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At least 181 records · Page 10

Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (k cat /K M 146 M -1 s -1 ). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (k cat /K M 103,000 M -1 s -1 ) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

59 BASIC BIOLOGICAL SCIENCES↗

Factors controlling marine aerosol size distributions and their climate effects over the northwest Atlantic Ocean region

Abstract. Aerosols over Earth's remote and spatially extensive ocean surfaces have important influences on planetary climate. However, these aerosols and their effects remain poorly understood, in part due to the remoteness and limited observations over these regions. In this study, we seek to understand factors that shape marine aerosol size distributions and composition in the northwest Atlantic Ocean region. We use the GEOS-Chem model with the TwO-Moment Aerosol Sectional (TOMAS) microphysics algorithm model to interpret measurements collected from ship and aircraft during the four seasonal campaigns of the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) conducted between 2015 and 2018. Observations from the NAAMES campaigns show enhancements in the campaign-median number of aerosols with diameters larger than 3 nm in the lower troposphere (below 6 km), most pronounced during the phytoplankton bloom maxima (May/June) below 2 km in the free troposphere. Our simulations, combined with NAAMES ship and aircraft measurements, suggest several key factors that contribute to aerosol number and size in the northwest Atlantic lower troposphere, with significant regional-mean (40–60∘ N and 20–50∘ W) cloud-albedo aerosol indirect effect (AIE) and direct radiative effect (DRE) processes during the phytoplankton bloom. These key factors and their associated simulated radiative effects in the region include the following: (1) particle formation near and above the marine boundary layer (MBL) top (AIE: −3.37 W m−2, DRE: −0.62 W m−2); (2) particle growth due to marine secondary organic aerosol (MSOA) as the nascent particles subside into the MBL, enabling them to become cloud-condensation-nuclei-sized particles (AIE: −2.27 W m−2, DRE: −0.10 W m−2); (3) particle formation and growth due to the products of dimethyl sulfide, above and within the MBL (−1.29 W m−2, DRE: −0.06 W m−2); (4) ship emissions (AIE: −0.62 W m−2, DRE: −0.05 W m−2); and (5) primary sea spray emissions (AIE: +0.04 W m−2, DRE: −0.79 W m−2). Our results suggest that a synergy of particle formation in the lower troposphere (particularly near and above the MBL top) and growth by MSOA contributes strongly to cloud-condensation-nuclei-sized particles with significant regional radiative effects in the northwest Atlantic. To gain confidence in radiative effect magnitudes, future work is needed to understand (1) the sources and temperature dependence of condensable marine vapors forming MSOA, (2) primary sea spray emissions, and (3) the species that can form new particles in the lower troposphere and grow these particles as they descend into the marine boundary layer.

54 ENVIRONMENTAL SCIENCES↗

Direct and semi-direct radiative forcing of biomass-burning aerosols over the southeast Atlantic (SEA) and its sensitivity to absorbing properties: a regional climate modeling study

Simulations are performed for the period 2000-2015 by two different regional climate models, ALADIN and RegCM, to quantify the direct and semi-direct radiative effects of biomass-burning aerosols (BBAs) in the southeast Atlantic (SEA) region. Different simulations have been performed using strongly absorbing BBAs in accordance with recent in situ observations over the SEA. For the July-August-September (JAS) season, the single scattering albedo (SSA) and total aerosol optical depth (AOD) simulated by the ALADIN and RegCM models are consistent with the MACv2 climatology and MERRA-2 and CAMS-RA reanalyses near the biomass-burning emission sources. However, the above-cloud AOD is slightly underestimated compared to satellite (MODIS and POLDER) data during the transport over the SEA. The direct radiative effect exerted at the continental and oceanic surfaces by BBAs is significant in both models and the radiative effects at the top of the atmosphere indicate a remarkable regional contrast over SEA (in all-sky conditions), with a cooling (warming) north (south) of 10°S, which is in agreement with the recent MACv2 climatology. In addition, the two models indicate that BBAs are responsible for an important shortwave radiative heating of ~0.5-1K per day over SEA during JAS with maxima between 2 and 4 km a.m.s.l. (above mean sea level). At these altitudes, BBAs increase air temperature by ~0.2-0.5 K, with the highest values being co-located with low stratocumulus clouds. Vertical changes in air temperature limit the subsidence of air mass over SEA, creating a cyclonic anomaly. The opposite effect is simulated over the continent due to the increase in lower troposphere stability. The BBA semi-direct effect on the lower troposphere circulation is found to be consistent between the two models. Changes in the cloud fraction are moderate in response to the presence of smoke, and the models differ over the Gulf of Guinea. Finally, the results indicate an important sensitivity of the direct and semi-direct effects to the absorbing properties of BBAs. Over the stratocumulus (Sc) region, DRE varies from +0.94 W m -2 (scattering BBAs) to +3.93 W m -2 (most absorbing BBAs).

54 ENVIRONMENTAL SCIENCES↗

A direct numerical simulation study for confined non-isothermal jet impingement at moderate nozzle-to-plate distances: Capturing jet-to-ambient density effects

A direct numerical simulation (DNS) campaign is deployed for a series of confined downward oriented, non-isothermal turbulent impinging jet configurations. A baseline Reynolds number of 9960 is obtained through a precursor DNS pipe flow simulation (Re τ = 505). Three jet temperature configurations (confinement height to nozzle diameter of three) enter a cylindrical domain that share ambient and impingement plate temperatures (298.15 K). The range of jet temperatures are crafted such that the ratio of inlet to ambient density varies from unity to 0.52, showcasing the effect of density disparity on flow characteristics such as core collapse, radial mixing of momentum and energy, near-wall stagnation behavior, wall-jet profiles, and large-scale vortical structures. Surface quantities provided include mean radial heat flux and wall-shear stress profiles, and heat flux histograms at select radial stations. Results showcase increased radial normal stresses for higher temperature jets that support increased mixing, resulting in large-scale recirculation structures that are smaller, while retaining similar normalized radial wall profiles for shear stress, heat flux and pressure. Furthermore, radial plots for wall shear stress and Nusselt number showcase strong radial decay as compared to previous configurations that share similar jet and ambient temperatures. For the 373.15 K case, a Gaussian-like histogram for heat fluxes at the impingement plate transitions to a log-normal profile as radial distances increase. In contrast, the 573.15 K configuration displays a bi-modal heat flux characteristic at the impingement plate, and in similar manner to the moderate temperature counterpart, transitions to a log-normal profile at larger radial distances.

33 ADVANCED PROPULSION SYSTEMS↗

Improving Performance and Durability of Low Temperature Direct Ammonia Fuel Cells: Effect of Backpressure and Oxygen Reduction Catalysts

Low temperature direct ammonia fuel cells (DAFCs) are attractive for transportation applications. The primary obstacle to their commercial use is their low performance and poor durability. In the present work, we focus on improving DAFCs performance and durability by examining the effect of operating backpressure and oxygen reduction reaction (ORR) catalysts such as Acta 4020, Pd/C and Pt/C. DAFCs with Acta 4020 cathode can reach a peak power density of 390 mW cm -2 which is among the best reported performance, but they can be operated for a period of 11 h at 300 mA cm -2 . DAFCs with Pd/C cathode offer a moderate performance with a peak power density of 304 mW cm -2 , but has a much improved durability - a continuous operation for up to 36 h with a slow decay rate of ~1 mV h -1 at 300 mA cm -2 . In addition, the degradation pathways for DAFCs with Pd/C cathode are probed by characterizing the initial and final electrodes by XPS, suggesting that cathodic Pd dissolution occurs during the durability test.

Electrochemistry↗

High-speed synchrotron X-ray imaging of directed energy deposition of titanium: effects of processing parameters on the formation of entrapped-gas pores

Laser based directed energy deposition (DED) is a competitive method for repairing and remanufacturing metallic parts used in numerous industries including aerospace and biomedical. However, the numerous dynamic phenomena associated with the DED process often result in defects such as entrapped-gas pores, lack of fusion, and undesirable anisotropic properties. The entrapped-gas pore, being one of the most common issues, not only influences melt-pool dynamics but also reduces the fabrication quality and mechanical properties of parts fabricated by the DED process. To reduce and further understand this issue, the real-time observation of the pore formation process needs to be studied first. To directly observe the phenomena in the melt pool, high-speed techniques are needed because rapid solidification leads to rapid pore formation and movement. In-situ high-speed X-ray has been proven to be an effective method in investigating the melt pool dynamics and pore formation mechanisms in the laser powder bed fusion process, in which the fabrication process is quite different from that in DED. Here, the high-speed X-ray method is extended to study the formation of entrapped-gas pores. The real-time formation and quantitative analysis of pores under each set of processing parameters (particle velocity, laser power, and spot welding dwelling time of stationary laser) in the DED process are investigated. We found that the DED with a higher particle velocity (3.19 m/s) produced a smaller average pore size of 27.8 µm and a lower pore area fraction of 0.52%. The DED under lower laser power (156 W) generated a smaller average pore size of 20.3 µm and a lower pore area fraction of 1.94%. The shorter dwelling time (10 ms) benefited the decrease of both average pore size and pore area fraction.

Defect↗

Improved representation of black carbon mixing structures suggests stronger direct radiative heating

Black carbon significantly influences the Earth system because of its strong solar radiation absorption. However, its direct radiative effect remains poorly understood in current climate models, partly because current climate models oversimplify the diverse structures formed when black carbon mixes with other atmospheric components. Here we show that incorporating more realistic, multi-mixing-structure representations of black carbon increases the direct radiative effect. We find that aged black carbon particles, with thicker coatings and higher embedded fractions, enhance the direct radiative effect more efficiently. Using machine learning alongside the Community Earth System Model, we show that the direct radiative effect at the top of the atmosphere in regions with heavy black carbon pollution is 31.6% greater when multi-mixing structures are considered. These findings highlight the importance of modeling complex mixing structures of particle-resolved black carbon to accurately capture their warming impacts on global atmosphere, particularly in highly polluted regions.

54 ENVIRONMENTAL SCIENCES↗

High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa

High temperatures alter the thermal sensitivities of numerous physiological and biochemical processes that impact tree growth and productivity. Foliar and root applications of methanol have been implicated in plant acclimation to high temperature via the C 1 pathway. Here, we characterized temperature acclimation at 35°C of leaf gas exchange, chlorophyll fluorescence and extractable metabolites of potted Populus trichocarpa saplings and examined potential influences of mM concentrations of methanol added during soil watering over a two-month period. Relative to plants grown under the low growth temperature (LGT), high growth temperature (HGT) plants showed a suppression of leaf water use and carbon cycling including transpiration (E), net photosynthesis (P n ), an estimate of photorespiration (R p ), and dark respiration (R d ), attributed to reductions in stomatal conductance and direct negative effects on gas exchange and photosynthetic machinery. In contrast, HGT plants showed an upregulation of non-photochemical quenching (NPQ t ), the optimum temperature for ETR, and leaf isoprene emissions at 40°C. A large number of metabolites (867) were induced under HGT, many implicated in flavonoid biosynthesis highlighting a potentially protective role for these compounds. Methanol application did not significantly alter leaf gas exchange but slightly reduced the suppression of R d and R p by the high growth temperature while slightly impairing ETR, Fv’/Fm’, and q p . However, we were unable to determine if soil methanol was sufficiently taken up by the plant to have a direct effect on foliar processes. A small number of extracted leaf tissue metabolites (55 out of 10,015) showed significantly altered abundances under LGT and methanol treatments relative to water controls, and this increased in compound number (222) at the HGT. The results demonstrate the large physiological and biochemical impacts of high growth temperature on poplar seedlings and highlights the enhancement of the optimum temperature of ETR as a rapid thermal acclimation mechanism. Finally, although no large effect on leaf physiology was observed, the results are consistent with methanol both impairing photochemistry of the light reactions via formaldehyde toxicity, and stimulating photosynthesis and dark respiration through formate oxidation to CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

Pluminate: Quantifying aerosol injection behavior from simulation, experimentation and observations

Marine aerosol injections are a key component in further understanding of both the potentials of deliberate injection for marine cloud brightening (MCB), a potential climate intervention (CI) strategy, and key aerosol-cloud interaction behaviors that currently form the largest uncertainty in global climate model (GCM) predictions of our climate. Since the rate of spread of aerosols in a marine environment directly translates to the effectiveness and ability of aerosol injections in impacting cloud radiative forcing, it is crucial to understand the spatial and temporal extent of injected-aerosol effects following direct injection into marine environments. The ubiquity of ship-injected aerosol tracks from satellite imagery renders observational validation of new parameterizations possible in 2D, however, 3D compatible data is more scarce, and necessary for the development of subgrid scale parameterizations of aerosol-cloud interactions in GCMs. This report introduces two novel parameterizations of atmospheric aerosol injection behavior suitable for both 3D (GCM-compatible) and 2D (observation-related) modeling. Their applicability is highlighted using a wealth of different observational data: small and larger scale salt-aerosol injection experiments conducted at SNL, 3D large eddy simulations of ship-injected aerosol tracks and 2D satellite images of ship tracks. The power of experimental data in enhancing knowledge of aerosol-cloud interactions is in particular emphasized by studying key aerosol microphysical and optical properties as observed through their mixing in cloud-like environments.

54 ENVIRONMENTAL SCIENCES↗

Investigating the effect of B T direction on W source-to-core pathways during the SAS-VW campaign on DIII-D

Experiments using the V-shaped closed slot tungsten (W) coated SAS-VW divertor in DIII-D studied the effects of the BT direction on core contamination of eroded tungsten from a closed slot divertor configuration. Core W content is inferred using soft-X ray tomography (SXR) and vacuum ultraviolet spectroscopy (SPRED), while W divertor erosion is inferred from visible spectroscopy of W emission (400.9 nm) measured by in-slot filterscopes (filtered photo-multipliers). Post-mortem analysis from the campaign discovered tile misalignment leading to suspected pronounced leading-edge erosion in the unfavorable BT direction (ion B ⃗×∇B ⃗ drift away from divertor) likely not captured by diagnostics. However, empirical findings show up to ~2-3x larger core contamination in the favorable BT direction even considering no additional W erosion from leading edges. A “source-to-core efficiency factor” is derived to estimate the effects of leading-edge erosion and compare W contamination for two pairs of H-mode discharges in opposite BT directions. While having differing absolute parameters, similar core impurity density gradients suggest comparable core impurity transport. These results show that favorable BT may have stronger source-to-core pathways for W impurities sourced from the outer divertor region. Possible explanations could include the effects of E ⃗×B ⃗ drifts on W transport in the scrape-off-layer (SOL) as well as previously determined fast SOL inner target directed flows in favorable BT.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fast Determination of Lithium Content in Spent Cathodes for Direct Battery Recycling

Determination of the lithium ion content in cathode materials, which is currently performed by inductively coupled plasma mass spectrometry (ICP-MS), involves tedious procedures and error-prone preparation. This work introduces a new methodology to quickly determine the lithium content in spent cathode materials (LiNix Mny Coz O2, x + y + z = 1, NMC) using a thermalgravimetric analysis, which bypasses the use of ICP-MS and significantly reduces the cost and time required for determining the lithium content. Based on this new method, a new approach is developed to identify spent cathode materials suitable for direct relithiation recycling. Finally, these new methods have been applied to investigate the effectiveness of direct electrochemical-relithiation on recycling the spent cathodes, and provide insights for future development of direct battery materials recycling.

cathode recycling↗

Superfluid effective field theory for dark matter direct detection

We develop an effective field theory (EFT) framework for superfluid 4 He to model the interactions among quasiparticles, helium atoms and probe particles. Our effective field theory approach brings together symmetry arguments and power-counting and matches to classical fluid dynamics. We then present the decay and scattering rates for the relevant processes involving quasiparticles and helium atoms. The presented EFT framework and results can be used to understand the dynamics of thermalization in the superfluid, and can be further applied to sub-GeV dark matter direct detection with superfluid 4 He.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Direct evidence of the effect of a moderate external magnetic field on stimulated Raman scattering in the kinetic regime

We present results from an experiment carried out at the OMEGA-EP laser facility that investigated the effect of a perpendicular magnetic field on stimulated Raman scattering (SRS) and report the first direct measurement of magnetic mitigation of SRS. A 13-T magnetic field generated by pulsed-power coils was imposed on a gas jet plasma, and a novel three-picket interaction beam was used to explore SRS reflectivity for several plasma conditions within single shots. The time-resolved backscattered light shows that SRS was mitigated by the external 13-T magnetic field in the kinetic regime (kλ D ∼ 0.3, where k is the electron plasma wave's wavenumber and λ D is electron Debye length) and at a density of n e /n cr ∼ 0.10. On the other hand, we also measured an enhancement of SRS reflectivity at lower density (n e /n cr < 0.08). We discuss experimental results in the context of magnetohydrodynamic and particle-in-cell simulations that scan SRS dynamics for a variety of plasma conditions. While the experimental evidence of SRS mitigation validates prior work on the kinetic simulation of SRS in an external magnetic field, we also find that other mechanisms such as SRS rescatter can lead to an enhancement of measured SRS reflectivity in simulations of parameters relevant to our experiment.

Gas jet↗

Chemical control of excited-state reactivity of the anionic green fluorescent protein chromophore

Controlling excited-state reactivity is a long-standing challenge in photochemistry, as a desired pathway may be inaccessible or compete with other unwanted channels. An important example is internal conversion of the anionic green fluorescent protein (GFP) chromophore where non-selective progress along two competing torsional modes (P: phenolate and I: imidazolinone) impairs and enables Z-to-E photoisomerization, respectively. Developing strategies to promote photoisomerization could drive new areas of applications of GFP-like proteins. Motivated by the charge-transfer dichotomy of the torsional modes, we explore chemical substitution on the P-ring of the chromophore as a way to control excited-state pathways and improve photoisomerization. As demonstrated by methoxylation, selective P-twisting appears difficult to achieve because the electron-donating potential effects of the substituents are counteracted by inertial effects that directly retard the motion. Conversely, these effects act in concert to promote I-twisting when introducing electron-withdrawing groups. Specifically, 2,3,5-trifluorination leads to both pathway selectivity and a more direct approach to the I-twisted intersection which, in turn, doubles the photoisomerization quantum yield. Our results suggest P-ring engineering as an effective approach to boost photoisomerization of the anionic GFP chromophore.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Propylamine Functionalized Porous Fiber Sorbents with High Oxidation Stability for Direct Air Capture

Amine-based sorbents are highly effective for direct air capture (DAC) due to their excellent CO2 capture efficiency under ultra-dilute conditions. However, these sorbents can suffer degradation when exposed to combinations of heat, oxygen, and other atmospheric components, indicating a need for improved sorbent stability. In this study, we developed amidoxime functionalized polymer of intrinsic microporosity (PIM-1-AO) fibers with tethered amines, specifically tris(2-aminoethyl)amine (TAEA) and tris(3-aminopropyl)amine (TAPA), denoted as PIM-1-AO-TAEA and PIM-1-AO-TAPA, respectively. In addition, large scale sorbent fiber spinning has been successfully performed by producing meters of fibers in the lab. We demonstrated that substituting TAEA with TAPA, which has propyl chains instead of ethyl chains, reduces oxidative degradation under regeneration conditions. The findings revealed that PIM-1-AO-TAPA not only significantly outperforms PIM-1-AO-TAEA after accelerated aging process, but also outperforms any other sorbent used in DAC aged under similar conditions. Moreover, PIM-1-AO-TAPA sorbent fibers showed one of the highest amine efficiencies (0.25) considering the low amine loading (21%) coupled with robust CO2 uptake performance (1.12 mmol/g) under DAC conditions.

amine-based sorbent↗