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At least 577 records · Page 32

A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior

Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.

36 MATERIALS SCIENCE↗

Tau tridents at accelerator neutrino facilities

We present the first detailed study of Standard Model neutrino tridents involving tau leptons at the near detectors of accelerator neutrino facilities. The rates of these processes were previously thought to be negligible, even at future facilities. Our full 2 → 4 calculation, including both coherent and incoherent scatterings, reveals that the DUNE near detector could observe a considerable number of tau tridents—an important background to new physics searches. We identify promising kinematic features that may allow distinction of tau tridents from the usual neutrino charged-current background at DUNE, and thus establish the observation of tau tridents for the first time. We also comment on the detection prospects at other accelerator and collider neutrino experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Topology-empowered membrane devices for terahertz photonics

Control of terahertz waves offers a profound platform for next-generation sensing, imaging, and information communications. However, all conventional terahertz components and systems suffer from bulky design, sensitivity to imperfections, and transmission loss. We propose and experimentally demonstrate on-chip integration and miniaturization of topological devices, which may address many existing drawbacks of the terahertz technology. We design and fabricate topological devices based on valley-Hall photonic structures that can be employed for various integrated components of on-chip terahertz systems. We demonstrate valley-locked asymmetric energy flow and mode conversion with topological waveguide, multiport couplers, wave division, and whispering gallery mode resonators. Our devices are based on topological membrane metasurfaces, which are of great importance for developing on-chip photonics and bring many features into terahertz technology.

47 OTHER INSTRUMENTATION↗

Structure of the EphB6 receptor ectodomain

Eph receptors are the largest group amongst the receptor tyrosine kinases and are divided into two subgroups, A and B, based on ligand binding specificities and sequence conservation. Through ligand-induced and ligand-independent activities, Ephs play central roles in diverse biological processes, including embryo development, regulation of neuronal signaling, immune responses, vasculogenesis, as well as tumor initiation, progression, and metastasis. The Eph extracellular regions (ECDs) are constituted of multiple domains, and previous structural studies of the A class receptors revealed how they interact with ephrin ligands and simultaneously mediate Eph-Eph clustering necessary for biological activity. Specifically, EphA structures highlighted a model, where clustering of ligand-bound receptors relies on two distinct receptor/receptor interfaces. Interestingly, most unliganded A class receptors also form an additional, third interface, between the ligand binding domain (LBD) and the fibronectin III domain (FN3) of neighboring molecules. Structures of B-class Eph ECDs, on the other hand, have never been reported. To further our understanding of Eph receptor function, we crystallized the EphB6-ECD and determined its three-dimensional structure using X-ray crystallography. EphB6 has important functions in both normal physiology and human malignancies and is especially interesting because this atypical receptor innately lacks kinase activity and our understanding of the mechanism of action is still incomplete. Our structural data reveals the overall EphB6-ECD architecture and shows EphB6-LBD/FN3 interactions similar to those observed for the unliganded A class receptors, suggesting that these unusual interactions are of general importance to the Eph group. We also observe unique structural features, which likely reflect the atypical signaling properties of EphB6, namely the need of co-receptor(s) for this kinase-inactive Eph. These findings provide new valuable information on the structural organization and mechanism of action of the B-class Ephs, and specifically EphB6, which in the future will assist in identifying clinically relevant targets for cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗

Advanced CMOS Reliability Update: Sub 20nm FinFET Assessment

Advances in FinFET design and fabrication enable manufacturing of denser, more compact integrated circuits (ICs) with substantially reduced leakage while shortening the channel-lengths. The same stress-induced leakage and breakdown degradation mechanisms that affect planar transistors also impact FinFET devices. Reliability concerns such as Bias Temperature Instability (BTI), Time Dependent Dielectric Breakdown (TDDB), and Hot Carrier Injection (HCI) become very important with changes to transistor geometry and fin sidewall crystal orientation. Recent testing has shown that FinFETs respond differently to radiation (radiation effects such as total ionizing dose) when compared to planar transistors. These reliability and radiation effects issues become very important when changing transistor geometry and scaling FinFETs towards smaller feature sizes (22-nm, 16-nm, 14- nm, 10-nm, and smaller critical dimensions). The comparable 2019 state of the art transistor densities in current high-volume manufacturing silicon-based foundries is 7-nm (ISMC, Samsung) and 10-nm (Intel) [www.anandtech.com,fuse.wikichip.org]. Released products include supporting components for the cellphone and commercial microprocessor markets respectively. Extensive development in the foundry industry is driving to a 5-nm technology node in late 2020.

47 OTHER INSTRUMENTATION↗

An Investigation of Strategies for Sensing Window Attachment Position: Survey of Candidate Technologies, Evaluation, and Deployment Recommendations

While windows are desirable feature in buildings for views, daylighting, and aesthetics, it is important to recognize that windows are a major contributor to a building’s energy load. Interior window coverings, such as shades and blinds, can help improve the energy performance of windows without sacrificing the benefits; however, while appropriate use of window coverings provide the potential for energy savings, there is little consensus regarding how occupants typically use these window attachments, which sometimes puts into question how much energy they actually save in an occupied home. Automated shading control strategies can reduce the uncertainty of energy savings; however, users can overwrite pre-defined schedules or write their own shade control programs to reach their personal comfort and privacy goals. Because it is difficult to identify how occupants interact with window shades, it is difficult to identify the energy savings potential of blinds. To address this problem, this study was developed to identify a candidate sensor that can be deployed to sense blind position. The intended application for this sensor is deployment in energy efficiency field studies so that shade usage can be measured to better understand results and identify the energy impact of specific window attachment technologies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Quantifying Turbine-Level Risk to Golden Eagles Using a High-Fidelity Updraft Model and a Stochastic Behavioral Model

To minimize the effects of wind farms on Golden Eagle (Aquila chrysaetos) populations while enabling sustainable development of renewable energy resources, it is important to understand how eagles interact with atmospheric flows, terrain features, and anthropogenic structures. Models that predict migratory flight paths provide one tool that helps us grasp how the location of wind farms may influence interactions and impacts on migrating Golden Eagles. The current state-of-the-art in predicting migratory flight paths uses a deterministic fluid-flow analogy to predict eagle trajectory using only an orographic updraft potential computed from topographical features. This model does not take into account variables, such as thermal updrafts and time varying atmospheric conditions that are known to influence migratory behavior. In this work, we improve on the model with the objective of developing tools that advance our understanding of how atmospheric flows and terrain features affect migratory eagle behavior and their interactions with wind farms. Specifically, we 1) incorporate both orographic and thermal updraft information in simulating eagle flight paths; 2) incorporate stochasticity into eagle travel patterns to better capture the influence of exogenous factors on, and the inherent stochasticity of eagle behavior; 3) consider spatio-temporal atmospheric data at wind-farm-scale when computing updraft potential; and 4) account for how atmospheric conditions and the direction of migration change seasonally and how these changes affect eagle migratory flight behavior. We tested the model using a 50km by 50km region with 50 m resolution in the western United States. We simulated 900 independent, probabilistic eagle tracks during southerly and northerly migration, assuming eagles solely rely on orographic updrafts. The preliminary results indicate that the inclusion of finer resolution atmospheric data allows for the inclusion of realistic conditions that an eagle experiences. The stochasticity in eagle tracks provides a platform to include uncertainty in eagle decision making and help produce robust eagle presence maps. We will deploy updraft and downdraft velocities computed using a high-fidelity, wind farm scale, computational fluid dynamics solver under development at National Renewable Energy Laboratory. This work is a first step in the development of a predictive and generalizable eagle behavior model at the wind farm scale that does not rely on empirical data collection. Although the current model is intended for migratory eagles, we will extend and refine this model to inform the development of additional behavioral modes, including resident eagle behavior. This modeling approach improves our ability to understand eagle use of the landscape at a fine scale, and it is our hope that this work will ultimately help advance strategies that minimize the impact of wind development on Golden Eagle populations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

Magnetization dynamics fingerprints of an excitonic condensate t 2 g 4 magnet

The competition between spin-orbit coupling (SOC) λ and electron-electron interaction U leads to a plethora of novel states of matter, extensively studied in the context of t 2 g 4 and t 2 g 5 materials, such as ruthenates and iridates. Excitonic magnets—the antiferromagnetic state of bounded electron-hole pairs-are prominent examples of phenomena driven by those competing energy scales. Interestingly, recent theoretical studies predicted that excitonic magnets can be found in the ground state of SOC t 2 g 4 Hubbard models. Here we present a detailed computational study of the magnetic excitations in that excitonic magnet, employing one-dimensional chains (via density matrix renormalization group) and small two-dimensional clusters (via Lanczos). Specifically, first we show that the low-energy spectrum is dominated by a dispersive (acoustic) magnonic mode, with extra features arising from the λ = 0 state in the phase diagram. Second, and more importantly, we found a novel magnetic excitation forming a high-energy optical mode with the highest intensity at wave-vector q → 0 . In the excitonic condensation regime at large U , we also have found a novel high-energy π mode composed solely of orbital excitations. Overall, these features do not appear all together in any of the neighboring states in the phase diagram and thus constitute unique fingerprints of the t 2 g 4 excitonic magnet, of importance in the analysis of neutron and resonant inelastic x-ray scattering experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Using limited neural networks to assess relative mechanistic influence on shock heating in granular solids

The rapid compaction of granular media results in localized heating that can induce chemical reactions, phase transformations, and melting. However, there are numerous mechanisms in play that can be dependent on a variety of microstructural features. Machine learning techniques such as neural networks offer a ubiquitous method to develop models for physical processes. Limiting what kind of microstructural information is used as an input and assessing normalized changes in network error, the relative importance of different mechanisms can be inferred. Here we utilize binned, initial density information as network inputs to predict local shock heating in a granular high explosive trained from large-scale molecular dynamics simulations. In this study, the spatial extent of the density field used in the network is altered to assess the importance and relevant length scales of the physical mechanisms in play, where different microstructural features result in different predictive capabilities.

36 MATERIALS SCIENCE↗

Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.

59 BASIC BIOLOGICAL SCIENCES↗

Comparing event generator predictions and ab initio calculations of ν- 12 C neutral-current quasielastic scattering at 1 GeV

The measurement of neutrino oscillations and exotic physics searches are important parts of the physics program in the near future, with new state-of-the-art experiments planned within the next decade. Future and modern experiments in these fields will make use of nuclear targets. Event generators (EGs) are software used in the analysis of neutrino oscillation experiments. EGs are used to predict kinematic observables for a range of neutrino energies. These simulations make use of simple models of nucleon dynamics. As such, they may fail to capture features of more rigorous theoretical calculations. This work compares EG performance to nuclear theory calculations by comparing observables generated in the two frameworks. We provide a common set of definitions between theory and experiment and assess the adequacy of the implementation of two nuclear physics models in EG simulations. Neutral-current quasielastic (NCQE) scattering events for neutrinos and antineutrinos on a 12 C target are simulated with a specific EG, NEUT, used by the T2K experiment for its analysis. The simulated cross sections are compared to analytic calculations from nuclear theory within the factorization scheme. We compare the NEUT implementation of two different models on nuclear spectral functions: the relativistic Fermi gas (RFG) and the correlated basis spectral function (CBF) to analytic calculations of the same models in the factorization scheme. For both nuclear physics models, we compare the appearance of features in the distributions relevant to experimental analyses. The peak of the cross section dσ/(dΩ dω) is consistent in energy transfer, ω, for RFG and CBF simulations. Qualitatively, the shape of the simulated distribution is similar to the one obtained through theory calculations; however, there are some discrepancies between the theory calculations and the NEUT simulation. While the EG simulations and analytic calculations with the same model of nuclear dynamics show similar overall features, there are still differences between the two. These results demonstrate the importance of benchmarking EGs so their nuclear physics implementations can be improved for the analysis of future experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A neural network for determination of latent dimensionality in Nonnegative Matrix Factorization

Non-negative Matrix Factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy datasets with applications in data mining, text recognition, dimension reduction, face recognition, anomaly detection, blind source separation, and many other fields. An important input for NMF is the latent dimensionality of the data, that is, the number of hidden features, K, present in the explored dataset. Unfortunately, and this quantity is rarely known a priori. The existing methods for determining latent dimensionality, such as Automatic Relevance Determination (ARD), are mostly heuristic and utilize different characteristics to estimate the number of hidden features. However, all of them require human presence to make a final determination of K. Here we utilize a supervised machine learning approach in combination with a recent method for model determination, called NMFk, to determine the number of hidden features automatically. NMFk performs a set of NMF simulations on an ensemble of matrices, obtained by bootstrapping the initial dataset, and estimates which K produces stable groups of latent features that reconstruct the initial dataset well. We then train a Multi-Layter Perceptron (MLP) classifier network to determine the correct number of latent features utilizing the statistics and characteristics of the NMF solution, obtained from NMFk. In order to train the MLP classifier, a training set of 58,660 matrices with predetermined latent features were factorized with NMFk. The MLP classifier in conjunction with NMFk maintains a greater than 95% success rate when applied to a held out test set. Additionally, when applied to two well-known benchmark datasets, the swimmer and MIT face data, NMFk/MLP correctly recovers the established number of hidden features. Finally, we compare the accuracy of our method to the ARD, AIC and Stability-based methods.

97 MATHEMATICS AND COMPUTING↗

Feature Classification for Control System Devices

Control systems are used to automate industrial processes, smart grids, and smart cities. Unfortunately, cyber attacks on control systems are on the rise. Additionally, control systems lack the plethora of tools available for commodity systems for forensic investigation. An important step towards the proper forensic investigation is to analyze device memory. To assist in identifying features of device memory, we present a machine learning-based technique that integrates ontology information for feature classification in a control system device’s memory.

ahmed mithu, M Rayhan↗

Recent advances in cooperative activation of CO 2 and N 2 O by bimetallic coordination complexes or binuclear reaction pathways

The gaseous small molecules, CO 2 and N 2 O, play important roles in climate change and ozone layer depletion, and they hold promise as underutilized reagents and chemical feedstocks. Furthermore, productive transformations of these heteroallenes are difficult to achieve because of their inertness. In nature, these gases are cycled through ecological systems by metalloenzymes featuring multimetallic active sites that employ cooperative mechanisms. Thus, cooperative bimetallic chemistry is an important strategy for synthetic systems, as well. In this Perspective, recent advances (since 2010) in cooperative activation of CO 2 and N 2 O are reviewed, including examples involving s-block, p-block, d-block, and f-block metals and different combinations thereof.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Overview of Atmospheric Features Over the Western North Atlantic Ocean and North American East Coast - Part 1: Analysis of Aerosols, Gases, and Wet Deposition Chemistry

The Western North Atlantic Ocean (WNAO) and adjoining East Coast of North America are of great importance for atmospheric research and have been extensively studied for several decades. This broad region exhibits complex meteorological features, diverse cloud types, and a wide range of conditions associated with gas and particulate species that originate from many sources regionally and from other continents. As Part 1 of a 2-part paper series, this work provides a characterization of quantities associated with atmospheric chemistry, including gases, aerosols, and wet deposition, based on satellite observations, ground-based data, model simulations, and reanalysis products. Key results include spatial and seasonal differences in composition along the North American East Coast and over the WNAO associated with varying sources of smoke and dust and meteorological drivers such as temperature, moisture, and precipitation. Spatial and seasonal variations of tropospheric carbon monoxide and ozone highlight different pathways towards accumulation of these species in the troposphere. Spatial distributions of speciated aerosol optical depth and vertical profiles of aerosol mass mixing ratios show a clear seasonal cycle highlighting the influence of both natural and anthropogenic sources in addition to the impact of intercontinental transport on their vertical profiles. Analysis of long-term climate model simulations of aerosol species and satellite observations of carbon monoxide confirm that there has been a significant decline in recent decades among anthropogenic constituents owing to regulatory activities. The results can inform current and future lines of research for the region.

Corral, Andrea↗

Ecological connectivity and habitat loss shape patterns of genetic diversity in a threatened salamander

Context The maintenance of genetic diversity is essential for preserving adaptive potential in populations, yet it is increasingly threatened by landscape alteration. The field of landscape genetics offers a framework for assessing how patch-level landscape conditions, modeled at multiple scales, influence genetic diversity. Objectives We sought to assess how local environmental features and connectivity influence genetic diversity across 74 four-toed salamander (Hemidactylium scutatum) breeding wetlands in the southeastern United States. Methods Using next-generation sequencing data and hierarchical Bayesian models, we examined genome-wide heterozygosity in relation to local landscape features and ecological connectivity. We also assessed the scale of effect of landscape features and tested for temporal lag effects. Results Genetic diversity was lower in wetlands with higher levels of historic deforestation and lower connectivity. An interaction between deforestation and connectivity indicated that deforestation had stronger negative effects in isolated wetlands but weaker effects in well-connected wetlands. Accounting for scale of effect and temporal lags was critical for detecting these relationships. Conclusions Our analyses highlight the importance of assessing the spatial scale (scale of effect) and temporal lag of landscape features to detect key drivers of genetic diversity. In line with population genetic theory, our results indicate that the genetic consequences of habitat loss do not affect populations uniformly and are most severe in isolated populations where gene flow cannot buffer against loss of diversity. Altogether, we highlight the importance of considering the interaction of habitat loss and connectivity in conservation genetic management.

Hemidactylium scutatum↗

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗

Explainable AI classification for parton density theory

Quantitatively connecting properties of parton distribution functions (PDFs, or parton densities) to the theoretical assumptions made within the QCD analyses which produce them has been a longstanding problem in HEP phenomenology. To confront this challenge, we introduce an ML-based explainability framework, XAI4PDF, to classify PDFs by parton flavor or underlying theoretical model using ResNet-like neural networks (NNs). By leveraging the differentiable nature of ResNet models, this approach deploys guided backpropagation to dissect relevant features of fitted PDFs, identifying x-dependent signatures of PDFs important to the ML model classifications. By applying our framework, we are able to sort PDFs according to the analysis which produced them while constructing quantitative, human-readable maps locating the x regions most affected by the internal theory assumptions going into each analysis. This technique expands the toolkit available to PDF analysis and adjacent particle phenomenology while pointing to promising generalizations.

Artificial Intelligence↗