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At least 37 records · Page 2

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Integration of DER Adoption Forecasting into Distribution Planning: Cooperative Research and Development Final Report, CRADA Number CRD-11-00430 (Project H)

The objective of this project is to improve distributed energy resources (DER) technology, time, and locational impact analysis by incorporating customer adoption intentions and preferences into distribution planning and operations. The National Renewable Energy Laboratory (NREL) shall collaborate with EPRI staff to contribute to the development of methodology, literature review, analysis, and write-up for two sections of a report "Identification and Overview of Methods for Mapping DER Adoption Forecasts” and “Comparative Analysis of Methods for Mapping DER Adoption Forecasts."

14 SOLAR ENERGY↗

Discovery of segmented Fermi surface induced by Cooper pair momentum

Imaging a peculiar Fermi surface Running a current through a superconductor can cause the superconducting gap to close on a section of the Fermi surface. However, observing this segmented Fermi surface directly is tricky. To do so, Zhu et al . worked with a thin film of the topological insulator bismuth telluride placed on top of superconducting niobium diselenide. A small applied magnetic field caused a screening current, which in turn led to a segmented Fermi surface in the topological insulator layer. Using a scanning tunneling microscope, the researchers were able to map out this Fermi surface. —JS

Science & Technology - Other Topics↗

The Role of Cooperative Interactions Among Surfaces, Solvents, and Reactive Intermediates on Catalysis at Liquid–Solid Interfaces (Final Report DE-SC0020224)

This project established quantitative links between inner‑sphere chemistry (active metal identity, coordination, and zeolite topology) and outer‑sphere organization (solvent identity, hydrogen‑bond networks, and pore condensation) that govern rates, activation barriers, and selectivities for alkene epoxidation and epoxide ring‑opening at solid–liquid and quasi‑liquid–solid interfaces. We deconvoluted contributions from covalent interactions at active sites and noncovalent, solvent‑mediated interactions within pores by pairing well‑defined metal substituted zeolites with controlled solvent environments. We then mapped those contributions onto measurable kinetics (ΔH‡, ΔS‡), adsorption thermodynamics (ITC), and in situ spectroscopy. The transferrable outcomes include a set of design rules that include the following understandings. First, tune silanol ((SiOH)x) density and pore topology to organize solvent networks that selectively stabilize transition states. Second, exploit activity‑coefficient‑normalized rates and adsorption– barrier correlations to diagnose when solvent reorganization rather than surface chemistry limits performance. Third, use partial pore condensation (e.g., acetonitrile, water but also generalizable to other solvents) to elicit liquid‑like stabilization effects even in nominally vapor‑phase reactors. Collectively, these results provide strategies to increase epoxidation rates, improve oxidant utilization (i.e., selectivities), and steer regioselectivity in zeolite‑based catalytic processes relevant to sustainable oxidation chemistry. These outcomes should be transferable to other classes of reactions that proceed in microporous materials and under confinement provided by organized solvents (e.g., electrochemical double layers).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bolometric Superconducting Optical Nanoscopy (BOSON)

Superconducting transition-edge sensors are renowned for their extraordinary photon sensitivity and energy resolution, finding applications spanning quantum information, astronomy, and nanophotonics. Here, we report the development of bolometric superconducting optical nanoscopy (BOSON), a novel platform that integrates bolometric detection at the superconducting transition edges with near-field optical techniques. BOSON enables the mapping of photoinduced changes in superconductivity with unprecedented spatial resolution and photon sensitivity. By incorporating BOSON with low-dimensional materials, we achieved polariton imaging at nanowatt excitation levels—at least 4 orders of magnitude lower than the power typically required in prior near-field nanoscopy experiments. Our findings highlight the potential for BOSON to advance scanning-probe-based optical platforms to enable the detection of photons, polaritons, and Cooper pair dynamics at the nanoscale. This paves the way for quantum sensing applications using single-polariton detection and can offer deeper insights into quasiparticle dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

SARS-CoV2 Docking Dataset

Description: Small-molecule conformations and docking scores for 1.4 billion molecules docked against 6 protein targets from SARS-CoV2: MPro 5R84, MPro 6WQF, NSP15 6WLC, PLPro 7JIR, Spike 6M0J, and a hand-optimized model of the RNA-dependent RNA polymerase. Docking was carried out using the Autodock-GPU program performing 20 independent structure minimizations per dock - saving 3 results per molecule. Scores reported include the Autodock free energy estimate as well as RF3 and VS-DUD-E v2 machine-learned rescoring models. Protein structure files and maps in the format input to Autodock-GPU are included. Literature Ref: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19, J. Chem. Inf. Model. 2020, 60(12): 5832–5852.

36 MATERIALS SCIENCE↗

The Synchronic Web

The Synchronic Web is a distributed network for securing data provenance on the World Wide Web. By enabling clients around the world to freely commit digital information into a single shared view of history, it provides a foundational basis of truth on which to build decentralized and scalable trust across the Internet. Its core cryptographical capability allows mutually distrusting parties to create and verify statements of the following form: “I commit to this information—and only this information—at this moment in time.” The backbone of the Synchronic Web infrastructure is a simple, small, and semantic-free blockchain that is accessible to any Internet-enabled entity. The infrastructure is maintained by a permissioned network of well-known servers, called notaries, and accessed by a permissionless group of clients, called journals. Through an evolving stack of flexible and composable semantic specifications, the parties cooperate to generate synchronic commitments over arbitrary data. When integrated with existing infrastructures, adapted to diverse domains, and scaled across the breadth of cyberspace, the Synchronic Web provides a ubiquitous mechanism to lock the world’s data into unique points in discrete time and digital space. This document provides a technical description of the core Synchronic Web system. The distinguishing innovation in our design—and the enabling mechanism behind the model—is the novel use of verifiable maps to place authenticated content into canonically defined locations off-chain. While concrete specifications and software implementations of the Synchronic Web continue to evolve, the information covered in the body of this document should remain stable. We aim to present this information clearly and concisely for technical non-experts to understand the essential functionality and value proposition of the network. In the interest of promoting discourse, we take some liberty in projecting the potential implications of the new model.

97 MATHEMATICS AND COMPUTING↗

Watching the Grand Ethiopian Renaissance Dam from a distance: Implications for sustainable water management of the Nile water

Increased demands for sustainable water and energy resources in densely populated basins have led to the construction of dams, which impound waters in artificial reservoirs. In many cases, scarce field data led to the development of models that underestimated the seepage losses from reservoirs and ignored the role of extensive fault networks as preferred pathways for groundwater flow. We adopt an integrated approach (remote sensing, hydrologic modeling, and field observations) to assess the magnitude and nature of seepage from such systems using the Grand Ethiopian Renaissance Dam (GERD), Africa's largest hydropower project, as a test site. The dam was constructed on the Blue Nile within steep, highly fractured, and weathered terrain in the western Ethiopian Highlands. The GERD Gravity Recovery and Climate Experiment Terrestrial Water Storage (GRACETWS), seasonal peak difference product, reveals significant mass accumulation (43 ± 5 BCM) in the reservoir and seepage in its surroundings with progressive south-southwest mass migration along mapped structures between 2019 and 2022. Seepage, but not a decrease in inflow or increase in outflow, could explain, at least in part, the observed drop in the reservoir's water level and volume following each of the three fillings. Using mass balance calculations and GRACETWS observations, we estimate significant seepage (19.8 ± 6 BCM) comparable to the reservoir's impounded waters (19.9 ± 1.2 BCM). Investigating and addressing the seepage from the GERD will ensure sustainable development and promote regional cooperation; overlooking the seepage would compromise hydrological modeling efforts on the Nile Basin and misinform ongoing negotiations on the Nile water management.

GRACE and GRACE-FO↗

Correlation of Injury Simulation with Clinical Assessment of Traumatic Brain Injury

This report contains a summary of our efforts to correlate head injury simulations predicting intracranial fluid cavitation with clinical assessments of brain injury from blunt impact to the head. Magnetic resonance imaging (MRI) data, collected on traumatic brain injury (TBI) subjects by researchers at the MIND Institute of New Mexico, was acquired for the current work. Specific blunt impact TBI case histories were selected from the TBI data for further study and possible correlation with simulation. Both group and single-subject case histories were examined. We found one single-subject case that was particularly suited for correlation with simulation. Diffusion tensor image (DTI) analysis of the TBI subject identified white matter regions within the brain displaying reductions in fractional anisotropy (FA), an indicator of local damage to the white matter axonal structures. Analysis of functional magnetic resonance image (fMRI) data collected on this individual identified localized regions of the brain displaying hypoactivity, another indicator of brain injury. We conducted high fidelity simulations of head impact experienced by the TBI subject using the Sandia head-neck-torso model and the shock physics computer code CTH. Intracranial fluid cavitation predictions were compared with maps of DTI fractional anisotropy and fMRI hypoactivity to assess whether a possible correlation exists. The ultimate goal of this work is to assess whether one can correlate simulation predictions of intracranial fluid cavitation with the brain injured sites identified by the fMRI and DTI analyses. The outcome of this effort is described in this report.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Hierarchical Self-Assembly of Carbon Dots into High-Aspect-Ratio Nanowires

Here, we report a spontaneous and hierarchical self-assembly mechanism of carbon dots prepared from citric acid and urea into nanowire structures with large aspect ratios (>50). Scattering-type scanning near-field optical microscopy (s-SNOM) with broadly tunable mid-IR excitation was used to interrogate details of the self-assembly process by generating nanoscopic chemical maps of local wire morphology and composition. s-SNOM images capture the evolution of wire formation and the complex interplay between different chemical constituents directing assembly over the nano- to microscopic length scales. We propose that residual citrate promotes tautomerization of melamine surface functionalities to produce supramolecular shape synthons comprised of melamine-cyanurate adducts capable of forming long-range and highly directional hydrogen-bonding networks. This intrinsic, heterogeneity-driven self-assembly mechanism reflects synergistic combinations of high chemical specificity and long-range cooperativity that may be harnessed to reproducibly fabricate functional structures on arbitrary surfaces.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

A Play-Based Exploration of CO 2 Storage in the Illinois Basin: Development and Application of the Play-Based Exploration Workflow

This report documents the workflow developed and applied for a play-based exploration (PBE) of carbon capture and storage (CCS) potential in the Illinois Basin, conducted under U.S. Department of Energy Cooperative Agreement DE-FE0032366. The project was led by the Illinois State Geological Survey (ISGS) at the University of Illinois Urbana-Champaign in collaboration with Visage Energy. The goal of this workflow is to identify locations where subsurface, surface, and societal conditions align to support safe and effective geologic CO 2 storage. To achieve this, the project team developed a systematic, seven-step workflow for conducting play-based exploration: (1) defining play elements, (2) collecting data, (3) constructing a geodatabase, (4) defining suitability criteria, (5) conducting suitability mapping, (6) generating Common Risk Segment (CRS) maps, and (7) creating composite play maps. The workflow is designed to be repeatable and adaptable for CCS assessments in other regions or for alternative subsurface energy applications such as hydrogen or natural gas storage.

01 COAL, LIGNITE, AND PEAT↗

Distinguishing finite-momentum superconducting pairing states with two-electron photoemission spectroscopy

Here, we show theoretically that double photoemission (2e-ARPES) may be used to identify the pairing state in superconductors in which the Cooper pairs have a nonzero center-of-mass momentum, q cm . We theoretically evaluate the 2e-ARPES counting rate P (2) for the cases of a d x 2 -y 2 -wave superconductor, a pair-density-wave (PDW) phase, and a Fulde-Ferrel-Larkin-Ovchinnikov (FFLO) phase. We show that P (2) provides direct insight into the center-of-mass momentum and spin state of the superconducting condensate, and thus can distinguish between these three different superconducting pairing states. In addition, P (2) can be used to map out the momentum dependence of the superconducting order parameter. Our results identify 2e-ARPES as an ideal tool for identifying and probing q cm ≠ 0 superconducting pairing states in superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DRIPS: Dynamic Rebalancing of Pipelined Streaming Applications on CGRAs

Coarse-grained reconfigurable arrays (CGRAs) provide higher flexibility than application-specific integrated circuits (ASICs) and higher efficiency than fine-grained reconfigurable devices such as Field Programmable Gate Arrays (FPGAs). However, CGRAs are generally designed to support offloading of a single kernel. While their design, based on communicating functional units, appears to naturally suit data streaming applications composed of multiple cooperating kernels, current approaches only statically partition the resources across application kernels. However, emerging streaming applications at the edge (scientific instruments, sensor networks, network processing) perform much more than digital signal processing and often are data and input dependent. This leads to extremely variable kernel execution times, severely impacting the throughput of the entire pipeline if resources are only statically allocated. Therefore, in this paper, we propose DRIPS — a coarse-grained, dynamically, and partially reconfigurable array for data-dependent streaming applications. We present a unified compiler framework to facilitate the mapping of a given streaming application onto the DRIPS CGRA architecture. The experimental results show that DRIPS achieves an average throughput improvement of 1.46$\times$ across a set of representative applications over a statically partitioned solution. The additional area overhead to enable dynamic rebalancing consumes 16.34% of the entire area for a 5x5 CGRA prototype.

Tan, Cheng↗

Free-moving Quantitative Gamma-ray Imaging

The ability to map and estimate the activity of radiological source distributions in unknown three-dimensional environments has applications in the prevention and response to radiological accidents or threats as well as the enforcement and verification of international nuclear non-proliferation agreements. Such a capability requires well-characterized detector response functions, accurate time-dependent detector position and orientation data, a digitized representation of the surrounding 3D environment, and appropriate image reconstruction and uncertainty quantification methods. We have previously demonstrated 3D mapping of gamma-ray emitters with free-moving detector systems on a relative intensity scale using a technique called Scene Data Fusion (SDF). Here we characterize the detector response of a multi-element gamma-ray imaging system using experimentally benchmarked Monte Carlo simulations and perform 3D mapping on an absolute intensity scale. We present experimental reconstruction results from hand-carried and airborne measurements with point-like and distributed sources in known configurations, demonstrating quantitative SDF in complex 3D environments.

47 OTHER INSTRUMENTATION↗

Grain boundary softening from stress assisted helium cavity coalescence in ultrafine-grained tungsten

The formation of helium cavities in coarse-grained materials produces hardening proportional to the number density and size of the cavities and due to the interaction of dislocations with intragranular helium defects. In nanostructured metals containing a high density of interfacial sinks, preferential cavity formation in the grain boundaries instead produces softening that is often attributed to enhanced interfacial plasticity. Here, employing two grades of ultrafine-grained tungsten, we explore this effect using targeted implantation studies to map cavity evolution as a function of the irradiation conditions and quantify its impact on the mechanical response through nanoindentation. Softening is reported at implantation temperatures above the threshold for preferential grain boundary cavity formation but at a sufficiently low fluence prior to the growth of intragranular cavities. Collective changes in the mean cavity size, density, and morphology beneath a residual impression on an implanted surface indicate that cavity coalescence accompanied the reduction in hardness. Complementary atomistic simulations demonstrate that, in tungsten grain structures exhibiting softening, grain boundary bubble coalescence is driven by stress concentrations that further act to localize strain in the grain boundaries through cooperative deformation processes involving local atomic shuffling and sliding, dislocation emission, and even the nucleation of unstable twinning events.

36 MATERIALS SCIENCE↗

Multiomics and deep learning dissect regulatory syntax in human development

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity. We identify ‘hard’ syntactic rules requiring precise motif spacing and orientation, ‘soft’ rules allowing flexible motif arrangements, and ubiquitous motifs inhibiting accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell-type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

59 BASIC BIOLOGICAL SCIENCES↗

Invariant Forms of Dissolution Fingers

Dissolution of fractured and porous media introduces a positive feedback between fluid flow and reactant transport, leading to the emergence of pronounced, fingerlike channels. We investigate the formation of these structures using a microfluidic Hele-Shaw cell with a soluble bottom. Our experiments show that the shape of dissolution fingers is invariant and reveals itself over time as the fingers extend into the system. Here, by combining reactive-transport theory and conformal mapping techniques we derive these invariant forms. We relate these results to natural dissolution fingers in karst landscapes, and illustrate how to determine the groundwater flow rate responsible for their formation based on the finger shape.

Flows in porous media↗

Improving Cyber Situational Understanding

Effective cybersecurity operations require the ability to analyze large amounts of information to assess security risks and formulate defensive strategies against adversaries. This has become more complex in recent years as the sprawl and interconnectivity of devices grows through implementation of virtualization, cloud computing, and Internet of Things (IoT). The amount of data and analysis required for effective cybersecurity command and control decisions far exceeds humans’ capacity to perform manually. We characterize the analysis problem as cyber situational understanding. The research presented to improve cyber situational understanding focuses on vulnerability analysis and threat intelligence. Regarding vulnerabilities, entities must analyze and plan work for between thousands and tens of thousands of software vulnerabilities annually. Entities heavily use network firewalls to limit vulnerability exposure. As a result, some of these vulnerabilities permit exposure to adversarial exploitation, whereas others are inaccessible and therefore present negligible risk of exploitation. Distinguishing between high and low risk software vulnerabilities requires a deep understanding of the vulnerability, network firewall protection, and characteristics of the targeted device. This problem is solved by extracting network service features from vulnerability data features using both machine-learning and natural language processing. Then, the network firewall topology is parsed to determine which vulnerabilities are reachable by adversaries. Ultimately, a state-based safety analysis ascertains which vulnerabilities are unsafe. A related vulnerability analysis problem occurs in cybersecurity operations when associating an entity’s hardware and software assets to public vulnerability databases. Assets often reveal hardware and software through installation artifacts and network service identification, and entities store these artifacts in inventory databases. However, software and hardware vendors apply a standard Common Platform Enumeration (CPE) naming convention when publicly reporting vulnerabilities. Associating these two datasets often requires many hours to days of manual inspection. The proposed solution automates the mapping approach of human analysts using fuzzy matching techniques, natural language processing, and, ultimately, machine learning to present a small set of recommendations for mapping the two datasets. The result significantly reduces human analysis time and reduces the occurrence of false positives in vulnerability notifications. Finally, cyber threat intelligence (CTI) requires associating cyber observable artifacts, such as IP addresses, URIs, and file hashes, with cyber threat tactics, techniques, and procedures. Unfortunately, most CTI data is compartmentalized across multiple organizations and cannot be shared due to the legal and reputational risk with cyber threat being associated with the entity. The approach to solving this problem inovlves using a distributed ledger with anonymous token spending and authentication. This allows a consortium of semi-trusted entities to share the workload of curating CTI for a threat sharing community’s cooperative benefit.

Huff, Philip↗