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At least 1,171 records · Page 65

Atomistic Simulation of Glasses and Amorphous Materials: Challenges and Opportunities for the Next Decade

Atomistic simulations have become indispensable tools for understanding glass structure, dynamics, and properties, yet persistent challenges limit their predictive power. This perspective examines three interconnected issues, namely glass formation procedures, interatomic potential development, and machine learning applications, which emerged from the 5th International Workshop on Challenges of Atomistic Simulations of Glasses and Amorphous Materials. We identify convergent community priorities for (i) standardized validation protocols, (ii) curated benchmark datasets with complete metadata, and (iii) open repositories for glasses. A systematic was forward is provided by a hierarchical validation framework for assessing the structural fidelity, property prediction, and behavioral realism of simulation techniques. Looking ahead, transformative advances are promised by the fusion of classical techniques with machine learning based approaches, for instance, by integrating swap Monte Carlo with machine-learning (ML) potentials, leveraging foundation models through transfer learning, and finetuning ML potentials with experimental data. Progress depends on the community committing to validated models, reproducible protocols, and sustained data sharing.

Krishnan, N. M. Anoop↗

The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions

The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review,we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.

59 BASIC BIOLOGICAL SCIENCES↗

An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots

The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. In this work, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.

59 BASIC BIOLOGICAL SCIENCES↗

A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large–scale systems–level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high–throughput enhanced yeast one–hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis–regulatory elements (CREs) in ER stress–responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Lastly, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription–regulatory mechanisms in the stress responses and crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗

Probing the in situ volumes of Arabidopsis leaf plastids using three‐dimensional confocal and scanning electron microscopy

SUMMARY Leaf plastids harbor a plethora of biochemical reactions including photosynthesis, one of the most important metabolic pathways on Earth. Scientists are eager to unveil the physiological processes within the organelle but also their interconnection with the rest of the plant cell. An increasingly important feature of this venture is to use experimental data in the design of metabolic models. A remaining obstacle has been the limited in situ volume information of plastids and other cell organelles. To fill this gap for chloroplasts, we established three microscopy protocols delivering in situ volumes based on: (i) chlorophyll fluorescence emerging from the thylakoid membrane, (ii) a CFP marker embedded in the envelope, and (iii) calculations from serial block‐face scanning electron microscopy (SBFSEM). The obtained data were corroborated by comparing wild‐type data with two mutant lines affected in the plastid division machinery known to produce small and large mesophyll chloroplasts, respectively. Furthermore, we also determined the volume of the much smaller guard cell plastids. Interestingly, their volume is not governed by the same components of the division machinery which defines mesophyll plastid size. Based on our three approaches, the average volume of a mature Col‐0 wild‐type mesophyll chloroplasts is 93 μm 3 . Wild‐type guard cell plastids are approximately 18 μm 3 . Lastly, our comparative analysis shows that the chlorophyll fluorescence analysis can accurately determine chloroplast volumes, providing an important tool to research groups without access to transgenic marker lines expressing genetically encoded fluorescence proteins or costly SBFSEM equipment.

Knoblauch, Jan↗

Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.

60 APPLIED LIFE SCIENCES↗

Artificial Neural Network Models for Octane Number and Octane Sensitivity: A Quantitative Structure Property Relationship Approach to Fuel Design

Octane sensitivity (OS), defined as the research octane number (RON) minus the motor octane number (MON) of a fuel, has gained interest among researchers due to its effect on knocking conditions in internal combustion engines. Compounds with a high OS enable higher efficiencies, especially within advanced compression ignition engines. RON/MON must be experimentally tested to determine OS, requiring time, funding, and specialized equipment. Thus, predictive models trained with existing experimental data and molecular descriptors (via quantitative structure-property relationships (QSPRs)) would allow for the preemptive screening of compounds prior to performing these experiments. Here, the present work proposes two methods for predicting the OS of a given compound: using artificial neural networks (ANNs) trained with QSPR descriptors to predict RON and MON individually to compute OS (derived octane sensitivity (dOS)), and using ANNs trained with QSPR descriptors to directly predict OS. Twenty-five ANNs were trained for both RON and MON and their test sets achieved an overall 6.4% and 5.2% error, respectively. Twenty-five additional ANNs were trained for both dOS and OS; dOS calculations were found to have 15.3% error while predicting OS directly resulted in 9.9% error. A chemical analysis of the top QSPR descriptors for RON/MON and OS is conducted, highlighting desirable structural features for high-performing molecules and offering insight into the inner mathematical workings of ANNs; such chemical interpretations study the interconnections between structural features, descriptors, and fuel performance showing that connectivity, structural diversity, and atomic hybridization consistently drive fuel performance.

09 BIOMASS FUELS↗

Analysis of Planar-Cavity Receiver Reactor for Solar Thermochemical Dry-Reforming

Concentrating solar thermal (CST) systems can be leveraged to provide not only heat for power generation, but also for energy storage and thermochemical fuel production. Such solar thermochemical processes have been studied conceptually, from solar thermochemical hydrogen production (STCH) and thermochemical energy storage (TCES), to gasification, reforming, and fuel upgrading by various means. The solar receiver and reactor are critical components in the conversion of solar energy into chemical energy in the form of 'solar fuels'. For effective conversion of solar energy within a coupled solar receiver-reactor, extremely high temperatures are required, thereby demanding a high solar concentration ratio (CR) for efficient operation. This creates a design challenge for the receiver-reactor, as many thermochemical processes involve gas or gas-solid systems that are limited by low heat transfer coefficients. A unique receiver design is proposed that has the potential to incorporate various high-temperature thermochemical processes such as TCES-assisted power generation, methane reforming, or STCH processes. Modeling this receiver and its potential applications requires a full three-dimensional model that accurately captures the interconnected effects of receiver geometry, spatial solar irradiance, complex radiation, reaction kinetics, fluid dynamics, and heat transfer. In this paper we analyze a CST system integrated with this unique planar-cavity receiver-reactor design using the developed model. The model presented in this paper showed where improved thermal management was needed to achieve suitable receiver performance when a dry-methane reforming process is implemented.

14 SOLAR ENERGY↗

FREQUENCY REGULATION WITH CONNECTED LIGHTING SYSTEMS

The management of end-use energy resources, e.g., commercial buildings, has been investigated as a promising source of services for the electric power grid. Lighting consumes about 17% electricity of U.S. commercial buildings; however, it may contribute significantly to services that improve the reliability and resilience of the grid due to its rapid speed of response. Connected lighting systems (CLS), which build upon solid-state lamp technology, can change their power demand more quickly than most other building electricity end uses. But the potential of CLS to provide grid services has not been considerably investigated. In this paper, we describe initial research to evaluate the potential of CLS for the grid service of frequency regulation. Frequency regulation is a reliability product that corrects in a matter of seconds for short-term changes in the balance between supply and demand in the balancing area that might affect the stability of the power system. Frequency regulation signals for a medium office building are generated from the normalized test signals for the PJM Interconnection Reg-A and Reg-D regulations services. Control of the CLS locally to follow the Reg-A or Reg-D signal is used to provide contributions to the corresponding frequency regulation service. The performance of CLS for frequency regulation is evaluated using the PJM 40-Minute Performance Score Template. The performance scores obtained for all CLS categories for both Reg-A and Reg-D signals far exceed the minimum score for the qualification, a very promising result for CLS to provide frequency regulation service.

Wang, Peng↗

MoorDyn V2: New Capabilities in Mooring System Components and Load Cases

MoorDyn, an open-source mooring dynamics model, is being expanded with capabilities for additional mooring system features and load cases. As floating wind turbine technology matures, mooring systems are becoming more sophisticated and more complex scenarios need to be considered in the design process. Mooring systems may have synthetic line materials, ballast/buoyancy bodies along the lines, or interconnections between platforms. Failure modes may involve multiple cascading line failures that depend on mooring system dynamics. Features recently added to MoorDyn aim to address these emerging needs. MoorDyn’s linear elasticity model has been supplemented to support user-defined stress-strain curves, which can be adjusted to represent synthetic mooring materials. Rigid six-degree-of-freedom bodies in the mooring system can now be modeled using two new model objects. “Rod” objects provide an option for rigid cylindrical bodies. They use the existing Morison equation-based hydrodynamics model and can be connected to mooring lines at either end. “Body” objects provide a generic six-degree-of-freedom rigid-body representation based on a lumped-parameter model of translational and rotational properties. Rod objects can be added to Body objects and mooring lines can be attached at any location, allowing a wide variety of submerged structures to be integrated into the mooring system. Lastly, a means of dynamically simulating mooring line failures has been implemented. These new features, currently in the C++ version of MoorDyn, are described and then demonstrated on a two-turbine shared-mooring array. A qualitative view of the results suggests the new features are functioning as expected.

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

Toward ultrafast, ultra-stable imaging arrays: Superlattice doping to enhance the performance of backside-illuminated 3D-hybridized silicon photodetectors

In this paper, the authors report the latest results on their development of superlattice-doped, thinned, backside-illuminated (BSI), 3D-integrated photodiode detectors—a step toward their ultimate goal of demonstrating ultrafast, ultrastable CMOS imaging arrays. As with most silicon-based photodetectors, backside-illumination and backside surface passivation are keys to achieve the highest performance capability. The two-dimensional (2D) doping technique developed at the Jet Propulsion Laboratory (JPL) has proved to result in a highly efficient, highly stable detector response when combined with a variety of detectors. Here, JPL's 2D-doping has been combined with Sandia's BSI photodetectors hybridized with custom fanout wafer via copper Direct Bond Interconnect (DBI®), a technology that is rapidly becoming industry standard for BSI CMOS imaging arrays. The prototype detectors were packaged and evaluated with respect to their response to low energy electrons. The authors find that the responsivity of 2D-doped BSI detectors is higher than devices prepared using other surface passivation techniques (i.e., ion implantation). The success of the work described herein verifies that the 2D-doping processes previously developed for Sandia's frontside-illuminated photodetectors are generally applicable to BSI detectors and demonstrates for the first time that JPL's 2D-doping process is compatible with the Cu-DBI® technology.

Jewell, April D.↗

Tutorial on forming through-silicon vias

Through-silicon vias (TSVs) are a critical technology for three-dimensional integrated circuit technology. These through-substrate interconnects allow electronic devices to be stacked vertically for a broad range of applications and performance improvements such as increased bandwidth, reduced signal delay, improved power management, and smaller form-factors. There are many interdependent processing steps involved in the successful integration of TSVs. This article provides a tutorial style review of the following semiconductor fabrication process steps that are commonly used in forming TSVs: deep etching of silicon to form the via, thin film deposition to provide insulation, barrier, and seed layers, electroplating of copper for the conductive metal, and wafer thinning to reveal the TSVs. Recent work in copper electrochemical deposition is highlighted, analyzing the effect of accelerator and suppressor additives in the electrolyte to enable void-free bottom-up filling from a conformally lined seed metal.

42 ENGINEERING↗

EarthShine: Observing our world as an exoplanet from the surface of the Moon

NASA’s return to the Moon coincides with explosive growth in exoplanet discovery. Missions are being formulated to search for habitable planets orbiting other stars, making this the ideal time to deploy an instrument suite to the lunar surface to help us recognize a habitable exoplanet when we see it. We present EarthShine, a technically mature, three-instrument suite to observe the whole Earth from the Moon as an exoplanet proxy. EarthShine data will validate and improve models critical for designing missions to image and characterize exoplanets, thus informing observing strategies for flagship missions to directly image exoplanets. EarthShine will answer interconnected questions in Earth and lunar science, exoplanets, and astrobiology, related to the credo “follow the water.” EarthShine can take advantage of current NASA programs to conduct science from the Moon with low-cost, mature space hardware to reduce risk and assure success. Like the 1968 Apollo Earthrise image of our home planet, lonely in the black sky, the appeal of EarthShine to a multidisciplinary array of researchers in Earth Science, Planetary Science, and astrophysics will maximize both its scientific impact and its impact on the general public.

79 ASTRONOMY AND ASTROPHYSICS↗

Demonstration of a third-order hierarchy of topological states in a three-dimensional acoustic metamaterial

Classical wave systems have constituted an excellent platform for emulating complex quantum phenomena, such as demonstrating topological phenomena in photonics and acoustics. Recently, a new class of topological states localized in more than one dimension of a D -dimensional system, referred to as higher-order topological (HOT) states, has been reported, offering an even more versatile platform to confine and control classical radiation and mechanical motion. Here, we design and experimentally study a 3D topological acoustic metamaterial supporting third-order (0D) topological corner states along with second-order (1D) edge states and first-order (2D) surface states within the same topological bandgap, thus establishing a full hierarchy of nontrivial bulk polarization–induced states in three dimensions. The assembled 3D topological metamaterial represents the acoustic analog of a pyrochlore lattice made of interconnected molecules, and is shown to exhibit topological bulk polarization, leading to the emergence of boundary states.

Science & Technology - Other Topics↗

Ultrahigh strength, modulus, and conductivity of graphitic fibers by macromolecular coalescence

Theoretical considerations suggest that the strength of carbon nanotube (CNT) fibers be exceptional; however, their mechanical performance values are much lower than the theoretical values. To achieve macroscopic fibers with ultrahigh performance, we developed a method to form multidimensional nanostructures by coalescence of individual nanotubes. The highly aligned wet-spun fibers of single- or double-walled nanotube bundles were graphitized to induce nanotube collapse and multi-inner walled structures. These advanced nanostructures formed a network of interconnected, close-packed graphitic domains. Their near-perfect alignment and high longitudinal crystallinity that increased the shear strength between CNTs while retaining notable flexibility. The resulting fibers have an exceptional combination of high tensile strength (6.57 GPa), modulus (629 GPa), thermal conductivity (482 W/m·K), and electrical conductivity (2.2 MS/m), thereby overcoming the limits associated with conventional synthetic fibers.

36 MATERIALS SCIENCE↗

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗