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At least 145 records · Page 8

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately a branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.

36 MATERIALS SCIENCE↗

Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation

Abstract Motivation Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conventional deep learning approaches rely purely on data-driven learning, which can limit robust model interpretability, particularly in high-dimensional settings with limited size samples. In computational biology, knowledge-guided learning has primarily leveraged network- and structural-based knowledge, leading to biologically interpretable representations and enhanced predictive performance compared to conventional approaches. However, curated biomarkers, one of the most accessible forms of biological knowledge, remain largely unexplored within knowledge-guided paradigms. Results In this study, we propose a model-agnostic training paradigm, Biomarker-driven Explainable Prior-guided Learning (BioExPL), that can be applied to any neural networks that incorporates curated prior knowledge. BioExPL enforces neural networks to reflect curated biomarker priors in their latent representations through a novel knowledge-alignment loss. BioExPL consistently demonstrated significantly improved predictive performance and enhanced model interpretability with minimized computational overhead in simulation studies and intensive experiments on multiple cancer datasets. BioExPL not only integrates prior curated knowledge into the model but also accurately identifies unknown associated signals additionally. BioExPL is model-agnostic and domain-independent, enabling its integration into diverse neural network architectures. Availability and implementation The open-source is publicly available at: https://github.com/datax-lab/BioExPL.

Baek, Beomsu [Department of Computer Science, Univ↗

Motivation and Design of the OCPP Security Service

Pacific Northwest National Laboratory is conducting in-depth research aimed at exploring how zero trust security principles can be effectively applied to electric vehicle charging infrastructure. This investigation seeks to enhance the resilience and reliability of these systems against cyber threats, ensuring secure and uninterrupted access to charging services for electric vehicle users and electric supply. Zero trust is a security concept centered on the belief that system operators should not automatically trust users or systems based on their location, whether inside or outside the organization, but instead must verify everything trying to connect to their systems before granting access. A key aspect of the project is to demonstrate and validate zero trust approaches targeted to electric vehicle (EV) charging infrastructure. It has been observed that both open-source and commercial solutions often overlook the specific protocols employed in managing EV charging stations and proceeded with a general, protocol-agnostic approach. While these strategies effectively block non-authorized routes to the charging infrastructure, they do not tackle the situations where attackers may exploit legitimate access channels, such as the inattentive operator model posited by the Idaho National Laboratory. To address this gap, this paper proposes and discusses a new security service targeted to the Open Charge Point Protocol (OCPP), which is the de facto protocol for the management of charging stations and serves a critical role in the broader adoption of electric vehicles. The design and architecture of the proposed OCPP security service are discussed in detail, outlining how it aims to safeguard charging station management system (CSMS) functions. The service is particularly important in scenarios where the charging station operator (CSO), responsible for the maintenance and operation of charging stations, and the charging network provider (CNP), which manages the charging network's accessibility and billing, are separate entities. This distinction is crucial because CSOs and CNPs often have different priorities, objectives, and operational responsibilities, which may not always align perfectly. For instance, a CSO might prioritize uptime and customer satisfaction, while a CNP might focus on maximizing revenue and network utilization. Such misalignment can create security vulnerabilities, as each entity might implement different policies and standards, potentially leaving gaps in the overall security posture.

33 ADVANCED PROPULSION SYSTEMS↗

Dual-band GPS antenna with horizontal polarization

An antenna array is described herein that is suitable for dual-band GPS reception. The antenna array includes a plurality of dipole antennas arranged in a circular pattern. The antenna array further includes a feed network, separated from the dipole antennas by an insulating plate, and that passes electrical signals output by the dipole antennas to a feed line. The feed network comprises a central plate in contact with the feed line, and a plurality of arms aligned with the dipoles and extending from the center plate toward the outer edges of the circular pattern. The arms cross over slots in each of the dipole antennas. Electromagnetic waves that impinge on the dipoles induce signals that travel down the slots in the dipoles and couple to the arms of the feed network where the arms cross over the slots. The signals then travel along the feed network to the feed line.

42 ENGINEERING↗

Mobile and replicated alignment of arrays in data-parallel programs

When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

Chatterjee, Siddhartha↗

Tribal Colleges and Universities/Advanced Manufacturing Network Initiative (Q3 FY2020 Progress Report)

The National Nuclear Security Agency (NNSA) initiated the Minority Serving Institution Partnership Plan (MSIPP) to 1) align investments in a university capacity and workforce development with the NNSA mission to develop the needed skills and talent for NNSA's enduring technical workforce at the laboratories and production plants, and 2) to enhance research and education at under-represented colleges and universities. Out of this effort, MSIPP launched a new consortium in early FY17 focused on Tribal Colleges and Universities (TCUs) known as the Advanced Manufacturing Network Initiative (AMNI). This consortium has been extended for FY20 and FY21. The following report summarizes the status update during this quarter.

42 ENGINEERING↗

Tribal Colleges and Universities/Advanced Manufacturing Network Initiative (Q4 FY2020 Progress Report)

The National Nuclear Security Agency (NNSA) initiated the Minority Serving Institution Partnership Plan (MSIPP) to 1) align investments in a university capacity and workforce development with the NNSA mission to develop the needed skills and talent for NNSA’s enduring technical workforce at the laboratories and production plants, and 2) to enhance research and education at under-represented colleges and universities. Out of this effort, MSIPP launched a new consortium in early FY17 focused on Tribal Colleges and Universities (TCUs) known as the Advanced Manufacturing Network Initiative (AMNI). This consortium has been extended for FY20 and FY21. The following report summarizes the status update during this quarter.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Alignment of the 12 Gev CEBAF Accelerator

Alignment of the 12 Gev CEBAF Accelerator Jefferson lab has just completed an upgrade to its CEBAF accelerator which allows for an increase in the energy of delivered beam from 6Gev to 12 Gev. The enhancements to the accelerator have included the addition of 10 new high performance cryomodules, and the removal, upgrade and refurbishment of almost 300 existing transport magnets. Outside of the main accelerator, a new experimental hall has been constructed, and the three existing halls are currently being upgraded to take advantage of the higher energies. For this project, a new survey network has been measured and almost every element in the accelerator has been re-aligned. Commissioning of the accelerator took place at the beginning of this year, during the course of which, it became apparent that there was a significant difference between the expected and the actual path length in the machine. This paper describes the measurements taken and analysis used to try and understand this situation.

Curtis, Christopher↗

Exploring drought-responsive crucial genes in Sorghum

Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance.

60 APPLIED LIFE SCIENCES↗

Modeling the Effects of Artificial Drainage on Agriculture-Dominated Watersheds Using a Fully Distributed Integrated Hydrology Model

In agriculture-dominated watersheds where natural drainage is poor, agricultural ditches (narrow engineered channels) and tile drains (perforated pipes) are widely employed to enhance surface and subsurface drainage, respectively. Despite their relatively small scale, these features exert substantial control over the hydro-biogeochemical function of watersheds and their effects need to be represented in the models. We introduce a novel strategy to incorporate the effects of artificial agricultural drainage into a fully distributed basin-scale integrated surface-subsurface hydrology models. In our approach, narrow agriculture ditches for surface drainage are resolved efficiently using ditch-aligned computational meshes that are hydrologically conditioned to ensure connectivity in the stream/ditch network. For tile drainage in the subsurface, we use the physically based Hooghoudt's drainage equation as a subgrid model and route the water drained through tiles to the nearest ditch. Without site-specific calibration, this model reproduced observed streamflow in the Portage River Watershed (>1,000 km 2 ) as recorded by a USGS gauge with good accuracy (normalized KGE = 0.81) and outperformed a calibrated SWAT model (normalized KGE = 0.68). Numerical experiments confirm that artificial drainage reduces surface inundations and effectively controls the water table. At the watershed scale, artificial drainage increases baseflow but has little effect on watershed discharges above the 90th percentile. The strong physical underpinnings and reduced need for calibration allow us to study the impacts of artificial drainage on distributed hydrological response in terms of fluxes and states and provide a platform for investigating watershed-scale nutrient transport.

54 ENVIRONMENTAL SCIENCES↗

Perovskite superlattices with efficient carrier dynamics

Compared with their three-dimensional (3D) counterparts, low-dimensional metal halide perovskites (2D and quasi-2D; B 2 A n-1 M n X 3n+1 , such as B = R-NH 3 + , A = HC(NH 2 ) 2 + , Cs + ; M = Pb 2+ , Sn 2+ ; X = Cl - , Br - , I - ) with periodic inorganic-organic structures have shown promising stability and hysteresis-free electrical performance. However, their unique multiple-quantum-well structure limits the device efficiencies because of the grain boundaries and randomly oriented quantum wells in polycrystals. In single crystals, the carrier transport through the thickness direction is hindered by the layered insulating organic spacers. Furthermore, the strong quantum confinement from the organic spacers limits the generation and transport of free carriers. Also, lead-free metal halide perovskites have been developed but their device performance is limited by their low crystallinity and structural instability 11 . Here, in this paper, we report a low-dimensional metal halide perovskite BA 2 MA n-1 Sn n I 3n+1 (BA, butylammonium; MA, methylammonium; n = 1, 3, 5) superlattice by chemical epitaxy. The inorganic slabs are aligned vertical to the substrate and interconnected in a criss-cross 2D network parallel to the substrate, leading to efficient carrier transport in three dimensions. A lattice-mismatched substrate compresses the organic spacers, which weakens the quantum confinement. The performance of a superlattice solar cell has been certified under the quasi-steady state, showing a stable 12.36% photoelectric conversion efficiency. Moreover, an intraband exciton relaxation process may have yielded an unusually high open-circuit voltage (V OC ).

36 MATERIALS SCIENCE↗

Observations of field-aligned currents, waves, and electric fields at substorm onset

Substorm onsets, identified Pi 2 pulsations observed on the Air Force Geophysics Laboratory Magnetometer Network, are studied using magnetometer and electric field data from ISEE 1 as well as magnetometer data from the geosynchronous satellites GOES 2 and 3. The mid-latitude magnetometer data provides the means of both timing and locating the substorm onset so that the spacecraft locations with respect to the substorm current systems are known. During two intervals, each containing several onsets or intensifications, ISEE 1 observed field-aligned current signatures beginning simultaneously with the mid-latitude Pi 2 pulsation. Close to the earth broadband bursts of wave noise were observed in the electric field data whenever field-aligned currents were detected. One onset occurred when ISEE 1 and GOES 2 were on the same field line but in opposite hemispheres. During this onset ISEE 1 and GOES 2 saw magnetic signatures which appear to be due to conjugate field-aligned currents flowing out of the western end of the westward auroral electrojets. The ISEE 1 signature is of a line current moving westward past the spacecraft. During the other interval, ISEE 1 was in the near-tail region near the midnight meridian. Plasma data confirms that the plasma sheet thinned and subsequently expanded at onset. Electric field data shows that the plasma moved in the opposite direction to the plasma sheet boundary as the boundary expanded which implies that there must have been an abundant source of hot plasma present. The plasma motion was towards the center of the plasma sheet and earthwards and consisted of a series of pulses rather than a steady flow.

Smits, D. P.↗

Architecture-based multiscale computational modeling of plant cell wall mechanics to examine the hydrogen-bonding hypothesis of cell wall network structure model

A primary plant cell wall network was computationally modeled using the finite element approach to study the hypothesis of hemicellulose (HC) tethering with the cellulose microfibrils (CMFs) as one of the major load-bearing mechanisms of the growing cell wall. A computational primary cell wall network fragment (10 × 10 μm) comprising typical compositions and properties of CMFs and HC was modeled with well-aligned CMFs. The tethering of HC to CMFs is modeled in accordance with the strength of the hydrogen bonding by implementing a specific load-bearing connection (i.e. the joint element). The introduction of the CMF-HC interaction to the computational cell wall network model is a key to the quantitative examination of the mechanical consequences of cell wall structure models, including the tethering HC model. When the cell wall network models with and without joint elements were compared, the hydrogen bond exhibited a significant contribution to the overall stiffness of the cell wall network fragment. When the cell wall network model was stretched 1% in the transverse direction, the tethering of CMF-HC via hydrogen bonds was not strong enough to maintain its integrity. When the cell wall network model was stretched 1% in the longitudinal direction, the tethering provided comparable strength to maintain its integrity. This substantial anisotropy suggests that the HC tethering with hydrogen bonds alone does not manifest sufficient energy to maintain the integrity of the cell wall during its growth (i.e. other mechanisms are present to ensure the cell wall shape).

59 BASIC BIOLOGICAL SCIENCES↗

Quantification of oil and gas methane emissions in the Delaware and Marcellus basins using a network of continuous tower-based measurements

Abstract. According to the United States Environmental Protection Agency (US EPA), emissions from oil and gas infrastructure contribute 30 % of all anthropogenic methane (CH4) emissions in the US. Studies in the last decade have shown emissions from this sector to be substantially larger than bottom-up assessments, including the EPA inventory, highlighting both the increased importance of methane emissions from the oil and gas sector in terms of their overall climatological impact and the need for independent monitoring of these emissions. In this study we present continuous monitoring of regional methane emissions from two oil and gas basins using tower-based observing networks. Continuous methane measurements were taken at four tower sites in the northeastern Marcellus basin from May 2015 through December 2016 and five tower sites in the Delaware basin in the western Permian from March 2020 through April 2022. These measurements, an atmospheric transport model, and prior emission fields are combined using an atmospheric inversion to estimate monthly methane emissions in the two regions. This study finds the mean overall emission rate from the Delaware basin during the measurement period to be 146–210 Mg CH4 h−1 (energy-normalized loss rate of 1.1 %–1.5 %, gas-normalized rate of 2.5 %–3.5 %). Strong temporal variability in the emissions was present, with the lowest emission rates occurring during the onset of the COVID-19 pandemic. Additionally, a synthetic model–data experiment performed using the Delaware tower network shows that the presence of intermittent sources is not a significant source of uncertainty in monthly quantification of the mean emission rate. In the Marcellus, this study finds the overall mean emission rate to be 19–28 Mg CH4 h−1 (gas-normalized loss rate of 0.30 %–0.45 %), with relative consistency in the emission rate over time. These totals align with aircraft top-down estimates from the same time periods. In both basins, the tower network was able to constrain monthly flux estimates within ±20 % uncertainty in the Delaware and ±24 % uncertainty in the Marcellus. The results from this study demonstrate the ability to monitor emissions continuously and detect changes in the emissions field, even in a basin with relatively low emissions and complex background conditions.

54 ENVIRONMENTAL SCIENCES↗

Differentiable hybrid neural network approach for enhancing reactor dynamics simulations

Reactor dynamics simulations provide essential insights into the time-dependent behavior of nuclear reactors under various operating conditions. However, high-fidelity simulations can be computationally intensive, requiring significant computational resources. Here, to address this challenge, this study employs a differentiable hybrid model that utilizes neural networks as a corrector to enhance the performance of a low-fidelity simulation, aligning its predictions with those of a high-fidelity simulation. Low-fidelity and high-fidelity simulations were obtained by adjusting the mesh size in the System Dynamics Analysis Tool. The differentiable hybrid model was trained in two approaches: time-step-wise and sequence-wise. It was then applied to simulate various transients in a molten salt reactor. Its performance was evaluated by comparing its responses to transients against those of the high-fidelity simulation. An additional approach was performed using a data-driven model to correct the low-fidelity simulation. In comparison, the differentiable hybrid model showed significant improvements in transient prediction, effectively addressing the limitations of the low-fidelity simulations. The results highlighted the robustness of the differentiable hybrid model in both training approaches. It delivered simulations that were at least 3.8 times faster than high-fidelity models. In the time-step-wise approach, it achieved at least a 39% improvement in accuracy. In the sequence-wise approach, it showed at least an 81% accuracy improvement over the full transient. This approach offers a promising path for improving computational efficiency without compromising accuracy in nuclear reactor simulations, making it suitable for real-time digital twin applications.

42 - ENGINEERING↗

Tribal Colleges and Universities/Advanced Manufacturing Network Initiative (Phase II) (Q1 FY2021 Progress Report)

The National Nuclear Security Agency (NNSA) initiated the Minority Serving Institution Partnership Plan (MSIPP) to 1) align investments in a university capacity and workforce development with the NNSA mission to develop the needed skills and talent for NNSA’s enduring technical workforce at the laboratories and production plants, and 2) to enhance research and education at under-represented colleges and universities. Out of this effort, MSIPP launched a new consortium in early FY17 focused on Tribal Colleges and Universities (TCUs) known as the Advanced Manufacturing Network Initiative (AMNI). This consortium has been extended for FY20 and FY21. The following report summarizes the status update during this quarter.

42 ENGINEERING↗

An Evaluation of Co-Simulation for Modeling Coupled Natural Gas and Electricity Networks

Reliance on natural gas for power generation has increased the coupling between gas and power networks. While this coupling can bring operational and economic benefits, it can also yield challenges, as the constraints in one system can impact the other. Co-simulation can capture the constraints and interactions between these systems, but so far, there has been limited comparison of co-simulation results to those of an integrated model. In this work, we develop a new co-simulation framework using the HELICS platform and the SAInt tool for modeling transient gas and AC optimal power flow. We evaluate this co-simulation framework against a fully integrated version of the SAInt power and gas simulators, thus providing a benchmarking of the co-simulation approach. We compare results across the two approaches for two test networks and a network representing the Belgian power and gas networks, testing both normal operating conditions and cases with compressor disruptions. In each of the cases tested, we find nearly identical results from the two approaches across various metrics of interest, such as nodal pressure, gas flow rates, and active power generation. This alignment suggests that co-simulation can yield comparable results to fully integrated models for modeling coupled gas and electricity networks.

03 NATURAL GAS↗