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DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗

DOE OSTI2021

422 Million intrinsic quality factor planar integrated all-waveguide resonator with sub-MHz linewidth

High quality-factor (Q) optical resonators are a key component for ultra-narrow linewidth lasers, frequency stabilization, precision spectroscopy and quantum applications. Integration in a photonic waveguide platform is key to reducing cost, size, power and sensitivity to environmental disturbances. However, to date, the Q of all-waveguide resonators has been relegated to below 260 Million. Here, we report a Si 3 N 4 resonator with 422 Million intrinsic and 3.4 Billion absorption-limited Qs. The resonator has 453 kHz intrinsic, 906 kHz loaded, and 57 kHz absorption-limited linewidths and the corresponding 0.060 dB m -1 loss is the lowest reported to date for waveguides with deposited oxide upper cladding. These results are achieved through a careful reduction of scattering and absorption losses that we simulate, quantify and correlate to measurements. This advancement in waveguide resonator technology paves the way to all-waveguide Billion Q cavities for applications including nonlinear optics, atomic clocks, quantum photonics and high-capacity fiber communications.

36 MATERIALS SCIENCE↗

DOE OSTI2020

On the Road to Achieving Safety Excellence at the Idaho Cleanup Project: The Initial Challenges, Solutions, and Positive Results of Striving to be the Best and Safest in the DOE Complex - 20518

When Fluor Idaho, LLC (Fluor Idaho) assumed the Idaho Cleanup Project Core contract (ICP Core) in mid-2016, it inherited the successful multi-faceted, employee-owned safety programs of two prior contractors supporting cleanup operations at the Idaho National Laboratory Site. Fluor Idaho incorporated the best of both safety programs along with Fluor Corporate's 106-year legacy of safety initiatives and successes. Fluor Idaho integrated the separate programs and cultures under a One Fluor approach - one project, one mission, One Fluor. Job changes, management changes, and procedures, processes, and system changes presented multiple challenges. Those challenges combined with the severe Winter of 2016/2017 resulted in numerous slips, trips, and falls first aids and reportable injuries. The road to safety excellence started off bumpy and stayed that way for some time. Since then, Fluor Idaho has successfully implemented several key initiatives including employee engagement; management engagement and time in the field; communications improvements; safety culture sustainment; injury/illness prevention; organizational learning; and DOE Voluntary Protection Program (VPP) readiness and preparation. Management became more engaged by making more workplace visits and increasing their supervision of 'life critical work' or complex activities. Additional training became mandatory for first-line supervisors and front-line workers. Most recently, Fluor Idaho increased its injury and illness prevention initiatives extensively. In the last year, things have turned around in a dramatic way. This shift is directly attributable to the significant number of initiatives launched in late 2017 and 2018. These initiatives addressed safety performance in the five key areas of the DOE VPP and promoted sustainability of the company's safety culture. The five key areas are: management leadership, employee involvement, work-site analysis, hazard prevention and control, and safety and health training. Employees and managers alike recommitted to making safety the highest value. The result of this laser-like focus on safety and accident and injury prevention is that injuries and first aids are a fraction of what they were. During FY 2019, employees worked more than 4.2 million hours without a serious injury or lost work-day and 1 million hours without a recordable injury. Fluor Idaho is proud of its safety trend. The company invested significant resources in improving its safety record, and that investment is paying off. Other contractors in the DOE Complex can learn and benefit from this discussion of the challenges Fluor Idaho faced, as well as its innovative safety initiatives that are producing results that are being recognized by our U.S. Department of Energy (DOE) customer. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Perspectives of active Si photonics devices for data communication and optical sensing

Si photonics has made rapid progress in research and commercialization in the past two decades. While it started with electronic–photonic integration on Si to overcome the interconnect bottleneck in data communications, Si photonics has now greatly expanded into optical sensing, light detection and ranging (LiDAR), optical computing, and microwave/RF photonics applications. From an applied physics point of view, this perspective discusses novel materials and integration schemes of active Si photonics devices for a broad range of applications in data communications, spectrally extended complementary metal–oxide–semiconductor (CMOS) image sensing, as well as 3D imaging for LiDAR systems. We also present a brief outlook of future synergy between Si photonic integrated circuits and Si CMOS image sensors toward ultrahigh capacity optical I/O, ultrafast imaging systems, and ultrahigh sensitivity lab-on-chip molecular biosensing.

electronic band structure↗

DOE OSTI2023

Ultrafast radiographic imaging and tracking: An overview of instruments, methods, data, and applications

Ultrafast radiographic imaging and tracking (U-RadIT) use state-of-the-art ionizing particle and light sources to experimentally study sub-nanosecond transients or dynamic processes in physics, chemistry, biology, geology, materials science and other fields. These processes are fundamental to modern technologies and applications, such as nuclear fusion energy, advanced manufacturing, communication, and green transportation, which often involve one mole or more atoms and elementary particles, and thus are challenging to compute by using the first principles of quantum physics or other forward models. One of the central problems in U-RadIT is to optimize information yield through, e.g. high-luminosity X-ray and particle sources, efficient imaging and tracking detectors, novel methods to collect data, and large-bandwidth online and offline data processing, regulated by the underlying physics, statistics, and computing power. We review and highlight recent progress in: (a.) Detectors such as high-speed complementary metal-oxide semiconductor (CMOS) cameras, hybrid pixelated array detectors integrated with Timepix4 and other application-specific integrated circuits (ASICs), and digital photon detectors; (b.) U-RadIT modalities such as dynamic phase contrast imaging, dynamic diffractive imaging, and four-dimensional (4D) particle tracking; (c.) U-RadIT data and algorithms such as neural networks and machine learning, and (d.) Applications in ultrafast dynamic material science using XFELs, synchrotrons and laser-driven sources. Hardware-centric approaches to U-RadIT optimization are constrained by detector material properties, low signal-to-noise ratio, high cost and long development cycles of critical hardware components such as ASICs. Interpretation of experimental data, including comparisons with forward models, is frequently hindered by sparse measurements, model and measurement uncertainties, and noise. Alternatively, U-RadIT make increasing use of data science and machine learning algorithms, including experimental implementations of compressed sensing. Machine learning and artificial intelligence approaches, refined by physics and materials information, may also contribute significantly to data interpretation, uncertainty quantification and U-RadIT optimization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Automation of Nanoparticle Synthesis Processes in a Plasma Environment Using LabVIEW

This work presents an automated control system for the synthesis of nanomaterials by plasma-enhanced chemical vapor deposition (PECVD), implemented using the LabVIEW software environment. The main objective of the study is to develop an integrated hardware-software platform that enables sequential control of the key stages of the PECVD process, including vacuum chamber preparation, pressure monitoring, working gas supply, plasma ignition, power matching, cyclic nanomaterial growth, and optical monitoring of nanoparticles in the plasma environment. The use of LabVIEW made it possible to integrate actuator control, experimental parameter acquisition, and realtime process visualization within a single automated system. The automated cycle begins with evacuation of the reaction chamber to a predefined base pressure. Transition to the next stage is permitted only after the specified pressure threshold has been reached, ensuring reproducible initial conditions for each experiment. The program then controls the supply of the working gas through mass flow controllers (MFCs). In this work, two gas-flow control modes were considered: analog control using a 0-5 V voltage signal and digital communication via RS-232 interface. It was shown that the analog approach requires accurate scaling of the control voltage, since applying 5 V corresponds to full-scale opening of the controller and results in the maximum gas flow. In contrast, the RS232 interface enables the gas flow rate to be specified directly in sccm, improving the accuracy, flexibility, and convenience of gas-environment control. After pressure stabilization, LabVIEW initiates RF plasma ignition and executes the RF matching algorithm aimed at minimizing reflected power and improving the stability of the plasma process. A separate software module implements the cyclic nanomaterial growth mode, in which the plasma-on time, plasma duration, and total number of synthesis cycles are predefined. This approach makes it possible to control material accumulation on the substrate and to correlate the process parameters with the morphological characteristics of the resulting nanostructures. The final module of the system is designed for optical monitoring of the nanoparticle cloud density in dusty plasma. For this purpose, the change in the intensity of laser radiation passing through the plasma region is recorded using a photodetector and a Keithley 2401 measuring unit connected to LabVIEW via RS-232 interface. The difference between the initial and modified optical signal intensity is used as a diagnostic parameter characterizing the formation and temporal evolution of nanoparticles. The developed system demonstrates that LabVIEW can be effectively applied not only for the automation of individual instruments, but also for the implementation of a complete digital control cycle for PECVD-based nanomaterial synthesis.

PECVD↗

DOE OSTI2022

Intersubband transitions in nonpolar and semipolar III-nitrides: Materials, devices, and applications

In the last two decades, the third-generation wide bandgap semiconductor III-nitrides have revolutionized a myriad of electronic and photonic devices and applications, including power electronics, extreme-environment electronics, RF amplifiers, and optoelectronics such as light-emitting diodes and laser diodes. Recently, III-nitride heterostructures (e.g., AlGaN/GaN) based intersubband transition (ISBT) has garnered considerable research interest for infrared (IR), terahertz (THz), and ultrafast optoelectronics (e.g., photodetectors and quantum cascade lasers) due to its large conduction band offset, large optical phonon energy, and promising room-temperature operation. This paper presents a comprehensive review on the recent progress and challenges of III-nitrides based ISBT from the perspectives of materials, structures, devices, and applications, with a focus on nonpolar and semipolar III-nitrides. Various device structures have been demonstrated for III-nitrides based ISBT, including quantum wells, dots, and wires, among which AlGaN/GaN quantum wells are the most widely used. The effects of device parameters, crystal orientations, and doping on the ISBT properties of AlGaN/GaN quantum wells are discussed. Although the room-temperature operation is still elusive, theoretical and experimental studies show that nonpolar and semipolar III-nitrides based ISBT exhibits tunable ISBT wavelength from far-IR to THz spectral range with higher efficiency compared with polar c-plane ISBT. This review can serve as a gateway to and an important reference for the recent progress and challenges of III-nitrides based ISBT and its potential applications in sensing, communication, ultrafast optoelectronics, and integrated photonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Communication—Controlling Etching of Germanium through Surface Charge Manipulation

Potassium hydroxide (KOH) aqueous solutions can effectively etch germanium. Etch rates were determined in an electrolytic etch cell. Electrically isolated Ge wafers were subject to an etch rate of 1.45 ± 0.07 nm min −1 , increasing to 12.6 ± 0.2 nm min −1 when grounded, 97 ± 2 nm min −1 when biased at −0.9 V, and 138 ± 2 nm min −1 with periodic biasing. Results suggest that the previously reported limited etching in KOH is associated with the recombination of holes with electrons injected from the surface reaction. The results of this study demonstrate that changing the hole concentration through biasing is an effective tool to control electrolytic etch rates, enabling future selective etching processes for germanium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

The case for digital twins in metal additive manufacturing

The digital twin (DT) is a relatively new concept that is finding increased acceptance in industry. A DT is generally considered as comprising a physical entity, its virtual replica, and two-way digital data communications in-between. Its primary purpose is to leverage the process intelligence captured within digital models—or usually their faster-solving surrogates—towards generating increased value from the physical entities. The surrogate models are created using machine learning based on data obtained from the field, experiments and digital models, which may be physics-based or statistics-based. Anomaly detection and correction, and diagnostic closed-loop process control are examples of how a process DT can be deployed. In the manufacturing industry, its use can achieve improvements in product quality and process productivity. Metal additive manufacturing (AM) stands to gain tremendously from the use of DTs. This is because the AM process is inherently chaotic, resulting in poor repeatability. However, a DT acting in a supervisory role can inject certainty into the process by actively keeping it within bounds through real-time control commands. Closed-loop feedforward control is achieved by observing the process through sensors that monitor critical parameters and, if there are any deviations from their respective optimal ranges, suitable corrective actions are triggered. The type of corrective action (e.g. a change in laser power or a modification to the scanning speed) and its magnitude are determined by interrogating the surrogate models. Because of their artificial intelligence (AI)-endowed predictive capabilities, which allow them to foresee a future state of the physical twin (e.g. the AM process), DTs proactively take context-sensitive preventative steps, whereas traditional closed-loop feedback control is usually reactive. Apart from assisting a build process in real-time, a DT can help with planning the build of a part by pinpointing the optimum processing window relevant to the desired outcome. Again, the surrogate models are consulted to obtain the required information. In this article, we explain how the application of DTs to the metal AM process can significantly widen its application space by making the process more repeatable (through quality assurance) and cheaper (by getting builds right the first time).

36 MATERIALS SCIENCE↗

DOE OSTI2023

Confidentiality-preserving machine learning algorithms for soft-failure detection in optical communication networks

Automated fault management is at the forefront of next-generation optical communication networks. The increase in complexity of modern networks has triggered the need for programmable and software-driven architectures to support the operation of agile and self-managed systems. In these scenarios, the European Telecommunications Standards Institute zero-touch network and service management approach is imperative. The need for machine learning algorithms to process the large volume of telemetry data brings safety concerns as distributed cloud-computing solutions become the preferred approach for deploying reliable communication network automation. This paper’s contribution is twofold. First, we propose a simple yet effective method to guarantee the confidentiality of the telemetry data based on feature scrambling. The method allows the operation of third-party computational services without direct access to the full content of the collected data. Additionally, the effectiveness of four unsupervised machine learning algorithms for soft-failure detection is evaluated when applied to the scrambled telemetry data. The methods are based on factor analysis, principal component analysis, nonlinear principal component analysis, and singular value decomposition. Most dimensionality reduction algorithms have the common property that they can maintain similar levels of fault classification performance while hiding the data structure from unauthorized access. Evaluations of the proposed algorithms demonstrate this capability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Sequential infiltration of two-photon polymerized 3D photonic crystals for mid-IR spectroscopic applications

Photonic crystals (PhCs) are spatially organized structures with lattice parameters equivalent to the operational wavelength of light. PhCs have been subject to extensive research efforts in the last two decades and are known for controlling light propagation with applications in sensing and time-delayed communication due to the slow-light phenomenon. Despite their exceptional properties, PhCs are difficult to fabricate using planar micromachining techniques due to their periodic structures. Techniques like two-photon stereolithography have been discussed for PhC fabrication in the literature, but the inherent disadvantage of poor refractive index (RI) contrast results in limited application. In this work, we present sequential infiltration synthesis performed on two-photon stereolithographically printed 3D PhCs for infiltration with zinc oxide to increase the RI of 3D PhCs. Further, finite element analysis was performed over a range of RI contrast values to study the change in photonic bandgap (PBG) with RI contrast. The transmission spectra were recorded on 3D PhCs before and after infiltration to demonstrate the change experimentally. An increase in the PBG width and absorbance is seen postinfiltration due to enhanced RI. This work presents the first, to our knowledge, sequentially infiltrated enhanced 3D PhC fabricated with two-photon stereolithography.

3D printing↗

DOE OSTI2024

Optical and microstructural studies of erbium-doped TiO 2 thin films on silicon, SrTiO 3 , and sapphire

Rare-earth ion doped oxide thin films integrated on silicon substrates provide a route toward scalable, chip-scale platforms for quantum coherent devices. Erbium-doped TiO 2 is an attractive candidate: the Er 3+ optical transition is compatible with C-band optical fiber communications, while TiO 2 is an insulating dielectric compatible with silicon process technology. Through structural and optical studies of Er-doped TiO 2 thin films grown via molecular beam deposition on silicon, SrTiO 3 , and sapphire substrates, we have explored the impact of polycrystallinity and microstructure on the optical properties of the Er emission. Comparing polycrystalline TiO 2 (rutile)/Si with single-crystalline TiO 2 (rutile)/r-sapphire and polycrystalline TiO 2 (anatase)/Si with single-crystalline TiO 2 (anatase)/SrTiO 3 , we observe that the inhomogeneous linewidth (Γ inh ) of the most prominent peak in the Er spectrum (the Y 1 –Z 1 transition, 1520 and 1533 nm in rutile and anatase TiO 2 ) is significantly narrower in the polycrystalline case. This implies a relative insensitivity to extended structural defects and grain boundaries in such films (as opposed to, e.g., point defects). We show that the growth of an undoped, underlying TiO 2 buffer on Si can reduce Γ inh by a factor of 4–5. Expectedly, Γ inh also reduces with decreasing Er concentrations: we observe a ∼2 order of magnitude reduction from ∼1000 ppm Er to ∼10 ppm Er. Γ inh then gets limited to a residual value of ∼5 GHz that is insensitive to further reduction in the Er concentration. Based upon the above results, we argue that the optical properties in these thin films are limited by the presence of high “grown-in” point defect concentrations.

Chemical elements↗

DOE OSTI2025

Sub-2 Kelvin Characterization of Nitrogen-Vacancy Centers in Silicon Carbide Nanopillars

The development of efficient quantum communication technologies depends on the innovation in multiple layers of its implementation, a challenge we address from the fundamental properties of the physical system at the nanoscale to the instrumentation level at the macroscale. We select a promising near-infrared quantum emitter, the nitrogen-vacancy (NV) center in 4H-SiC, and integrate it, at an ensemble level, with nanopillar structures that enhance photon collection efficiency into an objective lens. Moreover, changes in collection efficiency in pillars compared to bulk can serve as indicators of color center orientation in the lattice. To characterize NV center properties at the unprecedented sub-2 K temperatures, we incorporate compatible superconducting nanowire single photon detectors inside the chamber of an optical cryostat and create the ICECAP, the Integrated Cryogenic system for Emission, Collection And Photon detection. ICECAP measurements show no significant line-width broadening of NV ensemble emission and up to 14-fold enhancement in collected emission. With additional filtering, we measure emitter lifetimes of NV centers in a basal ( hk ) and axial ( kk ) orientation, unveiling their cryogenic values of 2.2 and 2.8 ns.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗