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At least 1,423 records · Page 79

Antisymmetric Spin-Orbit Coupling in a d-p Model on a Zigzag Chain

In this paper, we theoretically investigate how an antisymmetric spin-orbit coupling emerges in electrons moving on lattice structures which are centrosymmetric but break the spatial inversion symme- try at atomic positions. We construct an effective d-p model on the simplest lattice structure, a zigzag chain of edge-sharing octahedra, with taking into account the crystalline electric field, the spin-orbit coupling, and on-site and inter-site d-p hybridizations. We show that an effective antisymmetric spin-orbit coupling arises in the sublattice-dependent form, which results in a hidden spin polarization in the band structure. Finally, we explicitly derive the effective antisymmetric spin-orbit coupling for d electrons, which not only explains the hidden spin polarization but also indicates how to enhance it.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Traveling wave solutions in a chain of periodically forced coupled nonlinear oscillators

Artificial perceptions of light called phosphenes were motivated by earlier studies. We analyze traveling wave solutions in a chain of periodically forced coupled nonlinear oscillators modeling this phenomenon. We examine the discrete model problem in its co-traveling frame and systematically obtain the corresponding traveling waves in one spatial dimension. Direct numerical simulations as well as linear stability analysis are employed to reveal the parameter regions where the traveling waves are stable, and these waves are, in turn, connected to the standing waves analyzed in earlier work. We also consider a two-dimensional extension of the model and demonstrate the robust evolution and stability of planar fronts. Moreover, our simulations also suggest the radial fronts tend to either annihilate or expand and flatten out, depending on the phase value inside and the parameter regime. Finally, we observe that solutions that initially feature two symmetric fronts with bulged centers evolve in qualitative agreement with experimental observations of phosphenes.

59 BASIC BIOLOGICAL SCIENCES↗

Breathers in a locally resonant granular chain with precompression

Here we study a locally resonant granular material in the form of a precompressed Hertzian chain with linear internal resonators. Using an asymptotic reduction, we derive an effective nonlinear Schrödinger (NLS) modulation equation. In turn, this leads us to provide analytical evidence, subsequently corroborated numerically, for the existence of two distinct types of discrete breathers related to acoustic or optical modes: (a) traveling bright breathers with a strain profile exponentially vanishing at infinity and (b) stationary and traveling dark breathers, exponentially localized, time-periodic states mounted on top of a non-vanishing background. Moreover, the stability and bifurcation structure of numerically computed exact stationary dark breathers is also examined. Stationary bright breathers cannot be identified using the NLS equation, which is defocusing at the upper edges of the phonon bands and becomes linear at the lower edge of the optical band.

97 MATHEMATICS AND COMPUTING↗

Exact intrinsic localized excitation of an anisotropic ferromagnetic spin chain in external magnetic field with Gilbert damping, spin current and PT -symmetry

In this work, we obtain the exact one-spin intrinsic localized excitation in an anisotropic Heisenberg ferromagnetic spin chain in a constant/variable external magnetic field with Gilbert damping included. We also point out how an appropriate magnitude spin current term in a spin transfer nano-oscillator (STNO) can stabilize the tendency towards damping. Further, we show how this excitation can be sustained in a recently suggested PT -symmetric magnetic nanostructure. We also briefly consider more general spin excitations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Experimental and kinetic modeling study of the low- temperature and high-pressure combustion chemistry of straight chain pentanol isomers: 1-, 2- and 3-Pentanol

Pentanols have received significant attention as a potential alternative fuel or fuel additive owing to their high energy densities and low vapor pressure. The development of robust chemical kinetic models for alternative fuels which can provide accurate and efficient predictions of combustion performance across a wide range of engine relevant conditions is important in developing cleaner, more efficient combustors. Although the high temperature oxidation kinetics of pentanol isomers has been researched considerably, their low temperature combustion chemistry needs further investigation. While previously proposed low temperature mechanisms for 1-pentanol based on analogy and rate rules need further refinement, the low temperature oxidation kinetics of 2-pentanol and 3-pentanol has not been studied previously by any means, experimentally or theoretically. A newly developed kinetic mechanism is presented in this work for the three straight chain pentanol isomers: 1-, 2- and 3-pentanol. Low temperature kinetics is based on a recent study by Lockwood et al., 2022 [20] involving theoretical calculations at the CCSD(T)/cc-pV∞Z level of theory for the oxidation pathways involving alcohol peroxy radicals. Rate of production analyses performed in this study highlight the importance of the newly added pressure-dependent reactions of the α-alcohol peroxy radical forming an RO 2 adduct. While the α-alcohol fuel radical reacts with O 2 to directly decompose via a chemically activated pathway at low pressures, the formation of the RO 2 adduct is favored at high pressures. Furthermore, the detailed model is comprehensively validated against new ignition experiments at low temperature and high pressure, together with the wide range of data available in the literature. Both qualitative and quantitative predictions of the experimental data using the proposed kinetic model are satisfactory for all three pentanol isomers studied here.

1-pentanol↗

The role of radical-radical chain-propagating pathways in the phenyl + propargyl reaction

Well-skipping radical-radical reactions can provide a chain-propagating pathway for formation of polycyclic radicals implicated in soot inception. Here we use controlled pyrolysis in a microreactor to isolate and examine the role of well-skipping channels in the phenyl (C 6 H 5 ) + propargyl (C 3 H 3 ) radical-radical reaction at temperatures of 800-1600 K and pressures near 25 Torr. The temperature and concentration dependence of the closed-shell (C 9 H 8 ) and radical (C 9 H 7 ) products are observed using electron-ionization mass spectrometry. The flow in the reactor is simulated using a boundary layer model employing a chemical mechanism based on recent rate coefficient calculations. Further, comparison between simulation and experiment shows reasonable agreement, within a factor of 3, while suggesting possible improvements to the model. In contrast, eliminating the well-skipping reactions from the chemistry mechanism causes a much larger discrepancy between simulation and experiment in the temperature dependence of the radical concentration, revealing that the well-skipping pathways, especially to form indenyl radical, are significant at temperatures of 1200 K and higher. While most C 9 H 7 forms by well-skipping at 25 Torr, an additional simulation indicates that the wellskipping channels only contribute around 3% of the C 9 H x yield at atmospheric pressure, thus indicating a negligible role of the well-skipping pathways at atmospheric and higher pressures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Perfluorooctanoic acid affects endocytosis involving clathrin light chain A and microRNA-133b-3p in mouse testes

Perfluorooctanoic acid (PFOA) is an abundant perfluoroalkyl substance widely applied in industrial and consumer products. Among its potential health hazards, testicular toxicity is of major concern. To explore the potential effect of miRNA on post-translational regulation after PFOA exposure, changes in miRNAs were detected via miRNA array. Seventeen miRNAs were differentially expressed (eight upregulated, nine downregulated) in male mouse testes after exposure to 5 mg/kg/d of PFOA for 28 d (> 1.5-fold and P < 0.05 compared with the control). Eight of these miRNAs were further selected for TaqMan qPCR analysis. Proteomic profile analysis indicated that many changed proteins after PFOA treatment, including intersectin 1 (ITSN1), serine protease inhibitor A3K (Serpina3k), and apolipoprotein a1 (APOA1), were involved in endocytosis and blood-testis barrier (BTB) processes. These changes were further verified by immunohistochemical and Western blot analyses. Endocytosis-related genes were selected for qPCR analysis, with many found to be significantly changed after PFOA treatment, including epidermal growth factor receptor pathway substrate 8 (Eps8), Eps15, cortactin, cofilin, espin, vinculin, and zyxin. We further predicted the potential interaction between changed miRNAs and proteins, which indicated that miRNAs might play a role in the post-translational regulation of gene expression after PFOA treatment in mouse testes. Among them, miR-133b-3p/clathrin light chain A (CLTA) was selected and verified in vitro by transfection and luciferase activity assay. Results showed that PFOA exposure affects endocytosis in mouse testes and that CLTA is a potential target of miR-133b-3p. - Highlights: • Endocytosis and blood-testis barrier proteins were changed after PFOA exposure. • Seventeen miRNAs were differentially expressed in testes after PFOA exposure. • MiRNAs might play a role in gene regulation in testes after PFOA exposure.CLTA is a potential target of miR-133b-3p.

60 APPLIED LIFE SCIENCES↗

A multi-echelon supply chain model for municipal solid waste management system

In this paper, a multi-echelon multi-period solid waste management system (MSWM) was developed by inoculating with multi-echelon supply chain. Waste managers, suppliers, industries and distributors could be engaged in joint strategic planning and operational execution. The principal of MSWM system is interactive planning of transportation and inventory for each organization in waste collection, delivery and disposal. An efficient inventory management plan for MSWM would lead to optimized productivity levels under available capacities (e.g., transportation and operational capacities). The applicability of the proposed system was illustrated by a case with three cities, one distribution and two waste disposal facilities. Solutions of the decision variable values under different significant levels indicate a consistent trend. With an increased significant level, the total generated waste would be decreased, and the total transported waste through distribution center to waste to energy and landfill would be decreased as well.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Stimulatory and inhibitory mechanisms of slow muscle-specific myosin heavy chain gene expression in fish: Transient and transgenic analysis of torafugu MYH{sub M86-2} promoter in zebrafish embryos

The myosin heavy chain gene, MYH{sub M86-2}, exhibited restricted expression in slow muscle fibers of torafugu embryos and larvae, suggesting its functional roles for embryonic and larval muscle development. However, the transcriptional mechanisms involved in its expression are still ambiguous. The present study is the first extensive analysis of slow muscle-specific MYH{sub M86-2} promoter in fish for identifying the cis-elements that are crucial for its expression. Combining both transient transfection and transgenic approaches, we demonstrated that the 2614 bp 5′-flanking sequences of MYH{sub M86-2} contain a sufficient promoter activity to drive gene expression specific to superficial slow muscle fibers. By cyclopamine treatment, we also demonstrated that the differentiation of such superficial slow muscle fibers depends on hedgehog signaling activity. The deletion analyses defined an upstream fragment necessary for repressing ectopic MYH{sub M86-2} expression in the fast muscle fibers. The transcriptional mechanism that prevents MYH{sub M86-2} expression in the fast muscle fibers is mediated through Sox6 binding elements. We also demonstrated that Sox6 may function as a transcriptional repressor of MYH{sub M86-2} expression. We further discovered that nuclear factor of activated T cells (NFAT) binding elements plays a key role and myocyte enhancer factor-2 (MEF2) binding elements participate in the transcriptional regulation of MYH{sub M86-2} expression. - Highlights: ► MYH{sub M86-2} is highly expressed in slow muscle fibers of torafugu embryos and larvae. ► MYH{sub M86-2} promoter activity depends on the hedgehog signaling. ► Sox6 binding elements inhibits MYH{sub M86-2} expression in fast muscle fibers. ► Sox6 elements function as transcriptional repressor of MYH{sub M86-2} promoter activity. ► NFAT and MEF2 binding elements play a key role for directing MYH{sub M86-2} expression.

60 APPLIED LIFE SCIENCES↗

Myosin-IIA heavy chain phosphorylation on S1943 regulates tumor metastasis

Highlights: • pS1943 NMHC-IIA is detected in orthotopic tumors and metastatic lesions. • S1943E NMHC-IIA drives gelatin degradation and MMP9 secretion. • S1943E NMHC-IIA S1943E increases experimental metastasis in vivo. • NMHC-IIA S1943 phosphorylation regulates breast cancer invasion and metastasis. Nonmuscle myosin-IIA (NMHC-IIA) heavy chain phosphorylation has gained recognition as an important feature of myosin-II regulation. In previous work, we showed that phosphorylation on S1943 promotes myosin-IIA filament disassembly in vitro and enhances EGF-stimulated lamellipod extension of breast tumor cells. However, the contribution of NMHC-IIA S1943 phosphorylation to the modulation of invasive cellular behavior and metastasis has not been examined. Stable expression of phosphomimetic (S1943E) or non-phosphorylatable (S1943A) NMHC-IIA in breast cancer cells revealed that S1943 phosphorylation enhances invadopodia function, and is critical for matrix degradation in vitro and experimental metastasis in vivo. These studies demonstrate a novel link between NMHC-IIA S1943 phosphorylation, the regulation of extracellular matrix degradation and tumor cell invasion and metastasis.

60 APPLIED LIFE SCIENCES↗

A hybrid full-wave Markov chain approach to calculating radio-frequency wave scattering from scrape-off layer filaments

The interaction of radio-frequency (RF) waves with edge turbulence modifies the incident wave spectrum, and can significantly affect RF heating and current drive in tokamaks. Previous lower hybrid (LH) scattering models have either used the weak-turbulence approximation, or treated more realistic, filamentary turbulence in the ray tracing limit. In this study, a new model is introduced which retains full-wave effects of RF scattering in filamentary turbulence. First, a Mie-scattering technique models the interaction of an incident wave with a single Gaussian filament. Next, an effective differential scattering width is derived for a statistical ensemble of filaments. Lastly, a Markov chain solves for the transmitted wave spectrum in slab geometry. This model is applied to LH launching for current drive. The resulting wave spectrum is asymmetrically broadened in angular wavenumber space. This asymmetry is not accounted for in previous LH scattering models. The modified wave spectrum is coupled to a ray tracing/Fokker–Planck solver (GENRAY/CQL3D) to study its impact on current drive. The resulting current profile is greatly altered, and there is significant increase in the on-axis current and decrease in the off-axis peaks. This is attributed to a portion of the modified wave spectrum that is strongly dampened on-axis during the first pass.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Uniformly 15N-Labeled Recombinant Ricin A-chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatography-Tandem Mass Spectrometry

Ricin, a toxic protein from the castor plant, is of forensic and biosecurity interest because of its high toxicity and common occurrence in crimes and attempted crimes. Qualitative methods to detect ricin are therefore needed. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics methods are well-suited because of their high speci-ficity. Specificity in LC-MS/MS comes from both the LC and MS components. However, modern untargeted proteomics methods often use nanoflow LC, which has less reproducible retention times than standard-flow LC, making it challenging to use retention time as a point of identification in a forensic assay. We address this challenge by using retention times rela-tive to a standard, namely uniformly 15N–labeled ricin A-chain produced recombinantly in a bacterial expression system. This material, added as an internal standard prior to trypsin digestion, produces a stable isotope labeled standard for every ricin tryptic peptide in the sample. We show that the MS signals for 15N and natural isotopic abundance ricin peptides are distinct, with mass shifts that correspond to the numbers of nitrogen atoms in each peptide or fragment. We also show that, as expected, labeled and unlabeled peptides coelute, with relative retention time differences of less than 0.2%.

ricin, mass spectrometry, isotope, nitrogen-15, re↗

Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family

The 11-cis-retinylidene chromophore of visual pigments isomerizes upon interaction with a photon, initiating a downstream cascade of signaling events that ultimately lead to visual perception. 11-cis-Retinylidene is regenerated through enzymatic transformations collectively called the visual cycle. The first and rate-limiting enzymatic reaction within this cycle, i.e., the reduction of all-trans-retinal to all-trans-retinol, is catalyzed by retinol dehydrogenases. Here, we determined the structure of Drosophila melanogaster photoreceptor retinol dehydrogenase (PDH) isoform C that belongs to the short-chain dehydrogenase/reductase (SDR) family. This is the first reported structure of a SDR that possesses this biologically important activity. Two crystal structures of the same enzyme grown under different conditions revealed a novel conformational change of the NAD + cofactor, likely representing a change during catalysis. Amide hydrogen–deuterium exchange of PDH demonstrated changes in the structure of the enzyme upon dinucleotide binding. In D. melanogaster, loss of PDH activity leads to photoreceptor degeneration that can be partially rescued by transgenic expression of human RDH12. As a result, based on the structure of PDH, we analyzed mutations causing Leber congenital amaurosis 13 in a homology model of human RDH12 to obtain insights into the molecular basis of RDH12 disease-causing mutations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Noncanonical 1,2-Propanediol Utilization Bacterial Microcompartment

Bacterial microcompartments (BMCs) are proteinaceous organelles that encapsulate enzymes involved in CO 2 fixation (carboxysomes). or carbon catabolism (metabolosomes). Metabolosomes share a common core of enzymes and a distinct signature enzyme for substrate degradation that defines the function of the BMC (e,g., propanediol or ethanolamine utilization BMCs, or glycyl-radical enzyme microcompartments). Loci encoding metabolosomes also typically contain genes for proteins that support organelle function, such as regulation, transport of substrate, and cofactor (e.g., vitamin B-12) synthesis and recycling. Flavoproteins are frequently among these ancillary gene products, suggesting that these redox active proteins play an undetermined function in many metabolosomes. Here in this paper, we report the first characterization of a BMC-associated flavodoxin (Fld1C), a small flavoprotein, derived from the noncanonical 1,2-propanediol utilization BMC locus (PDU1C) of Lactobacillus reuteri. The 2.0 angstrom X-ray structure of Fld1C displays the alpha/beta flavodoxin fold, which noncovalently binds a single flavin mononucleotide molecule. Fld1C is a short-chain flavodoxin with redox potentials of -240 +/- 3 mV oxidized/semiquinone and -344 +/- 1 mV semiquinone/hydroquinone versus the standard hydrogen electrode at pH 7.5. It can participate in an electron transfer reaction with a photoreductant to form a stable semiquinone species. Collectively, our structural and functional results suggest that PDU1C BMCs encapsulate Fld1C to store and transfer electrons for the reactivation and/or recycling of the B 12 cofactor utilized by the signature enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily

Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-α-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, the dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-α-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 Å or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. Furthermore, on the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies

Self-assembly of recombinant proteins within the biosilica of living diatoms represents a means to construct functional materials in a reproducible and scalable manner that enable applications that harness the inherent specificities of proteins to sense and respond to environmental cues. Here we describe the use of a silaffin-derived lysine-rich 39 amino-acid targeting sequence (Sil3T8) to direct a single chain fragment variable (scFv) antibody or an enhanced green fluorescent protein (EGFP) to assemble within the biosilica frustule, resulting in abundances in excess of 200,000 proteins per frustule. The fluorescence of either a derivative of trinitrotoluene (TNT) bound to the scFv or the endogenous fluorescence of EGFP was used to monitor pro-tein conformational dynamics, accessibility to external quenchers, binding affinity, and conformational stability. We find that proteins within isolated frustules undergo isotropic rotational motions with two-fold increases in rotational correlation times, which are indicative of weak macromolecular associations within the biosilica. Solvent accessibilities and high-affinity (pM) binding are comparable to those in solution. In contrast to solution conditions, scFv antibod-ies within the biosilica matrix retain their binding affinity in the presence of chaotropic agents (i.e., 8 M urea). These results argue that dramatic increases in protein conforma-tional stability within the biosilica frustule matrices arise through molecular crowding, acting to retain native protein folds and associated functionality to allow the utility of engineered proteins under a range of harsh environmental conditions associated with environmental sensing and industrial catalytic transformations.

Biosilica↗

From Linear Molecular Chains to Extended Polycyclic Networks: Polymerization of Dicyanoacetylene

Dicyanoacetylene (C 4 N 2 ) is an unusual energetic molecule with alternating triple and single bonds (think miniature, nitrogen-capped carbyne), which represents an interesting starting point for the transformation into extended carbon–nitrogen solids. While pressure-induced polymerization has been documented for a wide variety of related molecular solids, precise mechanistic details of reaction pathways are often poorly understood and the characterization of recovered products is typically incomplete. In this work, we study the high-pressure behavior of C 4 N 2 and demonstrate polymerization into a disordered carbon–nitrogen network that is recoverable to ambient conditions. The reaction proceeds via activation of linear molecules into buckled molecular chains, which spontaneously assemble into a polycyclic network that lacks long-range order. The recovered product was characterized using a variety of optical spectroscopies, X-ray methods, and theoretical simulations and is described as a predominately sp 2 network comprising “pyrrolic” and “pyridinic” rings with an overall tendency toward a two-dimensional structure. This understanding offers valuable mechanistic insights into design guidelines for next-generation carbon nitride materials with unique structures and compositions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-Boltzmann Effects in Chain Branching and Pathway Branching for Diethyl Ether Oxidation

Low-temperature (LT) engine applications have several potential benefits, including reduced emissions and increased efficiency. Attaining these benefits requires accurate kinetic modeling of LT chain branching, which depends heavily on ketohydroperoxide (KHP) decomposition. For diethyl ether (DEE), a promising biofuel, current estimates of the KHP decomposition rate constant are largely based on empirical fits to data. In this study, we investigate the most important KHP isomer in DEE LT oxidation by applying variable reaction coordinate transition state theory to the main pathway for KHP decomposition: OO bond fission to produce •OH and a keto-alkoxy radical, •OQ'O. We also use ab initio kinetics methods to investigate the decomposition of •OQ'O, where we find dominant branching to acetic acid, with the remaining flux going to CH 3 C(O)OCHO. Additionally, new time-resolved measurements of DEE and acetic acid concentrations during LT (450–600 K) DEE oxidation are obtained in a laser photolysis flow reactor coupled with multiplexed photoionization mass spectrometry. These new experimental data, along with jet-stirred reactor data in the literature, are compared with the predictions of a recent DEE mechanism (Tran et al. Proc. Comb. Inst. 2019, 37, 511-519) that was modified with the newly calculated ab initio rate constants for KHP and •OQ'O decomposition. The predictions of the modified mechanism are quite poor when compared to the experimental data; this is primarily due to the new KHP ⇌ •OQ'O + •OH rate constant, which is 1–2 orders of magnitude slower than empirical values employed in recent mechanisms. To reconcile the new KHP rate constant and the experimental data, we explore and quantify the possible role of non-Boltzmann (nB) reaction sequences. The nB reactions have a substantial effect on both the overall mechanism reactivity and the •OQ'O branching to acetic acid. We also provide guidance on the proper implementation of nB reactions in kinetic mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗