include buoyancy effects, shape of the puff, and droplet evaporation rate, (ii) obtain values of closure parameters, which include location and time of the virtual origin, and puff entrainment and drag coefficients, and (iii) evaluate the accuracy of the theory in predicting the shape, size, and location of the puff, as well as droplet number density long after ejection. The theory adequately predicts global puff properties including size, velocity, and distance traveled, the largest size of droplets that exit the puff due to settling, and the droplet size distribution within the puff long after ejection.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗