Structural analyses of an RNA stability element interacting with poly(A)
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Atmospheric-pressure plasmas sustained in packed bed reactors (PBRs) are being investigated for chemical conversion of gases and pollution control. Metallic catalysts added to the surfaces of the dielectric beads of PBRs can increase the energy efficiency and selectivity of chemical processes by reducing operating temperature and providing additional reaction pathways. In this paper, results from a computational investigation of plasma surface interactions between micron-scale metallic catalysts and humid-air plasmas in PBRs are discussed. Here we found that high plasma density regions form in the proximity of the metallic catalysts. These higher-density plasma regions were confirmed experimentally using ICCD imaging. The intense plasmas result from geometrical electric field enhancement and redistribution of charges within the conductive particles, leading to further enhancement. The high electric field at the triple points of the catalysts can produce electric field emission of electrons, which provides a pre-ionization source or additional source of electrons. These regions of high electric field and sources of electrons guide discharges towards the catalysts and increases fluxes of excited species, ions, electrons and photons to their surfaces. These fluxes are focused primarily at the triple points between the metal, dielectric and gas. As a result, the catalyst is locally heated, which could lead to further increased rates of thermocatalytic reactions on the surface. Surface roughness of the metal inclusions can lead to additional electric field enhancement, which changes the character of the discharges in the vicinity of the catalysts while reducing breakdown voltage.
Mitigation of the multiple risks associated with disruptions and runaway electrons in tokamaks involves competing demands. Success requires that each risk be understood sufficiently that appropriate compromises can be made. Here the focus is on the interaction of short timescale magnetic-perturbations with the structure in ITER that is closest to the plasma, blanket modules covered by separated beryllium tiles. The effect of this tiled surface on the perturbations and on the forces on structures is subtle. Indeterminacy can be introduced by tile-to-tile shorting. A determinate subtlety is introduced because electrically separated tiles can act as a conducting surface for magnetic perturbations that have a normal component to the surface. A practical method for including this determinate subtlety into plasma simulations is developed. The shorter the timescales and the greater the localization, particularly in the toroidal direction, the more important the magnetic effects of the tiles become.
In this paper, we present a method to accurately and efficiently calculate many-body states of interacting carriers in quantum nanostructures based on a combination of iterative selection of configurations and perturbation theory. This method enables investigations of large excitonic complexes and multielectron systems with near full configuration interaction accuracy, even though only a small subspace of the full many-body Hilbert space is sampled, thus saving orders of magnitudes in computational resources. Important advantages of this method are that the convergence is controlled by a single parameter, the threshold, and that ground and excited states can be treated on an equal footing. On the example of InAsP nanowire quantum dots described using a million-atom tight-binding approach, we demonstrate the extreme efficiency of the method by numerical studies of large excitonic complexes filling up to the fourth electronic shell. We find that the method generally converges fast as a function of the threshold, profiting from a significant acceleration due to the perturbative corrections. The role of the choice of single-particle basis states is discussed. It is found that the algorithm converges faster in the Hartree-Fock basis only for highly charged systems, where Coulomb repulsion dominates. Finally, based on the observation that second-order perturbative energy corrections only depend on off-diagonal elements of the many-body Hamiltonian, we present a way to accurately calculate many-body states that requires only a relatively small number of Coulomb matrix elements.
Smart buildings, especially Grid-interactive Efficient Buildings (GEBs), suffer from cyber-attacks and physical faults due to the integration of a large number of sensors and controls, connected devices, and associated communication networks. This study demonstrated a real-time advanced building resilient platform, called CYber Defense and REsilient System (CYDRES), which is deployable for existing and emerging Building Automation Systems (BASs). CYDRES aims to empower GEBs with cyber-attack-immune capabilities through multi-layer prevention and adaptation mechanisms to monitor, detect, and respond to cyber-attacks and physical operational faults. CYDRES is demonstrated through real-time experiments in a Hardware-in-the-Loop (HIL) testbed.
Boiling water reactors (BWRs) represent approximately one-third of the operating fleet in the United States, contributing significantly towards the global effort in reducing carbon emissions. Even though most of the operating fleet has been in operation for quite some time, continued advancements in new nuclear fuel (such as accident tolerant fuel) or operating regimes (such as power up-rates and higher burnup operation) necessitates similar advancements in modeling and simulation capabilities. Bison, a component of the Virtual Environment for Reactor Applications (VERA), is a high-fidelity fuel performance code able to explore the fuel performance of a wide variety of fuel types in one-, two-, and three-dimensions. Until recently, the code had not been used for analyses of BWRs. Modeling capabilities have been added for Gd-bearing UO{sub 2} and pure zirconium liners. New models have been added based upon the U.S. Nuclear Regulatory Commission (NRC) guide-lines for hydrogen pickup in Zircaloy-2 claddings and pellet-clad mechanical interaction (PCMI) failure during a reactivity insertion accident (RIA), known as a rod drop accident (CRDA) in BWRs. Implementing and/or improving Bison modeling capabilities extended its analytical reach to areas beyond its original intended purpose. This paper demonstrates one of these capabilities as a proof of concept. Recently developed models enable Bison to provide an alternate approach for cladding integrity determination in CRDA evaluations, which currently use bounding conservative estimates. As part of this demonstration, NRC guidance on hydrogen-pickup and PCMI failure models were utilized in this research. Even though more research is needed in establishing right inputs and process in this area, this paper demonstrates Bison's ability to determine cladding integrity in a CRDA evaluation. This first of a kind demonstration is a proof of concept in this area, which could potentially be extended to a number of other areas where a more accurate cladding integrity determination would be needed. (authors)
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
Efficient realization of the scientific potential of the Electron Ion Collider (EIC) calls for addition of a future second Interaction Region (2nd IR) and a detector in the RHIC IR8 region after the EIC project completion. The second IR and detector are needed to independently cross-check the results of the first detector, and to provide measurements with complementary acceptance. The available space in the existing RHIC IR8 and maximum fields achievable with NbTi superconducting magnet technology impose constraints on the 2nd IR performance. Since commissioning of the 2nd IR is envisioned in a few years after the first IR, such a long time frame allows for more R&D on the Nb₃Sn magnet technology. Thus, it could provide a potential alternative technology choice for the 2nd IR magnets. Presently, we are exploring its potential benefits for the 2nd IR performance, such as improvement of the luminosity and acceptance, and are also assessing the technical risks associated with use of Nb₃Sn magnets. In this paper, we present the current progress of this work.
Surface fine particulate matter (PM 2.5 ) pollution can be enhanced by feedback processes induced by aerosol–radiation interactions (ARIs) and aerosol–cloud interactions (ACIs). Many previous studies have reported enhanced PM 2.5 concentrations induced by ARIs and ACIs for episodic events in China. However, few studies have examined the changes in the ARI- and ACI-induced PM 2.5 enhancements over a long period, though the anthropogenic emissions have changed substantially in the last decade. In this study, we quantify the ARI- and ACI-induced PM 2.5 changes for 2013–2021 under different meteorology and emission scenarios using the Weather Research and Forecasting model with Chemistry (WRF-Chem), and we investigate the driving factors behind the changes. Our results show that, in January 2013, when China suffered from the worst PM 2.5 pollution, the PM 2.5 enhancement induced by ARIs in eastern China (5.59 µg m −3 ) was larger than that induced by ACIs (3.96 µg m −3 ). However, the ACI-induced PM 2.5 enhancement showed a significantly smaller decrease ratio (51 %) than the ARI-induced enhancement (75 %) for 2013–2021, making ACIs more important for enhancing PM 2.5 concentrations in January 2021. Our analyses suggest that the anthropogenic emission reductions played a key role in this shift. Owing to only anthropogenic emission reductions, the ACI-induced PM 2.5 enhancement decreased by 43 % in January, which was lower than the decrease ratio of the ARI-induced enhancement (57 %). The relative change in ARI- and ACI-induced PM 2.5 enhancement in July was similar to the pattern observed in January, caused by anthropogenic emission reductions. The primary reason for this phenomenon is that the decrease in ambient PM 2.5 for 2013–2021 caused a disproportionately small decrease in the liquid water path (LWP) and an increase in the cloud effective radius (Re) under the condition of high PM 2.5 concentrations. Therefore, the surface solar radiation attenuation (and, hence, the boundary layer height reduction) caused by ACIs decreased slower than that caused by ARIs. Moreover, the lower decrease ratio of the ACI-induced PM 2.5 enhancement was dominated by the lower decrease ratio of ACI-induced secondary PM 2.5 component enhancement, which was additionally caused by the smaller decrease ratio of the air temperature reduction and the relative humidity (RH) increase. Our findings indicate that, with the decrease in ambient PM 2.5 , the ACI-induced PM 2.5 enhancement inevitably becomes more important. This needs to be considered in the formulation of control policies to meet the national PM 2.5 air quality standard.
Understanding protein-protein interactions (PPIs) between viruses and host organisms is crucial for uncovering infection mechanisms and identifying potential therapeutic targets. The ability to generalize PPI predictive models across understudied viruses presents a significant challenge. In this work, we use arenavirus-human PPIs to illustrate the difficulties associated with model generalization, which are compounded by a lack of both positive and negative data. We employ a Transfer Learning approach to investigate arenavirus-human PPIs by utilizing models trained on better-studied virus-human and human-human PPIs. Additionally, we curate and assess four types of negative sampling datasets to evaluate their impact on model performance. Despite the overall high accuracies (93–99 %) and AUPRC scores (0.8–0.9) appearing promising, further analysis indicates that these performance metrics can be misleading due to data leakage, data bias, and overfitting, especially concerning under-represented viral proteins. We reveal these gaps and assess the impact of data imbalance using standard k-fold cross-validation and Independent Blind Testing with a Balanced Dataset, resulting in a drop in accuracy below 50 %. We propose a viral protein-specific evaluation framework that categorizes viral proteins into majority and minority classes based on their representation in the dataset, enabling comparison of model performance across these groups using balanced accuracies. This framework offers a more robust evaluation of model generalizability, addressing biases inherent in standard evaluation techniques and paving the way for more reliable PPI prediction models for understudied viruses.
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The diffusion behavior of Mg 2+ in electrolytes is not as readily accessible as that from Li + or Na + utilizing PFG NMR, due to the low sensitivity, poor resolution, and rapid relaxation encountered when attempting 25 Mg NMR. In MgTFSI 2 /DME solutions, “bound” DME (coordinating to Mg 2+ ) and “free” DME (bulk) are distinguishable from 1 H NMR. With the exchange rates between them obtained from 2D 1 H EXSY NMR, we can extract the self-diffusivities of free DME and bound DME (which are equal to that of Mg 2+ ) before the exchange occurs using PFG diffusion NMR measurements coupled with analytical formulas describing diffusion under two-site exchange. Further, the high activation enthalpy for exhange (65–70 kJ/mol) can be explained by the structural change of bound DME as evidenced by its reduced C–H bond length. Comparison of the diffusion behaviors of Mg 2+ , TFSI – , DME, and Li + reveals a relative restriction to Mg 2+ diffusion that is caused by the long-range interaction between Mg 2+ and solvent molecules, especially those with suppressed motions at high concentrations and low temperatures.