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At least 829 records · Page 46

Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress

Background The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Results Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and ion mobility-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing 117 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein–protein dynamics. Conclusions The label-free scProteomic approach presented here represents a significant advance through the demonstration of a facile protoplast isolation method combined with deep and precise proteomic coverage of Arabidopsis leaf mesophyll cell types. We believe this study will serve as an informative reference to future plant scProteomic investigations.

Arabidopsis↗

A Quantum Mechanical MP2 Study of the Electronic Effect of Nonplanarity on the Carbon Pyramidalization of Fullerene C 60

Among C 60 ’s diverse functionalities, its potential application in CO 2 sequestration has gained increasing interest. However, the processes involved are sensitive to the molecule’s electronic structure, aspects of which remain debated and require greater precision. To address this, we performed structural optimization of fullerene C 60 using the QM MP2/6–31G* method. The nonplanarity of the optimized icosahedron is characterized by two types of dihedral angles: 138° and 143°. The 120 dihedrals of 138° occur between two hexagons intersecting at C–C bonds of 1.42 Å, while the 60 dihedrals of 143° are observed between hexagons and pentagons at C–C bonds of 1.47 Å. NBO analysis reveals less pyramidal sp 1.78 hybridization for carbons at the 1.42 Å bonds and more pyramidal sp 2.13 hybridization for the 1.47 Å bonds. Electrostatic potential charges range from -0.04 a.u. to 0.04 a.u. on the carbon atoms. Second-order perturbation analysis indicates that delocalization interactions in the C–C bonds of 1.42 Å (143.70 kcal/mol) and 1.47 Å (34.98 kcal/mol) are 22% and 38% higher, respectively, than those in benzene. MP2/Def2SVP calculations yield a correlation energy of 13.49 kcal/mol per electron for C 60 , slightly higher than the 11.68 kcal/mol for benzene. However, the results from HOMO-LUMO calculations should be interpreted with caution. This study may assist in the rational design of fullerene C 60 derivatives for CO 2 reduction systems.

36 MATERIALS SCIENCE↗

Marine and continental stratocumulus cloud microphysical properties obtained from routine ARM Cimel sunphotometer observations

This study investigates marine and continental stratocumulus (Sc) cloud properties obtained from an automated implementation of a multispectral photometer retrieval. Photometer methods simultaneously retrieve cloud optical depth (τ) and cloud droplet effective radius (r e ), with estimates for liquid water path (LWP) calculated on the availability of those quantities. These applied methods evaluate retrieved cloud properties for Sc identified during a recent 6 year period over the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) program sites in Oklahoma, USA (SGP) and in the Azores, Portugal (ENA). Modest agreement in key quantity retrievals is found between the routine photometer products and multisensor collocated profiling references. Cumulative breakdowns contingent on cloud thickness indicate increases in all retrieved quantities in thicker clouds, with larger discrepancies in the relative performance between the retrievals collected in the presence of drizzle. Under continental cloud conditions, the clouds of a similar thickness and r e to those sampled under marine conditions report a factor of 1.5 larger τ and LWP. An r 2 ≅0.65 is found between photometer τ retrievals and shadowband radiometer measurements, with photometer retrievals reporting a high (relative) bias. The τ intercomparisons indicate that variability between retrievals is a factor of three larger than errors reported from individual retrieval input perturbation tests. Photometer r e retrievals suggest a low r 2 (< 0.1) having a standard deviation ≅ 3 µm when compared to ARM baseline multi-sensor radar/radiometer references (accounting for offsets in the cloud droplet number concentration assumptions of the latter). However, photometer LWP calculations remain relatively unbiased in non-drizzling conditions, with errors O (50 g m −2 ) and r 2 ≅0.5 to collocated radiometer and interferometer references. Additional sensitivity tests for island influences on marine Sc properties suggest that while island-influenced winds may promote larger cloud LWP or thickness, the influence could be within retrieval method uncertainty and/or collocated instrument variability.

54 ENVIRONMENTAL SCIENCES↗

Modeling of resistive plasma response in toroidal geometry using an asymptotic matching approach

The method of solving the linear resistive plasma response, based on the asymptotic matching approach, is developed for full toroidal tokamaks by upgrading the resistive DCON code [A. H. Glasser, Z. R. Wang, and J.-K. Park, Phys. Plasmas 23, 112506 (2016)]. The derived matching matrix, asymptotically matching the outer and inner regions, indicates that the applied three dimension (3-D) magnetic perturbations contribute additional small solutions at each resonant surface due to the toroidal coupling of poloidal modes. In contrast, the resonant harmonic only affects the corresponding resonant surface in the cylindrical plasma. Additionally, the solution of the ideal outer region is critical to the asymptotic matching and is challenging in toroidal geometry due to the singular power series solution at the resonant surfaces. Thus, a systematic verification of the outer region Δ' matrix is made by reproducing the well-known analytical Δ' result in Furth et al. [Phys. Fluids 16, 1054–1063 (1073)] and by making a quantitative benchmark with the PEST3 code [A. Pletzer and R. L. Dewar, J. Plasma Phys. 45, 427–451 (1991)]. Finally, the reconstructed numerical solution of the resistive plasma response from the toroidal matching matrix is presented. Compared with the ideal plasma response, the global structure of the response can be affected by the small finite island at the resonant surfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Adiabatic matching of particle bunches in a plasma-based accelerator in the presence of ion motion

Witness beam stability and preservation of its ultra-low emittance have been identified as critical challenges toward realizing a TeV-class, plasma-based linear collider. In fact, the witness bunch parameters required by a future TeV-class collider have been expected to trigger hosing instability and background ion motion, leading to emittance degradation and, potentially, to bunch loss. Recently, it has been shown that ion motion suppresses the hosing instability, and proper longitudinal bunch shaping can eliminate the ion-motion-induced emittance growth. Here, we propose and analyze a plasma-based method to generate the shaped bunches that enable emittance preservation in the presence of ion motion. The method is based on an adiabatic matching procedure, where a bunch with an initially untapered profile is injected in the plasma accelerator stage with an energy low enough that ion motion effects are initially small. As the bunch accelerates, it is adiabatically compressed, ion motion is gradually triggered, and the bunch slowly but continuously readjusts itself in the ion motion-perturbed wakefield acquiring the desired taper. The production of tapered witness bunch profiles that minimize energy spread and preserve emittance for collider-relevant parameters could enable the use of plasma-based accelerators for high-energy physics applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Flow field characteristics of a 127-pin rod bundle with hexagonal spacer grids

A determination of nominal flow phenomena in liquid metal fast reactor (LMFR) fuel assemblies is critical toward generation-IV reactor development. Axially positioned spacer grids are used to maintain the geometry of hexagonal rod bundles and simultaneously introduce perturbations in the flow. Three-dimensional (3D) printed asymmetric honeycomb spacer grids were installed in a prototypical 127-pin LMFR fuel assembly model to study complex fluid dynamics interactions induced by the spacer grid and rods. To characterize flow dynamics in this intricate geometry, time-resolved particle image velocimetry (TR-PIV) using the matched-index-of-refraction method was employed to obtain non-intrusive velocity measurements for three axial planes (one near-wall and two interior planes) at a Reynolds number of 6000. The statistical TR-PIV results compared sub-channel-dependent normalized time-averaged velocity, velocity fluctuations, Reynolds stress, vorticity, and turbulence kinetic energy distributions. TR-PIV line profiles characterized downstream spacer grid flow dynamics. Two-point spatial and spatial–temporal cross-correlation fields revealed local coherent structures and quantified convection velocities of traveling vortices. Spatial–temporal decomposition using dynamic mode decomposition (DMD) applied to the near-wall vorticity fields extracted turbulent structures and flow instabilities in the wake region of the spacer grid, along with their decay and frequency rates. Reduced-order velocity fields from DMD reconstructions identified the most energy-containing coherent structures persistent in the near-wall region. This research provides experimental data sets and analyses of flow behavior in rod bundles with hexagonal spacer grids. In conclusion, the results are critical toward LMFR design and geometry optimization, crucial for the validation of computational fluid dynamics and reduced-order flow models.

42 ENGINEERING↗

Regulating loops in de Sitter spacetime

Perturbative quantum field theory (QFT) calculations in de Sitter space are riddled with contributions that diverge over time. These contributions often arise from loop integrals, which are notoriously hard to compute in de Sitter. We discuss an approach to evaluate loop integrals that contribute to equal-time correlators of a scalar field theory in a fixed de Sitter background. Our method is based on the Mellin-Barnes representation of correlation functions, which allows us to regulate loop divergences by adjusting the masses of the fields, or by gently deforming the underlying de Sitter spacetime. The resulting expressions have a similar structure as a standard answer from dimensional regularization in flat space QFT. These features of the regulator are illustrated with two examples, worked out in detail. Along the way, we illuminate the physical origin of these divergences and their interpretation with the machinery of the dynamical renormalization group. Our approach regulates the IR divergences of massless and massive particles in the same way. For massless scalars, the loop corrections can be incorporated as systematic improvements to the stochastic inflation framework, allowing for a more precise description of the IR dynamics of such fields in de Sitter. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Time propagation of electronic wavefunctions using nonorthogonal determinant expansions

The use of truncated configuration interaction in real-time time-dependent simulations of electron dynamics provides a balance of computational cost and accuracy, while avoiding some of the failures associated with real-time time-dependent density functional theory. However, low-order truncated configuration interaction also has limitations, such as overestimation of polarizability in configuration interaction singles, even when perturbative doubles are included. Increasing the size of the determinant expansion may not be computationally feasible, and so, in this work, we investigate the use of nonorthogonality in the determinant expansion to establish the extent to which higher-order substitutions can be recovered, providing an improved description of electron dynamics. Model systems are investigated to quantify the extent to which different methods accurately reproduce the (hyper)polarizability, including the high-harmonic generation spectrum of H 2 , water, and butadiene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An influence of manufacturing tolerances on Pin-Cell k-infinity of MOX fuel using data from the FUBILA experiment program

An influence of manufacturing tolerances (MTs) was evaluated on the pin-cell k-infinity of MOX fuel through the random sampling of CASMO5 calculations. The data from the FUBILA experiment program was used as the manufacturing parameters. For the uncertainties of element/isotope mass fractions, their covariance matrices were calculated by the generalized least square method. The total k-infinity uncertainty was 120-250 pcm (percent mille). From the breakdown of k-infinity uncertainty per materials, the MTs of fuel pellet had a dominant influence. The individual influences were also evaluated for element/isotope mass fractions, an inner/outer diameter, and a density. Those of element/isotope mass fractions were less than a few dozen pcm. Since the perturbations of fuel pellet diameter and density caused large variations to the total amount of heavy metals and effect of spatial self-shielding, they had a negative correlation with the k-infinity perturbation. On the AG3 (Al-Mg alloy) over-cladding, the inner/outer diameter perturbations had both negative and positive correlations. The negative one was due to decrease in amount of light water and the positive one was due to increase in amount of AG3. Since the effect of neutron slowing-down by light water had a dominant influence, the influence of the former negative correlation was larger than that of the latter positive correlation. It is, therefore, concluded that the consideration of the MTs that had a large influence on the effect of neutron slowing-down is important for precise quantification of the pin-cell k-infinity uncertainty of MOX fuel. (author)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

On the S-matrix of Ising field theory in two dimensions

We explore the analytic structure of the non-perturbative S-matrix in arguably the simplest family of massive non-integrable quantum field theories: the Ising field theory (IFT) in two dimensions, which may be viewed as the Ising CFT deformed by its two relevant operators, or equivalently, the scaling limit of the Ising model in a magnetic field. Our strategy is that of collider physics: we employ Hamiltonian truncation method (TFFSA) to extract the scattering phase of the lightest particles in the elastic regime, and combine it with S-matrix bootstrap methods based on unitarity and analyticity assumptions to determine the analytic continuation of the 2 → 2 S-matrix element to the complex s-plane. Focusing primarily on the “high temperature” regime in which the IFT interpolates between that of a weakly coupled massive fermion and the E 8 affine Toda theory, we will numerically determine 3-particle amplitudes, follow the evolution of poles and certain resonances of the S-matrix, and exclude the possibility of unknown wide resonances up to reasonably high energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Urbanization Impact on Regional Climate and Extreme Weather: Current Understanding, Uncertainties, and Future Research Directions

Abstract Urban environments lie at the confluence of social, cultural, and economic activities and have unique biophysical characteristics due to continued infrastructure development that generally replaces natural landscapes with built-up structures. The vast majority of studies on urban perturbation of local weather and climate have been centered on the urban heat island (UHI) effect, referring to the higher temperature in cities compared to their natural surroundings. Besides the UHI effect and heat waves, urbanization also impacts atmospheric moisture, wind, boundary layer structure, cloud formation, dispersion of air pollutants, precipitation, and storms. In this review article, we first introduce the datasets and methods used in studying urban areas and their impacts through both observation and modeling and then summarize the scientific insights on the impact of urbanization on various aspects of regional climate and extreme weather based on more than 500 studies. We also highlight the major research gaps and challenges in our understanding of the impacts of urbanization and provide our perspective and recommendations for future research priorities and directions.

54 ENVIRONMENTAL SCIENCES↗

Excitation of long electrostatic solitary waves in ion beam neutralization process

Unusually long electrostatic solitary waves (ESWs) are discovered in a particle-in-cell simulation study of the process of ion beam neutralization by electron emission from a filament. These ESWs are long because the density perturbation responses to the potential wells created by the ESWs are very small. Notably, the density perturbation is small because the trapped (positive) and untrapped (negative) electron density perturbations nearly compensate each other because of a non-Maxwellian electron velocity distribution in the beam.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

FY22 Progress on Multicontinuum Methods in Containment

Estimation of two-phase fluid flow properties is important to understand and predict water and gas movement through the vadose zone for agricultural, hydrogeological, and engineering applications, such as containment transport and/or containment of gases in the subsurface. To estimate rock fluid flow properties and subsequently predict physically realistic processes such as patterns and timing of water, gas, and energy (e.g., heat) movement in the subsurface, laboratory spontaneous water imbibition with simultaneous temperature measurement and numerical modeling methods are presented in the FY22 progress report. A multiple-overlapping-continua conceptual model is used to explain and predict observed complex multi-phenomenological laboratory test behavior during spontaneous imbibition experiments. This report primarily addresses two complexities that arise during the experiments: 1) capturing the late-time behavior of spontaneous imbibition tests with dual porosity; and 2) understanding the thermal perturbation observed at or ahead of the imbibing wetting front, which are associated with adsorption of water in initially dry samples. We use numerical approaches to explore some of these issues, but also lay out a plan for further laboratory experimentation and modeling to best understand and leverage these unique observations.

58 GEOSCIENCES↗

Elimination of QCD Renormalization Scale and Scheme Ambiguities

The setting of the renormalization scale (μ r ) in the perturbative QCD (pQCD) is one of the crucial problems for achieving precise fixed-order pQCD predictions. The conventional prescription is to take its value as the typical momentum transfer Q in a given process, and theoretical uncertainties are then evaluated by varying it over an arbitrary range. The conventional scale-setting procedure introduces arbitrary scheme-and-scale ambiguities in fixed-order pQCD predictions. The principle of maximum conformality (PMC) provides a systematic way to eliminate the renormalization scheme-and-scale ambiguities. The PMC method has rigorous theoretical foundations; it satisfies the renormalization group invariance (RGI) and all of the self-consistency conditions derived from the renormalization group. The PMC has now been successfully applied to many physical processes. In this paper, we summarize recent PMC applications, including event shape observables and heavy quark pair production near the threshold region in e + e – annihilation and top-quark decay at hadronic colliders. In addition, estimating the contributions related to the uncalculated higher-order terms is also summarized. These results show that the major theoretical uncertainties caused by different choices of μ r are eliminated, and the improved pQCD predictions are thus obtained, demonstrating the generality and applicability of the PMC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nonresonant Raman Control of Ferroelectric Polarization

Important advances is recently made in the search for materials with complex multi-phase landscapes that host photoinduced metastable collective states with exotic functionalities. In almost all cases so far, the desired phases are accessed by exploiting light–matter interactions via the imaginary part of the dielectric function through above-bandgap or resonant mode excitation. Nonresonant Raman excitation of coherent modes is experimentally observed and proposed for dynamic material control, but the resulting atomic excursion is limited to perturbative levels. Here, in this study, this challenge is overcome by employing nonresonant ultrashort pulses with low photon energies well below the bandgap. Using mid-infrared pulses, ferroelectric reversal is induced in lithium niobate, and the large-amplitude mode displacements are characterized through femtosecond stimulated Raman scattering and second harmonic generation. This approach, validated by first-principle calculations, defines a novel method for synthesizing hidden phases with unique functional properties and manipulating complex energy landscapes at reduced energy consumption and ultrafast speeds.

Shi, Jiaojian [Stanford Univ., CA (United States);↗

Locating fast-varying line disturbances with the frequency mismatch

In an attempt to provide an efficient method for line disturbance identification in complex networks of diffusively coupled agents, we recently proposed to leverage the frequency mismatch. The frequency mismatch filters out the intricate combination of interactions induced by the network structure and quantifies to what extent the trajectory of each agent is affected by the disturbance. In this previous work, we provided some analytical evidence of its efficiency when the perturbation is assumed to be slow. Here we claim that the frequency mismatch performs actually well for most disturbance regimes. This is shown through a series of simulations and is backed up by an analytical argument. Therefore, we argue that the frequency mismatch is an efficient and elegant tool for line disturbance location in complex networks of diffusively coupled agents.

97 MATHEMATICS AND COMPUTING↗

Scalable Heterogeneous Execution of a Coupled-Cluster Model with Perturbative Triples

The CCSD(T) coupled-cluster model with perturbative triples is considered a gold standard for computational modeling of the correlated behavior of electrons in molecular systems. A fundamental constraint is the relatively small global-memory capacity in GPUs compared to the main-memory capacity on host nodes, necessitating relatively smaller tile sizes for high-dimensional tensor contractions in NWChem's GPU-accelerated implementation of the CCSD(T) method. A coordinated redesign is described to address this limitation and associated data movement overheads, including a novel fused GPU kernel for a set of tensor contractions, along with inter-node communication optimization and data caching. The new implementation of GPU-accelerated CCSD(T) improves overall performance by 3.4x. Finally, we discuss the trade-offs in using this fused algorithm on current and future supercomputing platforms.

Kim, Jinsung↗

Fine structure of current noise spectra in nanoelectromechanical resonators

Here, we study the frequency-dependent noise of a suspended carbon nanotube quantum dot nanoelectromechanical resonator induced by electron-vibration coupling. Using a rigorous Keldysh diagrammatic technique, we establish a formal framework connecting the vibrational properties to electrical measurements. We find that the noise power spectrum exhibits a narrow resonant peak at the frequency of the vibrational modes. However, this fine structure tends to disappear due to a coherent cancellation effect when the tunneling barriers are tuned to a symmetric point. Notably, measuring the electrical current noise spectra provides a sensitive alternative method for detecting the damping and dephasing of quantum vibrational modes.

Electric measurements↗