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At least 703 records · Page 39

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during salt-induced disassembly of canonical NCPs. We find that H2A–H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. Furthermore, the link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.

59 BASIC BIOLOGICAL SCIENCES↗

In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale

The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca 2+ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.

59 BASIC BIOLOGICAL SCIENCES↗

Multiphysics analysis system for heat pipe cooled micro-reactors employing PRAGMA-OpenFOAM-ANLHTP

A multiphysics analysis system for neutronics/thermo-mechanical/heat-pipe analysis of heat pipe cooled micro-reactors was developed using the PRAGMA code as the neutronics engine. PRAGMA, which used to be a GPU-based continuous-energy MC code for power reactor applications, now has an extended geometry package to handle geometries with unstructured meshes generated by the ANSYS Design-Modeler and Meshing. The NVIDIA ray tracing engine OptiX was exploited for efficient neutron transport on unstructured geometry. On the multiphysics side, the open-source CFD tool OpenFOAM and one-dimensional heat pipe analysis code ANLHTP were adopted. The manager-worker system based on the MPI dynamic process management (DPM) model enables efficient coupling of codes employing different parallelization schemes. With all the features, the multiphysics analysis of the one-sixth symmetrical MegaPower 2D core was performed and it demonstrated the benefit of the tight integration of the three-way coupling system and one-to-one geometry coupling strategy. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Operando 3D imaging of defects dynamics of twinned-nanocrystal during catalysis

Using operando Bragg coherent x-ray diffraction imaging, we visualised three-dimensionally a single twinned-gold nanocrystal during the CO oxidation reaction. We describe the defect dynamics process occurring under operating conditions and indicate the correlation between the nucleation of highly strained regions at the surface of the nanocrystal and its catalytic activity. Understanding the twinning deformation mechanism sheds light on the creation of active sites, and could well contribute to the understanding of the catalytic behaviour of other catalysts. Furthermore, with the start-up of 4th generation synchrotron sources, we anticipate that coherent hard x-ray diffraction imaging techniques will play a major role in imaging in situ chemical processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-pressure studies with x-rays using diamond anvil cells

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials' properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. These HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Black holes and gravitational waves in models of minicharged dark matter

In viable models of minicharged dark matter, astrophysical black holes might be charged under a hidden U(1) symmetry and are formally described by the same Kerr-Newman solution of Einstein-Maxwell theory. These objects are unique probes of minicharged dark matter and dark photons. We show that the recent gravitational-wave detection of a binary black-hole coalescence by aLIGO provides various observational bounds on the black hole’s charge, regardless of its nature. The pre-merger inspiral phase can be used to constrain the dipolar emission of (ordinary and dark) photons, whereas the detection of the quasinormal modes set an upper limit on the final black hole’s charge. By using a toy model of a point charge plunging into a Reissner-Nordstrom black hole, we also show that in dynamical processes the (hidden) electromagnetic quasinormal modes of the final object are excited to considerable amplitude in the gravitational-wave spectrum only when the black hole is nearly extremal. The coalescence produces a burst of low-frequency dark photons which might provide a possible electromagnetic counterpart to black-hole mergers in these scenarios.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Much of zero emissions commitment occurs before reaching net zero emissions

Abstract We explore the response of the Earth’s coupled climate and carbon system to an idealized sequential addition and removal of CO 2 to the atmosphere, following a symmetric and continuous emissions pathway, in contrast to the discontinuous emissions pathways that have largely informed our understanding of the climate response to net zero and net negative emissions to date. We find, using both an Earth system model and an ensemble of simple climate model realizations, that warming during the emissions reduction and negative emissions phases is defined by a combination of a proportionality of warming to cumulative emissions characterized by the transient climate response to emissions (TCRE), and a deviation from that proportionality that is governed by the zero emissions commitment (ZEC). About half of the ZEC is realized before reaching zero emissions, and the ZEC thus also controls the timing between peak cumulative CO 2 emissions and peak temperature, such that peak temperature may occur before peak cumulative emissions if ZEC is negative, underscoring the importance of ZEC in climate policies aimed to limit peak warming. Thus we argue that ZEC is better defined as the committed warming relative to the expected TCRE proportionality, rather than as the additional committed warming that will occur after reaching net zero CO 2 emissions. Once established, the combined TCRE and ZEC relationship holds almost to complete removal of prior cumulative CO 2 emissions. As cumulative CO 2 emissions approach zero through negative CO 2 emissions, CO 2 concentrations drop below preindustrial values, while residual long-term climate change continues, governed by multicentennial dynamical processes.

54 ENVIRONMENTAL SCIENCES↗

Probing reaction channels via reinforcement learning

Abstract Chemical reactions are dynamical processes involving the correlated reorganization of atomic configurations, driving the conversion of an initial reactant into a result product. By virtue of the metastability of both the reactants and products, chemical reactions are rare events, proceeding fleetingly. Reaction pathways can be modelled probabilistically by using the notion of reactive density in the phase space of the molecular system. Such density is related to a function known as the committor function, which describes the likelihood of a configuration evolving to one of the nearby metastable regions. In theory, the committor function can be obtained by solving the backward Kolmogorov equation (BKE), which is a partial differential equation (PDE) defined in the full dimensional phase space. However, using traditional methods to solve this problem is not practical for high dimensional systems. In this work, we propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an ensemble of states that concentrate on the transition path ensemble. This configuration ensemble can be effectively employed in a neural network-based PDE solver to obtain an approximation solution of a restricted BKE, even when the dimension of the problem is very high. The resulting solution provides an approximation for the committor function that encodes mechanistic information for the reaction, paving a new way for understanding of complex chemical reactions and evaluation of reaction rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Star-forming S0 galaxies in the SDSS-IV MaNGA survey

ABSTRACT To investigate star-forming activities in early-type galaxies, we select a sample of 52 star-forming S0 galaxies (SFS0s) from the SDSS-IV MaNGA survey. We find that SFS0s have smaller stellar masses compared to normal S0s in MaNGA. After matching the stellar mass to select the control sample, we find that the mean Sérsic index of SFS0 bulges (1.76 ± 0.21) is significantly smaller than that of the control sample (2.57 ± 0.20), suggesting the existence of pseudo-bulges in SFS0s. After introducing the environmental information, SFS0s show smaller spin parameters in the field than in groups, while the control sample has no obvious difference in different environments, which may suggest different dynamical processes in SFS0s. Furthermore, with derived N/O and O/H abundance ratios, SFS0s in the field show nitrogen enrichment, providing evidence for the accretion of metal-poor gas in the field environment. To study the star-formation relation, we show that the slope of the spatially resolved star-formation main sequence is nearly 1.0 with MaNGA integral field unit data, confirming the self-regulation of star-formation activity on kpc scales.

79 ASTRONOMY AND ASTROPHYSICS↗

The evolution of the Milky Way’s thin disc radial metallicity gradient with K2 asteroseismic ages

ABSTRACT The radial metallicity distribution of the Milky Way’s disc is an important observational constraint for models of the formation and evolution of our Galaxy. It informs our understanding of the chemical enrichment of the Galactic disc and the dynamical processes therein, particularly radial migration. We investigate how the metallicity changes with guiding radius in the thin disc using a sample of red giant stars with robust astrometric, spectroscopic, and asteroseismic parameters. Our sample contains 668 stars with guiding radii 4 < Rg < 11 kpc and asteroseismic ages covering the whole history of the thin disc with precision ${\approx} 25 {{\, \rm per\ cent}}$. We use MCMC analysis to measure the gradient and its intrinsic spread in bins of age and construct a hierarchical Bayesian model to investigate the evolution of these parameters independently of the bins. We find a smooth evolution of the gradient from ≈−0.07 dex kpc−1 in the youngest stars to ≈−0.04 dex kpc−1 in stars older than 10 Gyr, with no break at intermediate ages. Our results are consistent with those based on asteroseismic ages from CoRoT, with that found in Cepheid variables for stars younger than 1 Gyr, and with open clusters for stars younger than 6 Gyr. For older stars we find a significantly lower metallicity in our sample than in the clusters, suggesting a survival bias favouring more metal-rich clusters. We also find that the chemical evolution model of Chiappini '09 is too metal poor in the early stages of disc formation. Our results provide strong new constraints for the growth and enrichment of the thin disc and radial migration, which will facilitate new tests of model conditions and physics.

79 ASTRONOMY AND ASTROPHYSICS↗

An ALMA view of star formation efficiency suppression in early-type galaxies after gas-rich minor mergers

Gas-rich minor mergers contribute significantly to the gas reservoir of early-type galaxies (ETGs) at low redshift, yet the star formation efficiency (SFE; the star formation rate divided by the molecular gas mass) appears to be strongly suppressed following some of these events, in contrast to the more well-known merger-driven starbursts. We present observations with the Atacama Large Millimeter/submillimeter Array (ALMA) of six ETGs, which have each recently undergone a gas-rich minor merger, as evidenced by their disturbed stellar morphologies. These galaxies were selected because they exhibit extremely low SFEs. We use the resolving power of ALMA to study the morphology and kinematics of the molecular gas. The majority of our galaxies exhibit spatial and kinematical irregularities, such as detached gas clouds, warps, and other asymmetries. These asymmetries support the interpretation that the suppression of the SFE is caused by dynamical effects stabilizing the gas against gravitational collapse. Through kinematic modelling we derive high velocity dispersions and Toomre Q stability parameters for the gas, but caution that such measurements in edge-on galaxies suffer from degeneracies. We estimate merger ages to be about 100 Myr based on the observed disturbances in the gas distribution. Furthermore, we determine that these galaxies lie, on average, two orders of magnitude below the Kennicutt–Schmidt relation for star-forming galaxies as well as below the relation for relaxed ETGs. We discuss potential dynamical processes responsible for this strong suppression of star formation surface density at fixed molecular gas surface density.

79 ASTRONOMY AND ASTROPHYSICS↗

Lie-algebraic classical simulations for quantum computing

The classical simulation of quantum dynamics plays an important role in our understanding of quantum complexity and in the development of quantum technologies. Efficient techniques such as those based on the Gottesman-Knill theorem for Clifford circuits, tensor networks for low entanglement-generating circuits, or Wick's theorem for fermionic Gaussian states have become central tools in quantum computing. In this work, we contribute to this body of knowledge by presenting a framework for classical simulations, dubbed “𝔤-sim”, which is based on the underlying Lie algebraic structure of the dynamical process. When the dimension of the algebra grows at most polynomially in the system size, there exist observables for which the simulation is efficient. Indeed, we show that 𝔤-sim enables new regimes for classical simulations, is able to deal with certain forms of noise in the evolution, as well as can be used to tackle several paradigmatic variational and nonvariational quantum computing tasks. For the former, we perform Lie-algebraic simulations to train and optimize parametrized quantum circuits (thus effectively showing that some variational models can be dequantized), design enhanced parameter initialization strategies, solve tasks of quantum circuit synthesis, and train a quantum-phase classifier. For the latter, we report large-scale noiseless and noisy simulations on benchmark problems. By comparing the limitations of 𝔤-sim and certain Wick's theorem-based simulations, we find that the two methods become inefficient for different types of states or observables, hinting at the existence of distinct, nonequivalent resources for classical simulation.

97 MATHEMATICS AND COMPUTING↗

Accelerating Ultrafast Spectroscopy with Compressive Sensing

We report ultrafast spectroscopy is an important tool for studying photoinduced dynamical processes in atoms, molecules, and nanostructures. Typically, the time to perform these experiments ranges from several minutes to hours depending on the choice of spectroscopic method. It is desirable to reduce this time overhead not only to shorten time and laboratory resources, but also to make it possible to examine fragile specimens that quickly degrade during long experiments. In this article, we motivate using compressive sensing to significantly shorten data acquisition time by reducing the total number of measurements in ultrafast spectroscopy. We apply this technique to experimental data from ultrafast transient absorption spectroscopy and ultrafast terahertz spectroscopy and show that good estimates can be obtained with as low as 15% of the total measurements, implying a sixfold reduction in the data acquisition time.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Geometrical-Based Generative Adversarial Network to Enhance Digital Rock Image Quality

X-ray microcomputed tomography (micro-CT) is a common tool for the study of porous media structures and properties. High-quality micro-CT data are required to accurately capture pore structures. Acquiring high-quality micro-CT data, however, is not always possible, owing to application limitations and experimental constraints. Therefore, we propose a geometrical-based generative adversarial network (GAN) to rapidly restore noisy micro-CT images to their clean counterparts. The training data and related ground-truth (GT) data are scanned for 7 min and 9.5 h, respectively. To evaluate the performance of the geometrical-based GAN, a 6003 voxel image that has never been used for training is reconstructed and compared with the corresponding GT image. Histogram matching and linear normalization are implemented to adjust the histogram of the reconstructed image to that of the GT image. A watershed-based segmentation method is then applied to delineate pore and solid phases. Lastly, we measure the Minkowski functionals and petrophysical properties, including absolute permeability, pore size distribution, drainage capillary pressure-saturation curve, and imbibition relative permeability, to estimate the physical accuracy of the denoised image. The results show that the proposed geometrical-based GAN can accurately restore noisy micro-CT data. By reducing the scanning time from 9.5 h to 7 min, the expenditure of collecting micro-CT can be decreased significantly. This is particularly important for applications where time-lapse images of a dynamic process are required, high-throughput imaging is necessary for real-time data analysis, or where the quantification of large sample volumes is required.

58 GEOSCIENCES↗

Topological sliding moiré heterostructure

In this work, we investigate the effect of the sliding motion of layers in moiré heterostructures on the electronic state. We show that the sliding moiré heterostructure can generate nontrivial topology characterized by the first and second Chern number in the high-dimensional manifold spanned by the physical dimensions and synthetic dimensions associated with the sliding displacement. The nontrivial topology implies a topological charge pumping caused by the sliding motion. We demonstrate the nontrivial topology and charge pumping explicitly in a one-dimensional bichain model and small-angle twisted bilayer graphene. Contrary to the conventional belief that the interlayer sliding in incommensurate moiré heterostructures does not affect the electronic structure, our results reveal that the sliding motion can generate nontrivial topology dynamically and hence cannot be neglected in the dynamical process.

36 MATERIALS SCIENCE↗

Energy transfer in random-matrix ensembles of Floquet Hamiltonians

Here, we explore the statistical properties of energy transfer in ensembles of doubly driven random-matrix Floquet Hamiltonians based on universal symmetry arguments. The energy-pumping efficiency distribution P⁡($\overline{E}$) is associated with the Hamiltonian parameter ensemble and the eigenvalue statistics of the Floquet operator. For specific Hamiltonian ensembles, P⁡($\overline{E}$) undergoes a transition which cannot be associated with a symmetry breaking of the instantaneous Hamiltonian. The Floquet eigenvalue spacing distribution indicates the considered ensembles constitute generic nonintegrable Hamiltonian families. As a step towards Hamiltonian engineering, we develop a machine-learning classifier to understand the relative parameter importance in resulting high-conversion efficiency. We propose random Floquet Hamiltonians as a general framework to investigate frequency conversion effects in a class of generic dynamical processes beyond adiabatic pumps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ultrafast quasiparticle dynamics in the correlated semimetal Ca 3 Ru 2 O 7

The correlated polar semimetal Ca 3 Ru 2 O 7 exhibits a rich phase diagram including two magnetic transitions (T N = 56 K and T C = 48 K) with the appearance of an insulating-like pseudogap (at T C ). In addition, there is a crossover back to metallic behavior at T* = 30 K, the origin of which is still under debate. We utilized ultrafast optical-pump optical-probe spectroscopy to investigate quasiparticle dynamics as a function of temperature in this enigmatic quantum material. We identify two dynamical processes, both of which are influenced by the onset of the pseudogap. This includes electron-phonon relaxation and, below T C , the onset of a phonon bottleneck hindering the relaxation of quasiparticles across the pseudogap. We introduce a gap-modified two-temperature model to describe the temperature dependence of electron-phonon thermalization, and use the Rothwarf-Taylor to model the phonon bottleneck. In conjunction with density functional theory, our experimental results synergistically reveal the origin of the T-dependent pseudogap. Further, our data and analysis indicate that T* emerges as a natural consequence of T-dependent gapping out of carriers, and does not correspond to a separate electronic transition. Furthermore, our results highlight the value of low-fluence ultrafast optics as a sensitive probe of low-energy electronic structure, thermodynamic parameters, and transport properties of Ruddlesden-Popper ruthenates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Influence of the tensor interaction on heavy-ion fusion cross sections

The tensor interaction has a measurable effect on the fusion cross sections of nuclei spanning the nuclear chart. The effect comes from both static effects present in the ground state and dynamic processes arising from the time evolution of the system. This motivates the development of a modern Skyrme parameter set that includes all time-odd and tensor terms and that studies moving forward should include the tensor force to ensure a more robust and complete description of nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗