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At least 505 records · Page 28

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase

Abstract The average eukaryotic transfer ribonucleic acid (tRNA) contains 13 post-transcriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully modified cellular tRNALys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNALys3 anticodon loop modifications S34 (mcm5s2U) and R37 (ms2t6A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNALys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNALys3 aminoacylation are structurally ordered; docking of the 3′-CCA end in the active site cannot proceed until the lysyl–adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS–tRNALys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium toward the 3′-CCA end “docked” conformation and allosterically increases h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it.

Devarkar, Swapnil C. (ORCID:000000029271243X)↗

Interfacial oxide and other species in trimethylaluminum-pretreated atomic layer deposition-Al 2 O 3 /GaN characterized by sputter-assisted ToF-SIMS

Deposition techniques, like atomic layer deposition (ALD), are used to form high-quality dielectrics for GaN-based metal–oxide–semiconductor (MOS) gate structures due to the lack of a reliable thermal oxide in GaN. Moreover, interfacial GaO x from pre-existing native oxides is thought to adversely impact channel carrier dynamics and induce undesired threshold voltage shifts in GaN-based MOS gate structures. Exposure of the GaN surface to the trimethylaluminum (TMA) precursor prior to standard alumina ALD decreases the native oxide layer on GaN, but the extent of chemical modification has not been well studied in the context of interface composition in a MOS gate structure. Herein, we compare annealed 55 nm Al 2 O 3 dielectric films on GaN grown using either a water-first ALD process or a process including sequential pulses of TMA immediately before the initiation of Al 2 O 3 ALD. Time-of-Flight Secondary Ion Mass Spectrometry measures differences in the interfacial GaO x content between each ALD film. Here, it also detects surface contaminant species like Si, F, S, and C. Furthermore, we report the formation of an AlN species at the Al 2 O 3 /GaN interface, which is more prominent for the film grown using the TMA pre-pulse step. In general, this work demonstrates that the TMA pre-pulse step is an effective strategy for cleaning substrate surfaces prior to ALD.

Atomic layer deposition↗

Bending and shear improvements in 3D-printed core sandwich composites through modification of resin uptake in the skin/core interphase region

Fused deposition modeling (FDM) printed polymers are rarely used as a structural material due to anisotropic and low mechanical properties compared with conventional composites. In recent years, greater need has been expressed for recycling of materials, such as recyclable FDM, at the end of service life to reduce environmental pollution and manufacture cost. However, how the amount of resin uptake in the skin and skin/core interphase affects the bending and shear performance of the sandwich composites when replacing the low strength and ductile core (conventional core) with a high strength and brittle core (FDM printed PLA (polylactic acid) core) still remains unclear. A new manufacturing routine is needed to improve the incorporation of FDM printed polymers in composite structures. In this work, FDM printed PLA was used as core material and sandwiched between two unidirectional glass fiber reinforced polymer (GFRP) skins to form a sandwich composite by compression-molding (CM) process, which provides a good manufacturing strategy for skin/core interphase modification. The significance of the CM process is proved by investigating the effect of resin uptake on bending and in-plane/out-of-plane shear performances. Current first order shear deformation (FSDT) theory lacks a direct connection between the in-plane shear stress and out-of-shear stress in the core region of sandwich composites. With the help of DIC, a connection between the in-plane shear and the out-of-plane shear strain was built and in-plane shear properties can acquire through out-of-plane shear properties, hence reducing the redundancy of sample preparation or the need for simulation. A significant improvement was found compared with the optimized resin uptake (Optimized resin uptake range: 20.43%–22.86 wt%) 3D-printed PLA core sandwich composite and lowest performance sandwich composite (Improvement: in-plane shear strength (~34%)/modulus (~29%), out-of-plane shear strength (~25%)/modulus (~31%), specific peak bending load (~19%)). Finally, compared with balsa core sandwich composites, the 3D-printed cores are suitable for use in composite sandwich structures in many applications with a satisfactory strength-to-weight ratio.

3D-printed core sandwich composite↗

PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation

PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1. Here, single-particle cryo-EM provides views of the full complement of PARP1 domains engaging a DNA single-strand break in the presence of HPF1 and a fragment of binding partner Timeless. Cryo-EM, single-molecule DNA dynamics, and small-angle X-ray scattering analysis indicate that PARP1 remains dynamic even when the multi-domain structure is organized on a DNA break, with the minimal catalytic region displaying high mobility relative to domains engaging damage. We propose that the organization of PARP1 domains on a DNA break releases a tethered, constitutively active catalytic region to modify molecules in a radius surrounding the DNA break site.

59 BASIC BIOLOGICAL SCIENCES↗

Thiol redox proteomics: Characterization of thiol-based post-translational modifications

Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.

59 BASIC BIOLOGICAL SCIENCES↗

Probing the Short-Distance Structure of the Quark-Gluon Plasma with Energy Correlators

Energy-energy correlators (EECs) are promising observables to study the dynamics of jet evolution in the quark-gluon plasma (QGP) through its imprint on angular scales in the energy flux of final-state particles. We carry out the first complete calculation of EECs using realistic simulations of high-energy heavy-ion collisions and dissect the different dynamics underlying the final distribution through analyses of jet propagation in a uniform medium. The EECs of γ -jets in heavy-ion collisions are found to be enhanced by the medium response from elastic scatterings instead of induced gluon radiation at large angles. In the meantime, EECs are suppressed at small angles due to energy loss and transverse momentum broadening of jet shower partons. These modifications are further shown to be sensitive to the angular scale of the in-medium interaction, as characterized by the Debye screening mass. Experimental verification and measurement of such modifications will shed light on this scale and the short-distance structure of the QGP in heavy-ion collisions. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Diterpenoid natural products serve critical functions in plant development and ecological adaptation and many diterpenoids have economic value as bioproducts. The family of class II diterpene synthases catalyzes the committed reactions in diterpenoid biosynthesis, converting a common geranylgeranyl diphosphate precursor into different bicyclic prenyl diphosphate scaffolds. Enzymatic rearrangement and modification of these precursors generate the diversity of bioactive diterpenoids. We report the crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase, GrTPS2, at 2.1 Å of resolution. GrTPS2 catalyzes the committed reaction in the biosynthesis of grindelic acid, which represents the signature metabolite in species of gumweed (Grindelia spp., Asteraceae). Grindelic acid has been explored as a potential source for drug leads and biofuel production. The GrTPS2 crystal structure adopts the conserved three-domain fold of class II diterpene synthases featuring a functional active site in the γβ-domain and a vestigial α-domain. Substrate docking into the active site of the GrTPS2 apo protein structure predicted catalytic amino acids. Biochemical characterization of protein variants identified residues with impact on enzyme activity and catalytic specificity. Specifically, mutagenesis of Y457 provided mechanistic insight into the position-specific deprotonation of the intermediary carbocation to form the characteristic 7,13 double bond of 7,13-copalyl diphosphate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structures of N-terminally processed KRAS provide insight into the role of N-acetylation

Although post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg 2+ -free structures of KRAS with flexible N-termini. In the Mg 2+ -free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg 2+ -free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg 2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg 2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg 2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamics of pectic homogalacturonan in cellular morphogenesis and adhesion, wall integrity sensing and plant development

Homogalacturonan (HG) is the most abundant pectin subtype in plant cell walls. Although it is a linear homopolymer, its modification states allow for complex molecular encoding. HG metabolism affects its structure, chemical properties, mobility and binding capacity, allowing it to interact dynamically with other polymers during wall assembly and remodelling and to facilitate anisotropic cell growth, cell adhesion and separation, and organ morphogenesis. HGs have also recently been found to function as signalling molecules that transmit information about wall integrity to the cell. Here we highlight recent advances in our understanding of the dual functions of HG as a dynamic structural component of the cell wall and an initiator of intrinsic and environmental signalling. Here, we also predict how HG might interconnect the cell wall, plasma membrane and intracellular components with transcriptional networks to regulate plant growth and development.

59 BASIC BIOLOGICAL SCIENCES↗

Single-particle detection of enhanced polarizability in Au-decorated semiconducting nanorods via scanning dielectric microscopy

Hybrid nanostructures that combine semiconducting and metallic components offer great potential for photothermal therapy, optoelectronics, and sensing, by integrating tunable optical properties with enhanced light absorption and charge transport. Boosting the integrated performance of these hybrid systems demands techniques capable of probing local variations of the physical properties inaccessible to bulk analysis. Here, we report the single-particle dielectric characterization of hybrid, semiconducting bismuth sulfide (Bi 2 S 3 ) nanorods (NR) decorated with metallic Au nanoparticles (NP), employing scanning dielectric microscopy, which uses electrostatic force microscopy in combination with finite-element numerical simulations. We reveal a pronounced enhancement in the local dielectric response of Bi2S3 upon Au decoration, attributed to interfacial polarization and electron transfer from Au to the Bi 2 S 3 matrix, thus suggesting a enhanced metallic-like polarizability at the single-particle level. Numerical simulations show that the response is dominated by the vertical component of the permittivity and that the decorating metallic Au NP produce only moderate shielding of the semiconductor Bi 2 S 3 NR core, indicating that the large increase in the dielectric response originates primarily from intrinsic modifications within the NR. Overall, these findings provide direct insight into structure–property relationships at the single-particle level, supporting the rational design of advanced hybrid nanostructures with tailored electronic functionalities.

36 MATERIALS SCIENCE↗

Enhanced Light Outcoupling from OLEDs Fabricated on Novel Low-Cost Patterned Plastic Substrates of Varying Periodicity

OLEDs continue to make strides in display applications, but their commercial utilization in solid-state lighting (SSL) is lagging. An ongoing challenge, in particular for manufacturing, is the need for enhanced efficiency and hence the necessity to increase in an inexpensive approach the extraction of the light generated inside the OLED into the forward (viewing) hemisphere. In conventional OLEDs fabricated on a transparent flat anode coated on glass, the external quantum efficiency (EQE) is only ~20%. About 50% of the light is lost to internal waveguiding in the high refractive index (RI) organic + ITO anode layers and to surface plasmon polaritons (SPPs) at the organic/metal cathode interface. Another ~30% of the light is externally waveguided in the substrate to its edges. While extraction of the externally waveguided light is commonly addressed by adding a microlens array (MLA) or a scattering layer at the substrate’s air-side, light outcoupling increases by only ~1.6-1.7x (vs up to 2.5x in improving from ~20% to ~50%). The use of a hemispherical lens or an index matching fluid (IMF) at the substrate/photodetector (PD) interface increases the outcoupling by at least 2x; these approaches however, are not viable industrially, and even a MLA is sometimes undesirable due to its non-planar, scattering structure. In multi-stack tandem OLEDs, where the metal cathode is far from the emitting zone(s), the impact of photons loss to SPPs decreases. Our project addressed the ~50% loss to the internally waveguided light and SPPs. We evaluated OLEDs fabricated on patterned or planarized plastic substrates manufactured in a cost-effective approach compatible with a roll-to-roll (R2R) process. The OLEDs were either (i) patterned to various degrees depending on the pitch a and height or depth h of the pattern features or (ii) planar, with a pattern buried under a flat high RI planarization layer. We demonstrated that the outcoupling from green patterned OLEDs reaches ~50% by mitigating plasmon–related loss and internal waveguiding, even without the addition of a MLA, a hemispherical lens, or IMF. Simulations conducted in parallel with the experimental effort demonstrated how diffraction by conformally corrugated OLEDs increases the outcoupling to >60%. Structures with varying pitch values were also simulated indicating that combining domains of varying pitch could increase outcoupling to 55-60%. Experimentally, we additionally assessed the role a and h in determining not only the OLED efficiencies, but also their structural properties, i.e., the uniformity and conformality throughout the OLED stack. As planar OLEDs are preferred over corrugated devices, we studied different patterns in plastic substrates that were planarized by a high RI formulation. Planar green OLEDs on such structures showed enhanced efficiencies with EQEs larger than 60% with the addition of an IMF (to extract the substrate mode) at the substrate/Si PD interface. White OLEDs showed EQEs of 45.5%. Plastic substrates are currently less attractive than glass substrates due to drawbacks such as permeability to water vapor and oxygen, and in some cases thermal instability. Plastic substrates however, are flexible and easy to handle unlike thin flexible glass, and once transparent thin barrier films are available, they will become more attractive; they are already of interest in medical applications. Importantly, as it is easy to generate various patterns in different plastic materials, they provide excellent means for assessing and optimizing enhancing extracting structures. Such structures can also be transferred to glass substrates with some process modifications. The technical effectiveness and economic feasibility of the project lie in the patterning of the extracting plastic substrates in an approach that is scalable to R2R manufacturing. R2R processes are of drastically lower-cost than batch or single-unit fabrication. The patterned plastic can be a part of an integrated substrate either plastic or glass, which includes also a MLA or a planar layer with embedded scattering particles, as well as a conductive metal mesh/electrode design. SSL is environmentally-friendly and as OLED SSL becomes more efficient it will reduce electricity consumption, and hence lighting cost, as well as produce less expensive attractive lighting fixtures. Our university-industry collaboration is hence of major benefit to the public as it demonstrates the feasibility of manufacturing optimized extracting substrates for highly efficient OLEDs for SSL in a future R2R process, which would drastically reduce the manufacturing cost and increase production in the USA. Moreover, newly developed methods by our team allow low-cost roll manufactured substrates to be transferred to flexible or rigid glass substrates, which solves the plastic substrate barrier issues, and when combined with device encapsulation will increase the OLEDs’ environmental stability.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Modeling the Interaction of Laser-Produced Proton Beams with Matter

A major goal of this project is to significantly increase our understanding of isochoric heating of matter using laser produced proton beams, and the associated high energy density (HED) and warm dense matter (WDM) regimes generated. This will benefit research fields such as planetary science, fusion energy, plasma physics, and material science. For example, it will enhance our understanding of WDM properties of iron and silica under conditions encountered in planetary interiors and diagnostic components in fusion devices exposed to high fluxes of energetic plasma ions. The project is motivated by recent experiments that irradiated Si targets with proton beams generated by the 20 TW-laser at the SLAC MEC end-station. The HED/WDM states are probed using the 50 fs hard X-rays available in the 3rd harmonic of the LCLS. As part of this project, results from the phase contrast X-ray imaging, which shows the generation of compression waves that produces rear surface spallation, are compared with results from the 3D multi-physics multi- material code, PISALE, that combines Arbitrary Lagrangian-Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR). This comparison required modifications to several physics models in the PISALE (Pacific Island Structured-AMR with ALE) code. An important aspect of this project is the continued training of graduate students in HED physics and in conducting complex multiphysics simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Use of Novel Diglycolamide Extractants in Liquid-liquid Separations of Light Rare Earths

Creation of a novel extractant that can improve rare earth separations both economically and environmentally will be pivotal for industry progression. Diglycolamide (DGA) extractants provide chemistries that support this goal by serving as an extractant with high affinity for lanthanides and improved separation factors for light rare earths as compared to current extractants like PC88A. Initial organic phase loading capacity and phase dispersion tests performed with various modified DGAs generated results that were unfavorable for industrial processing, but further modification of the DGA alkyl chain substituents have resulted in new structures with promising results. Dispersion time measurements taken in small scale batch contacts of the extractant with a simulated leach liquor containing La, Ce, Nd, and Pr support implementation in both mixer-settlers and centrifugal contactors for larger scale separations. Furthermore, this confirmation allowed for preliminary flowsheet design using extraction equilibria at various organic to aqueous flow ratios (O/A) for extraction, scrubbing, and stripping stages. These values along with expected product/effluent compositions for each section aid in the testing for specific distribution ratios and final flowsheet design. Implementation of the DGA extractant into solvent extraction equipment will provide essential information for the next steps of this project and how this extractant may be optimized for future applications.

42 ENGINEERING↗

O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology

Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer’s and Parkinson’s disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the determinants contributing to the formation of different amyloid features could open new avenues for developing disease-specific diagnostics and therapies. Here we report that O-GlcNAc modification of α-synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by cryogenic electron microscopy, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson’s disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc-modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the α-synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that posttranslational modifications, such as O-GlcNAc modification, of α-synuclein are key determinants of α-synuclein amyloid strains and pathogenicity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Across the Scales of the Nucleus: Understanding Short Range Correlations from Medium Modification to Probe Independence

The atomic nucleus presents an intricate system due to the non-linear forces described by Quantum Chromodynamics (QCD) that govern its structure. The range of scales involved is remarkable; the most massive nuclei weigh approximately five orders of magnitude more than the quarks that compose them. The nucleus can be analyzed at various levels, from quarks to hadrons to the nucleus as a whole. Short-Range Correlations (SRCs) within the nucleus play a significant role that spans these diverse scales. At the most fundamental level, SRCs influence the interaction between nucleons. The nucleon-nucleon (NN) interaction, arising from QCD, is crucial in determining nuclear properties. SRCs serve as valuable probes for measuring this NN interaction, as the nucleons within SRCs become effectively decoupled from the rest of the nucleus. Multiple experimental techniques, including electron scattering, have been employed to investigate the NN interaction through SRCs. However, our first project demonstrates that inclusive measurements alone are inadequate to constrain this interaction fully. Moving to the scale of the nucleus, SRCs contribute to the high-momentum tail of the nuclear spectral function. While the low-momentum region is characterized by nucleons exhibiting bulk properties, nucleons begin to pair into SRCs at higher momenta. Our research aims to bridge the understanding between the mean-field portion of the nucleus and its high-momentum SRC components. Additionally, SRCs affect the quark structure of protons, as evidenced by the EMC effect, which indicates that quarks behave differently when protons are embedded within a nucleus—an effect referred to as medium modification. This thesis explores the correlation between SRCs and medium modification across various experimental setups. Finally, we seek to establish an interpretation of the nuclear ground state. Accomplishing this requires demonstrating that our SRC observables are independent of the probe’s scale and scheme. The concluding project of this thesis illustrates how we utilize triple coincidence quasi-elastic scattering across a range of (Q2) values to develop a model-dependent framework for understanding SRC distributions within the nucleus’s ground-state wavefunction.

Denniston, A. W. Denniston [University of Tel Aviv↗

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

Background: Fibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible “cryptic” epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen. Methods: Here, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. Results: Our data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions. Conclusion: Further, this work provides a molecular basis for the structural “dynamism” of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

59 BASIC BIOLOGICAL SCIENCES↗

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗

High-Sensitivity Low-Energy Ion Spectroscopy with Sub-Nanometer Depth Resolution Reveals Oxidation Resistance of MoS 2 Increases with Film Density and Shear-Induced Nanostructural Modifications of the Surface

For decades, density has been attributed as a critical aspect of the structure of sputter-deposited nanocrystalline molybdenum disulfide (MoS 2 ) coatings impacting oxidation resistance and wear resistance. Despite its importance, there are few examples in the literature that explicitly investigate the relationship between the density and oxidation behaviors of MoS 2 coatings. Aging and oxidation are primary considerations for the use of MoS 2 coatings in aerospace applications as they inevitably experience prolonged storage in water and oxygen-rich environments prior to use. Oxidation that is either limited to the first few nanometers or through the bulk of the coating can result in seizure due to high initial coefficients of friction or component failure from excessive wear. High-sensitivity low-energy ion spectroscopy (HS-LEIS) and Rutherford backscattering spectrometry (RBS) are both used to understand the extent of oxidation throughout the first ~10 nanometers of the surface of pure sputtered nanocrystalline MoS 2 coatings after high-temperature aging and how it is impacted by the density of coatings as measured by RBS. Results show that low-density coatings (ρ = 3.55 g/cm 3 ) exhibit a more columnar microstructure and voiding, which act as pathways for oxidative species to penetrate and interact with edge sites, causing severe surface and subsurface oxidation. Furthermore, HS-LEIS of surfaces sheared prior to oxidation reveals that the oxidation resistance of low-density MoS 2 coatings can be significantly improved by shear-induced reorientation of the surface microstructure to a basal orientation and elimination of pathways for oxygen into the bulk through compaction of surface and subsurface voids.

36 MATERIALS SCIENCE↗