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At least 703 records · Page 39

Structural basis of ECF-σ-factor-dependent transcription initiation

Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.

60 APPLIED LIFE SCIENCES↗

Observation of formation and local structures of metal-organic layers via complementary electron microscopy techniques

Abstract Metal-organic layers (MOLs) are highly attractive for application in catalysis, separation, sensing and biomedicine, owing to their tunable framework structure. However, it is challenging to obtain comprehensive information about the formation and local structures of MOLs using standard electron microscopy methods due to serious damage under electron beam irradiation. Here, we investigate the growth processes and local structures of MOLs utilizing a combination of liquid-phase transmission electron microscopy, cryogenic electron microscopy and electron ptychography. Our results show a multistep formation process, where precursor clusters first form in solution, then they are complexed with ligands to form non-crystalline solids, followed by the arrangement of the cluster-ligand complex into crystalline sheets, with additional possible growth by the addition of clusters to surface edges. Moreover, high-resolution imaging allows us to identify missing clusters, dislocations, loop and flat surface terminations and ligand connectors in the MOLs. Our observations provide insights into controllable MOL crystal morphology, defect engineering, and surface modification, thus assisting novel MOL design and synthesis.

36 MATERIALS SCIENCE↗

Structure-induced switching of interpolymer adhesion at a solid–polymer melt interface

In this paper, we report a link between the interfacial structure and adhesive property of homopolymer chains physically adsorbed (i.e., via physisorption) onto solids. Polyethylene oxide (PEO) was used as a model and two different chain conformations of the adsorbed polymer were created on silicon substrates via the well-established Guiselin's approach: “flattened chains” which lie flat on the solid and are densely packed, and “loosely adsorbed polymer chains” which form bridges jointing up nearby empty sites on the solid surface and cover the flattened chains. We investigated the adhesion properties of the two different adsorbed chains using a custom-built adhesion testing device. Bilayers of a thick PEO overlayer on top of the flattened chains or loosely adsorbed chains were subjected to the adhesion test. The results revealed that the flattened chains do not show any adhesion even with the chemically identical free polymer on top, while the loosely adsorbed chains exhibit adhesion. Neutron reflectivity experiments corroborated that the difference in the interfacial adhesion is not attributed to the interfacial brodening at the free polymer–adsorbed polymer interface. Instead, coarse-grained molecular dynamics simulation results suggest that the tail parts of the loosely adsorbed chains act as “connector molecules”, bridging the free chains and substrate surface and improving the interfacial adhesion. Finally, these findings not only shed light on the structure–property relationship at the interface, but also provide a novel approach for developing sticking/anti-sticking technologies through precise control of the interfacial polymer nanostructures.

36 MATERIALS SCIENCE↗

Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

DNA self-assembly is a highly programmable method to construct arbitrary architectures based on sequence complementarity. Among various constructs, DNA crystals are macroscopic crystalline materials formed by assembling motifs via sticky end association. Due to their high structural integrity and size ranging from tens to hundreds of micrometers, DNA crystals offer unique opportunities to study the structural properties and deformation behaviors of DNA assemblies. For example, enzymatic ligation of sticky ends can selectively seal nicks resulting in more robust structures with enhanced mechanical properties. However, the research efforts have been mostly on experiments involving different motif designs, structural optimization, or new synthesis methods, while their mechanics are not yet fully understood. The complex properties of DNA crystals are difficult to study via experiments alone, and numerical simulation can complement and aid the experiments. The coarse-grained molecular dynamics (MD) simulation is a powerful tool that can probe the mechanics of DNA assemblies. Here, we investigate DNA crystals made of four different motif lengths with various ligation patterns (full ligation, major directions, connectors, and in-plane) using oxDNA, an open-source, coarse-grained MD platform. We found that several distinct deformation stages emerge in response to mechanical loading and that the number and the location of ligated nucleotides can significantly modulate structural behaviors. These findings should be useful for predicting crystal properties and thus improving the design.

DNA crystal↗

Engineering modular enzyme assembly: synthetic interface strategies for natural products biosynthesis applications

Covering: 2020 to 2025Natural products remain indispensable sources of therapeutic and bioactive compounds, yet traditional discovery strategies are constrained by compound rediscovery. Modular biosynthetic enzymes, such as type I polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs), offer promising platforms for combinatorial biosynthesis owing to their programmable architectures. However, practical implementation is frequently limited by inter-modular incompatibility and domain-specific interactions. This review highlights recent advances in modular enzyme assembly enabled by synthetic interfaces-including cognate docking domains, synthetic coiled-coils, SpyTag/SpyCatcher, and split inteins-which function as orthogonal, standardized connectors to facilitate post-translational complex formation. These interfaces support rational investigations into substrate specificity, module compatibility, and pathway derivatization as well as general enzyme clustering applications beyond PKS and NRPS systems. Synthetic interfaces can be integrated with computational tools to support a more systematic and scalable framework for modular enzyme engineering by providing predictive insights into domain compatibility and interface design. These approaches within iterative design-build-test-learn workflows can accelerate the programmable assembly of biosynthetic systems and expand the accessible chemical space for natural products.

Kim, Gahyeon↗

Mapping Critical Vulnerabilities in Natural Gas Pipeline Systems through Network Centrality and GIS Analytics

Natural gas plays a central role in the US energy landscape, providing 43% of electricity generation in 2023. Its exclusive recovery ability on pipelines for transmission underscores the importance of understanding the disruption recovery ability of this infrastructure. This study employs a network-based analytical framework integrating geographic information systems (GIS) with multiple centrality measures—betweenness, closeness, degree, and eigenvector—to pinpoint key segments and evaluate the structural robustness of the national pipeline network. Pipelines are grouped by System ID and Operator ID to capture variations across organizational and physical structures. The analysis reveals uneven patterns of network influence, where certain pipelines function as critical connectors or dominant hubs. Spatial mapping highlights geographic dependencies and potential chokepoints, offering a clear view of where targeted risk prevention measures would be most effective. The findings provide practical guidance for prioritizing maintenance, enhancing system robustness, and mitigating risks to ensure a stable and secure energy supply. Future research will expand the framework to incorporate dynamic operational data and real-time network behavior.

Peterson, Steven [ORNL] (ORCID:0000000287672998)↗

Analysis of the failures and corrective actions for the LHC cryogenics radiation tolerant electronics and its field instruments

The LHC cryogenic system radiation tolerant electronics and their associated field instruments have been in nominal conditions since before the commissioning of the first LHC beams in September 2008. This system is made of about 15’000 field instruments (thermometers, pressure sensors, liquid helium level gauges, electrical heaters and position switches), 7’500 electronic cards and 853 electronic crates. Since mid-2008 a software tool has been deployed, this allows an operator to report a problem and then lists the corrective actions. The tool is a great help in detecting recurrent problems that may be tackled by a hardware or software consolidation. The corrective actions range from simple resets, exchange of defective equipment, repair of electrical connectors, etc. However a recurrent problem that heals by itself is present on some channels. This type of fault is extremely difficult to diagnose and it appears as a temporary opening of an electrical circuit; its duration can range from a few minutes to several months. This paper presents the main type of problems encountered during the last four years, their evolution over time, the various hardware or software consolidations that have resulted and whether they have had an impact in the availability of the LHC beam.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

All-semiconductor metamaterial-based optical circuit board at the microscale

The newly introduced metamaterial-based optical circuit, an analogue of electronic circuit, is becoming a forefront topic in the fields of electronics, optics, plasmonics, and metamaterials. However, metals, as the commonly used plasmonic elements in an optical circuit, suffer from large losses at the visible and infrared wavelengths. We propose here a low-loss, all-semiconductor metamaterial-based optical circuit board at the microscale by using interleaved intrinsic GaAs and doped GaAs, and present the detailed design process for various lumped optical circuit elements, including lumped optical inductors, optical capacitors, optical conductors, and optical insulators. By properly combining these optical circuit elements and arranging anisotropic optical connectors, we obtain a subwavelength optical filter, which can always hold band-stop filtering function for various polarization states of the incident electromagnetic wave. All-semiconductor optical circuits may provide a new opportunity in developing low-power and ultrafast components and devices for optical information processing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Upgrades to the in-vessel calibration light source on JET

Since 2010, an in-vessel calibration light source (ICLS) has been used periodically on JET to calibrate a range of diagnostics at UV, visible, and IR wavelengths. During shutdowns, the ICLS (which is essentially an integrating sphere) is positioned within the vacuum vessel by the remote handling (RH) system. Following the 2013 calibration runs, several changes were made to improve the efficiency and quality of the calibrations. Among these was the replacement of a 20 m “umbilical” cable which carried power and other electrical signals through a vessel port to/from a control cubicle. A lightweight 2 m cable now plugs directly into a single connector on the RH manipulator system, greatly reducing the time required for deployment and improving operational flexibility; e.g., the vessel access “floor” no longer needs to be installed. This change also means the system would be compatible with calibrations after a high neutron-fluence period of operation. An on-board micro-spectrometer now allows for real-time verification of the emitted spectrum. Finally, new “baffles” were designed and installed within the integrating sphere itself, greatly improving the spectral radiance uniformity at non-normal viewing angles (necessary due to orientation uncertainties with the RH system).

Conway, N. J.↗

W-band system-on-chip electron cyclotron emission imaging system on DIII-D

Monolithic, millimeter wave “system-on-chip” (SoC) technology has been employed in heterodyne receiver integrated circuit radiometers in a newly developed Electron Cyclotron Emission Imaging (ECEI) system on the DIII-D tokamak for 2D electron temperature profile and fluctuation evolution diagnostics. Here, a prototype module operating in E-band (72-80 GHz) was first employed in a 2 x 10 element array that demonstrated significant improvements over the previous quasi-optical Schottky diode mixer arrays during the 2018 operational campaign of the DIII-D tokamak. For compatibility with International Thermonuclear Experimental Reactor (ITER) relevant scenarios on DIII-D, the SoC ECEI system was upgraded with 20 horn-waveguide receiver modules. Each individual module contains a University of California at Davis designed W-band (75 -110 GHz) receiver die that integrates a broadband low noise amplifier (LNA), a double balanced down-converting mixer, and a x4 multiplier on the local oscillator (LO) chain. A x2 multiplier and two IF amplifiers are packaged and selected to further boost the signal strength as well as downconvert the signal frequency. The upgraded W-band array exhibits > 30 dB additional gain and 20x improvement in noise temperature comparing with the previous Schottky diode radio frequency (RF) mixer input systems; an internal 8 times multiplier chain is used to bring down the LO frequency below 12 GHz, thereby obviating the need for a large aperture for quasi-optical LO coupling and replacing it with coaxial connectors. The horn-waveguide shielding housing avoids out-of-band noise interference on each individual module. The upgraded ECEI system plays an important role for absolute electron temperature evolution and fluctuation measurements for edge and core region transport physics studies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Radio frequency mixing modules for superconducting qubit room temperature control systems

As the number of qubits in nascent quantum processing units increases, the connectorized RF (radio frequency) analog circuits used in first generation experiments become exceedingly complex. The physical size, cost, and electrical failure rate all become limiting factors in the extensibility of control systems. We have developed a series of compact RF mixing boards to address this challenge by integrating I/Q quadrature mixing, intermediate frequency/LO (local oscillator)/RF power level adjustments, and direct current bias fine tuning on a 40 × 80 mm 2 four-layer printed circuit board with electromagnetic interference shielding. The RF mixing module is designed to work with RF and LO frequencies between 2.5 and 8.5 GHz. The typical image rejection and adjacent channel isolation are measured to be ~27 dBc and ~50 dB. By scanning the drive phase in a loopback test, the module short-term amplitude and phase linearity are typically measured to be 5 ×10 -4 (V pp /V mean ) and 1 ×10 -3 radian (pk-pk). The operation of the RF mixing board was validated by integrating it into the room temperature control system of a superconducting quantum processor and executing randomized benchmarking characterization of single and two qubit gates. We measured a single-qubit process infidelity of 9.3(3) × 10 -4 and a two-qubit process infidelity of 2.7(1) × 10 -2 .

47 OTHER INSTRUMENTATION↗

The ultrafast pixel array camera system and its applications in high energy density physics

Diagnostics in high energy density physics, shock physics, and related fields are primarily driven by a need to record rapidly time-evolving signals in single-shot events. These measurements are often limited by channel count and signal degradation issues on cable links between the detector and digitizer. Here we present the Ultrafast Pixel Array Camera (UPAC), a compact and flexible detector readout system with 32 waveform-recording channels at up to 10 Gsample/s and 1.8 GHz analog bandwidth. The compact footprint allows the UPAC to be directly embedded in the detector environment. A key enabling technology is the PSEC4A chip, an eight-channel switch-capacitor array sampling device with up to 1056 samples/channel. The UPAC system includes a high-density input connector that can plug directly into an application-specific detector board, programmable control, and serial readout, with less than 5 W of power consumption in full operation. We present the UPAC design and characterization, including a measured timing resolution of ~20 ps or better on acquisitions of sub-nanosecond pulses with minimal system calibrations. Example applications of the UPAC are also shown to demonstrate operation of a solid-state streak camera, an ultrafast imaging array, and a neutron time-of-flight spectrometer.

47 OTHER INSTRUMENTATION↗

Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. In this paper, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain’s β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. Finally, this finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Temperature dependent striction effect in a single crystalline Nd 2 Fe 14 B revealed using a novel high temperature resistivity measurement technique

In this work, we studied the temperature dependence of resistivity in a single crystalline Nd 2 Fe 14 B using a newly developed high temperature probe. This novel probe employs mechanical pin connectors instead of conducting glue/paste. From warming and cooling curves, the Curie temperature was consistently measured around T c = 580 K. In addition, anomalous discrete jumps were found only in cooling curves between 400 and 500 K, but not shown in warming curves. More interestingly, when the jumps occurred during cooling, the resistivity was increased. This phenomenon could possibly be due to a temperature dependent striction effect induced by the re-orientation of magnetic domains well below the Curie temperature. Further microscopic study is needed to confirm this effect.

permanent magnet↗

Development of an ADC radiation tolerance characterization system for the upgrade of the ATLAS LAr calorimeter

ATLAS LAr calorimeter will undergo its Phase-I upgrade during the long shutdown (LS2) in 2018, and a new LAr Trigger Digitizer Board (LTDB) will be designed and installed. Several commercial-off-the-shelf (COTS) multi-channel high-speed ADCs have been selected as possible backups of the radiation tolerant ADC ASICs for the LTDB. Here, to evaluate the radiation tolerance of these backup commercial ADCs, we developed an ADC radiation tolerance characterization system, which includes the ADC boards, data acquisition (DAQ) board, signal generator, external power supplies and a host computer. The ADC board is custom designed for different ADCs, with ADC drivers and clock distribution circuits integrated on board. The Xilinx ZC706 FPGA development board is used as a DAQ board. The data from the ADC are routed to the FPGA through the FMC (FPGA Mezzanine Card) connector, de-serialized and monitored by the FPGA, and then transmitted to the host computer through the Gigabit Ethernet. A software program has been developed with Python, and all the commands are sent to the DAQ board through Gigabit Ethernet by this program. Two ADC boards have been designed for the ADC, ADS52J90 from Texas Instruments and AD9249 from Analog Devices respectively. TID tests for both ADCs have been performed at BNL, and an SEE test for the ADS52J90 has been performed at Massachusetts General Hospital (MGH). Test results have been analyzed and presented. The test results demonstrate that this test system is very versatile, and works well for the radiation tolerance characterization of commercial multi-channel high-speed ADCs for the upgrade of the ATLAS LAr calorimeter. It is applicable to other collider physics experiments where radiation tolerance is required as well.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Characterization of UV optical components for photon detector calibration in liquid argon TPCs

Large liquid argon time projection chambers (LArTPCs)require stable and well-characterized delivery of ultraviolet (UV)light for in situ calibration of photosensors at cryogenictemperatures. This article reports bench-top and cryogenicmeasurements of the optical components used in a UV lightcalibration system, including multi-mode fused-silica fibers,SMA-to-SMA connectors, optical fiber feedthroughs, andlight-diffuser assemblies. Light loss in several fiber types and SMAconnectors was measured across wavelengths from275–970 mm. In addition,light-loss measurements of the tested fibers after severalliquid-nitrogen thermal cycles showed no statistically significantdegradation relative to baseline measurements, and high-rate pulsedexposure (30–90 million pulses from a275 nm LED) likewise showed nomeasurable aging in jacketed fibers. A compact, palm-sized,3D-printed PEEK diffuser housing with stacked UV-grade fused-silicadiffusers yields Lambertian emission and the most uniform angulardistribution. Optical components exhibiting improved UV transmissionwere deployed successfully in multiple DUNE small- and large-scaleprototypes, demonstrating reliable operation of UV light calibrationsystem. These findings inform component selection and calibrationprocedures for achieving reliable, uniform UV light delivery inlarge-scale cryogenic detectors such as DUNE.

Behera, B. [South Dakota Sch. Mines Tech.] (ORCID:↗

ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor

Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA–gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a ‘Z’-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.

59 BASIC BIOLOGICAL SCIENCES↗

Dielectric Spectroscopy on Thermally Aged, Intact Poly-vinyl Chloride/Ethylene Propylene Rubber (PVC/EPR) Multipolar Cables

As a contribution to condition monitoring diagnostics on low voltage cables used in nuclear power plants, this work shows that broadband dielectric spectroscopy can be an effective technique to assess aging state of these cables. Broadband dielectric spectroscopy has been performed on three-conductor (tri-core) cables, insulated by EPR with PVC jacket. The main challenge has been to perform the measurement on the intact cables, by means of a custom-built connector, conceiving a non-destructive and non-intrusive technique. Results show that capacitance and dissipation factor can provide information about the aging state of the cable, without the need to destroy the sample in the measurement process.

dielectric spectroscopy, nondestructive evaluation↗