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RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA
Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G·T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5- carboxylcytosine (caC), which are generated from mC by Tet (ten–eleven translocation) enzymes. Using improved crystallization conditions, we solved high resolution (up to 1.45 A) structures of TDG enzyme– ' product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water mediated enzyme–substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNAfree TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme–product complex.
Connected and disconnected sea partons from the CT18 parametrization of PDFs
Not Available
p -adic reconstruction of rational functions in multiloop amplitudes
Numerical reconstruction techniques are widely employed in the calculation of multiloop scattering amplitudes. In recent years, it has been observed that the rational functions in multiloop calculations greatly simplify under partial fractioning. In this article, we present a technique to reconstruct rational functions directly in partial-fractioned form, by evaluating the functions at special integer points chosen for their properties under a p -adic metric. As an application, we apply this technique to reconstruct the largest rational function in the integration-by-parts reduction of one of the rank-5 integrals appearing in two-loop five-point full-color massless amplitude calculations in quantum chromodynamics. The number of required numerical probes (per prime field) is found to be around 25 times smaller than in conventional techniques, and the obtained result is 130 times smaller. The reconstructed result displays signs of additional structure that could be used to further reduce its size and the number of required probes. Published by the American Physical Society 2024
Calculation of electron-ion temperature equilibration rates and friction coefficients in plasmas and liquid metals using quantum molecular dynamics
In this work, we discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals, and hot solids. Promising results from this method were recently reported for various materials and physical conditions. Like other ab initio calculations, the approach offers a very useful comparison with the experimental measurements and permits an extension into conditions not covered by the experiments. The energy relaxation rate is related to the friction coefficients felt by individual ions due to their nonadiabatic interactions with electrons. Each coefficient satisfies a Kubo relation given by the time integral of the autocorrelation function of the interaction force between an ion and the electrons. These Kubo relations are evaluated using the output of quantum molecular dynamics calculations in which electrons are treated in the framework of finite-temperature density functional theory. The calculation presents difficulties that are unlike those encountered with the Kubo formulas for the electrical and thermal conductivities. In particular, the widely used Kubo-Greenwood approximation is inapplicable here. Indeed, the friction coefficients and the energy relaxation rate diverge in this approximation since it does not properly account for the electronic screening of electron-ion interactions. The inclusion of screening effects considerably complicates the calculations. We discuss the physically motivated approximations we applied to deal with these complications in order to investigate a widest range of materials and physical conditions. Unlike the standard method used for the electronic conductivities, the Kubo formulas are evaluated directly in the time domain and not in the energy domain, which spares one from needing to introduce an extraneous undetermined numerical parameter to account for the discrete character of the numerical density of states. We highlight interesting properties of the energy relaxation rate not shared by other electronic properties, in particular its self-averaging character. We then present a detailed parametric and convergence study with the numerical parameters, including the system size, the number of bands and k-points, and the physical approximations for the dielectric function and the exchange-correlation energy.
Experimentation in Exploring Photovoltaic Inverter Dynamics Under Different Irradiance Levels Through a Data-Driven Approach
As conventional direct connections of synchronous generators are being phased out, inverter-based resources (IBRs) with grid support functions are increasingly being integrated into power systems. This transition requires the development of accurate dynamic models for IBRs to predict how power systems will adapt to varying levels of IBRs penetration, establish grid code requirements, and ensure compliance. Here, this study introduces an active probing signal-based data-driven modeling technique to accurately derive the dynamics model of a smart photovoltaic inverter operating in Volt-Watt and Freq-Watt modes, in compliance with the IEEE 1547–2018 standard. The paper focuses on investigating how the dynamics of the PV inverter model respond to fluctuations in solar irradiance, utilizing real-time digital simulator experimentation. The experimental analysis demonstrates that the amplitude of dynamics fluctuates with changes in irradiance across both operational modes and confirms the active power’s dependence on irradiance levels. Furthermore, the nature of inverter dynamics varies distinctly between the different modes of activation. Critically, our findings indicate that dynamic models require DC-gain adjustments to accommodate contrasting irradiance levels, highlighting a negative gradient linear relationship between the DC-gain of each model and the irradiance.
A Multi-Agent System Concept for Rapid Energy Storage Development
Many energy storage systems that use technologies such as batteries are composed of power electronics conditioning systems and battery management systems. These are often produced by multiple manufacturers and require hardware and software integration for full grid functionality. This paper proposes an agent-based framework to support the development of an energy storage system with standardized communications. This framework can be utilized with different power conversion systems with an appropriate hardware interface.
Cross-sectional transport imaging in a multijunction solar cell
Here, we combine a highly localized electron-beam point source excitation to generate excess free carriers with the spatial resolution of optical near-field imaging to map recombination in a cross-sectioned multijunction (Ga 0.5 In 0.5 P/GaIn 0.01 As/Ge) solar cell. By mapping the spatial variations in emission of light for fixed generation (as opposed to traditional cathodoluminescence (CL), which maps integrated emission as a function of position of generation), it is possible to directly monitor the motion of carriers and photons. We observe carrier diffusion throughout the full width of the middle (GaInAs) cell, as well as luminescent coupling from point source excitation in the top cell GaInP to the middle cell. Supporting CL and near-field photoluminescence (PL) measurements demonstrate the excitation-dependent Fermi level splitting effects that influence cross-sectioned spectroscopy results, as well as transport limitations on the spatial resolution of conventional cross-sectional far-field measurements.
Surf-Deformer: Mitigating Dynamic Defects on Surface Code via Adaptive Deformation
In this paper, we introduce Surf-Deformer, a code deformation framework that seamlessly integrates adaptive defect mitigation functionality into the current surface code workflow. It crafts several basic deformation instructions based on fundamental gauge transformations, which can be combined to explore a larger design space than previous methods. This enables more optimized deformation processes tailored to specific defect situations, restoring the QEC capability of deformed codes more efficiently with minimal qubit resources. Additionally, we design an adaptive code layout that accommodates our defect mitigation strategy while ensuring efficient execution of logical operations. Our evaluation shows that Surf-Deformer outperforms previous methods by significantly reducing the end-to-end failure rate of various quantum programs by 35× to 70×, while requiring only about 50% of the qubit resources compared to the previous method to achieve the same level of failure rate. Ablation studies show that Surf-Deformer surpasses previous defect removal methods in preserving QEC capability and facilitates surface code communication by achieving nearly optimal throughput.
Deconstructing the root system of grasses through an exploration of development, anatomy and function
Abstract Well‐adapted root systems allow plants to grow under resource‐limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below‐ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts‐list of elements that function together in an integrated root system to promote survival and crop productivity.
Special Section on InterPACK 2017—Part 1
InterPACK is a premier international forum for exchange of state-of-the-art knowledge in research, development, manufacturing, and applications of micro-electronics packaging. It is the flagship conference of the ASME Electronic and Photonic Packaging Division (EPPD) founded in 1992 as an ASME-JSME joint biannual conference. Rapid changes in the semiconductor landscape together with findings from InterPACK Pathfinding workshop (IPW) in 2016 led to a significant reset of InterPACK conference priorities and focus to comprehensively address needs of the InterPACK community. As a result, starting in 2017, InterPACK has become an annual conference and the scope of the conference has increased significantly together with a systems-focus to include some of the most cutting-edge topics in electronics packaging, device integration, and reliability. These topics are organized across five different tracks: (1) heterogeneous integration: microsystems with diverse functionality, (2) servers of the future, (3) structural and physical health monitoring, (4) energy conversion and storage, and (5) transportation: autonomous and electric vehicles.
Review of metal-containing resists in electron beam lithography: perspectives for extreme ultraviolet patterning
Background: Metal-containing resists entered the mainstream semiconductor industry process flow to mitigate the low absorbance of extreme ultraviolet (EUV) radiation by thin films of organic resists that lead to poor sensitivity and their inability to handle rigors of development and etching conditions. Aim: The long and rich history of using metal-containing resists in electron beam lithography can offer interesting lessons, pointers, and insights to the relatively newcomer EUV lithography, which is slightly over a decade old. Approach: Electron beam lithography has been enjoying a considerable amount of freedom in the choice of resist materials for close to 50 years; especially the use of metal-containing resists to attain not only single digit nanometer resolution, higher sensitivity, and etch resistance but also lower line-edge roughness. Here, we make a comprehensive historical review of the progress made in the patterning of metal-containing resists in electron beam lithography and derive insights that can be potentially useful in EUV patterning. Perspectives: Small molecular weight resists are proven to be crucial for achieving higher resolution with low line-edge roughness. Simplifying process flow by reducing etch-stack-layers is conceivable with metal-containing resists, along with direct-patterning of functional materials for heterogeneous integration. Efficient contact hole patterning at tighter pitches may be incumbent on progress in positive-tone resist research.
Dosimetry in differentiated thyroid carcinoma (12-1402R)
Purpose: The aim of this study has been to perform a dosimetric study in the treatments of differentiated thyroid cancer (DTC) performed in our center in order to find a dose-effect correlation. Methods: Thirty patients treated for DTC with 3700 MBq of {sup 131}I have been included in this study. For reasons of radiological protection all of them spent two nights as inpatients. Dose rate at 1 m from all patients was measured approximately 20 and 44 h after the administration of the radioiodine and a whole body scan in the gamma camera was performed approximately 1 week later. With those measurements and by using a model of two compartments the activities in thyroid bed remnants and in the whole body were calculated as a function of time. The integration of both activities yields the corresponding cumulated activities. Absorbed doses to thyroid bed remnants and to the whole body can be calculated following the MIRDOSE method-that is, by multiplying the corresponding cumulated activities by the corresponding S factors. Results: The absorbed doses to thyroid bed remnants calculated in this study fall into a very wide range (13-1161 Gy) and showed the highest correlation factors with the following parameters: the absorbed dose rate to thyroid bed remnants, the cumulated activity in thyroid bed remnants, and the maximum radioiodine uptake in thyroid bed remnants. The absorbed doses to the whole body range from 0.12 to 0.23 Gy. The ablation was successful in all patients, and in spite of the wide range of absorbed doses to thyroid bed remnants obtained, no dose-effect correlation could be obtained. Conclusions: Facing DTC treatments from a dosimetric viewpoint in which a predosimetry to calculate the activity of {sup 131}I to be administered is performed is a subject difficult to handle. This statement is based on the fact that although a very wide range of absorbed doses to thyroid bed remnants was obtained (including several absorbed doses well below some dose thresholds previously published to achieve ablation of thyroid bed remnants), ablation of thyroid bed remnants was successful for all patients and therefore no dose-effect correlation could be determined.
SU-F-J-20: Commissioning and Acceptance Testing of the C-Rad CatalystHD Surface Imaging System
Introduction: With the increasing use of surface-based, nonionizing image-guided radiotherapy (IGRT) systems, a comprehensive set of clinical acceptance and commissioning procedures are needed to ensure correct functionality and proper clinical integration. Although TG-147 provides a specific set of parameters, measurement methodologies have yet to be described. The aim of this study was to provide a comprehensive overview of the commissioning and acceptance analysis performed for the C-Rad CatalystHD imaging system. Methods and Materials: Methodology for the commissioning and acceptance of the C-Rad CatalystHD imaging system was developed using commercially available clinical equipment. Following TG-147 guidelines, the following tests were performed: integration of peripheral equipment, system drift, static spatial reproducibility and localization accuracy, static end-to-end analysis, static rotational accuracy, dynamic spatial accuracy, dynamic temporal accuracy, dynamic radiation delivery and a comprehensive end-to-end analysis. Results: The field of view (FOV) of the CatalystHD was 105×109×83 cm3 in the lateral, longitudinal and vertical directions. For thermal equilibrium and system drift, a thermal drift of 1.0mm was noted. A 45 min warmup time is recommended if the system has been shut off an extended period of time (>24 hours) before the QA procedure to eliminate any thermal drift. Spatial reproducibility was found to be 0.05±0.03 mm using a rigid phantom. For the static localization accuracy, system agreement with couch shifts was within 0.1±0.1 mm and positioning agreement with kV-CBCT was 0.16±0.10 mm. For static rotational accuracy, system agreement with a high precision rotational stage (0.01 deg precision) was within 0.10±0.07 deg. Dynamic spatial and temporal localization accuracy was found to be within 0.2±0.1 mm. Conclusion: A comprehensive commissioning and acceptance study was performed using commercially available phantoms and in-house methodologies to provide a performance evaluation of the CatalystHD imaging system.
Quantum transport equation for systems with rough surfaces and its application to ultracold neutrons in a quantizing gravity field
We discuss transport of particles along random rough surfaces in quantum size effect conditions. As an intriguing application, we analyze gravitationally quantized ultracold neutrons in rough waveguides in conjunction with GRANIT experiments (ILL, Grenoble). We present a theoretical description of these experiments in the biased diffusion approximation for neutron mirrors with both one- and two-dimensional (1D and 2D) roughness. All system parameters collapse into a single constant which determines the depletion times for the gravitational quantum states and the exit neutron count. This constant is determined by a complicated integral of the correlation function (CF) of surface roughness. The reliable identification of this CF is always hindered by the presence of long fluctuation-driven correlation tails in finite-size samples. We report numerical experiments relevant for the identification of roughness of a new GRANIT waveguide and make predictions for ongoing experiments. We also propose a radically new design for the rough waveguide.
Quantum electron levels in the field of a charged black hole
Stationary solutions of the Dirac equation in the metric of the charged Reissner–Nordstrom black hole are found. In the case of an extremal black hole, the normalization integral of the wave functions is finite, and the regular stationary solution is physically self-consistent. The presence of quantum electron levels under the Cauchy horizon can have an impact on the final stage of the Hawking evaporation of the black hole, as well as on the particle scattering in the field of the black hole.