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At least 613 records · Page 34

Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography

Abstract The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic properties of 316l stainless steel repaired using electron beam additive manufacturing

Additive manufacturing has the potential to be used for repair of high-value parts, but the strength and integrity of such repaired parts, especially under dynamic loading, in still unknown. This work presents the results of high strain-rate dynamic testing of additively repaired stainless steel samples. The 316L samples were intentionally damaged and subsequently repaired with 308L stainless steel wire using electron beam additive manufacturing. The repaired samples were subjected to gas-gun impact testing to induce incipient damage and determine the role played by the repaired region in dictating damage and failure. The results show the following: 1) the equation of state of the repaired region is comparable to the original material as shown by the unchanged spall plane location, 2) the deformation behavior is similar to the original material as shown by the similar Hugoniot Elastic limit, 3) the spall strength of the repaired region is slightly higher than the original material due to varying grain size, and 4) the damage morphology in the repaired region is different and involves a high rate of void coalescence. In conclusion, despite these minor differences in the spall strength and the damage morphology, the overall dynamic response of the original material and repaired samples is similar suggesting that AM is a promising approach for repairing high-value components.

36 MATERIALS SCIENCE↗

Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy

Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained atomic-scale corrugations that were absent in the other systems which comprised unsubstituted aliphatic and aromatic side chains. We hypothesize that these corrugations are due to the dipolar characteristics of the brominated phenyl group and interactions between this group and water molecules. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

Broadband 2DES detection of vibrational coherence in the S x state of canthaxanthin

The nonadiabatic mechanism that mediates nonradiative decay of the bright S 2 state to the dark S 1 state of carotenoids involves population of a bridging intermediate state, S x , in several examples. The nature of S x remains to be determined definitively, but it has been recently suggested that S x corresponds to conformationally distorted molecules evolving along out-of-plane coordinates of the isoprenoid backbone near a low barrier between planar and distorted conformations on the S 2 potential surface. Here, the electronic and vibrational dynamics accompanying the formation of S x in toluene solutions of the ketocarotenoid canthaxanthin (CAN) are characterized with broadband two-dimensional electronic spectroscopy (2DES) with 7.8 fs excitation pulses and detection of the linear polarization components of the third-order nonlinear optical signal. A stimulated-emission cross peak in the 2DES spectrum accompanies the formation of S x in <20 fs following excitation of the main absorption band. S x is prepared instantaneously, however, with excitation of hot-band transitions associated with distorted conformations of CAN’s isoprenoid backbone in the low frequency onset of the main absorption band. Vibrational coherence oscillation maps and modulated anisotropy transients show that S x undergoes displacements from the Franck–Condon S 2 state along out-of-plane coordinates as it passes to the S 1 state. The results are consistent with the conclusion that CAN’s carbonyl-substituted β-ionone rings impart an intramolecular charge-transfer character that frictionally slows the passage from S x to S 1 compared to carotenoids lacking carbonyl substitution. Despite the longer lifetime, the S 1 state of CAN is formed with retention of vibrational coherence after passing through a conical intersection seam with the S x state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Connectivity-Dependent Exciton–Phonon Coupling in Cesium Bismuth Halide Quantum Dots

Metal halide octahedra form the fundamental functional building blocks of metal halide perovskites, dictating their structures, optical properties, electronic structures, and dynamics. Here, in this study, we show that the connectivity of bismuth halide octahedra in Cs 3 Bi 2 Br 9 and Cs 3 Bi 2 I 9 quantum dots (QDs) changes with different halide elements. We use first-principles calculations to reveal the key role of the connectivity of bismuth halide octahedra on the wave function symmetry, Huang-Rhys factor, and exciton-phonon interaction strength. Following QD synthesis via a ligand-mediated transport method, the effect of connectivity is verified with transient absorption spectroscopy, where we contrast Cs 3 Bi 2 Br 9 and Cs 3 Bi 2 I 9 QD exciton dynamics. In photoexcited Cs 3 Bi 2 I 9 QDs, phonons related to the vibrational motions of face-sharing [BiI 6 ] 3- bioctahedra couple strongly to the electronic state and drive rapid carrier relaxation. Equivalent signals are not observed for photoexcited Cs 3 Bi 2 Br 9 QDs, implying a lack of phonon involvement in band-edge absorption and subsequent exciton relaxation. Our findings suggest that structural engineering can effectively tune the exciton-phonon coupling and therefore influence exciton relaxation and recombination in perovskite nanomaterials.

TDDFT↗

Plasma decay of nanosecond pulsed laser-produced Ar and Ar–H 2 O sparks at atmospheric pressure

Time-resolved diagnostics were applied to investigate free-electron properties in nanosecond laser-produced discharges generated in atmospheric pressure Ar and in Ar–3%H 2 O. The discharges were generated using 23 ns, 1064 nm laser pulses. Broadband plasma imaging and laser Thomson scattering were combined with optical emission spectroscopy, with particular emphasis on the Stark broadening of the H α and H β lines. The plasma exhibited a bright emission that persists for up to 30–40 µs after breakdown. Plasma emission was then followed by a very weak glow emission that persisted for up to 19 ms after breakdown. Peak electron number density of ∼2 × 10 17 cm −3 and electron temperature of ∼7 eV were measured. An excellent agreement between both techniques was obtained regarding absolute electron number densities. The inferred free-electron temporal decay dynamics are consistent with processes dominated by hydrodynamic expansion and two- and three-body electron–ion recombination. These results provide benchmark data for modeling nanosecond laser discharges and demonstrate the reliability of combining Thomson scattering with Stark broadening in atmospheric laser sparks.

Thomson scattering↗

Ultrafast thermal modification of strong coupling in an organic microcavity

There is growing interest in using strongly coupled organic microcavities to tune molecular dynamics, including the electronic and vibrational properties of molecules. However, very little attention has been paid to the utility of cavity polaritons as sensors for out-of-equilibrium phenomena, including thermal excitations. Here, we demonstrate that non-resonant infrared excitation of an organic microcavity system induces a transient response in the visible spectral range near the cavity polariton resonances. We show how these optical responses can be understood in terms of ultrafast heating of electrons in the metal cavity mirror, which modifies the effective refractive index and subsequently the strong coupling conditions. The temporal dynamics of the microcavity are strictly determined by carriers in the metal, including the cooling of electrons via electron–phonon coupling and excitation of propagating coherent acoustic modes in the lattice. We rule out multiphoton excitation processes and verify that no real polariton population exists despite their strong transient features. These results suggest the cavity polaritons to be promising as sensitive probes of non-equilibrium phenomena.

36 MATERIALS SCIENCE↗

Collisionless plasma transport mechanisms in stochastic open magnetic field lines in tokamaks

The collisionless plasma transport in stochastic magnetic fields connecting to wall boundary has been studied to understand the underlying mechanisms of thermal quench physics in tokamak disruption. In this study, we present a comprehensive understanding of the plasma dynamics in three-dimensional stochastic open magnetic field lines, taking into account the consistent coupling of electron and ion dynamics through the ambipolar electric field. The open stochastic field lines act as a 3D magnetic mirror consisting of the magnetic well and hill regions. It was found that the magnetic hill regions play a critical role in enhancing electron thermal transport. When the plasma collapses to the wall, the 3D ambipolar potential arises in the stochastic layer to maintain the quasi-neutrality of the plasma. The E × B vortices induced by the 3D ambipolar potential mix the plasma across stochastic field lines and enhance the radial transport. Particularly, the E × B mixing between the magnetic well and hill regions provides a collisionless detrapping mechanism that plays a major role in the loss of high-energy trapped electrons. As a result, the electron temperature steadily decreases at a rate of about -0.5 keV ms -1 , comparable to the rate observed in thermal quench experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Revealing the dynamics of the alloying and segregation of Pt-Co nanoparticles via in-situ environmental transmission electron microscopy

Thermal treatment is a general and efficient way to synthesize intermetallic catalysts and may involve complicated physical processes. So far, the mechanisms leading to the size and composition heterogeneity, as well as the phase segregation behavior in Pt-Co nanoparticles (NPs) are still not well understood. Here, via in-situ environmental transmission electron microscopy, the formation dynamics and segregation behaviors of Pt-Co alloyed NPs during the thermal treatment were investigated. It is found that Pt-Co NPs on zeolitic imidazolate frameworks-67-derived nanocarbon (NC) are formed consecutively through both particle migration coalescence and the Ostwald ripening process. The existence of Pt NPs is found to affect the movement of Co NPs during their migration. With the help of theoretical calculations, the correlations between the composition and migration of the Pt and Co during the ripening process were uncovered. Herein, these complex alloying processes are revealed as key factors leading to the heterogeneity of the synthesized Pt-Co alloyed NPs. Under oxidation environment, the Pt-Co NPs become surface faceted gradually, which can be attributed to the oxygen facilitated relatively higher segregation rate of Co from the (111) surface. This work advances the fundamental understanding of design, synthesis, and durability of the Pt-based nanocatalysts.

36 MATERIALS SCIENCE↗

Momentum-Space Observation of Optically Excited Nonthermal Electrons in Graphene with Persistent Pseudospin Polarization

The unique optical properties of graphene, with broadband absorption and ultrafast response, make it a critical component of optoelectronic and spintronic devices. Using time-resolved momentum microscopy with high data rate and high dynamic range, we report momentum-space measurements of electrons promoted to the graphene conduction band with visible light and their subsequent relaxation. Here, we observe a pronounced nonthermal distribution of nascent photoexcited electrons with lattice pseudospin polarization in remarkable agreement with results of simple tight-binding theory. By varying the excitation fluence, we vary the relative importance of electron-electron vs electron-phonon scattering in the relaxation of the initial distribution. Increasing the excitation fluence results in increased noncollinear electron-electron scattering and reduced pseudospin polarization, although up-scattered electrons retain a degree of polarization. These detailed momentum-resolved electron dynamics in graphene demonstrate the capabilities of high-performance time-resolved momentum microscopy in the study of 2D materials and can inform the design of graphene devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From Electronic Structure to Ion Transport: Photoelectron Spectroscopy and Molecular Dynamics Simulations Reveal the Role of Anions in Lithium Battery Electrolytes

Electrolyte anions are pivotal for lithium battery performance, yet their fundamental electronic structural properties are not well understood. In this work, we employ a combination of negative-ion photoelectron spectroscopy (NIPES), ab initio calculations, and molecular dynamics (MD) simulations to investigate the electronic structures of three representative electrolyte anions. This multiscale approach enables us to elucidate how their intrinsic electronic properties govern anion–solvent interactions in gas-phase clusters, as well as lithium-ion (Li + ) solvation structures and ion transport behavior in the condensed phase. NIPES reveals that difluoro(oxalato)borate (DFOB – ), bis(fluorosulfonyl)imide (FSI – ), and bis(oxalato)borate (BOB – ) all exhibit high electron binding energies, with vertical/adiabatic detachment energies increasing from DFOB – (6.09/5.70 eV) to FSI – (6.80/6.10 eV) to BOB – (6.82/6.40 eV), correlating with enhanced oxidation stability. Ab initio calculations reveal that DFOB – /FSI – –solvent complexes bind Li + ∼ 10 kcal/mol stronger than BOB – series, aligning with the strength of a Li + –anion model. DFOB – exhibits pronounced charge localization on both oxygen and fluorine atoms, enabling their involvement in Li + coordination. In contrast, fluorine atoms in FSI – are largely electron-depleted and remain excluded from direct Li + binding. MD simulations further demonstrate that LiDFOB and LiFSI systems exhibit Li + diffusion coefficients three and five times higher than those of LiBOB across four common solvents. Notably, LiFSI salt in acetonitrile (AN) exhibits the fastest Li + diffusion among 12 electrolyte systems, highlighting the synergistic effect of FSI – and AN in promoting ion mobility. In conclusion, these findings provide a molecular-level understanding of the critical roles of anion and its microsolvation in optimizing Li + diffusion dynamics, once again emphasizing the positioning of FSI – and DFOB – as prime candidates for next-generation electrolytes.

25 ENERGY STORAGE↗

Latent Mechanisms of Polarization Switching from In Situ Electron Microscopy Observations

In situ scanning transmission electron microscopy enables observation of the domain dynamics in ferroelectric materials as a function of externally applied bias and temperature. The resultant data sets contain a wealth of information on polarization switching and phase transition mechanisms. However, identification of these mechanisms from observational data sets has remained a problem due to a large variety of possible configurations, many of which are degenerate. Here, an approach based on a combination of deep learning-based semantic segmentation, rotationally invariant variational autoencoder (VAE), and non-negative matrix factorization to enable learning of a latent space representation of the data with multiple real-space rotationally equivalent variants mapped to the same latent space descriptors is introduced. By varying the size of training sub-images in the VAE, the degree of complexity in the structural descriptors is tuned from simple domain wall detection to the identification of switching pathways. Importantly, this yields a powerful tool for the exploration of the dynamic data in mesoscopic electron, scanning probe, optical, and chemical imaging. Moreover, this work adds to the growing body of knowledge of incorporating physical constraints into the machine and deep-learning methods to improve learned descriptors of physical phenomena.

36 MATERIALS SCIENCE↗

Resonant inelastic x-ray scattering in warm-dense Fe compounds beyond the SASE FEL resolution limit

Resonant inelastic x-ray scattering (RIXS) is a widely used spectroscopic technique, providing access to the electronic structure and dynamics of atoms, molecules, and solids. However, RIXS requires a narrow bandwidth x-ray probe to achieve high spectral resolution. The challenges in delivering an energetic monochromated beam from an x-ray free electron laser (XFEL) thus limit its use in few-shot experiments, including for the study of high energy density systems. Here we demonstrate that by correlating the measurements of the self-amplified spontaneous emission (SASE) spectrum of an XFEL with the RIXS signal, using a dynamic kernel deconvolution with a neural surrogate, we can achieve electronic structure resolutions substantially higher than those normally afforded by the bandwidth of the incoming x-ray beam. We further show how this technique allows us to discriminate between the valence structures of Fe and Fe2O3, and provides access to temperature measurements as well as M-shell binding energies estimates in warm-dense Fe compounds.

74 ATOMIC AND MOLECULAR PHYSICS↗

ELECTRONIC STRUCTURE METHODS AND PROTOCOLS WITH APPLICATION TO DYNAMICS, KINETICS AND THERMOCHEMISTRY

Hydrocarbon combustion involves the reaction dynamics of a tremendous number of species beginning with many-component fuel mixtures and proceeding via a complex system of intermediates to form primary and secondary products. Combustion conditions corresponding to new advanced engines and/or alternative fuels rely increasingly on autoignition and low-temperature-combustion chemistry. In these regimes various transient radical species such as HO2, ROO·, ·QOOH, HCO, NO2, HOCO, and Criegee intermediates play important roles in determining the detailed as well as more general dynamics. A clear understanding and accurate representation of these processes is needed for effective modeling. Given the difficulties associated with making reliable experimental measurements of these systems, computation can play an important role in developing these energy technologies. Accurate calculations have their own challenges since even within the simplest dynamical approximations such as transition state theory, the rates depend exponentially on critical barrier heights and these may be sensitive to the level of quantum chemistry. Moreover, it is well-known that in many cases it is necessary to go beyond statistical theories and consider the dynamics. Quantum tunneling, resonances, radiative transitions, and non-adiabatic effects governed by spin-orbit or derivative coupling can be determining factors in those dynamics. Building upon progress made during a period of prior support through the DOE Early Career Program, this project combines developments in the areas of potential energy surface (PES) fitting and multistate multireference quantum chemistry to allow spectroscopically and dynamically/kinetically accurate investigations of key molecular systems (such as those mentioned above), many of which are radicals with strong multireference character and have the possibility of multiple electronic states contributing to the observed dynamics. An ongoing area of investigation is to develop general strategies for robustly convergent electronic structure theory for global multichannel reactive surfaces including diabatization of energy and other relevant surfaces such as dipole transition. Combining advances in ab initio methods with automated interpolative PES fitting allows the construction of high-quality PESs (incorporating thousands of high-level data) to be done rapidly through parallel processing on high-performance computing (HPC) clusters. In addition, new methods and approaches to electronic structure theory will be developed and tested through applications. This project will explore limitations in traditional multireference calculations (e.g., MRCI) such as those imposed by internal contraction, lack of high-order correlation treatment and poor scaling. Methods such as DMRG-based extended active-space CASSCF and various Quantum Monte Carlo (QMC) methods will be applied (including VMC/DMC and FCIQMC). Insight into the relative significance of different orbital spaces and the robustness of application of these approaches on leadership class computing architectures will be gained. Synergy with other components of this research program such as automated PES fitting and multireference quantum chemistry will be used to address challenges encountered by the standard approaches to computational thermochemistry (those being single-reference quantum chemistry and perturbative treatments of the anharmonic vibrational energy, which break down for some cases of electronic structure or floppy strongly coupled vibrational modes).

74 ATOMIC AND MOLECULAR PHYSICS↗

Breakdown front dynamics of streamer-like discharge in electron-charged polymethyl methacrylate

We present the results of an experimental study of fast breakdown in electron-charged polymethyl methacrylate. We irradiate bulk polymethyl methacrylate disks with diameters up to one meter at different implanted charge densities and measure the discharge current during the forced electrical breakdown of the material. We infer the breakdown dynamics from these current waveforms, including the velocity and time dependence of the electric field driving the breakdown, and compare these results with the physical electrical tree patterns left behind in the material. We find that the dynamics and physical characteristics of the breakdown channels in electron-irradiated solids depart from typical expectations of electrical treeing behavior in solid materials. Thus, we interpret these results as an expression of streamer discharges in dense gases motivated by the existence of trapped gases in the solid due to radiation damage. We show that the dynamics of the breakdown channels in the electron-charged solid dielectric material is well described by applying standard streamer physics to this physical system. The results show that the dynamics of breakdown channels in solid dielectric material is a promising avenue to further understand streamer discharges in different media under extreme conditions.

36 MATERIALS SCIENCE↗

Valley relaxation of resident electrons and holes in a monolayer semiconductor: Dependence on carrier density and the role of substrate-induced disorder

Using time-resolved optical Kerr rotation, here we measure the low-temperature valley dynamics of resident electrons and holes in exfoliated WSe 2 monolayers as a systematic function of carrier density. In an effort to reconcile the many disparate timescales of carrier valley dynamics in monolayer semiconductors reported to date, we directly compare the doping-dependent valley relaxation in two electrostatically gated WSe 2 monolayers having different dielectric environments. In a fully encapsulated structure ( hBN / WSe 2 / hBN , where hBN is hexagonal boron nitride), valley relaxation is found to be monoexponential. The valley relaxation time τ v is quite long ( ~ 10 μ s ) at low carrier densities, but decreases rapidly to less than 100 ns at high electron or hole densities ≳ 2 × 10 12 cm – 2 . In contrast, in a partially encapsulated WSe 2 monolayer placed directly on silicon dioxide ( hBN / WSe 2 / SiO 2 ) , carrier valley relaxation is multiexponential at low carrier densities. The difference is attributed to environmental disorder from the SiO 2 substrate. Unexpectedly, very small out-of-plane magnetic fields can increase τ v , especially in the hBN / WSe 2 / SiO 2 structure, suggesting that localized states induced by disorder can play an important role in depolarizing spins and mediating the valley relaxation of resident carriers in monolayer transition-metal dichalcogenide semiconductors.

36 MATERIALS SCIENCE↗

Graph-based quantum response theory and shadow Born–Oppenheimer molecular dynamics

Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born–Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. Further, the proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗

Relativistic and correlation effects in the photoionization dynamics of oganesson ( Z = 118): Spin-orbit-interaction-activated interchannel coupling effects

High-Z atoms are excellent laboratories to study the combination of relativistic and many-electron correlation effects in electronic structure and dynamics. In the present work, the relativistic-random-phase approximation at different levels of truncation is employed to explore the final-state correlation effects in the photoelectron dynamics of the heaviest known element in the Periodic Table: oganesson (Og) with Z = 118. Here, the focus of this work is to illustrate the relativistic effects resulting from coupling different photoionization channels arising from spin-orbit split subshells, termed the spin-orbit-interaction-activated interchannel coupling effect. Comparison with the photoelectron dynamics of Rn on a qualitative level is also carried out, since Og is a homologue of Rn. The photoelectron dynamics of 7p, 7s, and 6d subshells are investigated and differences between Og and Rn, due to enhanced relativistic effects, are investigated.

74 ATOMIC AND MOLECULAR PHYSICS↗