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At least 685 records · Page 38

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

The Electron Spectro-Microscopy (ESM) Beamline at NSLS-II

Photoelectron spectroscopy is a primary tool for the study of the electronic structure of materials and the chemical composition of surfaces. High-resolution angle-resolved photoemission spectroscopy (ARPES) has the unique ability to map the energy bands in momentum space. Furthermore, going beyond the single particle picture, the self-energy corrections caused by correlations in solids can be extracted from the analysis of the emission line shape. The current level of refinement, in terms of energy and angular resolution (ΔE < 1 meV, Δθ < 0.1°), makes the technique sensitive to the lowest energy excitations and the dynamics of electrons, which in turn virtually determine all the macroscopic properties of any system and govern the chemical, electrical, magnetic, and physical processes. Similarly important, X-ray photoelectron microscopy (XPEEM), combined with the low-energy electron microscopy (LEEM), is indispensable in probing the complexity of chemical, structural, electronic and magnetic properties of surfaces and shallow interfaces, with the spatial resolution of few tens of nanometer (nm). The Electron-Spectro-Microscopy beamline (ESM) has been recently commissioned at NSLS-II and is now in operation. The primary spectroscopic technique is photoemission, performed over a wide energy range with control of light polarization and in a variety of flux/resolution conditions. The beamline has two experimental end stations that allow to perform ARPES and XPEEM/LEEM, separately. The ARPES end station focuses on high energy-resolution work, with spot-size of a few microns. The XPEEM/LEEM end station is a full-field microscope (XPEEM) operating either with the synchrotron generated X-rays (XPEEM), or with an internal electron gun (LEEM). Spatial resolution is crucial in studies of newly synthesized complex materials since they are often initially available only as small specimens (typically micron size). Furthermore, chemical inhomogeneities on surfaces are often an integral part of surface chemical processes. Finally, the ESM beamline with X-ray spots of few microns is optimized to study the electronic structure of novel materials with microscopy capabilities.

47 OTHER INSTRUMENTATION↗

Electron-irradiation induced creep in amorphous alloys

Electron-irradiation induced creep rates in amorphous alloys, a-SiO2, Fe79B16Si5, Cu60Ta40, and Cu50Ti50, were measured at room temperature using a miniaturized beam-bending apparatus within a transmission electron microscope operated at 200 keV. The creep rates of these amorphous samples increased nearly linearly with both e-beam current density and applied stress, while a reference crystalline (c-)SiO2 sample failed to creep under the same conditions. The irradiation induced creep compliance of a-SiO2 was ~ 15 times larger than that of Fe79B16Si5 and over 1,000 times larger than that of the two Cu alloys. Molecular dynamics computer simulations were employed to simulate electron irradiation induced creep using interatomic potentials representing amorphous Cu75Zr25, Ni80P20, and SiO2 as model systems. The irradiation induced creep compliances calculated for Cu75Zr25 during 200 keV electron irradiation provided good quantitative agreement with the two Cu-based alloys, but that for a-SiO2 was ~ 180 times too small. These results indicate that unlike neutron or ion-beam induced creep in a-SiO2, creep under electron irradiation is dominated by the effects of ionization owing largely to the far higher ratio of electronic stopping to nuclear stopping for electrons than for ions.

36 MATERIALS SCIENCE↗

Influence of neutrino-electron scattering and neutrino-pair annihilation on hypermassive neutron star

Here, we investigate the influence of inelastic neutrino microphysics in general-relativistic magnetohydrodynamics simulations of a hypermassive neutron star. In particular, we include species/energy groups coupled neutrino-matter interactions, such as inelastic neutrino-electron scattering and electron-positron annihilation kernels, into simulations up to 50 ms. Neutrino-electron inelastic scattering is known to have effective neutrino-matter energy exchange. We show that, with neutrino-electron inelastic scattering, simulations predict 75% higher disc mass with slightly different mass-averaged compositions, and 18% more ejected mass with similar distributions. The enhancement of the mass of the disc and the ejecta results in stronger baryon pollution, leading to less favorable jet launching environments. Furthermore, neutrino luminosities are about 50%, 40%, and 30% higher for electron neutrino, electron antineutrino, and heavy-lepton neutrinos. In contrast, we do not see any significant impacts due to electron-positron annihilation.

79 ASTRONOMY AND ASTROPHYSICS↗

Numerical investigation of nonequilibrium electron effects on the collisional ionization rate in the collisional-radiative model

In this study, the interplay of kinetic electron physics and atomic processes in ultrashort laser-plasma interactions provides a comprehensive understanding of the impact of the electron energy distribution on plasma properties. Notably, nonequilibrium electrons play a vital role in collisional ionization, influencing ionization degrees and spectra. This paper introduces a computational model that integrates the physics of kinetic electrons and atomic processes, utilizing a Boltzmann equation for nonequilibrium electrons and a collisional-radiative model for atomic state populations. The model is used to investigate the influence of nonequilibrium electrons on collisional ionization rates and its effect on the population distribution, as observed in a widely known experiment. The study reveals a significant nonequilibrium electron presence during XFEL-matter interactions, profoundly affecting collisional ionization rates in the gas plasma, thereby necessitating careful consideration of the Collisional-Radiative model applied to such systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Anomalous Resistivity and Electron Heating by Lower Hybrid Drift Waves during Magnetic Reconnection with a Guide Field

The lower hybrid drift wave (LHDW) has been a candidate for anomalous resistivity and electron heating inside the electron diffusion region of magnetic reconnection. In a laboratory reconnection layer with a finite guide field, quasielectrostatic LHDW (ES-LHDW) propagating along the direction nearly perpendicular to the local magnetic field is excited in the electron diffusion region. ES-LHDW generates large density fluctuations ($δn_{\text e}$, about 25% of the mean density) that are correlated with fluctuations in the out-of-plane electric field ($δE_Y$, about twice larger than the mean reconnection electric field). With a small phase difference (~ 30°) between two fluctuating quantities, the anomalous resistivity associated with the observed ES-LHDW is twice larger than the classical resistivity and accounts for 20% of the mean reconnection electric field. After we verify the linear relationship between $δn_{\text e}$ and $δE_Y$, anomalous electron heating by LHDW is estimated by a quasilinear analysis. The estimated electron heating is about 2.6 ± 0.3 MW / m 3 , which exceeds the classical Ohmic heating of about 2.0 ± 0.2 MW / m 3 . This LHDW-driven heating is consistent with the observed trend of higher electron temperatures when the wave amplitude is larger. Finally, presented results provide the first direct estimate of anomalous resistivity and electron heating power by LHDW, which demonstrates the importance of wave-particle interactions in magnetic reconnection.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Electronic Band Structure of a Superconducting Nickelate Probed by the Seebeck Coefficient in the Disordered Limit

Superconducting nickelates are a new family of strongly correlated electron materials with a phase diagram closely resembling that of superconducting cuprates. While analogy with the cuprates is natural, very little is known about the metallic state of the nickelates, making these comparisons difficult. We probe the electronic dispersion of thin-film superconducting five-layer ( n = 5 ) and metallic three-layer ( n = 3 ) nickelates by measuring the Seebeck coefficient S . We find a temperature-independent and negative S / T for both n = 5 and n = 3 nickelates. These results are in stark contrast to the strongly temperature-dependent S / T measured at similar electron filling in the cuprate La 1.36 Nd 0.4 Sr 0.24 CuO 4 . The electronic structure calculated from density-functional theory can reproduce the temperature dependence, sign, and amplitude of S / T in the nickelates using Boltzmann transport theory. This demonstrates that the electronic structure obtained from first-principles calculations provides a reliable description of the fermiology of superconducting nickelates and suggests that, despite indications of strong electronic correlations, there are well-defined quasiparticles in the metallic state. Finally, we explain the differences in the Seebeck coefficient between nickelates and cuprates as originating in strong dissimilarities in impurity concentrations. Our study demonstrates that the high elastic scattering limit of the Seebeck coefficient reflects only the underlying band structure of a metal, analogous to the high magnetic field limit of the Hall coefficient. This opens a new avenue for Seebeck measurements to probe the electronic band structures of relatively disordered quantum materials. Published by the American Physical Society 2024

Grissonnanche, G. (ORCID:0000000251153125)↗

Probing Electronic Coherence between Core-Level Vacancies at Different Atomic Sites

The detailed understanding of electronic coherence in quantum systems requires measurements on the attosecond timescale. Attosecond x-ray pulses enable the study of electronic coherence in core-excited molecular systems. Here we report on the coherent motion of electrons in the 1,1-difluoroethylene ion following ionization of the K shell of the two nonequivalent carbon sites with a subfemtosecond x-ray pulse. Using the angular streaking technique to track the Auger-Meitner decay, we observe temporal modulations of the emission, indicating the electronic coherence of the core-excited ionic states, and extract a 6.5 ± 0.8 fs average lifetime of the core-level vacancies. A quantum-mechanical model is employed to interpret the measurement, and we find the observed temporal modulations are independent of charge density oscillations. This work opens a new regime of coherent electronic motion, beyond charge migration, where electronic coherence manifests in the nonlocal quantum correlation between atomic sites while charge density oscillation is absent. Our results broaden the landscape of electronic coherence in molecular systems. Published by the American Physical Society 2025

Wang, Jun (ORCID:000000031962895X)↗

Study of electron-induced chemical transformations in polymers

In extreme ultraviolet (EUV) photoresist exposure, the primary and secondary electrons drive chemistry rather than the EUV photons themselves. These electrons have a wide range of energies below approximately 80 eV, which are capable of complex network of reactions during exposure. To better understand the ability of electrons of different energies within the EUV primary and secondary electron range, we want to characterize and compare the chemistry induced in pure polymer films by direct exposure to electrons. Thin films of poly(tert-butyl methacrylate), poly(methyl methacrylate), and poly(4-hydroxystyrene) were exposed to a 20 to 80 eV electron beam. Outgassing during exposure was characterized in-situ using a quadrupole residual gas analyzer. The thickness changes were measured using ellipsometry and chemical bond structure data were collected using Fourier-transform infrared spectroscopy (FTIR) after exposure to compare different exposure conditions. Poly(4-hydroxystyrene) demonstrated stability during electron exposures. Exposures of the other two materials led to outgassing of protecting groups, the intensity of which decayed in time. Outgassing, FTIR, and thickness loss data exhibited approximately linear relationships to each other.

Mueller, Maximillian↗

Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source

ABSTRACT Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures (“py”’) demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c - and b -type cytochromes was observed in “py,” pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells’ photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(−), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet’s history.

59 BASIC BIOLOGICAL SCIENCES↗

Electron Spin Polarization in Large Electric Fields

This project investigated the effects of large electric fields on electron spin polarization in semiconductors, which is of interest for spin-based electronics (“spintronics”) and quantum information processing. It has been theoretically proposed that large electric fields could potentially preserve or amplify electron spin polarization, which would make it easier to generate, transport, and detect spin polarization in spin-based devices; however, previous measurements had not measured the response of electron spin polarization at large electric fields. During this project, methods to perform measurements of electron spin polarization at large electric fields were developed and performed using ultrafast time- and spatially-resolved magneto-optical spectroscopy, high-voltage pulses, and lock-in detection. The device geometry was engineered to reduce the threshold voltage required to reach the Gunn threshold, and the effect of optical illumination on the sample conductivity and Gunn oscillations was investigated. Electron spin polarization measurements were performed at electric fields up to and beyond the Gunn threshold for the device. The measurements showed that the electron spin polarization magnitude decreased with increasing electric field in the devices measured, and a spin amplification effect was not observed. However, these effects could potentially exist in a different material or in a material with a different doping concentration or in a different device geometry.

36 MATERIALS SCIENCE↗

Oblique instability of quasi-parallel whistler waves in the presence of cold and warm electron populations

Whistler waves propagating nearly parallel to the ambient magnetic field experience a nonlinear instability due to transverse currents when the background plasma has a population of sufficiently low energy electrons. Intriguingly, this nonlinear process may generate oblique electrostatic waves, including whistlers near the resonance cone with properties resembling oblique chorus waves in the Earth’s magnetosphere. Focusing on the generation of oblique whistlers, earlier analysis of the instability is extended here to the case where low-energy background plasma consists of both a “cold” population with energy of a few eV and a “warm” electron component with energy of the order of 100 eV. This is motivated by spacecraft observations in the Earth’s magnetosphere where oblique chorus waves were shown to interact resonantly with the warm electrons. The main new results are: 1) the instability producing oblique electrostatic waves is sensitive to the shape of the electron distribution at low energies. In the whistler range of frequencies, two distinct peaks in the growth rate are typically present for the model considered: a peak associated with the warm electron population at relatively low wavenumbers and a peak associated with the cold electron population at relatively high wavenumbers; 2) overall, the instability producing oblique whistler waves near the resonance cone persists (with a reduced growth rate) even in the cases where the temperature of the cold population is relatively high, including cases where cold population is absent and only the warm population is included; 3) particle-in-cell simulations show that the instability leads to heating of the background plasma and formation of characteristic plateau and beam features in the parallel electron distribution function in the range of energies resonant with the instability. The plateau/beam features have been previously detected in spacecraft observations of oblique chorus waves. However, they have been attributed to external sources and have been proposed to be the mechanism generating oblique chorus. In the present scenario, the causality link is reversed and the instability generating oblique whistler waves is shown to be a possible mechanism for formation of the plateau and beam features.

79 ASTRONOMY AND ASTROPHYSICS↗

Characterizing the Excited States and Electronic Absorption Spectra of Small Alkylperoxy (RO 2 •) and Hydroperoxy (•QOOH) Radicals

Organic peroxy (ROO•) and hydroperoxy (•QOOH) radicals are key reactive intermediates that are formed via the oxidation of volatile organic compounds during combustion or in the Earth’s atmosphere. Their primary fate is continued unimolecular decay or bimolecular chemistry, the relative branching for which is heavily structure- and temperature-dependent. This article outlines a combined single- and multi-reference quantum chemical study to characterize the near-UV accessible electronically excited states of the prototypical ROO• and •QOOH intermediates, tert-butyl peroxy and hydroperoxy-tert-butyl radicals—the ground-state chemistries of which have been well studied both experimentally and computationally. Additionally, we simulate the electronic absorption profiles of these ROO• and •QOOH intermediates with a variety of multi- and single-reference methods. The results show an interesting conformer dependence on the electronically excited-state character and electronic absorption maxima of •QOOH. The results show promise for electronic absorption spectroscopy to be used as a selected probe for determining •QOOH conformers. Additionally, electronic absorption may contribute to the daytime removal of long-lived •QOOH intermediates formed in the troposphere. We expect that our studies will motivate experiments on the electronic absorption spectra of experimentally achievable ROO• and •QOOH.

excited states↗

Electron Heating in 2D Particle-in-cell Simulations of Quasi-perpendicular Low-beta Shocks

Abstract We measure the thermal electron energization in 1D and 2D particle-in-cell simulations of quasi-perpendicular, low-beta ( β p = 0.25) collisionless ion–electron shocks with mass ratio m i / m e = 200, fast Mach number M ms = 1 –4, and upstream magnetic field angle θ Bn = 55°–85° from the shock normal n ˆ . It is known that shock electron heating is described by an ambipolar, B -parallel electric potential jump, Δ ϕ ∥ , that scales roughly linearly with the electron temperature jump. Our simulations have Δ ϕ ∥ / ( 0.5 m i u sh 2 ) ∼ 0.1 –0.2 in units of the pre-shock ions’ bulk kinetic energy, in agreement with prior measurements and simulations. Different ways to measure ϕ ∥ , including the use of de Hoffmann–Teller frame fields, agree to tens-of-percent accuracy. Neglecting off-diagonal electron pressure tensor terms can lead to a systematic underestimate of ϕ ∥ in our low- β p shocks. We further focus on two θ Bn = 65° shocks: a M s = 4 ( M A = 1.8 ) case with a long, 30 d i precursor of whistler waves along n ˆ , and a M s = 7 ( M A = 3.2 ) case with a shorter, 5 d i precursor of whistlers oblique to both n ˆ and B ; d i is the ion skin depth. Within the precursors, ϕ ∥ has a secular rise toward the shock along multiple whistler wavelengths and also has localized spikes within magnetic troughs. In a 1D simulation of the M s = 4 , θ Bn = 65° case, ϕ ∥ shows a weak dependence on the electron plasma-to-cyclotron frequency ratio ω pe /Ω ce , and ϕ ∥ decreases by a factor of 2 as m i / m e is raised to the true proton–electron value of 1836.

Tran, Aaron (ORCID:0000000334834890)↗

Energy Conversion and Electron Acceleration and Transport in 3D Simulations of Solar Flares

Recent observations and simulations indicate that solar flares undergo extremely complex 3D evolution, making 3D particle transport models essential for understanding electron acceleration and interpreting flare emissions. In this study, we investigate this problem by solving Parker’s transport equation with 3D MHD simulations of solar flares. By examining energy conversion in the 3D system, we evaluate the roles of different acceleration mechanisms, including reconnection current sheet (CS), termination shock (TS), and supra-arcade downflows (SADs). We find that large-amplitude turbulent fluctuations are generated and sustained in the 3D system. The model results demonstrate that a significant number of electrons are accelerated to hundreds of keV and even a few MeV, forming power-law energy spectra. These energetic particles are widely distributed, with concentrations at the TS and in the flare looptop region, consistent with results derived from recent hard X-ray (HXR) and microwave (MW) observations. By selectively turning particle acceleration on or off in specific regions, we find that the CS and SADs effectively accelerate electrons to several hundred keV, while the TS enables further acceleration to MeV. However, no single mechanism can independently account for the significant number of energetic electrons observed. Instead, the mechanisms work synergistically to produce a large population of accelerated electrons. Our model provides spatially and temporally resolved electron distributions in the whole flare region and at the flare footpoints, enabling synthetic HXR and MW emission modeling for comparison with observations. These results offer important insights into electron acceleration and transport in 3D solar flare regions.

79 ASTRONOMY AND ASTROPHYSICS↗

Monochromation of pulsed electron beams with terahertz radiation at a planar mirror

Exquisite control of electron beam energy is required for many electron spectroscopy and imaging applications. For both continuous and pulsed beams, the beam energy spread is fundamentally limited by the electron source, and is typically a sizable fraction of an electron-volt. In this paper, we present a means to reduce electron beam energy spread after emission to the level of a few 10s of meV rms using femtosecond photoemission and an interaction with laser-derived single- to few-cycle terahertz (THz) radiation. We show analytically and in particle tracking simulations that this interaction can remove energy spread stored in both the transverse and longitudinal degrees of freedom. We analytically formulate the limit of energy spread that this technique can achieve, and map the non-ideal affects arising at high frequencies. The interaction is mediated by the beam's passage through a mirror which is reflective to terahertz radiation but allows transmission of the majority of the electron beam (e.g. a wire mesh). This method then only requires beam current losses of a few tens of percent, far smaller than what is achieved in prism and slit-based electron monochromators.

Accelerator Physics (physics.acc-ph)↗

SM91: Observations of interchange between acceleration and thermalization processes in auroral electrons

Results from a Nike-Tomahawk sounding rocket flight launched from Fort Churchill are presented. The rocket was launched into a breakup aurora at magnetic local midnight on 21 March 1968. The rocket was instrumented to measure electrons with an electrostatic analyzer electron spectrometer which made 29 measurements in the energy interval 0.5 KeV to 30 KeV. Complete energy spectra were obtained at a rate of 10/sec. Pitch angle information is presented via 3 computed average per rocket spin. The dumped electron average corresponds to averages over electrons moving nearly parallel to the B vector. The mirroring electron average corresponds to averages over electrons moving nearly perpendicular to the B vector. The average was also computed over the entire downward hemisphere (the precipitated electron average). The observations were obtained in an altitude range of 10 km at 230 km altitude.

Pongratz, M.↗

Explorer 35 observations of solar-wind electron density, temperature, and anisotropy.

Measurement of the solar wind electron integral spectrum yielding electron temperatures ranging from 100,000 to 400,000 K and having an average value of 182,000 K, electron densities having an average value of 4.6 per cu cm, and electron-temperature anisotropies ranging from 1 to 1.4. The electron temperature is found to be independent of solar-wind speed over the range from 290 to 675 km/sec. Comparison of the simultaneous alignment of the local magnetic-field vector with the direction of the electron-temperature anisotropy reveals a high correlation. Necessary conditions for the fire-hose instabilities were satisfied in the electron and proton components of the solar-wind plasma immediately behind an interplanetary shock.

Serbu, G. P.↗