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Correction for ‘Interfacial rheology of lanthanide binding peptide surfactants at the air–water interface’ by Stephen A. Crane et al. , Soft Matter , 2024, 20 , 9161–9173, https://doi.org/10.1039/D4SM00493K.
We measure the current expansion rate of the Universe, Hubble’s constant $H_0$, by calibrating the absolute magnitudes of supernovae to distances measured by baryon acoustic oscillations (BAO). This ‘inverse distance ladder’ technique provides an alternative to calibrating supernovae using nearby absolute distance measurements, replacing the calibration with a high-redshift anchor. We use the recent release of 1829 supernovae from the Dark Energy Survey spanning $0.01\lt z\lt 1.13$ anchored to the recent baryon acoustic oscillation measurements from Dark Energy Spectroscopic Instrument (DESI) spanning $0.30 \lt z_{\mathrm{eff}}\lt 2.33$. To trace cosmology to $z=0$, we use the third-, fourth-, and fifth-order cosmographic models, which, by design, are agnostic about the energy content and expansion history of the universe. With the inclusion of the higher redshift DESI-BAO data, the third-order model is a poor fit to both data sets, with the fourth-order model being preferred by the Akaike Information Criterion. Using the fourth-order cosmographic model, we find $H_0=67.19^{+0.66}_{-0.64}\mathrm{~km} \mathrm{~s}^{-1} \mathrm{~Mpc}^{-1}$, in agreement with the value found by Planck without the need to assume Flat-$\Lambda$CDM. However, the best-fitting expansion history differs from that of Planck, providing continued motivation to investigate these tensions.
Electron ptychography is a powerful computational method for atomic-resolution imaging with high contrast for weakly and strongly scattering elements. Modern algorithms coupled with fast and efficient detectors allow imaging specimens with tens of nanometers thicknesses with sub-0.5 Ångstrom lateral resolution. However, the axial resolution in these approaches is currently limited to a few nanometers, limiting their ability to solve novel atomic structures ab initio. Here, we experimentally demonstrate multi-slice ptychographic electron tomography, which allows atomic resolution three-dimensional phase-contrast imaging in a volume surpassing the depth of field limits. We reconstruct tilt-series 4D-STEM measurements of a $\mathrm{Co_3O_4}$ nanocube, yielding 2 Å axial and 0.7 Å transverse resolution in a reconstructed volume of $\mathrm{(18.2\,nm)^3}$. Our results demonstrate a 13.5-fold improvement in axial resolution compared to multi-slice ptychography while retaining the atomic lateral resolution and the capability to image volumes beyond the depth of field limit. Multi-slice ptychographic electron tomography significantly expands the volume of materials accessible using high-resolution electron microscopy. We discuss further experimental and algorithmic improvements necessary to also resolve single weakly scattering atoms in 3D.
The field of Integrated Computational Materials Engineering (ICME) combines a broad range of methods to study materials’ responses over a spectrum of length scales. A relatively unexplored aspect of microstructure-sensitive materials design is uncertainty propagation and quantification (UP/UQ) of materials’ microstructure, as well as establishing process-structure–property (PSP) relationships for inverse material design. In this study, an efficient UP technique built on the idea of changing probability measures and a deep generative unsupervised representative machine learning method for microstructure-based design of thermal conductivity of materials is proposed. Probability measures are used to represent microstructure space, and Wasserstein metrics are used to test the efficiency of the UP method. By using deep Variational AutoEncoder (VAE), we identify the correlations between the material/process parameters and the thermal conductivity of heterogeneous dual-phase microstructures. Through high-throughput screening, UP, and the deep-generative VAE method, PSP relationships that are too complex can be revealed by exploiting the materials’ design space with an emphasis on microstructures. As a last point, we demonstrate generative machine learning serves as a useful tool for inverse microstructure-centered materials design, and we demonstrate this by examining the inverse design of thermal conductivity in nano-structured materials. Here, the results reveal the effects of morphology, volume fraction, characteristic length scale, and the individual thermal diffusivity of phases on the thermal conductivity of dual-phase alloys. Our findings emphasize the advantages of high-throughput phase-field modeling and generative deep learning for linking PSP and inverse microstructure-centered materials design.
Magnetic nanomaterials are gaining interest for their many applications in technological areas from information science and computing to next-generation quantum energy materials. While magnetic materials have historically been nanostructured through techniques such as lithography and molecular beam epitaxy, there has recently been growing interest in using soft matter self-assembly. In this work, a triblock terpolymer, poly(isoprene-block-styrene-block-ethylene oxide) (ISO), is used as a structure directing agent for aluminosilicate sol nanoparticles and magnetic material precursors to generate organic–inorganic bulk hybrid films with co-continuous morphology. After thermal processing into mesoporous materials, results from a combination of small angle X-ray scattering (SAXS) and scanning electron microscopy (SEM) are consistent with the double gyroid morphology. Nitrogen sorption measurements reveal a type IV isotherm with H1 hysteresis, and yield a specific surface area of around 200 m 2 g −1 and an average pore size of 23 nm. The magnetization of the mesostructured material as a function of applied field shows magnetic hysteresis and coercivity at 300 K and 10 K. Comparison of magnetic measurements between the mesoporous gyroid and an unstructured bulk magnetic material, derived from the identical inorganic precursors, reveals the structured material exhibits a coercivity of 250 Oe, opposed to 148 Oe for the unstructured at 10 K, and presence of remnant magnetic moment not conventionally found in bulk hematite; both of these properties are attributed to the mesostructure. This scalable route to mesoporous magnetic materials with co-continuous morphologies from block copolymer self-assembly may provide a pathway to advanced magnetic nanomaterials with a range of potential applications.
Abstract Large language models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 32 total projects developed during the second annual LLM hackathon for applications in materials science and chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.
Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.
Purpose: TomoTherapy (Accuray Co.) has an image-guided radiotherapy system with megavoltage (MV) X-ray source and the on-board imaging device. With the MV computed tomography (MVCT), it became feasible to perform the efficient daily-3D registration of the patient position before each treatment delivery. This system also allows one to acquire the delivery sinogram during the actual treatment, which partly includes the information of the irradiated object. In this study, we try to develop the image reconstruction during treatment in helical Tomotherapy. Methods: Sinogram data were acquired during helical Tomotherapy delivery using an arc-shaped detector array that consists of 738 xenon-gas filled detector cells. In preprocessing, these were normalized by full air-scan data. A software program was developed that reconstructs 3D images during treatment with corrections as; (1) the regions outside the field were masked not to be added in the backprojection (a masking correction), and (2) each voxel of the reconstructed image was divided by the number of the X-ray passing through its voxel (a ray-passing correction). Results: Without masking and ray-passing corrections, the image reconstruction was failed. The masking correction made the image clear, however, the streak artifact was accompanied. The ray-passing correction reduced this artifact. Although the SNR (the ratio of mean to standard deviation in homogeneous region) and the contrast of the reconstructed image were slightly improved with the ray-passing correction, the masking correction only is enough for the visualization purpose. Conclusion: The visualization of the treatment area was feasible by use of the sinogram in helical Tomotherapy. This proposed method can be utilized in the treatment verification. This work was partly supported by JSPS KAKENHI 24234567. No COI, but the data in this paper were prepared by collaborators in Accuray.
The promise of machine learning interatomic potentials (MLIPs) has led to an abundance of public quantum mechanical (QM) training datasets. The quality of an MLIP is directly limited by the accuracy of the energies and atomic forces in the training dataset. Unfortunately, most of these datasets are computed with relatively low-accuracy QM methods, e.g. density functional theory with a moderate basis set. Due to the increased computational cost of more accurate QM methods, e.g. coupled-cluster theory with a complete basis set (CBS) extrapolation, most high-accuracy datasets are much smaller and often do not contain atomic forces. The lack of high-accuracy atomic forces is quite troubling, as training with force data greatly improves the stability and quality of the MLIP compared to training to energy alone. Because most datasets are computed with a unique level of theory, traditional single-fidelity (SF) learning is not capable of leveraging the vast amounts of published QM data. In this study, we apply multi-fidelity learning (MFL) to train an MLIP to multiple QM datasets of different levels of accuracy, i.e. levels of fidelity. Specifically, we perform three test cases to demonstrate that MFL with both low-level forces and high-level energies yields an extremely accurate MLIP—far more accurate than a SF MLIP trained solely to high-level energies and almost as accurate as a SF MLIP trained directly to high-level energies and forces. Therefore, MFL greatly alleviates the need for generating large and expensive datasets containing high-accuracy atomic forces and allows for more effective training to existing high-accuracy energy-only datasets. Indeed, low-accuracy atomic forces and high-accuracy energies are all that are needed to achieve a high-accuracy MLIP with MFL.
The massive data generated by scientists daily serve as both a major catalyst for new discoveries and innovations, as well as a significant roadblock that restricts access to the data. Here, our paper introduces a new approach to removing Big Data barriers and democratizing access to petascale data for the broader scientific community. Our novel data fabric abstraction layer allows user-friendly querying of scientific information while hiding the complexities of dealing with file systems or cloud services. We enable FAIR (Findable, Accessible, Interoperable, and Reusable) access to datasets such as NASA’s petascale climate datasets. Our paper presents an approach to managing, visualizing, and analyzing petabytes of data within a browser on equipment ranging from the top NASA supercomputer to commodity hardware like a laptop. Our novel data fabric abstraction utilizes state-of-the art progressive compression algorithms and machine-learning insights to power scalable visualization dashboards for petascale data. The result provides users with the ability to identify extreme events or trends dynamically, expanding access to scientific data and further enabling discoveries. We validate our approach by improving the ability of climate scientists to visually explore their data via three fully interactive dashboards. We further validate our approach by deploying the dashboards and simplified training materials in the classroom at a minority-serving institution. These dashboards, released in simplified form to the general public, contribute significantly to a broader push to democratize the access and use of climate data.
We present improved cosmological constraints from a re-analysis of the Dark Energy Survey (DES) 5-year sample of Type Ia supernovae (DES-SN5YR). This re-analysis includes an improved photometric cross-calibration, recent white dwarf observations to cross-calibrate between DES and low-redshift surveys, retraining the salt3 light-curve model and fixing a numerical approximation in the host-galaxy colour law. Our fully recalibrated sample, which we call DES-Dovekie, comprises ~1600 likely Type Ia SNe from DES and ~200 low-redshift SNe from other surveys. With DES-Dovekie, we obtain Ω m = 0.330 ± 0.015 in flat Lambda-cold dark matter (ΛCDM) which changes Ω m by –0.022 compared to DES-SN5YR. Combining DES-Dovekie with cosmic microwave background data from Planck, Atacama Cosmology Telescope, and South Pole Telescope and the DESI DR2 measurements in a flat CDM cosmology, we find ω 0 = –0.803 ± 0.054 and ω a = –0.72 ± 0.21. Our results hold a significance of 3.2σ, reduced from 4.2σ for DES-SN5YR, to reject the null hypothesis that the data are compatible with the cosmological constant. This significance is equivalent to a Bayesian model preference odds of approximately 5:1 in favour of the flat ω 0 ω a CDM model. Using generally accepted thresholds for model preference, our updated data exhibits only a weak preference for evolving dark energy.
Coronary artery disease (CAD) is highly prevalent and associated with adverse events. Challenges have emerged in the treatment of intermediate coronary artery stenoses. These lesions are often interrogated with fractional flow reserve (FFR) testing to determine if a stenosis is likely to be causative for ischemia in a cardiac territory. This invasive test requires insertion of a pressure wire into a coronary vessel. Recently computational fluid dynamics (CFD) has been used to noninvasively assess fractional flow reserve in vessels reconstructed from medical imaging data. However, many of these simulations are unable to provide additional information about intravascular hemodynamics, including velocity, endothelial shear stress (ESS), and vorticity. We hypothesized that vorticity, which has demonstrated utility in the assessment of ventricular and aortic diseases, would also be an important hemodynamic factor in CAD. Three-dimensional (3D), patient-specific coronary artery geometries that included all vessels >1 mm in diameter were created from angiography data obtained from 10 patients who underwent diagnostic angiography and FFR testing (n = 9). A massively parallel CFD solver (HARVEY) was used to calculate coronary hemodynamic parameters including pressure, velocity, ESS, and vorticity. These simulations were validated by comparing velocity flow fields from simulation to both velocities derived from in vitro particle image velocimetry and to invasively acquired pressure wire-based data from clinical testing. There was strong agreement between findings from CFD simulations and particle image velocimetry experimental testing (p < 0.01). CFD-FFR was also highly correlated with invasively measured FFR (ρ = 0.77, p = 0.01) with an average error of 5.9 ± 0.1%. CFD-FFR also had a strong inverse correlation with the vorticity (ρ = -0.86, p = 0.001). Simulations to determine the effect of the coronary stenosis on intravascular hemodynamics demonstrated significant differences in velocity and vorticity (both p < 0.05). Further evaluation of an angiographically normal appearing non-FFR coronary vessel in patients with CAD also demonstrated differences in vorticity when compared with FFR vessels (p < 0.05). The use of highly accurate 3D CFD-derived intravascular hemodynamics provides additional information beyond pressure measurements that can be used to calculate FFR. Vorticity is one parameter that is modified by a coronary stenosis and appears to be abnormal in angiographically normal vessels in patients with CAD, highlighting a possible use-case in preventative screening for early coronary disease.
Computational chemistry was used to help provide a molecular level description of the interactions of Gram-negative microbial membranes with subsurface materials. The goal is to develop a better understanding of the molecular processes involved in microbial metal binding, microbial attachment to mineral surfaces, and, eventually, oxidation/reduction reactions (electron transfer) that can occur at these surfaces and are mediated by the bacterial exterior surface. The project focused on the interaction of the outer microbial membrane, which is dominated by an exterior lipopolysaccharide (LPS) portion, of Pseudomonas aeruginosa with the mineral goethite and with solvated ions in the environment. This was originally a collaborative project with T.P. Straatsma and B. Lowery of the Pacific Northwest National Laboratory. The University of Alabama effort used electronic structure calculations to predict the molecular behavior of ions in solution and the behavior of the sugars which form a critical part of the LPS. The interactions of the sugars with metal ions are expected to dominate much of the microscopic structure and transport phenomena in the LPS. This work, in combination with the molecular dynamics simulations of Straatsma and the experimental electrochemistry and microscopy measurements of Lowry, both at PNNL, is providing new insights into the detailed molecular behavior of these membranes in geochemical environments. The effort at The University of Alabama has three components: solvation energies and structures of ions in solution, prediction of the acidity of the critical groups in the sugars in the LPS, and binding of metal ions to the sugar anions. An important aspect of the structure of the LPS membrane as well as ion transport in the LPS is the ability of the sugar side groups such as the carboxylic acids and the phosphates to bind positively charged ions. We are studying the acidity of the acidic side groups in order to better understand the ability of these groups to bind metal ions. We need to understand the solvation properties of the metal ions in solution and their ability to bind not only to the sugars but to proteins and to other anions. Our goal is then to be able to predict the ability of the side groups to bind metal ions. One result from the earlier molecular dynamics simulations is the exclusion of water from the inner hydrophobic part of the membrane. We thus need to investigate the binding of the cations in media with different dielectric constants.
High-End computing (HEC) has been a driver for advances in science and engineering for the past four decades. Increasingly HEC has become a significant element in the national security, economic vitality, and competitiveness of the United States. Advances in HEC provide results that cut across traditional disciplinary and organizational boundaries. This program provides opportunities to share information about HEC systems and computational techniques across multiple disciplines and organizations through conferences and exhibitions of HEC advances held in Washington DC so that mission agency staff, scientists, and industry can come together with White House, Congressional and Legislative staff in an environment conducive to the sharing of technical information, accomplishments, goals, and plans. A common thread across this series of conferences is the understanding of computational science and applied mathematics techniques across a diverse set of application areas of interest to the Nation. The specific objectives of this program are: Program Objective 1. To provide opportunities to share information about advances in high-end computing systems and computational techniques between mission critical agencies, agency laboratories, academics, and industry. Program Objective 2. To gather pertinent data, address specific topics of wide interest to mission critical agencies. Program Objective 3. To promote a continuing discussion of critical issues in high-end computing. Program Objective 4. To provide a venue where a multidisciplinary scientific audience can discuss the difficulties applying computational science techniques to specific problems and can specify future research that, if successful, will eliminate these problems.
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.
We conduct a search for strong gravitational lenses in the Dark Energy Survey (DES) Year 6 imaging data. We implement a pre-trained Vision Transformer (ViT) for our machine learning (ML) architecture and adopt interactive machine learning to construct a training sample with multiple classes to address common types of false positives. Our ML model reduces ∼236 million DES cutout images to 22,564 targets of interest, including ∼85% of previously reported galaxy–galaxy lens candidates discovered in DES. These targets were visually inspected by citizen scientists, who ruled out ∼90% as false positives. Of the remaining 2618 candidates, 149 were expert-classified as “definite” lenses and 516 as “probable” lenses, for a total of 665 systems, with 147 of these candidates being newly identified. Additionally, we trained a second ViT to find double-source plane lens systems, finding at least one double-source system. Our main ViT excels at identifying galaxy–galaxy lenses, consistently assigning high scores to candidates with high expert assessments. The top 800 ViT-scored images include ∼100 of our “definite” lens candidates. This selection is an order of magnitude higher in purity than previous convolutional neural-network-based lens searches and demonstrates the feasibility of applying our methodology for discovering large samples of lenses in future surveys.
The ATLAS experiment has developed extensive software and distributed computing systems for Run 3 of the LHC. These systems are described in detail, including software infrastructure and workflows, distributed data and workload management, database infrastructure, and validation. The use of these systems to prepare the data for physics analysis and assess its quality are described, along with the software tools used for data analysis itself. An outlook for the development of these projects towards Run 4 is also provided.
A widely utilized tool in reactor analysis is passive tracers that report the residence time distribution, allowing estimation of the conversion and other properties of the system. Recently, advances in microrobotics have introduced powered and functional entities with sizes comparable to some traditional tracers. This has motivated the concept of Smart Tracers that could record the local chemical concentrations, temperature, or other conditions as they progress through reactors. Herein, the design constraints and advantages of Smart Tracers by simulating their operation in a laminar flow reactor model conducting chemical reactions of various orders are analyzed. It is noted that far fewer particles are necessary to completely map even the most complex concentration gradients compared with their conventional counterparts. Design criteria explored herein include sampling frequency, memory storage capacity, and ensemble number necessary to achieve the required accuracy to inform a reactor model. Cases of severe particle diffusion and sensor noise appear to bind the functional upper limit of such probes and require consideration for future design. The results of the study provide a starting framework for applying the new technology of microrobotics to the broad and impactful set of problems classified as chemical reactor analysis.