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At least 145 records · Page 8

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of “undruggability” for an intracellular target. Structural studies reveal extensive protein–WDB002 and protein–protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise “undruggable” targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

59 BASIC BIOLOGICAL SCIENCES↗

STM/S Grid LDOS Data and Analysis Code for Deciphering Majorana Zero Modes in Topological Superconductor

This dataset provides raw millikelvin scanning tunneling microscopy/spectroscopy (STM/S) grid spectroscopy data and Python analysis scripts supporting the manuscript “Deciphering Majorana Zero Modes in Topological Superconductor FeTe0.55Se0.45 with Machine-Learning-Assisted Spectral Deconvolution.” The dataset includes a raw grid spectroscopy file acquired on FeTe0.55Se0.45 at 40 mK under magnetic field, together with Python/Jupytext analysis scripts used for STM/S data processing, visualization, spectral deconvolution, Lorentzian peak fitting, feature extraction, machine-learning-assisted clustering, and figure generation. These files support the analysis of vortex-core local density of states and the identification of zero-bias-peak-related spectral components from complex in-gap states. The dataset is intended to provide a citable archival record of the data and analysis code associated with the published manuscript and to support transparency and reproducibility of the reported STM/S and machine-learning workflow.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The National Grid Project: A system overview

The National Grid Project (NGP) is a comprehensive numerical grid generation software system that is being developed at the National Science Foundation (NSF) Engineering Research Center (ERC) for Computational Field Simulation (CFS) at Mississippi State University (MSU). NGP is supported by a coalition of U.S. industries and federal laboratories. The objective of the NGP is to significantly decrease the amount of time it takes to generate a numerical grid for complex geometries and to increase the quality of these grids to enable computational field simulations for applications in industry. A geometric configuration can be discretized into grids (or meshes) that have two fundamental forms: structured and unstructured. Structured grids are formed by intersecting curvilinear coordinate lines and are composed of quadrilateral (2D) and hexahedral (3D) logically rectangular cells. The connectivity of a structured grid provides for trivial identification of neighboring points by incrementing coordinate indices. Unstructured grids are composed of cells of any shape (commonly triangles, quadrilaterals, tetrahedra and hexahedra), but do not have trivial identification of neighbors by incrementing an index. For unstructured grids, a set of points and an associated connectivity table is generated to define unstructured cell shapes and neighboring points. Hybrid grids are a combination of structured grids and unstructured grids. Chimera (overset) grids are intersecting or overlapping structured grids. The NGP system currently provides a user interface that integrates both 2D and 3D structured and unstructured grid generation, a solid modeling topology data management system, an internal Computer Aided Design (CAD) system based on Non-Uniform Rational B-Splines (NURBS), a journaling language, and a grid/solution visualization system.

Gaither, Adam↗

Improving ICARUS track reconstruction algorithms

The ICARUS experiment is part of the Short-Baseline Neutrino program at Fermilab. Its primary objective is to explore the possible existence of sterile neutrinos in the O(1 eV) mass range and to clarify the anomalies observed in the Liquid Scintillator Neutrino Detector and MiniBooNE experiments. The ICARUS-T600 detector is a Liquid Argon Time Projection Chamber, capable of producing high-resolution 3D images and precise calorimetric measurements of ionizing particles. This technology allows for a detailed study of neutrino interactions across a broad energy range, from a few keV to several hundred GeV. The track reconstruction is achieved through a software framework that applies a series of pattern recognition algorithms, transforming raw detector signals into fully reconstructed event topologies. This process involves identifying interaction vertices, particle tracks, and electromagnetic showers within the TPC. However, in certain cases, these algorithms may mistakenly break a single particle track into several shorter segments, interpreting each as a distinct particle. Since track length is used to estimate the particle's energy, such fragmentation can result in an energy underestimation of several hundred MeV. Furthermore, when a track is split into multiple segments, the particle identification (which relies on analyzing the energy loss as a function of the residual range) may fail, potentially leading to the loss of the entire event. To mitigate this problem, we have developed a dedicated algorithm designed to identify and reconnect (“stitch”) the tracks that were erroneously divided into multiple segments.

Ricci, Alessandro Maria [Pisa U.; INFN, Pisa] (ORC↗

Pressure-induced creation and annihilation of Weyl points in T d - Mo 0.5 W 0.5 Te 2 and 1 T " - Mo 0.5 W 0.5 Te 2

By means of first-principles density-functional theory calculations, we investigate the role of hydrostatic pressure in the electronic structure of the T d (Pmn2 1 ) and 1T" (Pm) phases of the Weyl semimetal Mo 0.5 W 0.5 Te 2 , which is a promising material for phase-change memory technology and superconductivity. We particularly focus on changes occurring in the distribution of the gapless Weyl points (WPs) within the 0 to 45 GPa pressure range. Here we further investigate the structural phase transition and lattice dynamics of the T d and 1T" phases within the aforementioned pressure range. Our calculations suggest that both the T d and 1T" phases of Mo 0.5 W 0.5 Te 2 host four WPs in their full Brillouin zone at zero pressure. The total number of WPs increases to 44 (36) with increasing pressure via pair creation up to 20 (15) GPa for the T d (1T") phase, and beyond this pressure pair annihilation of WPs starts occurring, leaving only 16 WPs at 45 GPa in both phases. The enthalpy versus pressure data reveal that the 1T" phase is more favorable below the critical pressure of 7.5 GPa; however, beyond this critical pressure the T d phase becomes enthalpically favorable. We also provide the calculated x-ray diffraction spectra along with the calculated Raman- and infrared-active phonon frequencies to facilitate the experimental identification of the studied phases

36 MATERIALS SCIENCE↗

Multilevel Monte Carlo Predictions of First Passage Times in Three-Dimensional Discrete Fracture Networks: A Graph-Based Approach

In this paper, we present a method combining multilevel Monte Carlo (MLMC) and a graph-based primary subnetwork identification algorithm to provide estimates of the mean and variance of the distribution of first passage times in fracture media at significantly lower computational cost than standard Monte Carlo (MC) methods. Simulations of solute transport are performed using a discrete fracture network (DFN), and instead of using various grid resolutions for levels in the MLMC, which is standard practice in MLMC, we identify a hierarchy of subnetworks in the DFN based on the shortest topological paths through the network using a graph-based method. While the mean of these ensembles is of critical importance, the variance is also essential in fractured media where uncertainty is an overarching theme, and understanding variability across an ensemble is a requirement for safety assessments. The method provides good estimates of the mean and variance at two orders of magnitude lower computational cost than MC.

54 ENVIRONMENTAL SCIENCES↗

Accommodating Actuator Failures in Flight Control Systems

A technique for the design of flight control systems that can accommodate a set of actuator failures is presented. As employed herein, an actuator failure is defined as any change in the parametric model of the actuator which can adversely affect actuator performance. The technique is based upon the formulation of a fixed feedback topology which ensures at least stability in the presence of the failures in the set. The fixed compensation is obtained from a loop-shaping design procedure similar to Quantitative Feedback Theory and provides stability robustness in the presence of uncertainty in the vehicle dynamics caused by the failures. System adaptation to improve performance after actuator failure(s) occurs through a static gain adjustment in the compensator followed by modification of the system prefilter. Precise identification of the vehicle dynamics is unnecessary. Application to a single-input, single-output design using a simplified model of the longitudinal dynamics of the NASA High Angle of Attack Research Vehicle is discussed. Non-real time simulations of the system including a model of the pilot demonstrate the effectiveness and limitations of the approach.

Hess, R. A.↗

Big Data Synchrophasor Monitoring and Analytics for Resiliency Tracking (BDSMART)

This report contains key findings from a project titled Big Data Synchrophasor Monitoring and Analytics for Resiliency Tracking (BDSMART), which was carried out through a collaborative effort of a team of researchers from Texas A&M Engineering Experiment Station, Temple University, and Quanta Technology, LLC. The in-kind support came from OSIsoft (acquired by AVEVA), which provided their PI Historian software to demonstrate the use case of streaming PMU data. The first section of the report describes the project goals and objectives related to the development of Machine Learning (ML) models capable of detecting and classifying events by processing phasor measurements captured in the field by Phasor Measurement Units (PMUs). The data for this study was contributed by the utilities/ISOs from the Western and Eastern interconnects and ERCOT, further referred to as Interconnect B (IC B), Interconnect A (IC A), and Interconnect C (IC C), respectively. The approach that the BDSMART Research Team proposed and the key research tasks defined by the team are outlined in this section. The next section describes the technical approach. We first discuss the data constraints related to the PMU measurements and data interpretation constraints imposed by the data contributors. They provided neither the topological information of the grid nor PMU placement locations and captured recorded data at very few locations in the system with the reporting rate of either 30 or 60 fps. The recordings are mostly positive sequence voltage, frequency, and ROCOF, and in some limited cases, three-phase voltages and currents. We then reflect on the bad data issues that stem from poor recording practices and vague definitions of the PMU status bits to supposedly be used for bad data identification. Finally, the data discovery points to imprecise time stamps with incomplete event start/end time, as well as inconsistent and incomplete event labeling, which combined make the implementation of the data models using supervising learning quite challenging. Following the data discovery study, we hypothesize that because the IC B data has the most complete labels, we should focus our model development on that data and then test it on data from other interconnects. We also define the common metrics used to evaluate the results from the ML algorithm tests. We concluded this section by summarizing the common ML models we used and explaining how we implemented and tested them. The issues from this section are expanded in the Training Dataset Report from this project. The final section of this report deals with the accomplishments and conclusions. As the accomplishments, we formulate the problem we are solving and what is achieved by solving the problem. We then reflect on each of the analytics tools we developed and point out the performance of each tool when applied to solving the mentioned problems. We reference this work for further details to the papers we published on each tool. In the conclusions, we give recommendations on how to improve future PMU recording practices to facilitate the ML algorithm implementation and guidance for the future standardization work aimed at clarifying the ambiguities associated with the PMU status bits. We finally list future tasks that can bring about further improvements in the proposed algorithms. The issues from this section are expanded in the Training, and Test Dataset Report filed at the project completion date.

97 MATHEMATICS AND COMPUTING↗

Characterization of Si (sub X)Ge (sub 1-x)/Si Heterostructures for Device Applications Using Spectroscopic Ellipsometry

Spectroscopic ellipsometry (SE) characterization of several complex Si (sub X)Ge (sub 1-x)/Si heterostructures prepared for device fabrication, including structures for heterojunction bipolar transistors (HBT), p-type and n-type heterostructure modulation doped field effect transistors, has been performed. We have shown that SE can simultaneously determine all active layer thicknesses, Si (sub X)Ge (sub 1-x) compositions, and the oxide overlayer thickness, with only a general knowledge of the structure topology needed a priori. The characterization of HBT material included the SE analysis of a Si (sub X)Ge (sub 1-x) layer deeply buried (600 nanometers) under the silicon emitter and cap layers. In the SE analysis of n-type heterostructures, we examined for the first time a silicon layer under tensile strain. We found that an excellent fit can be obtained using optical constants of unstrained silicon to represent the strained silicon conduction layer. We also used SE to measure lateral sample homogeneity, providing quantitative identification of the inhomogeneous layer. Surface overlayers resulting from prior sample processing were also detected and measured quantitatively. These results should allow SE to be used extensively as a non-destructive means of characterizing Si (sub X)Ge (sub 1-x)/Si heterostructures prior to device fabrication and testing.

Sieg, R. M.↗

Discovery and construction of surface kagome electronic states induced by p-d electronic hybridization in Co3Sn2S2

Abstract Kagome-lattice materials possess attractive properties for quantum computing applications, but their synthesis remains challenging. Herein, based on the compelling identification of the two cleavable surfaces of Co 3 Sn 2 S 2 , we show surface kagome electronic states (SKESs) on a Sn-terminated triangular Co 3 Sn 2 S 2 surface. Such SKESs are imprinted by vertical p-d electronic hybridization between the surface Sn (subsurface S) atoms and the buried Co kagome-lattice network in the Co 3 Sn layer under the surface. Owing to the subsequent lateral hybridization of the Sn and S atoms in a corner-sharing manner, the kagome symmetry and topological electronic properties of the Co 3 Sn layer is proximate to the Sn surface. The SKESs and both hybridizations were verified via qPlus non-contact atomic force microscopy (nc-AFM) and density functional theory calculations. The construction of SKESs with tunable properties can be achieved by the atomic substitution of surface Sn (subsurface S) with other group III-V elements (Se or Te), which was demonstrated theoretically. This work exhibits the powerful capacity of nc-AFM in characterizing localized topological states and reveals the strategy for synthesis of large-area transition-metal-based kagome-lattice materials using conventional surface deposition techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Roadmap for Photonics with 2D Materials

Triggered by advances in atomic-layer exfoliation and growth techniques, along with the identification of a wide range of extraordinary physical properties in self-standing films consisting of one or a few atomic layers, two-dimensional (2D) materials such as graphene, transition metal dichalcogenides (TMDs), and other van der Waals (vdW) crystals now constitute a broad research field expanding in multiple directions through the combination of layer stacking and twisting, nanofabrication, surface-science methods, and integration into nanostructured environments. Photonics encompasses a multidisciplinary subset of those directions, where 2D materials contribute remarkable nonlinearities, long-lived and ultraconfined polaritons, strong excitons, topological and chiral effects, susceptibility to external stimuli, accessibility, robustness, and a completely new range of photonic materials based on layer stacking, gating, and the formation of moiré patterns. These properties are being leveraged to develop applications in electro-optical modulation, light emission and detection, imaging and metasurfaces, integrated optics, sensing, and quantum physics across a broad spectral range extending from the far-infrared to the ultraviolet, as well as enabling hybridization with spin and momentum textures of electronic band structures and magnetic degrees of freedom. The rapid expansion of photonics with 2D materials as a dynamic research arena is yielding breakthroughs, which this Roadmap summarizes while identifying challenges and opportunities for future goals and how to meet them through a wide collection of topical sections prepared by leading practitioners.

2D materials↗

Competing magnetic phases and fluctuation-driven scalar spin chirality in the kagome metal YMn 6 Sn 6

Identification, understanding, and manipulation of novel magnetic textures are essential for the discovery of new quantum materials for future spin-based electronic devices. In particular, materials that manifest a large response to external stimuli such as a magnetic field are subject to intense investigation. Here, we study the kagome-net magnet YMn 6 Sn 6 by magnetometry, transport, and neutron diffraction measurements combined with first-principles calculations. We identify a number of nontrivial magnetic phases, explain their microscopic nature, and demonstrate that one of them hosts a large topological Hall effect (THE). We propose a previously unidentified fluctuation-driven mechanism, which leads to the THE at elevated temperatures. This interesting physics comes from parametrically frustrated interplanar exchange interactions that trigger strong magnetic fluctuations. Our results pave a path to chiral spin textures, promising for novel spintronics.

36 MATERIALS SCIENCE↗

Topological Surface and Bulk States in Dirac Semimetal Alpha-Sn Thin Films

Supported by this DOE grant, we made significant advancements in the study and application of topological surface states (TSS) in topological Dirac semimetal (TDS) α-Sn thin films. Our key findings include: (1) the successful growth of TDS α-Sn thin films via sputtering, an industry-friendly technique, on Si and InSb substrates, marking a breakthrough over previous molecular beam epitaxy methods, (2) the demonstration of enhanced damping in adjacent NiFe thin films due to the TSS of α-Sn, (3) the first observation of a strong bilinear magneto-electric resistance (BMER) effect in TDS materials at room temperature, with responses surpassing previous results, (4) the identification of quantum oscillations in α-Sn thin films associated with the TSS, revealing critical quantum transport characteristics such as Berry phase and quantum mobility, (5) the first experimental observation of negative magnetoresistance in α-Sn, and (6) the demonstration of spinorbit torque-driven, field-free magnetization switching in an α-Sn/Ag/CoFeB trilayer, achieving efficiency levels higher than conventional heavy-metal-based structures, highlighting the essential role of TSS in enabling the switching process.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Flight Readiness of Mochii S: Portable Spectroscopic Scanning Electron Microscope Facility on the International Space Station (ISS)

The ISS (International Space Station) currently lacks the capability to image and chemically analyze nano-to-micron scale particles from numerous engineering systems. To identify these particles, we must wait for a re-entry vehicle to return them from low earth orbit for ground-based SEM (Scanning Electron Microscope) / EDS (Energy Dispersive X-Ray Spectroscopy) analysis. This may take months, potentially delaying the affected system. Having an EDS-equipped SEM (Mochii S) aboard the ISS will accelerate response time thereby enhancing crew and vehicle safety by rapid and accurate identification of microscopic threats, especially in time-critical situations.The Mochii S payload will be stationed in the Japanese Experiment Module (JEM) powered by 120 VAC (Volts Alternating Current) inverter and connected to station Ethernet and WiFi (Fig. 1). To date the Mochii S payload has undergone testing for command and data handling, power quality, flight vibration, and radiation testing at Johnson Space Center (JSC). Mochii's high-RPM (Revolutions Per Minute) rotating vacuum pumps and high voltage systems have been reviewed to meet safety standards by JSC (Johnson Space Center) Engineering. Topology of the system in the JEM module has been baselined by ISS Safety and JAXA (Japan Space Exploration Agency). Digital controls to and from ISS over Joint Station LAN (Local Area Network) uplink have been simulated and the latencies and data rates have been found to be sufficient for successful operation of the payload from ground.Transporting sensitive electron optical instruments aboard a rocket that sustains 7G acceleration for 8 minutes and then operating it the unique microgravity (micro-g) environment is no trivial matter. To meet strict safety requirements and increase robustness for mission success, over 500 unique verifications must be completed before the payload is certified for spaceflight. Two of which will be discussed in detail are: vibroacoustic testing and magnetic susceptibility shielding and validation.

Mochii↗

Topological graph-based analysis of solid-state ion migration

To accelerate the development of ion conducting materials, we present a general graph-theoretic analysis framework for ion migration in any crystalline structure. The nodes of the graph represent metastable sites of the migrating ion and the edges represent discrete migration events between adjacent sites. Starting from a collection of possible metastable migration sites, the framework assigns a weight to the edges by calculating the individual migration energy barriers between those sites. Connected pathways in the periodic simulation cell corresponding to macroscopic ion migration are identified by searching for the lowest-cost cycle in the periodic migration graph. To exemplify the utility of the framework, we present the automatic analyses of Li migration in different polymorphs of VO(PO 4 ), with the resulting identification of two distinct crystal structures with simple migration pathways demonstrating overall <300 meV migration barriers.

36 MATERIALS SCIENCE↗

Observables for recoil identification in high-definition Gas Time Projection Chambers

Directional detection of nuclear recoils is broadly desirable in nuclear and particle physics. At low recoil energies, this capability may be used to confirm the cosmological origin of a dark matter signal, to penetrate the so-called neutrino floor, or to distinguish between different neutrino sources. Gas Time Projection Chambers (TPCs) can enable directional recoil detection if the readout granularity is sufficiently high, as is the case when micro-pattern gaseous detectors (MPGDs) are utilized. A key challenge in such detectors is identifying and rejecting background electron recoil events caused by gamma rays from radioactive contaminants in the detector materials and the environment. We define new observables that can distinguish electron and nuclear recoils, even at keV-scale energies, based on the simulated ionization's topology. Here we perform a simulation study that shows these observables outperform the traditionally used discriminant, dE/dx, by up to three orders of magnitude. Furthermore, these new observables work well even at ionization energies well below 10keV and remain robust even in the regime where directionality fails.

79 ASTRONOMY AND ASTROPHYSICS↗

Method and apparatus for chemical and topographical microanalysis

A scanning probe microscope is combined with a laser induced breakdown spectrometer to provide spatially resolved chemical analysis of the surface correlated with the surface topography. Topographical analysis is achieved by scanning a sharp probe across the sample at constant distance from the surface. Chemical analysis is achieved by the means of laser induced breakdown spectroscopy by delivering pulsed laser radiation to the sample surface through the same sharp probe, and consequent collection and analysis of emission spectra from plasma generated on the sample by the laser radiation. The method comprises performing microtopographical analysis of the sample with a scanning probe, selecting a scanned topological site on the sample, generating a plasma plume at the selected scanned topological site, and measuring a spectrum of optical emission from the plasma at the selected scanned topological site. The apparatus comprises a scanning probe, a pulsed laser optically coupled to the probe, an optical spectrometer, and a controller coupled to the scanner, laser and spectrometer for controlling the operation of the scanner, laser and spectrometer. The probe and scanner are used for topographical profiling the sample. The probe is also used for laser radiation delivery to the sample for generating a plasma plume from the sample. Optical emission from the plasma plume is collected and delivered to the optical spectrometer so that analysis of emission spectrum by the optical spectrometer allows for identification of chemical composition of the sample at user selected sites.

Kossakovski, Dmitri A.↗