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At least 775 records · Page 43

Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy

Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. Furthermore, these structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.

36 MATERIALS SCIENCE↗

Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation

As efforts to move a renewable economy grow, it will be necessary to make use of microbial conversion strategies for the production of novel materials or the upgrading of waste to high-value products. One critical technical challenge currently limiting waste upgrading remains the difficulty in obtaining single-pot conversion techniques where physical, chemical, and biological conversion are performed in a single step. To overcome this challenge, a detailed understanding of how different stresses impact microbial membrane stability will be necessary. In this work, using all-atom molecular dynamics simulations, we examine the impacts of moderate concentrations of NaCl and CaCl 2 on a model yeast plasma membrane. Weak, though statistically significant, changes in membrane morphology and dynamics functions are observed that are consistent with swelling and stiffening. Additionally, an examination of the ion-lipid contacts and the behavior of water at the water-membrane interface suggests that the impacts of these common salts may, in part, be mediated through changes to water-membrane hydrogen-bonding and hydration water dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Numerical Prediction of Oscillation Behaviors of a Multiphase Core–Shell Droplet During Interfacial Tension Measurement

Interfacial tension between molten high-temperature materials is to be measured using the electrostatic levitation furnace (ELF) and the electromagnetic levitator (ISS-EML) aboard the International Space Station. A levitated compound droplet of a concentric core–shell structure is excited either by an impulsive electromagnetic field or by a superimposed electrostatic field. The oscillation behavior of the compound droplet is analyzed to measure interfacial tension at the interface of the two phases. In support of the space experiments, a computational fluid dynamic model was developed to characterize the oscillation behavior of multiphase core–shell droplet. The developed model predicted the interfacial tension between molten copper-rich and cobalt-rich phases with a difference of 3.3 pct compared to the values reported in literature. The developed model is being utilized to investigate the influence of various test parameters on measured surface tension and also being extended for molten steel–molten slag systems.

36 MATERIALS SCIENCE↗

Mixing across stable density interfaces in forced stratified turbulence

Understanding how turbulence enhances irreversible scalar mixing in density-stratified fluids is a central problem in geophysical fluid dynamics. While isotropic overturning regions are commonly the focus of mixing analyses, we here investigate whether significant mixing may arise in anisotropic statically stable regions of the flow. Focusing on a single forced direct numerical simulation of stratified turbulence, we analyse spatial correlations between the vertical density gradient $\partial \rho /\partial z$ and the dissipation rates of kinetic energy $\epsilon$ and scalar variance $\chi$ , the latter quantifying scalar mixing. The domain is characterized by relatively well-mixed density layers separated by sharp stable interfaces that are correlated with high vertical shear. While static instability is most prevalent within the mixed layers, much of the scalar mixing is localized to the intervening interfaces, a phenomenon not apparent if considering local static instability or $\epsilon$ alone. While the majority of the domain is characterized by the canonical flux coefficient $\varGamma \equiv \chi /\epsilon =0.2$ , often assumed in ocean mixing parametrizations, extreme values of $\chi$ within the statically stable interfaces, associated with elevated $\varGamma$ , strongly skew the bulk statistics. Our findings suggest that current parametrizations of turbulent mixing may be biased by undersampling, such that the most common, but not necessarily the most significant, mixing events are overweighted. Having focused here on a single simulation of stratified turbulence, it is hoped that our results motivate a broader investigation into the role played by stable density interfaces in mixing, across a wider range of parameters and forcing schemes representative of ocean turbulence.

Couchman, Miles M. P. (ORCID:0000000246676829)↗

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Abstract Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis , here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗

A solid electrolyte interphase to protect the sulfurized polyacrylonitrile (SPAN) composite for Li–S batteries: computational approach addressing the electrolyte/SPAN interfacial reactivity

This study addresses the reactivity of multiple solvents and lithium bis(fluorosulfonyl)imide (LiFSI) at the interface with sulfurized polyacrylonitrile (SPAN) in multiple stages of lithiation via ab initio molecular dynamics simulations. Here, both ether 1,3-dioxolane (DOL) and dimethyl carbonate (DMC) proved stable on the lithiated SPAN surface regardless of the lithium content, meaning that neither of these species likely contributes to growing a solid electrolyte interphase (SEI) coating to protect the SPAN composite. Conversely, cyclic carbonates, ethylene carbonate (EC) and fluoroethylene carbonate (FEC) are shown to be very active. The EC reduction occurs only on a highly lithiated surface with a 3.0 Li/S molar ratio, the equivalent of the SPAN composite in an over-discharge regime with voltages close to 0.0 V vs. Li/Li + . The FEC reduction starts with a 2.0 Li/S molar ratio and above, suggesting that FEC could act as a useful additive in electrolyte formulations with EC. Both EC and FEC follow multiple reduction mechanisms to produce complex reduction products and LiF in the FEC case. We provide a mechanistic description for each detected decomposition path. The LiFSI salt also proves reactive against the lithiated SPAN surface. The FSI – defluorination is the dominant reduction path. However, the SO 2 NSO 2 F – and SO 2 NSO 2 2– species proved stable against S–N cleavage. This behavior makes the LiFSI salt a potential candidate for SPAN-based Li–S batteries because it produces LiF without releasing SO 2 .

25 ENERGY STORAGE↗

Charge transfer dynamics and interlayer exciton formation in MoS 2 /VOPc mixed dimensional heterojunction

Mixed-dimensional van der Waals heterojunctions involve interfacing materials with different dimensionalities, such as a 2D transition metal dichalcogenide and a 0D organic semiconductor. These heterojunctions have shown unique interfacial properties not found in either individual component. Here, we use femtosecond transient absorption to reveal photoinduced charge transfer and interlayer exciton formation in a mixed-dimensional type-II heterojunction between monolayer MoS 2 and vanadyl phthalocyanine (VOPc). Selective excitation of the MoS 2 exciton leads to hole transfer from the MoS 2 valence band to VOPc highest occupied molecular orbit in ~710 fs. On the contrary, selective photoexcitation of the VOPc layer leads to instantaneous electron transfer from its excited state to the conduction band of MoS 2 in less than 100 fs. Further, this light-initiated ultrafast separation of electrons and holes across the heterojunction interface leads to the formation of an interlayer exciton. These interlayer excitons formed across the interface lead to longer-lived charge-separated states of up to 2.5 ns, longer than in each individual layer of this heterojunction. Thus, the longer charge-separated state along with ultrafast charge transfer times provide promising results for photovoltaic and optoelectronic device applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Shuffling mode competition leads to directionally anisotropic mobility of faceted Σ11 boundaries in fcc metals

Faceted grain boundaries can migrate in interesting and unexpected ways. For example, faceted Σ11 <110> tilt grain boundaries were observed to exhibit mobility values that could be strongly dependent on the direction of migration. In order to understand whether this directionally-anisotropic mobility is a general phenomenon and to isolate mechanistic explanations for this behavior, molecular dynamics simulations of bicrystals evolved under an artificial driving force are used to study interface migration for a range of boundary plane inclination angles and temperatures in multiple face centered cubic metals (Al, Ni, and Cu). We find that directionally anisotropic mobility is active in a large fraction of these boundaries in Ni and Cu and should therefore impact the coarsening of polycrystalline materials. On the other hand, no such anisotropy is observed in any of the Al boundaries, showing that this behavior is material-dependent. Migration of the faceted boundaries is accomplished through transformation events at facet nodes and incommensurate boundary plane facets, which are termed shuffling modes. Three major shuffling modes have been identified, namely Shockley shuffling, slip plane shuffling, and disordered shuffling. A shift from the first two ordered modes to the third disordered mode is found to be responsible for reducing or removing directionally-anisotropic mobility, especially at the highest temperatures studied.

36 MATERIALS SCIENCE↗

Atomistic simulations for investigation of substrate and salt effects on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study

In-source fragmentation (ISF) poses a significant challenge in secondary ion mass spectrometry (SIMS). These fragment ions increase the spectral complexity and can lead to incorrect annotation of fragments as intact species. The presence of salt that is ubiquitous in biological samples can influence the fragmentation and ionization of analytes in a significant manner, but their influences on SIMS have not been well characterized. To elucidate the effect of substrates and salt on ISF in SIMS, we have employed experimental SIMS in combination with atomistic simulations of a sphingolipid on a gold surface with various NaCl concentrations as a model system. Our results revealed that a combination of bond dissociation energy and binding energy between N-palmitoyl-sphingomyelin and a gold surface is a good predictor of fragment ion intensities in the absence of salt. However, ion-fragment interactions play a significant role in determining fragment yields in the presence of salt. Additionally, the charge distribution on fragment species may be a major contributor to the varying effects of salt on fragmentation. This study demonstrates that atomistic modeling can help predict ionization potential when salts are present, providing insights for more accurate interpretations of complex biological spectra.

74 ATOMIC AND MOLECULAR PHYSICS↗

Reactor wall effects in Si–Cl 2 –Ar atomic layer etching

This work complements our previous manuscript [J. Vac. Sci. Technol. A41, 062602 (2023)] where predictions from molecular dynamics (MD) simulations of silicon–chlorine–argon (Si–Cl 2 –Ar) atomic layer etching (ALE) are compared to experiments. When etch product distributions for atomic chlorine (Cl) and silicon chlorides were initially compared to optical emission spectroscopy (OES) signals, it appeared that there was a discrepancy between the MD predictions and experimental results at higher ion fluences. Experiments showed a relatively long period of nearly constant Cl-containing etch products released from the ion-bombarded surface (referred to as the “plateau”) but this effect was not observed in MD simulations. In this report, we demonstrate that the “plateau” observed in the OES signals is most likely due to the desorption of Cl-containing etch products from the walls of the reactor and subsequent adsorption on the Si substrate. Experiments varying the gas residence time in the chamber while keeping incoming gas concentrations and pressure constant support this interpretation. We also conducted experiments with an additional Ar-only flow in the chamber to reduce the concentration of Cl-containing species on the chamber walls. For both sets of flow modification experiments, we observe results consistent with the hypothesis that Cl-containing species desorbing from chamber walls are a significant cause of the observed discrepancy between MD predictions and experimental observations. If the measured OES signals are corrected for this “additional” source of Cl-containing species at the surface, the MD predictions and measured OES signals are in excellent agreement. This further supports the predictive capability of MD simulations to accurately capture the relevant physical and chemical processes in plasma-assisted ALE processes. We provide an order of magnitude estimate of the required density of Cl-containing species that would account for the additional etch products observed. Finally, we discuss the implications of this effect on ALE in plasma nanofabrication.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Comparison of unfolding methods using RooFitUnfold

In this study we describe RooFitUnfold, an extension of the RooFit statistical software package to treat unfolding problems, and which includes most of the unfolding methods that commonly used in particle physics. The package provides a common interface to these algorithms as well as common uniform methods to evaluate their performance in terms of bias, variance and coverage. In this paper we exploit this common interface of RooFitUnfold to compare the performance of unfolding with the Richardson–Lucy, Iterative Dynamically Stabilized, Tikhonov, Gaussian Process, bin-by-bin and inversion methods on several example problems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Effect of Soluble Corrosion Products on Electrical Double Layer in LiCl-KCl Molten Salts

Corrosion in molten salts greatly hampers the application for renewable energy applications like molten salt reactors. To develop effective strategies for corrosion mitigation, understanding the interfacial structures and properties such as specific ion adsorption and electrical double layer capacitance are crucial. Using cyclic voltammetry and electrochemical impedance spectroscopy, we systematically studied the interfaces on various model electrodes including W (solid), Bi (liquid), and the stainless steel 316 in LiCl-KCl eutectic molten salts with the addition of corrosion species CrCl 2 and FeCl 2 . Both Cr 2+ and Fe 2+ ions increased electrical double layer capacitance, with Cr 2+ showing specific adsorption behavior and shifting the potential of zero charge, while Fe 2+ had minimal effect on point of zero charge. Two-working electrode measurements revealed increasing open-circuit potential and electrical double layer capacitance during the exposure of stainless steel 316, indicating its progressive corrosion and ion accumulation at the interface. X-ray photoelectron spectroscopy and Raman confirmed Cr enrichment at the interface. This work highlights the strong correlation between electrical double layer behavior and corrosion dynamics in molten salts and suggests electrical double layer capacitance as a sensitive, in situ indicator for corrosion monitoring.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A File Format and API for Dynamic Radar Cross Section Data

Often the Radar Cross-Section (RCS) of a target is incorrectly assumed to be a single number by those unfamiliar with electromagnetic scattering. In actuality, a target's RCS depends on many factors. These factors include radar signal frequency, radar observation angle, as well as target orientation. Another possible parameter (often not considered) is time. The RCS of targets may change over time due to movement, environmental changes, etc. In order to accurately represent the dynamic RCS of a target in a time-stepped analysis, the ability to interface with large RCS datasets efficiently is desired. To this end, a file format and API (written in C++) were developed and are described in this report.

42 ENGINEERING↗

The Scientific Case for Concurrent Neutron and X-ray Scattering and Spectroscopy

The interrogation of materials with X-rays or neutrons to determine the structure, energetics, and dynamics of materials is fundamental to advancing materials' physical and chemical science and developing innovative material technologies. A transcending challenge in developing novel materials is that progress hinges on understanding the structure and dynamics across multiple time and length scales in complex materials that feature multiple components, interfaces, and compositions. Despite the ever-growing demands on materials’ characterization, existing approaches are almost exclusively based on isolated X-ray or neutron scattering, i.e., an approach commensurate with the more narrowly defined needs of fifty years ago. A three-day workshop sponsored by the U.S. National Science Foundation (NSF) analyzed the demand for concurrent neutron and X-ray (NeX) experiments. It was held at the Spring Hill Suites, San Jose, California, from June 2 to 4, 2022. In this workshop, 70 national and international experts ascertained the crucial need to establish NeX capabilities to advance the science of complex materials and systems in the US. Here, we illustrate the need for NeX scattering and spectroscopy experiments by showcasing examples that span areas as diverse as biomaterials, energy science, soft matter, and nanomaterials. To provide NeX capability will require new instrumentation that enables concurrent experiments. Affected areas include chemistry, soft matter, quantum materials, pure and applied chemistry, bioscience, geoscience, and applied materials. NeX benefits research outcomes due to the complementarity of the two techniques, which is essential for better model refinement. While joint refinement of data from separate neutron and X-ray experiments is critical to avoid ambiguities, especially in multiphase-multicomponent materials, concurrent experiments overcome scientific and technical barriers associated with single measurements, separated by location and, thus, time. Among all the examples, these factors introduce uncertainties in the results that complicate data analysis. [1,2] [3] While models are strongly sample-dependent, the principles of joint refinement are generally applicable to these disciplines, including the development of advanced parameterization, modeling, and analysis techniques that also consider the temporal and spatial resolutions of the two methods, leading to unambiguous data interpretation. Solutions for technical barriers must be found to realize NeX experiments, including developing robust sample environments that meet the optical requirements of neutrons and X-rays.

36 MATERIALS SCIENCE↗

Characterizing Bioavailable Soil Nutrients Across Coastal Systems: Western Lake Erie and Chesapeake Bay

Terrestrial Aquatic Interfaces (TAIs), defined as where land meets water, exhibit important hydrological, biological, and biogeochemical dynamics and play a critical role in the Earth’s carbon cycle. Current Earth System Models improperly represent this role due to the complexity of these systems and the disproportionally large impact TAIs have relative to their area. To improve our predictive capacity of coastal system dynamics, a better understanding of carbon and nutrient cycling across TAI’s is needed. Coastal Observations, Mechanisms, and Predictions Across Systems and Scales (COMPASS) aims to achieve this through field observations and laboratory incubations throughout the Western Lake Erie and Chesapeake Bay regions. Here, we report on preliminary results from a soil characterization experiment across the WLE and CB regions. This experiment was conducted as part of the 2-year field, measurements, and experiments (FME) pilot study portion of COMPASS to provide initial baseline data for the sites and to characterize the spatial variability of our analytes. Soil samples were collected from three locations along the TAI transect (upland forest, transitional forest, and wetland) and analyzed for bioavailable nutrients using three types of extractions: (a) water extractions, (b) 2M KCl extractions, and (c) 1M NH4Cl extractions to analyze (a) water soluble organic carbon (WSOC), (b) ammonium and nitrate, and (c) base cations, including Ca, Mg, Na, K, and Fe. These analyses, in conjunction with other bulk physicochemical analyses, will help establish baseline understanding of these sites to drive future research and design focused experiments that will ultimately improve our predictive understanding of these freshwater and marine coastal TAIs and their response to short and long-term changes.

54 ENVIRONMENTAL SCIENCES↗

From Femtoseconds to Gigaseconds: The SolDeg Project to Analyze and Mitigate the Performance Degradation of a-Si:H/c-Si Heterojunction Solar Cells

We pursued two major projects. In the first, we studied the degradation of a-Si/c-Si Heterojunction cells. We substantially expanded our previously developed SolDeg platform, and incorporated hydrogen into it. We also expanded the capabilities of SolDeg by developing a three channel model for a very efficient way to determine long term junction dynamics. The first main result was that we identified hydrogen drifting away from the interface as a key degradation channel. The second was that we developed and proposed the concept of a “reverse silicon density gradient” in the a-Si layer that had the promise of reducing degradation by up to 80%. In the second project, we studied the degradation of TOPCon solar cells. We again identified a key degradation channel, which in these cells was the formation of pinholes across the oxide layer. We then again were able to develop and to propose a way to dramatically reduce degradation by discovering that tuning the hydrogen concentration forms a sharp and deep minimum of the recombination current.

14 SOLAR ENERGY↗

Microscale mechanical modeling of deformable geomaterials with dynamic contacts based on the numerical manifold method

Abstract Micromechanical modeling of geomaterials is challenging because of the complex geometry of discontinuities and potentially large number of deformable material bodies that contact each other dynamically. In this study, we have developed a numerical approach for micromechanical analysis of deformable geomaterials with dynamic contacts. In our approach, we detect contacts among multiple blocks with arbitrary shapes, enforce different contact constraints for three different contact states of separated, bonded, and sliding, and iterate within each time step to ensure convergence of contact states. With these features, we are able to simulate the dynamic contact evolution at the microscale for realistic geomaterials having arbitrary shapes of grains and interfaces. We demonstrate the capability with several examples, including a rough fracture with different geometric surface asperity characteristics, settling of clay aggregates, compaction of a loosely packed sand, and failure of an intact marble sample. With our model, we are able to accurately analyze (1) large displacements and/or deformation, (2) the process of high stress accumulated at contact areas, (3) the failure of a mineral cemented rock samples under high stress, and (4) post-failure fragmentation. The analysis highlights the importance of accurately capturing (1) the sequential evolution of geomaterials responding to stress as motion, deformation, and high stress; (2) large geometric features outside the norms (such as large asperities and sharp corners) as such features can dominate the micromechanical behavior; and (3) different mechanical behavior between loosely packed and tightly packed granular systems.

58 GEOSCIENCES↗

Effect of indium alloying on the charge carrier dynamics of thick-shell InP/ZnSe quantum dots

In this work, thick-shell InP/ZnSe III–V/II–VI quantum dots (QDs) were synthesized with two distinct interfaces between the InP core and ZnSe shell: alloy and core/shell. Despite sharing similar optical properties in the spectral domain, these two QD systems have differing amounts of indium incorporation in the shell as determined by high-resolution energy-dispersive x-ray spectroscopy scanning transmission electron microscopy. Ultrafast fluorescence upconversion spectroscopy was used to probe the charge carrier dynamics of these two systems and shows substantial charge carrier trapping in both systems that prevents radiative recombination and reduces the photoluminescence quantum yield. The alloy and core/shell QDs show slight differences in the extent of charge carrier localization with more extensive trapping observed in the alloy nanocrystals. Despite the ability to grow a thick shell, structural defects caused by III–V/II–VI charge carrier imbalances still need to be mitigated to further improve InP QDs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗