Learning to Evolve Structural Ensembles of Unfolded and Disordered Proteins Using Experimental Solution Data

We have developed a Generative Recurrent Neural Networks (GRNN) that learns the probability of the next residue torsions $X_{i+1}=\ [\phi_{i+1},\psi_{i+1},\omega _{i+1}, \chi_{i+1}]$from the previous residue in the sequence$X_i$ to generate new IDP conformations. In addition, we couple the GRNN with a Bayesian model, X-EISD, in a reinforcement learning step that biases the probability distributions of torsions to take advantage of experimental data types such as J-couplingss, NOEs and PREs. We show that updating the generative model parameters according to the reward feedback on the basis of the agreement between structures and data improves upon existing approaches that simply reweight static structural pools for disordered proteins. Instead the GRNN "DynamICE" model learns to physically change the conformations of the underlying pool to those that better agree with experiment

Water Formation Reaction under Interfacial Confinement: Al0.25Si0.75O2 on O-Ru(0001)

Confined nanosized spaces at the interface between a metal and a seemingly inert material, such as a silicate, have recently been shown to influence the chemistry at the metal surface. In prior work, we observed that a bilayer (BL) silica on Ru(0001) can change the reaction pathway of the water formation reaction (WFR) near room temperature when compared to the bare metal. In this work, we looked at the effect of doping the silicate with Al, resulting in a stoichiometry of AlSiO . We investigated the kinetics of WFR at elevated H pressures and various temperatures under interfacial confinement using ambient pressure X-ray photoelectron spectroscopy. The apparent activation energy was lower than that on bare Ru(0001) but higher than that on the BL-silica/Ru(0001). The apparent reaction order with respect to H was also determined. The increased residence time of water at the surface, resulting from the presence of the BL-aluminosilicate (and its subsequent electrostatic stabilization), favors the so-called disproportionation reaction pathway (*HO + *O ↔ 2 *OH), but with a higher energy barrier than for pure BL-silica.Research was carried out in part at the 23-ID-2 (IOS) beamline of the National Synchrotron Light Source II and the Center for Functional Nanomaterials, which are U.S. DOE Office of Science Facilities, and the Scientific Data and Computing Center, a component of the Computational Science Initiative, at Brookhaven National Laboratory under Contract No. DE-SC0012704. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. J.C. thanks the Spanish Ministry of Science, Innovation and Universities for a “Severo Ochoa” grant (BES-2015-075748) through “Severo Ochoa” Excellence Programme (SEV-2016-0683). Z.D. is supported by ACS PRF grant #61059-ND5

A blood-based predictor for neocortical Aβ burden in Alzheimer\u27s disease: results from the AIBL study

Dementia is a global epidemic with Alzheimer’s disease (AD) being the leading cause. Early identification of patients at risk of developing AD is now becoming an international priority. Neocortical Aβ (extracellular β-amyloid) burden (NAB), as assessed by positron emission tomography (PET), represents one such marker for early identification. These scans are expensive and are not widely available, thus, there is a need for cheaper and more widely accessible alternatives. Addressing this need, a blood biomarker-based signature having efficacy for the prediction of NAB and which can be easily adapted for population screening is described. Blood data (176 analytes measured in plasma) and Pittsburgh Compound B (PiB)-PET measurements from 273 participants from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study were utilised. Univariate analysis was conducted to assess the difference of plasma measures between high and low NAB groups, and cross-validated machine-learning models were generated for predicting NAB. These models were applied to 817 non-imaged AIBL subjects and 82 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) for validation. Five analytes showed significant difference between subjects with high compared to low NAB. A machine-learning model (based on nine markers) achieved sensitivity and specificity of 80 and 82%, respectively, for predicting NAB. Validation using the ADNI cohort yielded similar results (sensitivity 79% and specificity 76%). These results show that a panel of blood-based biomarkers is able to accurately predict NAB, supporting the hypothesis for a relationship between a blood-based signature and Aβ accumulation, therefore, providing a platform for developing a population-based scree

Ultrathin Magnesium-based Coating as an Efficient Oxygen Barrier for Superconducting Circuit Materials

Scaling up superconducting quantum circuits based on transmon qubits necessitates substantial enhancements in qubit coherence time. Among the materials considered for transmon qubits, tantalum (Ta) has emerged as a promising candidate, surpassing conventional counterparts in terms of coherence time. However, the presence of an amorphous surface Ta oxide layer introduces dielectric loss, ultimately placing a limit on the coherence time. In this study, we present a novel approach for suppressing the formation of tantalum oxide using an ultrathin magnesium (Mg) capping layer deposited on top of tantalum. Synchrotron-based X-ray photoelectron spectroscopy (XPS) studies demonstrate that oxide is confined to an extremely thin region directly beneath the Mg/Ta interface. Additionally, we demonstrate that the superconducting properties of thin Ta films are improved following the Mg capping, exhibiting sharper and higher-temperature transitions to superconductive and magnetically ordered states. Based on the experimental data and computational modeling, we establish an atomic-scale mechanistic understanding of the role of the capping layer in protecting Ta from oxidation. This work provides valuable insights into the formation mechanism and functionality of surface tantalum oxide, as well as a new materials design principle with the potential to reduce dielectric loss in superconducting quantum materials. Ultimately, our findings pave the way for the realization of large-scale, high-performance quantum computing systems

In situ characterization of the deposition of anatase TiO2 on rutile TiO2(110)

Growing additional TiO2 thin films on TiO2 substrates in ultrahigh vacuum (UHV)-compatible chambers have many applications for sample preparation, such as smoothing surface morphologies, templating, and covering impurities. However, there has been little study into how to control the morphology of TiO2 films deposited onto TiO2 substrates, especially using atomic layer deposition (ALD) precursors. Here, the authors show the growth of a TiO2 film on a rutile TiO2(110) surface using titanium tetraisopropoxide (TTIP) and water as the precursors at pressures well below those used in common ALD reactors. X-ray absorption spectroscopy suggests that the relatively low sample temperature (175 °C) results in an anatase film despite the rutile template of the substrate. Using ambient pressure x-ray photoelectron spectroscopy, the adsorption of TTIP was found to be self-limiting, even at room temperature. No molecular water was found to adsorb on the surface. The deposited thickness suggests that an alternate chemical vapor deposition growth mechanism may be dominating the growth process. This study highlights the possibility that metal oxide film deposition from molecular precursors is an option for sample preparations in common UHV-compatible chambers

Chemical profiles of the oxides on tantalum in state of the art superconducting circuits

Over the past decades, superconducting qubits have emerged as one of the leading hardware platforms for realizing a quantum processor. Consequently, researchers have made significant effort to understand the loss channels that limit the coherence times of superconducting qubits. A major source of loss has been attributed to two level systems that are present at the material interfaces. We recently showed that replacing the metal in the capacitor of a transmon with tantalum yields record relaxation and coherence times for superconducting qubits, motivating a detailed study of the tantalum surface. In this work, we study the chemical profile of the surface of tantalum films grown on c-plane sapphire using variable energy X-ray photoelectron spectroscopy (VEXPS). We identify the different oxidation states of tantalum that are present in the native oxide resulting from exposure to air, and we measure their distribution through the depth of the film. Furthermore, we show how the volume and depth distribution of these tantalum oxidation states can be altered by various chemical treatments. By correlating these measurements with detailed measurements of quantum devices, we can improve our understanding of the microscopic device losses

Aqueous dune-like bedforms in Athabasca Valles and neighbouring locations utilized in palaeoflood reconstruction

Putative fluvial dunes have been identified within the Athabasca Valles and associated network of channels on Mars. Previous published work identified and measured bedforms in Athabasca Valles using photoclinometry methods on 2–3 m/pixel resolution Mars Orbiter Camera Narrow Angle images, and argued that these were created by an aqueous megaflood that occurred between 2 and 8 million years ago. This event is likely to have occurred due to geological activity associated with the Cerberus Fossae fracture system at the source of Athabasca Vallis. The present study has used higher resolution, 25 cm/pixel images from the Mars Reconnaissance Orbiter HiRISE camera, as well as stereo-derived digital terrain models and GIS software, to re-measure and evaluate these bedforms together with data from newly discovered neighbouring fields of bedforms. The analysis indicates that the bedforms are aqueous dunes, in that they occur in channel locations where dunes would be expected to be preserved and moreover they have geometries very similar to megaflood dunes on Earth. Dune geometries are used to estimate megaflood discharge rates, including uncertainty, which results support previous flood estimates that indicate that a flood with a discharge of ∼2 × 106m3s−1 created these bedforms

Amazonian chemical weathering rate derived from stony meteorite finds at Meridiani Planum on Mars

© The Author(s) 2016.Spacecraft exploring Mars such as the Mars Exploration Rovers Spirit and Opportunity, as well as the Mars Science Laboratory or Curiosity rover, have accumulated evidence for wet and habitable conditions on early Mars more than 3 billion years ago. Current conditions, by contrast, are cold, extremely arid and seemingly inhospitable. To evaluate exactly how dry today's environment is, it is important to understand the ongoing current weathering processes. Here we present chemical weathering rates determined for Mars. We use the oxidation of iron in stony meteorites investigated by the Mars Exploration Rover Opportunity at Meridiani Planum. Their maximum exposure age is constrained by the formation of Victoria crater and their minimum age by erosion of the meteorites. The chemical weathering rates thus derived are ~1 to 4 orders of magnitude slower than that of similar meteorites found in Antarctica where the slowest rates are observed on Earth