High density photosynthetic CO2 response curves of hybrid poplar, New York, USA, 2019
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Anderson, Jeremiah↗
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Correction: Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods
Correction for ‘Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods’ by Daniel R. Nascimento et al. , Phys. Chem. Chem. Phys. , 2022, 24 , 14680–14691, https://doi.org/10.1039/D2CP01132H.
Nascimento, Daniel R.↗
Parametrizing the detector response with neural networks
In high energy physics, characterizing the response of a detector to radiation is one of the most important and fundamental experimental tasks. In many cases, this task is accomplished by parameterizing summary statistics of the full detector response probability density. The parameterized detector response can then be used for calibration as well as for directly improving physics analysis sensitivity. This paper reports on how to parameterize summary statistics of the detector response using neural networks. Specifically, neural networks are powerful tools for incorporating multidimensional data and the loss function used during training determines which summary statistic is learned. One common summary statistic that has not been combined with deep learning (as far as the authors are aware) is the mode. A neural network-based approach to mode learning is proposed and empirically demonstrated in the context of high energy jet calibrations. Altogether, the neural network-based toolkit for detector response parameterization can enhance the utility of data collected at high energy physics experiments and beyond.
47 OTHER INSTRUMENTATION↗
The Silencing of U.S. Campuses Following the COVID-19 Response: Evaluating Root Mean Square Seismic Amplitudes Using Power Spectral Density Data
In response to the COVID-19 global pandemic, many populated and active regions have become deserted and show significant reductions in their background seismicity, especially campuses across the United States (U.S.). Seismic sensors located in the vicinity of or within U.S. campuses show that anthropogenic seismic noise remains elevated during the ordinary, nonpandemic, academic year, only subduing during periods of recess (e.g., winter break). Here, we use power spectral density (PSD) data computed by the Incorporated Research Institutions for Seismology Data Management Center for quality assessment to calculate root mean square (rms) amplitude and analyze the effects of the COVID-19 school closures. We processed and analyzed PSD data for 46 seismic stations located within 50 m of a U.S. university or college. Results show that 42 campus stations show an overall rms drop following a statewide school closure.
58 GEOSCIENCES↗
(U) A Linear Response Model Predicts Reactivity From a Density Profile
We tested the ability to predict the system reactivity, described by alpha, given a density profile using a simple linear system response. We generated a suite of 1-dimensional density profiles that consisted of nominal density, a discontinuity, and a decay. These profiles were prescribed a functional form and the mass was conserved in all cases. From these density profiles, we calculated the alpha value of the 3-dimensional system.We calculated a linear response function given a training set of the 1-dimensional density profiles, and the system reactivity described by alpha. We tested the robustness of the response function using the remaining test data. Our results showed very good agreement between the predicted and calculated test values, where the distribution of alpha differences was centered about zero and had a standard deviation of 0.005 gens/shake. The predicted and calculated alpha values did not significantly differ (t=-0.0009 p<0.99). We used Singular Value Decomposition (SVD) to reduce the matrix rank by retaining95% of the cumulative singular value contributions. This reduced the matrix rank by 91.7%. We generated the linear response matrix and calculated the difference between the predicted and calculated alpha values. Using the reduced order matrix, we showed good agreement between the predicted and calculated alpha values where the distribution of differences was centered near zero, the standard deviation was 0.006 gens/shake, and the statistical t-test showed good agreement (t=0.02, p<0.98). These results show a linear relationship between a series of 1-dimensional density profiles,where the mass was conserved, and the system reactivity. The next steps of this work will be to investigate the linear response using 2-dimensional density profiles.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
State Interaction Linear Response Time-Dependent Density Functional Theory with Perturbative Spin–Orbit Coupling: Benchmark and Perspectives
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods
Time-dependent density functional theory provides a sufficiently accurate framework to study X-ray spectroscopies.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Reconfigurable plasma-dielectric hybrid photonic crystal as a platform for electromagnetic wave manipulation and computing
The introduction of 3D printing has enabled fabrication of photonic crystal devices with complex crystal structures that would be challenging to construct using other fabrication methods. In this paper, we construct and characterize a photonic crystal consisting of two 4 x 8 x 8 cubic lattices composed of spherical silicon nitride elements straddling a layer of 8 plasma discharge tubes, creating a 3D hybrid plasma photonic crystal device. Integrating under-dense gaseous plasma elements provides a unique coupling dynamic between the dielectric spheres and the cylindrical plasma discharges, creating a monolithic hybrid photonic crystal with solid state and reconfigurable elements. The device has resonant modes that have attenuation peaks that are either switchable, tunable in amplitude, or tunable in frequency with variations in plasma density. The response of these bands seen with varying plasma density is confirmed through simulations when effects due to the heating of the photonic crystal from the gaseous plasma elements are accounted for in the experiments. We discuss how this reconfigurable device may be used and expanded upon for applications in photonic artificial neural networks and optical computing systems.
3D printing↗
Optical response from charge-density waves in Weyl semimetals
Not Available
McKay, Robert C. (ORCID:0000000276846059)↗
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↗
Stochastic Framework for Optimal Control of Planetary Reentry Trajectories Under Multilevel Uncertainties
We present a novel stochastic optimal control framework that accounts for various types of uncertainties, with application to reentry trajectory planning. The formulation of the optimal trajectory control problem is presented in the context of an indirect method where a functional objective associated with the terminal vehicle speed is to be minimized. Uncertain input parameters in the optimal trajectory control model, including aerodynamic parameters and initial and terminal conditions, are modeled as aleatory random variables, while the statistical parameters of these aleatory distributions are themselves random variables. The parametric and model uncertainties are simultaneously propagated through an extended polynomial chaos expansion (EPCE) formalism. Several metrics are described to evaluate response statistics and presented as insightful tools for robust decision making. Specifically, the response probability density function (PDF) reflecting influence of both epistemic and aleatory uncertainties is obtained. By sampling over the random variables representing model error, an ensemble of response PDFs is generated and the associated failure probability is estimated as a random variable with its own polynomial chaos expansion. Besides, the sensitivity index functions of response PDF with respect to the statistical parameters are evaluated. Coupling parametric and model uncertainties within the EPCE framework leads to a robust and efficient paradigm for multilevel uncertainty propagation and PDF characterization in general optimal control problems.
Engineering↗
Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers
Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure–function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density–voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium–indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Introductory lecture: when the density of the noninteracting reference system is not the density of the physical system in density functional theory
We develop expressions for electron density defined through the linear response for general density functional approximations, demonstrating results for orbital functionals and for many-body perturbation theory, and explore the connections to developments in DFT.
Jin, Ye↗
On-the-fly response function generation method for composite coarse mesh
The hybrid stochastic deterministic transport code COMET, based on the incident response expansion theory, is used to model reactor cores with high fidelity and formidable computational speed. COMET models a reactor core using a library of incident flux response expansion coefficients that are pre computed for all the unique lattice cells (e.g., fuel assemblies, reflector blocks, etc.) in the core. In order to further improve its computational efficiency in pre-calculating the response library a new response function generation method is developed to compute the response functions for the composite coarse meshes made of a smaller set of unique lattices on the fly within the COMET's deterministic transport core sweep. The efficiency is achieved by eliminating a number of unique lattices that can be made up from the reduced set of unique meshes on the fly. The numerical process consists of the following steps. First, the boundary condition on composite coarse mesh boundaries is projected onto the expansion basis to compute the incident flux moments on external surfaces of all the basic (reduced set of unique) coarse meshes. Secondly, the deterministic sweeping solver in COMET is used to converge on the outgoing/incoming flux expansion moments crossing interfaces between the basic coarse meshes. Thirdly, the response functions for the composite coarse meshes are constructed as a superposition on the fly. The new response function generation method was tested on 88 composite coarse meshes consisting of CANDU fuel bundles and moderator blocks. It was found that response functions generated by the new method agree very well with those generated by direct Monte Carlo calculations. The average and maximum relative differences in the surface-to-surface response coefficients computed by the two methods are 0.10% and 0.20%, respectively. Similarly, the average and maximum relative differences in the response fission densities are 0.13% and 0.43%, respectively. These discrepancies are within one standard deviation of the stochastic uncertainties. The new method is five times faster than the original direct Monte Carlo method. The size of the response function library for the new method is five times smaller than that for the original method, leading to significantly less requirement for the computer hard drive space and memory. (authors)
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Engineering quantitative stomatal trait variation and local adaptation potential by cis‐regulatory editing
Summary Cis‐regulatory element editing can generate quantitative trait variation that mitigates extreme phenotypes and harmful pleiotropy associated with coding sequence mutations. Here, we applied a multiplexed CRISPR/Cas9 approach, informed by bioinformatic datasets, to generate genotypic variation in the promoter ofOsSTOMAGEN, a positive regulator of rice stomatal density. Engineered genotypic variation corresponded to broad and continuous variation in stomatal density, ranging from 70% to 120% of wild‐type stomatal density. This panel of stomatal variants was leveraged in physiological assays to establish discrete relationships between stomatal morphological variation and stomatal conductance, carbon assimilation and intrinsic water use efficiency in steady‐state and fluctuating light conditions. Additionally, promoter alleles were subjected to vegetative drought regimes to assay the effects of the edited alleles on developmental response to drought. Notably, the capacity for drought‐responsive stomatal density reprogramming instomagenand two cis‐regulatory edited alleles was reduced. Collectively our data demonstrate that cis‐regulatory element editing can generate near‐isogenic trait variation that can be leveraged for establishing relationships between anatomy and physiology, providing a basis for optimizing traits across diverse environments.
Biotechnology & Applied Microbiology↗
Spin waves in doped graphene: A time-dependent spin density functional approach to collective excitations in paramagnetic two-dimensional Dirac fermion gases
In spin-polarized itinerant electron systems, collective spin-wave modes arise from dynamical exchange and correlation (xc) effects. We consider here spin waves in doped paramagnetic graphene with adjustable Zeeman-type band splitting. The spin waves are described using time-dependent spin density functional response theory, treating dynamical xc effects within the Slater and Singwi-Tosi-Land-Sjölander approximations. We obtain spin-wave dispersions and spin stiffnesses as a function of doping and spin polarization, and we discuss the prospects for their experimental observation.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Level-set topology optimization with PDE generated conformal meshes
This paper presents a level-set topology optimization approach that uses conformal meshes for the analysis of the displacement field. The structure’s boundary is represented by the iso-contour of a level-set field discretized on a fixed background design mesh. The conformal mesh is updated for each design iteration via a PDE based mesh morphing process that identifies the set of facets in the background mesh that are homeomorphic to the boundary and relaxes the homeomorphic mesh to conform to the structure’s boundary and ensure high element quality. The conformal mesh allows for a more accurate computation of the response versus density and some level-set based methods which interpolate material properties using the volume fraction. Numerical examples illustrate the proposed approach by optimizing linear-elastic two- and three-dimensional structures, wherein insight into the performance of the mesh morphing process is provided. The examples also highlight the scalability of the approach.
42 ENGINEERING↗
Field-Dependent Magnetic Domain Behavior in van der Waals Fe 3 GeTe 2
Two-dimensional magnetic van der Waals (vdW) materials can show a variety of topological nontrivial spin textures, such as Bloch- or Néel-type stripe, skyrmion, or bubble domains under certain external stimuli. It is critical to understand the magnetic domain behavior in vdW materials in order to control their size and density in response to external stimuli, such as electric and magnetic fields. In this study, we examine the magnetic field dependence of topologically non-trivial magnetization spin textures in vdW Fe 3 GeTe 2 . Néel-type stripe domains and skyrmions are formed depending on the magnetic field-cooling protocol used during in situ Lorentz transmission electron microscopy (LTEM) experiments. Use of quantitative reconstruction of magnetic induction maps and micromagnetic simulations allow for the understanding of the LTEM results of Néel-type stripe domains as well as skyrmions. In addition, the deformation of skyrmion contrast is observed as a result of the introduction of an in-plane magnetic field. We demonstrate the stability of the stripe domains and skyrmions in response to an externally applied magnetic field due to an energy barrier for domain wall annihilation. Our results establish an understanding of the energy landscape that governs the behavior of the topologically non-trivial spin textures in vdW materials which can be harnessed for spintronic applications.
36 MATERIALS SCIENCE↗