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At least 1,747 records · Page 97

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↗

Structure of Ionic Liquids Under Nanoconfinement in Energy Applications

Room temperature ionic liquids are widely regarded as the most promising next-generation electrolyte for energy storage. However, their structure, which dictates a device’s ability to store electrical charge, at interfaces and under nanoconfinement remains poorly understood. By integrating cutting-edge X-ray characterization tools, advanced nanocarbon synthesis and nanofabrication, and ab initio molecular dynamics simulation, this work probed with spatial and chemical detail the structure of ionic liquids confined in carbon nanopores. This provides mechanistic understanding toward optimizing ionic liquid-solid electrode interfaces and developing design rules that could dramatically increasing capacity and charge/discharge rates of future supercapacitor devices. Nevertheless, the ability to probe ions at interfaces is also critical in other areas such as batteries, desalination, electrocatalysis, and biological and chemical sensors.

36 MATERIALS SCIENCE↗

Hybridization-Induced Carrier Localization at the C60/ZnO Interface

Electronic coupling and ground-state charge transfer at the C60/ZnO hybrid interface is shown to localize carriers in the C60 phase. This effect, revealed by resonant X-ray photoemission, arises from interfacial hybridization between C60 and ZnO. Such localization at carrier-selective electrodes and interlayers may lead to severely reduced carrier harvesting efficiencies and increased recombination rates in organic electronic devices.

14 SOLAR ENERGY↗

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)↗

Molecular Investigation of Oxidized Graphene: Anatomy of the Double-Layer Structure and Ion Dynamics

We investigated the influence of surface oxidization of planar graphene electrodes on charge storage and ion dynamics of supercapacitors. Our approach compared two distinct ionic liquid (IL) electrolytes: tetraethylammonium tetrafluoroborate solvated in acetonitrile (TEA-BF4/ACN) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide solvated in acetonitrile (EMIm-TFSI/ACN). Both experimental electrochemical tests and molecular dynamics (MD) simulations showed positive, electrolyte-specific influences of hydroxyl-free electrode interfaces on capacitance. In the EMIm-TFSI/ACN system, the hydroxylated surface, because of its strong interaction with anions, impeded surface charge storage. On the other hand, in the case of TEA-BF4/ACN, the distribution and orientation of ACN across the system exerted vital influence on the capacitance, especially on the positive hydroxyl-free electrode. Furthermore, MD simulations of ion mobility with respect to the electrode surface in the lateral and perpendicular directions revealed significantly slower diffusion performance on the oxidized surface. Our efforts enhanced the level of fundamental understanding of the effects of hydroxyl groups on electrode–electrolyte interfaces and resulting supercapacitor performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Emergent Properties of Antiagglomerant Films Control Methane Transport: Implications for Hydrate Management

The relationship between collective properties and performance of antiagglomerants (AAs) used in hydrate management is handled using molecular dynamics simulations and enhanced sampling techniques. A thin film of AAs adsorbed at the interface between one flat sII methane hydrate substrate and a fluid hydrocarbon mixture containing methane and $n$-dodecane is studied. The AA considered is a surface-active compound with a complex hydrophilic head that contains both amide and tertiary ammonium cation groups and hydrophobic tails. At a sufficiently high AA density, the interplay between the surfactant layer and the liquid hydrocarbon excludes methane from the interfacial region. In this scenario, we combine metadynamics and umbrella sampling frameworks to study accurately the free-energy landscape and the equilibrium rates associated with the transport of one methane molecule across the AA film. We observe that the local configurational changes of the liquid hydrocarbon packed within the AA film are associated with high free-energy barriers for methane transport. The time scales estimated for the transport of methane across the AA film can be, in some cases, comparable to those reported in the literature for the growth of hydrates, suggesting that one possible mechanism by which AAs delay the formation of hydrate plugs could be providing a barrier to methane transport. Considering the interplay between the structural design and collective properties of AAs might be of relevance to improve their performance in flow assurance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase-referenced nonlinear spectroscopy of the α-quartz/water interface

Probing the polarization of water molecules at charged interfaces by second harmonic generation spectroscopy has been heretofore limited to isotropic materials. Here we report non-resonant nonlinear optical measurements at the interface of anisotropic z-cut α-quartz and water under conditions of dynamically changing ionic strength and bulk solution pH. We find that the product of the third-order susceptibility and the interfacial potential, χ (3) × Φ(0), is given by (χ1 (3) –iχ2 (3) ) × Φ(0), and that the interference between this product and the second-order susceptibility of bulk quartz depends on the rotation angle of α-quartz around the z axis. Our experiments show that this newly identified term, iχ (3) × Φ(0), which is out of phase from the surface terms, is of bulk origin. Lastly, the possibility of internally phase referencing the interfacial response for the interfacial orientation analysis of species or materials in contact with α-quartz is discussed along with the implications for conditions of resonance enhancement.

74 ATOMIC AND MOLECULAR PHYSICS↗

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↗

Comparative Implementation of High Performance Computing for Power System Dynamic Simulations

Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP). These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.

97 MATHEMATICS AND COMPUTING↗

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↗

NEW EPICS/RTEMS IOC BASED ON ALTERA SOC AT JEFFERSON LAB

A new EPICS/RTEMS IOC based on the Altera System-on-Chip (SoC) FPGA is being designed at Jefferson Lab. The Altera SoC FPGA integrates a dual ARM Cortex-A9 Hard Processor System (HPS) consisting of processor, peripherals and memory interfaces tied seamlessly with the FPGA fabric using a high-bandwidth interconnect backbone. The embedded Altera SoC IOC has features of remote network boot via U-Boot from SD card or QSPI Flash, 1Gig Ethernet, 1GB DDR3 SDRAM on HPS, UART serial ports, and ISA bus interface. RTEMS for the ARM processor BSP were built with CEXP shell, which will dynamically load the EPICS applications at runtime. U-Boot is the primary bootloader to remotely load the kernel image into local memory from a DHCP/TFTP server over Ethernet, and automatically run RTEMS and EPICS. The first design of the SoC IOC will be compatible with Jefferson Lab’s current PC104 IOCs, which have been running in CEBAF 10 years. The next design would be mounting in a chassis and connected to a daughter card via standard HSMC connectors. This standard SoC IOC will become the next generation of low-level IOC for the accelerator controls at Jefferson Lab.

Yan, Jianxun↗