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Dynamic entity formed by protein and its hydration water

The interaction between protein and water plays a pivotal role in shaping the structure, dynamics, and function of biomacromolecules. A comprehensive understanding of this intricate interplay necessitates a systematic evaluation of interaction strength and its consequential impact on the dynamics of proteins and water across diverse protein systems. Despite numerous works on understanding the dynamics of water and proteins and the coupling between them, there are still unanswered questions. Here, we combine neutron scattering and isotope labeling to probe the dynamics of proteins and their hydration water in a variety of protein systems. We consider proteins of different structures and varying thermostability as well as proteins within living cells with distinct growth temperatures. Simultaneous characterization of protein and hydration water dynamics across diverse systems was achieved. Moreover, we performed water sorption isothermal measurements on three representative proteins to correlate the observed dynamics with the strength of the interaction energies governing each system. The experimental results underscore that proteins manifesting stronger attractive interactions with water display diffusionlike dynamics with higher flexibility upon hydration, concomitant with a reduced mobility in hydration water. Significantly, our findings suggest that, in fact, it is the interaction between protein and its hydration water that facilitates the transfer of mobility from water to protein, with stronger interactions correlating to greater protein flexibility and slower hydration water diffusion. Published by the American Physical Society 2024

Ye, Yongfeng (ORCID:0009000792374198)↗

Stakeholder-guided holistic, Adaptive Framework for enhancing community Energy Resilience (SAFER) (Final Technical Report)

The Stakeholder-guided holistic, Adaptive Framework for enhancing community Energy Resilience (SAFER) project advances resilience science and engineering by addressing challenges in rural Kansas communities where aging infrastructure, extreme weather, and socioeconomic disparities heighten vulnerability to energy disruptions. Traditional approaches often focus on technical performance while overlooking community concerns and priorities. SAFER responds by integrating community perspectives with advanced analytical frameworks to create a holistic model for measuring and improving resilience. Project objectives included developing novel resilience metrics, advancing modeling frameworks that capture interdependencies across infrastructures, and embedding community-centric indicators directly into planning processes for distributed energy resources. The key technical innovations included the creation of self-organizing map (SOM)-based indices for objective resilience quantification, hetero-functional graph theory (HFGT) models linking power, water, transportation, and community assets, and graph neural network (GNN) tools for identifying critical nodes in complex systems. Community-centric energy planning was demonstrated through optimal siting and sizing of (photovoltaic) PV and battery storage, ensuring resilience enhancements also addressed energy burden and energy insecurity. SAFER engaged community partners in Dodge City and Ford County through surveys, focus groups, and workshops, generating more than 600 responses that established baseline measures of energy burden, financial insecurity, and willingness-to-pay to avoid outages. This data, organized in terms of a community capitals framework, informed the development of weighted reliability indices that better reflect community costs than traditional utility metrics. SAFER’s GNN-based critical node identification framework identified expert-labelled critical nodes with over 99% accuracy, while also uncovering additional functionalities essential for proactive resilience planning. The project’s models demonstrated that optimal PV and storage deployment could improve resilience indices by over 11 percent, with dispatch strategies further enhancing outcomes, confirming both the technical effectiveness and economic feasibility of these approaches. Through its combined emphasis on rigorous modeling, community-focused planning, and community engagement, SAFER advances the state of resilience research while delivering direct benefits to rural communities. The project provides tools, guidelines, and resilience heatmaps that help utilities, local governments, and residents better anticipate disruptions, prioritize investments, and strengthen the capacity to withstand and recover from energy-related hazards. Furthermore, the developed HFG and GNN frameworks are designed for transferability, allowing them to be adapted for resilience planning in other communities with minimal retraining. This inductive learning capability provides a scalable pathway to extend the SAFER project’s impact. Thus, creating a foundation for a nationally applicable model of infrastructure resilience. Additionally, the HFG can also be extended to include other FEMA community lifelines.

14 SOLAR ENERGY↗

Broadband coherent anti-Stokes Raman scattering (BCARS) microscopy for rapid, label-free biological imaging

Broadband coherent anti-Stokes Raman scattering (BCARS) microscopy is a label-free imaging approach that provides detailed chemical information at high spatial resolution in a sample through nonlinear, coherent excitation of molecular vibrations and detection of Raman spectra. While its utility for biological imaging has been demonstrated, many aspects of this technique must mature before it can be widely adopted. One of the areas of required improvement is imaging speed—most BCARS implementations involve sample rastering, which limits imaging speed. Beam scanning can provide faster BCARS imaging but presents some unique challenges. Here, we describe a beam-scanning BCARS microscopy system that improves spatial resolution twofold and imaging speed by fivefold over a previous beam-scanning implementation. These enhancements were enabled by an improvement in supercontinuum power and the use of a sCMOS camera for its high data transfer rate and low read noise. Implementation of the sCMOS camera required correction for the significant pixel-to-pixel background and photon response nonuniformity. Here, we report on the method that we implemented for calibrating and correcting the pixel-to-pixel differences in sCMOS camera noise.

Dixon, Jessica Z. [Georgia Institute of Technology↗

Warming and elevated CO 2 promote rapid incorporation and degradation of plant‐derived organic matter in an ombrotrophic peatland

Abstract Rising temperatures have the potential to directly affect carbon cycling in peatlands by enhancing organic matter (OM) decomposition, contributing to the release of CO 2 and CH 4 to the atmosphere. In turn, increasing atmospheric CO 2 concentration may stimulate photosynthesis, potentially increasing plant litter inputs belowground and transferring carbon from the atmosphere into terrestrial ecosystems. Key questions remain about the magnitude and rate of these interacting and opposing environmental change drivers. Here, we assess the incorporation and degradation of plant‐ and microbe‐derived OM in an ombrotrophic peatland after 4 years of whole‐ecosystem warming (+0, +2.25, +4.5, +6.75 and +9°C) and two years of elevated CO 2 manipulation (500 ppm above ambient). We show that OM molecular composition was substantially altered in the aerobic acrotelm, highlighting the sensitivity of acrotelm carbon to rising temperatures and atmospheric CO 2 concentration. While warming accelerated OM decomposition under ambient CO 2 , new carbon incorporation into peat increased in warming × elevated CO 2 treatments for both plant‐ and microbe‐derived OM. Using the isotopic signature of the applied CO 2 enrichment as a label for recently photosynthesized OM, our data demonstrate that new plant inputs have been rapidly incorporated into peat carbon. Our results suggest that under current hydrological conditions, rising temperatures and atmospheric CO 2 levels will likely offset each other in boreal peatlands.

59 BASIC BIOLOGICAL SCIENCES↗

Particle track classification using quantum associative memory

Pattern recognition algorithms are commonly employed to simplify the challenging and necessary step of track reconstruction in sub-atomic physics experiments. Aiding in the discrimination of relevant interactions, pattern recognition seeks to accelerate track reconstruction by isolating signals of interest. In high collision rate experiments, such algorithms can be particularly crucial for determining whether to retain or discard information from a given interaction even before the data is transferred to tape. As data rates, detector resolution, noise, and inefficiencies increase, pattern recognition becomes more computationally challenging, motivating the development of higher efficiency algorithms and techniques. Quantum associative memory is an approach that seeks to exploits quantum mechanical phenomena to gain advantage in learning capacity, or the number of patterns that can be stored and accurately recalled. Here, we study quantum associative memory based on quantum annealing and apply it to the particle track classification. We focus on discrimination models based on Ising formulations of quantum associative memory model (QAMM) recall and quantum content-addressable memory (QCAM) recall. We characterize classification performance of these approaches as a function detector resolution, pattern library size, and detector inefficiencies, using the D-Wave 2000Q processor as a testbed. Discrimination criteria is set using both solution-state energy and classification labels embedded in solution states. We find that energy-based QAMM classification performs well in regimes of small pattern density and low detector inefficiency. In contrast, state-based QCAM achieves reasonably high accuracy recall for large pattern density and the greatest recall accuracy robustness to a variety of detector noise sources.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Coastal bacteria and protists assimilate viral carbon and nitrogen

Abstract Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements with single-cell resolution and flow cytometry, we quantified the flux of viral C and N into virovorous protists and bacteria and compared the loss of viruses due to abiotic vs biotic factors. We found that some protists can obtain most of their C and N requirements from viral particles and that viral C and N get incorporated into bacterial biomass. We found that bacteria and protists were responsible for increasing the daily removal rate of viruses by 33% to 85%, respectively, compared to abiotic processes alone. Our laboratory incubation experiments showed that abiotic processes removed roughly 50% of the viruses within a week, and adding biotic processes led to a removal of 83% to 91%. Our data provide direct evidence for the transfer of viral C and N back into the microbial loop through protist grazing and bacterial breakdown, representing a globally significant flux that needs to be investigated further to better understand and predictably model the C and N cycles of the hydrosphere.

59 BASIC BIOLOGICAL SCIENCES↗

Rays for Roots - Integrating Backscatter X-Ray Phenotyping, Modeling and Genetics to Increase Carbon Sequestration and Switchgrass Resource Use (Final Report)

To increase carbon (C) deposition in the soil and enhance crop resource use efficiency, characterizing root form and function is essential. Several root and soil traits have been linked to increased root-to-soil C transfer. Technology that could provide high-resolution characterization of many of these traits in field conditions would revolutionize our ability to study and understand how to increase C sequestration. In this effort, we developed an initial early prototype backscatter X-ray system for non-destructive imaging of root traits. We collected initial backscatter X-ray data in field and lab settings and carried out early analysis of these data. Along with this prototype, we also developed a suite of root phenotyping approaches including advanced minirhizotron image analysis, soil core imaging, and mesocosm imaging. Minirhizotron (MR) tubes are clear tubes inserted into the soil in the field and used to image roots and the surrounding soil. Our team has developed deep learning-based methods that can segment roots from soil that can learn from imprecise image-level labels. The ability to learn or fine-tune our deep learning algorithms from image-level labels allows easier and faster application of these approaches to new locations and new plant species. We have successfully implemented and applied our MR analysis approaches to thousands of switchgrass MR images collected across geographical regions. An advantage of MR imaging is the ability to collect root and soil images over time. Our soil core analysis included collecting hundreds of soil core samples from harvested switchgrass fields and imaging these cores with both X-ray CT and backscatter X-ray imaging. Initial segmentation approaches for the X-ray CT images of these cores have been developed and applied. An advantage of soil core analysis is that it preserves the three-dimensional structures of the roots and soil in the core collected. Our group also developed photogrammetry-based mesocosm root imaging and phenotyping approaches. In this approach, a plant was grown in a large mesocosm with a three-dimensional grid of thin supporting lines inserted throughout the mesocosm. After the plant (and, correspondingly, the root architecture is grown and established) the soil media was removed and the supporting lines approximately preserved the three-dimensional root architecture. Then, we applied photogrammetry techniques to create a three-dimensional digital representation of the root architecture for which we developed analysis algorithms including skeletonization. We carried out our phenotyping development with powerful switchgrass resources and physiological and agroecosystem modeling to deliver novel technology. This project contributes to multiple ARPA-E missions including reduction of foreign imports of energy, reduction of energy-related emissions including greenhouse gases, and ensuring that the United States maintains a technological lead in developing and deploying advanced energy technology. Furthermore, the developed tools could transform public and private plant breeding and could be broadly applicable to other crops and, potentially, other application areas. Our team of engineers, plant and soil scientists, and modelers i) developed an early prototype backscatter X-ray platform that can operate in field conditions; ii) developed a suite of root phenotyping and characterization approaches as described above; iii) developed and carried out plant biology and physiology roots studies and; iv) developed and implemented mechanistic physiological modeling.

42 ENGINEERING↗

Design and Characterization of the 162.5 MHz RF Component Layout for Fermilab's PIP-II Reference Line

The Proton Improvement Plan II (PIP-II) Reference Line at Fermi National Accelerator Laboratory distributes phase-stable radio-frequency (RF) signals throughout the accelerator. PIP-II requires stable timing and phase reference signals so its accelerating cavities transfer energy to the particle beam at the correct point in each RF cycle. The full system includes 162.5, 325, and 650 MHz sections corresponding to the frequency sections of the PIP-II Linac, with this project focusing on the 162.5 MHz section. The Reference Line must provide a phase stable source signal while responding to phase changes caused by environmental conditions or system drift. Its RF components will be mounted on aluminum heat plates inside a temperature controlled enclosure to further limit temperature-driven phase changes. To prepare the system for manufacture, the project reviewed component functions and dimensions, developed a computer-aided design (CAD) model, and arranged the hardware to support short cable paths, grounding, fastener access, and maintenance. Several full scale, three dimensional printed prototypes allowed the available components to be mounted and inspected. These fit checks revealed mechanical conflicts and guided revisions to component placement, countersink geometry, labeling, and plate thickness. Electrical characterization was also performed on selected RF hardware to compare its measured behavior with the performance metrics that were set for our design. Overall, the project produced a manufacturable 162.5 MHz layout, physical fit-check prototypes, and documented electrical measurements that support review before metal fabrication. The 325 and 650 MHz layouts remain future work because they require additional minor mechanical changes.

Subedi, Harsheet [Unlisted, US, CA] (ORCID:0009000↗

Automated defect identification in electroluminescence images of solar modules

Solar photovoltaic (PV) modules are susceptible to manufacturing defects, mishandling problems or extreme weather events that can limit energy production or cause early device failure. Trained professionals use electroluminescence (EL) images to identify defects in modules, however, field surveys or inline image acquisition can generate millions of EL images, which are infeasible to analyze by rote inspection. Here, we develop a rapid automatic computer vision pipeline (~0.5 seconds/module) to analyze EL images and identify defects including cracks, intra-cell defects, oxygen-induced defects, and solder disconnections. Defect identification is achieved with a machine learning model (Random Forest, ResNet models and YOLO) trained on 762 manually-labeled EL images of PV modules. We compare model performance on an imbalanced real-world validation set containing 134 EL images and determine that ResNet18 and YOLO are the optimal models; we next evaluated these models on a dedicated testing set (129 module images) with resulting macro F1 scores of 0.83 (ResNet18) and 0.78 (YOLO). Using a field EL survey of a PV power plant damaged in a vegetation fire, we analyze 18,954 EL images (2.4 million cells) and inspect the spatial distribution of defects on the solar modules. The results find increased frequency of ‘crack’, ‘solder’ and ‘intra-cell’ defects on the edges of the solar module closest to the ground after fire. We also find an abnormal increase of striation rings on cells which were assumed to be caused mainly in fabrication process. Our methods are published as open-source software. It can also be used to identify other kinds of defects or process different types of solar cells with minor modification on models by transfer learning.

14 SOLAR ENERGY↗

MnEdgeNet for accurate decomposition of mixed oxidation states for Mn XAS and EELS L2,3 edges without reference and calibration

Accurate decomposition of the mixed Mn oxidation states is highly important for characterizing the electronic structures, charge transfer and redox centers for electronic, and electrocatalytic and energy storage materials that contain Mn. Electron energy loss spectroscopy (EELS) and soft X-ray absorption spectroscopy (XAS) measurements of the Mn L2,3 edges are widely used for this purpose. To date, although the measurements of the Mn L2,3 edges are straightforward given the sample is prepared properly, an accurate decomposition of the mix valence states of Mn remains non-trivial. For both EELS and XAS, 2+, 3+, and 4+ reference spectra need to be taken on the same instrument/beamline and preferably in the same experimental session because the instrumental resolution and the energy axis offset could vary from one session to another. To circumvent this hurdle, in this study, we adopted a deep learning approach and developed a calibration-free and reference-free method to decompose the oxidation state of Mn L2,3 edges for both EELS and XAS. A deep learning regression model is trained to accurately predict the composition of the mix valence state of Mn. To synthesize physics-informed and ground-truth labeled training datasets, we created a forward model that takes into account plural scattering, instrumentation broadening, noise, and energy axis offset. With that, we created a 1.2 million-spectrum database with 1-by-3 oxidation state composition ground truth vectors. The library includes a sufficient variety of data including both EELS and XAS spectra. By training on this large database, our convolutional neural network achieves 85% accuracy on the validation dataset. We tested the model and found it is robust against noise (down to PSNR of 10) and plural scattering (up to t/λ = 1). We further validated the model against spectral data that were not used in training. In particular, the model shows high accuracy and high sensitivity for the decomposition of Mn 3 O 4 , MnO, Mn 2 O 3 , and MnO 2 . The accurate decomposition of Mn 3 O 4 experimental data shows the model is quantitatively correct and can be deployed for real experimental data. Our model will not only be a valuable tool to researchers and material scientists but also can assist experienced electron microscopists and synchrotron scientists in the automated analysis of Mn L edge data.

25 ENERGY STORAGE↗

AMF diversity promotes plant community phosphorus acquisition and reduces carbon costs per unit of phosphorus

Plants may benefit from more diverse communities of arbuscular mycorrhizal fungi (AMF), as functional complementarity of AMF may allow for increased resource acquisition, and because a high AMF diversity increases the probability of plants matching with an optimal AMF symbiont. Here, we repeatedly radiolabeled plants and AMF in the glasshouse over c. 9 months to test how AMF species richness (SR) influences the exchange of plant C ( 14 C) for AMF P ( 32 P & 33 P) and resulting shoot nutrients and mass from a biodiversity–ecosystem functioning perspective. Plant P acquisition via AMF increased with sown AMF SR, as did shoot biomass, shoot P, and shoot N. The rate of plant C transferred to AMF for this P (C:P) decreased with sown AMF SR. Plants in plant communities benefit from inoculation with a variety of AMF species via more favorable resource exchange. Surprisingly, this effect did not differ among functionally distinct communities comprised entirely of either legumes, nonlegume forbs, or C3 grasses.

arbuscular mycorrhizal fungi↗

Mechanism for Acetone and Crotonaldehyde Production during Steam Reforming of Ethanol over La 0.7 Sr 0.3 MnO 3–x Perovskite: Evidence for a Shared C4 Aldol Addition Intermediate

Here a mechanistic study was conducted on the catalytic conversion of ethanol over La 0.7 Sr 0.3 MnO 3–x perovskite catalysts in the presence and absence of water. The study sought insights into the path of C–C coupling toward acetone and crotonaldehyde and also into clarifying whether the lack of previous reports of C–C coupling over La 0.7 Sr 0.3 MnO 3–x (100) could be due to a “pressure gap”. Several types of experiments were performed at 400–800 K: flow experiments with a torr range reactant gas flown over La 0.7 Sr 0.3 MnO 3–x powders; ultra-high vacuum experiments with continuous gas exposures to a La 0.7 Sr 0.3 MnO 3–x (100) single-crystal sample; and torr range continuous gas exposures to a La 0.7 Sr 0.3 MnO 3–x (100) single-crystal sample. When ethanol and water were flown over La 0.7 Sr 0.3 MnO 3–x powders at 400–800 K, the products detected were ethene, acetaldehyde, acetone, crotonaldehyde, CO, CO 2 , and H 2 . Acetone was catalytically produced over both the La 0.7 Sr 0.3 MnO 3–x powder and the La 0.7 Sr 0.3 MnO 3–x (100) single-crystal sample at temperatures of 700–800 K when reaction conditions were on the order of 1 Torr of reactant gas and with an excess of water relative to ethanol (1 ethanol/9 water). Isotopic labeling with deuterium was used to gain insights into the C–C coupling reaction mechanism and paths in species with three and four carbons (C 3 and C 4 species). Additionally, steady-state isotopic transient kinetic analysis (SSITKA) experiments + simulations using carbon labeling of the ethanol feed were performed. Three mechanistic paths were considered for the C–C coupling step: the first two paths, A and B, involve coupling between two intermediates which are both in oxygen vacancies; and the third path, C, involves coupling between one intermediate in an oxygen vacancy and one intermediate outside of an oxygen vacancy. The results suggest that the dominant path to the C 3 product, acetone, depends on the conditions. The less active path (attributed to path A or B) occurs at 600–700 K and involves coupling between two irreversibly bound species. The more active path (attributed to path C) requires an excess of water, becomes dominant at 600–800 K, and involves coupling between one irreversibly bound species and one reversibly bound species. Based on these various observations from experiments and simulations, an elementary step is proposed for acetone formation involving a previously unreported C 4 transition state that is formed after aldol addition. Density functional theory calculations were performed based on this hypothesis, and it confirmed that this specific and previously unreported aldol addition path to acetone does exist and that this path consistent with the experimental data. In this path, C–C formation occurs to create a C 4 intermediate that is bound to an oxygen vacancy, then a hydrogen transfer with C–C bond breaking occurs that results in the production of the acetone molecule. The proposed mechanism is also consistent with the experimental observation that acetone formation has a greater than first-order dependence on the water vapor pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive Cybersecurity for Distributed Energy Resources (AdCyDER): Online Reinforcement Learning with Stackelberg-Optimized Defenses — Pipeline Architecture, Evaluation Methodology, and Findings from a Synthetic-Data Evaluation

This report documents the design and evaluation of an integrated online-learning pipeline developed within the AdCyDER project for Distributed Energy Resource (DER) cybersecurity. The pipeline couples a Reinforcement Learning (RL) attack classifier — which produces an attack-type probability distribution — with a Stackelberg game-theoretic (GT) defense selector that consumes those distributions alongside SME-encoded priors over (defense, attack) effectiveness pairings and perdefense costs to choose grid-health-preserving defenses. The objective is not attack classification per se but production of distributions that drive effective defense selection through the Stackelberg layer, learned from delayed grid-health feedback rather than labeled attack data. AdCyDER as a whole is broader than the work presented here; this report covers the specific RL/GT loop integration and its evaluation. We present the integrated pipeline (SCADA telemetry with Fronius inverter physics, Suricata IDS, time-windowed aggregation, per-facility LSTM classifier, Stackelberg optimizer, OpenC2 actuators), an experimental campaign of 28 eight-hour iterations across three baseline modes, and a pipeline-ordered diagnostic protocol. The protocol identifies two distinct failure modes within the loop: paired supervised ceilings on the same features establish that the deployed online RL classifier (macro F1 ≈ 0.07) sits at least 4.7× below a same-architecture supervised LSTM (≈ 0.34) and 10–11× below a linear feature-signal ceiling (≈ 0.70–0.79 depending on per-facility isolation), localizing the dominant failure to the training procedure; and the reward signal driving online updates carries weak directional coupling with classifier correctness in the methodology-expected direction (multi-lens convergent: top-decile P(true) records produce more frequent state changes and slightly larger improvements, top-vs-bot Cohen’s 𝑑 ≈ −0.19), but at effect magnitudes too small to drive gradient-based learning at the campaign sample size. The original learning hypothesis is not supported by the data. The primary contributions are the diagnostic methodology — proposed as a transferable falsification protocol for online RL/GT defense pipelines learning from delayed environmental reward — and the open, reproducible experimental infrastructure. We outline reward reformulation as the highest-priority aspirational next step given the underpowered-but-aligned Q6 reading, with hardware-in-the-loop evaluation as the broadest scope-expansion option.

Blakely, Benjamin [Argonne National Laboratory (AN↗

Bioinspired Activation of N 2 on Asymmetrical Coordinated Fe Grafted 1T MoS 2 at Room Temperature

Inspired by the nitrogen fixation process on MoFe nitrogenase, asymmetrical coordinated Fe grafted onto 1T MoS 2 were successfully synthesized. The unique electron -rich structure with asymmetrical coordination made the 1T Fe 0.1 Mo 0.9 S 2 layered material actively react with water and dinitrogen at room temperature and atmosphere pressure. Subsequently, ammonia can be produced with a yield of 800 pmol (NH 4 + ) g -1 (12.5% yield in mole). The activation, fixation and reduction of dinitrogen were confirmed by isotopically labeled experiments. The location and the specific coordination environment of grafted Fe in Fe-Mo-S were further determined by X-ray absorption spectroscopy analysis. Our work demonstrates that the nitrogen fixation and reduction for ammonia at room temperature without any chemical and electrochemical assistance is distinctly different from traditional bionic -inspired nitrogen fixation process. The mechanism of the activation and reduction of N 2 was further investigated by density functional theory calculation and Raman spectra. Compared with 1T MoS 2 , the enriched electron nature and asymmetrical coordination of Fe in Fe-Mo-S materials play a critical role in the bioinspired activation of N 2 at ambient condition.

1T MoS2↗

Synergistic Integration of Chemo-Resistive and SERS Sensing for Label-Free Multiplex Gas Detection

Practical sensing applications such as real-time safety alerts and clinical diagnoses require sensor devices to differentiate between various target molecules with high sensitivity and selectivity, yet conventional devices such as oxide-based chemo-resistive sensors and metal-based surface-enhanced Raman spectroscopy (SERS) sensors usually do not satisfy such requirements. In this report a label-free, chemo-resistive/SERS multimodal sensor based on a systematically assembled 3D cross-point multifunctional nanoarchitecture (3D-CMA), which has unusually strong enhancements in both “chemo-resistive” and “SERS” sensing characteristics is introduced. 3D-CMA combines several sensing mechanisms and sensing elements via 3D integration of semiconducting SnO 2 nanowire frameworks and dual-functioning Au metallic nanoparticles. It is shown that the multimodal sensor can successfully estimate mixed-gas compositions selectively and quantitatively at the sub-100 ppm level, even for mixtures of gaseous aromatic compounds (nitrobenzene and toluene) with very similar molecular structures. This is enabled by combined chemo-resistive and SERS multimodal sensing providing complementary information.

36 MATERIALS SCIENCE↗

NSFnets (Navier-Stokes flow nets): Physics-informed neural networks for the incompressible Navier-Stokes equations

In the last 50 years there has been a tremendous progress in solving numerically the Navier-Stokes equations using finite differences, finite elements, spectral, and even meshless methods. Yet, in many real cases, we still cannot incorporate seamlessly (multi-fidelity) data into existing algorithms, and for industrial-complexity applications the mesh generation is time consuming and still an art. Moreover, solving ill-posed problems (e.g., lacking boundary conditions) or inverse problems is often prohibitively expensive and requires different formulations and new computer codes. Here, we employ physics-informed neural networks (PINNs), encoding the governing equations directly into the deep neural network via automatic differentiation, to overcome some of the aforementioned limitations for simulating incompressible laminar and turbulent flows. We develop the Navier-Stokes flow nets (NSFnets) by considering two different mathematical formulations of the Navier-Stokes equations: the velocity-pressure (VP) formulation and the vorticity-velocity (VV) formulation. Since this is a new approach, we first select some standard benchmark problems to assess the accuracy, convergence rate, computational cost and flexibility of NSFnets; analytical solutions and direct numerical simulation (DNS) databases provide proper initial and boundary conditions for the NSFnet simulations. The spatial and temporal coordinates are the inputs of the NSFnets, while the instantaneous velocity and pressure fields are the outputs for the VP-NSFnet, and the instantaneous velocity and vorticity fields are the outputs for the VV-NSFnet. This is unsupervised learning and, hence, no labeled data are required beyond boundary and initial conditions and the fluid properties. The residuals of the VP or VV governing equations, together with the initial and boundary conditions, are embedded into the loss function of the NSFnets. No data is provided for the pressure to the VP-NSFnet, which is a hidden state and is obtained via the incompressibility constraint without extra computational cost. Unlike the traditional numerical methods, NSFnets inherit the properties of neural networks (NNs), hence the total error is composed of the approximation, the optimization, and the generalization errors. Here, we empirically attempt to quantify these errors by varying the sampling (“residual”) points, the iterative solvers, and the size of the NN architecture. For the laminar flow solutions, we show that both the VP and the VV formulations are comparable in accuracy but their best performance corresponds to different NN architectures. The initial convergence rate is fast but the error eventually saturates to a plateau due to the dominance of the optimization error. For the turbulent channel flow, we show that NSFnets can sustain turbulence at , but due to expensive training we only consider part of the channel domain and enforce velocity boundary conditions on the subdomain boundaries provided by the DNS data base. We also perform a systematic study on the weights used in the loss function for balancing the data and physics components, and investigate a new way of computing the weights dynamically to accelerate training and enhance accuracy. In the last part, we demonstrate how NSFnets should be used in practice, namely for ill-posed problems with incomplete or noisy boundary conditions as well as for inverse problems. We obtain reasonably accurate solutions for such cases as well without the need to change the NSFnets and at the same computational cost as in the forward well-posed problems. As a result, we also present a simple example of transfer learning that will aid in accelerating the training of NSFnets for different parameter settings.

97 MATHEMATICS AND COMPUTING↗

CyBERT: Cybersecurity Claim Classification by Fine-Tuning the BERT Language Model

We introduce CyBERT, a cybersecurity feature claims classifier based on bidirectional encoder representations from transformers and a key component in our semi-automated cybersecurity vetting for industrial control systems (ICS). To train CyBERT, we created a corpus of labeled sequences from ICS device documentation collected across a wide range of vendors and devices. This corpus provides the foundation for fine-tuning BERT’s language model, including a prediction-guided relabeling process. We propose an approach to obtain optimal hyperparameters, including the learning rate, the number of dense layers, and their configuration, to increase the accuracy of our classifier. Fine-tuning all hyperparameters of the resulting model led to an increase in classification accuracy from 76% obtained with BertForSequenceClassification’s original architecture to 94.4% obtained with CyBERT. Furthermore, we evaluated CyBERT for the impact of randomness in the initialization, training, and data-sampling phases. CyBERT demonstrated a standard deviation of ±0.6% during validation across 100 random seed values. Finally, we also compared the performance of CyBERT to other well-established language models including GPT2, ULMFiT, and ELMo, as well as neural network models such as CNN, LSTM, and BiLSTM. The results showed that CyBERT outperforms these models on the validation accuracy and the F1 score, validating CyBERT’s robustness and accuracy as a cybersecurity feature claims classifier.

97 MATHEMATICS AND COMPUTING↗

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗