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At least 415 records · Page 23

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗

High-Energy Coherent X-Ray Dffraction Microscopy of Polycrystal Grains: First Steps Towards a Multi-Scale Approach

Here, we present proof-of-concept imaging measurements of a polycrystalline material that integrate the elements of conventional high-energy x-ray diffraction microscopy with coherent diffraction-imaging techniques, and that can enable in situ strain-sensitive imaging of lattice structure in ensembles of deeply embedded crystals over five decades of length scale upon full realization. We demonstrate that the combination of these two characterization methods enables a more complete picture of the crystal-lattice strain than either method is capable of providing individually. Such complementary imaging capabilities are critical to addressing questions in a variety of research areas such as materials science and engineering, chemistry, and solid-state physics. Towards this eventual goal, the following key aspects are demonstrated: (1) high-energy Bragg coherent diffraction imaging (HE BCDI) of submicron-scale crystallites at 52 keV at current third-generation synchrotron light sources, (2) HE BCDI performed in conjunction with far-field high-energy diffraction microscopy (FF HEDM) on the grains of a polycrystalline sample in a smoothly integrated manner, and (3) the orientation information of an ensemble of grains obtained via FF HEDM used to perform complementary HE BCDI on multiple Bragg reflections of a single targeted grain. The imaged structures are seen to be 477 ± 50 nm or smaller in size, with an estimated strain resolution of 2.5 x 10 -4 . These steps lay the foundation for integration of HE BCDI, which typically provides a spatial resolution tens of nanometers, into a broad suite of well-established HEDM methods, extending HEDM beyond the few-micrometer resolution bound and into the nanoscale, and positioning the approach to take full advantage of the orders-of-magnitude improvement of x-ray coherence expected at fourth-generation light sources presently being built and commissioned worldwide.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗

Distribution of centrality measures on undirected random networks via the cavity method

The Katz centrality of a node in a complex network is a measure of the node’s importance as far as the flow of information across the network is concerned. For ensembles of locally tree-like undirected random graphs, this observable is a random variable. Its full probability distribution is of interest but difficult to handle analytically because of its “global” character and its definition in terms of a matrix inverse. Leveraging a fast Gaussian Belief Propagation-Cavity algorithm to solve linear systems on tree-like structures, we show that i) the Katz centrality of a single instance can be computed recursively in a very fast way, and ii) the probability P ( K ) that a random node in the ensemble of undirected random graphs has centrality K satisfies a set of recursive distributional equations, which can be analytically characterized and efficiently solved using a population dynamics algorithm. We test our solution on ensembles of Erdős-Rényi and Scale Free networks in the locally tree-like regime, with excellent agreement. The analytical distribution of centrality for the configuration model conditioned on the degree of each node can be employed as a benchmark to identify nodes of empirical networks with over- and underexpressed centrality relative to a null baseline. We also provide an approximate formula based on a rank- 1 projection that works well if the network is not too sparse, and we argue that an extension of our method could be efficiently extended to tackle analytical distributions of other centrality measures such as PageRank for directed networks in a transparent and user-friendly way.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Machine Learning Framework for Modeling Ensemble Properties of Atomically Disordered Materials

Atomic disorder can strongly influence material properties such as charge transport, optical response, and catalytic activity. However, efficiently modeling these disorder effects remains challenging for first-principles methods due to the cost of sampling large configurational spaces and computing complex physical quantities. Recent advances of machine learning techniques, particularly graph neural networks (GNNs), has enabled the efficient and accurate predictions of complex material properties, offering promising tools for studying disordered systems. In this work, we present a general machine-learning-assisted computational framework that integrates equivariant GNNs with Monte Carlo simulations to compute the thermodynamic and ensemble-averaged functional properties of disordered materials. Using the surface-termination-disordered MXene monolayer Ti 3 C 2 T 2–x as a representative system, we find that electrical conductivity exhibits an emergent peak near the order–disorder phase transition temperature due to the interplay between electron scattering and doping. In contrast, optical conductivity remains largely insensitive to local atomic disorder and reflects the global surface chemical composition. These results highlight the role of atomic disorder in affecting material properties and demonstrate the potential of our approach for statistically modeling disorder effects in a wide range of materials such as high-entropy alloys and spin liquids.

MXene↗

Future Changes in Midwest Extreme Precipitation Depend on Storm Type

Midwestern U.S. extreme precipitation is associated with multiple storm types including mesoscale convective systems (MCSs) and/or training thunderstorms, tropical cyclone (TC) remnants, and winter storms. Anthropogenic warming is expected to increase climatological precipitation globally, however, there may be little correspondence with regional storm-based changes. Furthermore, uncertainty remains in precipitation-temperature scaling due to use of convective parameterization in most global models. In this study, we investigated historically impactful extreme precipitation events from multiple types of Midwest storms using the Weather Research and Forecasting model at convection-permitting resolution. We simulated five-member ensembles of historical hindcasts and experiments representing the storms in the future using the pseudo-global warming method. We found that future precipitation changes depend on storm type, with increases near Clausius-Clapeyron (CC) for winter storms, no consensus for MCSs and/or training thunderstorms, and sub-CC increases for TC remnants. This research highlights the importance of considering storm type in future extreme precipitation projections.

54 ENVIRONMENTAL SCIENCES↗

Two- and three-meson scattering amplitudes with physical quark masses from lattice QCD

We study systems of two and three mesons composed of pions and kaons at maximal isospin using four CLS ensembles with 𝑎 ≈ 0.063 fm, including one with approximately physical quark masses. Using the stochastic Laplacian-Heaviside method, we determine the energy spectrum of these systems including many levels in different momentum frames and irreducible representations. Using the relativistic two- and three-body finite-volume formalism, we constrain the two- and three-meson K matrices, including not only the leading 𝑠 wave, but also 𝑝 and 𝑑 waves. By solving the three-body integral equations, we determine, for the first time, the physical-point scattering amplitudes for 3⁢𝜋 + , 3⁢𝐾 + , 𝜋 + ⁢𝜋 + ⁢𝐾 + , and 𝐾 + ⁢𝐾 + ⁢𝜋 + systems. These are determined for total angular momentum 𝐽 𝑃 = 0 − , 1 + , and 2 − . We also obtain accurate results for 2⁢𝜋 + , 𝜋 + ⁢𝐾 + , and 2⁢𝐾 + phase shifts. We compare our results to chiral perturbation theory and to phenomenological fits.

FOS: Physical sciences↗

Spin Squeezing by Rydberg Dressing in an Array of Atomic Ensembles

Here, we report on the creation of an array of spin-squeezed ensembles of cesium atoms via Rydberg dressing, a technique that offers optical control over local interactions between neutral atoms. We optimize the coherence of the interactions by a stroboscopic dressing sequence that suppresses super-Poissonian loss. We thereby prepare squeezed states of N = 200 atoms with a metrological squeezing parameter ξ 2 = 0.77⁢(9) quantifying the reduction in phase variance below the standard quantum limit. We realize metrological gain across three spatially separated ensembles in parallel, with the strength of squeezing controlled by the local intensity of the dressing light. Our method can be applied to enhance the precision of tests of fundamental physics based on arrays of atomic clocks and to enable quantum-enhanced imaging of electromagnetic fields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Matilda v1.0: An R package for probabilistic climate projections using a reduced complexity climate model

A primary advantage to using reduced complexity climate models (RCMs) has been their ability to quickly conduct probabilistic climate projections, a key component of uncertainty quantification in many impact studies and multisector systems. Providing frameworks for such analyses has been a target of several RCMs used in studies of the future co-evolution of the human and Earth systems. In this paper, we present Matilda, an open-science R software package that facilitates probabilistic climate projection analysis, implemented here using the Hector simple climate model in a seamless and easily applied framework. The primary goal of Matilda is to provide the user with a turn-key method to build parameter sets from literature-based prior distributions, run Hector iteratively to produce perturbed parameter ensembles (PPEs), weight ensembles for realism against observed historical climate data, and compute probabilistic projections for different climate variables. This workflow gives the user the ability to explore viable parameter space and propagate uncertainty to model ensembles with just a few lines of code. The package provides significant freedom to select different scoring criteria and algorithms to weight ensemble members, as well as the flexibility to implement custom criteria. Additionally, the architecture of the package simplifies the process of building and analyzing PPEs without requiring significant programming expertise, to accommodate diverse use cases. We present a case study that provides illustrative results of a probabilistic analysis of mean global surface temperature as an example of the software application.

54 ENVIRONMENTAL SCIENCES↗

Multilevel Monte Carlo methods for the Grad-Shafranov free boundary problem

The equilibrium configuration of a plasma in an axially symmetric reactor is described mathematically by a free boundary problem associated with the celebrated Grad-Shafranov equation. The presence of uncertainty in the model parameters introduces the need to quantify the variability in the predictions. This is often done by computing a large number of model solutions on a computational grid for an ensemble of parameter values and then obtaining estimates for the statistical properties of solutions. In this study, we explore the savings that can be obtained using multilevel Monte Carlo methods, which reduce costs by performing the bulk of the computations on a sequence of spatial grids that are coarser than the one that would typically be used for a simple Monte Carlo simulation. We examine this approach using both a set of uniformly refined grids and a set of adaptively refined grids guided by a discrete error estimator. Numerical experiments show that multilevel methods dramatically reduce the cost of simulation, with cost reductions typically on the order of 60 or more and possibly as large as 200. Furthermore, adaptive griding results in more accurate computation of geometric quantities such as x-points associated with the model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fault location in High Voltage Multi-terminal dc Networks Using Ensemble Learning

Precise location of faults for large distance power transmission networks is essential for faster repair and restoration process. High Voltage direct current (HVdc) networks using modular multi-level converter (MMC) technology has found its prominence for interconnected multi-terminal networks. This allows for large distance bulk power transmission at lower costs. However, they cope with the challenge of dc faults. Fast and efficient methods to isolate the network under dc faults have been widely studied and investigated. After successful isolation, it is essential to precisely locate the fault. The post-fault voltage and current signatures are a function of multiple factors and thus accurately locating faults on a multi-terminal network is challenging. In this paper, we discuss a novel data-driven ensemble learning based approach for accurate fault location. Here we utilize the eXtreme Gradient Boosting (XGB) method for accurate fault location. The sensitivity of the proposed algorithm to measurement noise, fault location, resistance and current limiting inductance are performed on a radial three-terminal MTdc network designed in Power System Computer Aided Design (PSCAD)/Electromagnetic Transients including dc (EMTdc).

24 POWER TRANSMISSION AND DISTRIBUTION↗

Using feature importance as an exploratory data analysis tool on Earth system models

Abstract. Machine learning (ML) models are commonly used to generate predictions, but these models can also support the discovery of new science. Generating accurate predictions necessitates that a model captures the structure of the underlying data. If the structure is properly extracted, ML could be a useful exploratory and evidential tool. In this paper, we present a case study that demonstrates the use of ML for exploratory data analysis (EDA) in the climate space. We apply the ML explainability method of spatiotemporal zeroed feature importance (stZFI) to understand how climate-variable associations evolve over space and time. Our analyses focus on data from ensembles of Earth system models (ESMs) which provide data on different climate states and conditions. We elect to work with ESM ensembles since they allow us to compare feature importance across alternative scenarios not available with observed data. The ensembles also account for natural variability so that we can distinguish between signal and noise due to natural climate variability when computing feature importance. The use of perturbed initial condition ensembles introduces variability mimicking the natural variability in the atmosphere; thus the signals emerging using feature importance (FI) can be evaluated against the natural variability in the climate system. For our analyses, we consider the 1991 volcanic eruption of Mount Pinatubo, which was a large stratospheric aerosol injection. We explore the climate pathway associated with the eruption from aerosols to radiation to temperature at both the near-surface and stratospheric levels. In addition to applying the method to data generated from two different ESMs, we apply stZFI to reanalysis data to compare the associations identified by stZFI. We show how stZFI tracks the importance of aerosol optical depth over time on forecasting temperatures. This case study illustrates usefulness of an ML tool (stZFI) for EDA on a well-studied climate exemplar.

Ries, Daniel (ORCID:0000000250294647)↗

Evidential Deep Learning: Enhancing Predictive Uncertainty Estimation for Earth System Science Applications

Abstract Robust quantification of predictive uncertainty is a critical addition needed for machine learning applied to weather and climate problems to improve the understanding of what is driving prediction sensitivity. Ensembles of machine learning models provide predictive uncertainty estimates in a conceptually simple way but require multiple models for training and prediction, increasing computational cost and latency. Parametric deep learning can estimate uncertainty with one model by predicting the parameters of a probability distribution but does not account for epistemic uncertainty. Evidential deep learning, a technique that extends parametric deep learning to higher-order distributions, can account for both aleatoric and epistemic uncertainties with one model. This study compares the uncertainty derived from evidential neural networks to that obtained from ensembles. Through applications of the classification of winter precipitation type and regression of surface-layer fluxes, we show evidential deep learning models attaining predictive accuracy rivaling standard methods while robustly quantifying both sources of uncertainty. We evaluate the uncertainty in terms of how well the predictions are calibrated and how well the uncertainty correlates with prediction error. Analyses of uncertainty in the context of the inputs reveal sensitivities to underlying meteorological processes, facilitating interpretation of the models. The conceptual simplicity, interpretability, and computational efficiency of evidential neural networks make them highly extensible, offering a promising approach for reliable and practical uncertainty quantification in Earth system science modeling. To encourage broader adoption of evidential deep learning, we have developed a new Python package, Machine Integration and Learning for Earth Systems (MILES) group Generalized Uncertainty for Earth System Science (GUESS) (MILES-GUESS) ( https://github.com/ai2es/miles-guess ), that enables users to train and evaluate both evidential and ensemble deep learning. Significance Statement This study demonstrates a new technique, evidential deep learning, for robust and computationally efficient uncertainty quantification in modeling the Earth system. The method integrates probabilistic principles into deep neural networks, enabling the estimation of both aleatoric uncertainty from noisy data and epistemic uncertainty from model limitations using a single model. Our analyses reveal how decomposing these uncertainties provides valuable insights into reliability, accuracy, and model shortcomings. We show that the approach can rival standard methods in classification and regression tasks within atmospheric science while offering practical advantages such as computational efficiency. With further advances, evidential networks have the potential to enhance risk assessment and decision-making across meteorology by improving uncertainty quantification, a longstanding challenge. This work establishes a strong foundation and motivation for the broader adoption of evidential learning, where properly quantifying uncertainties is critical yet lacking.

Schreck, John S.↗

Quantum Simulations of Radiation Damage in a Molecular Polyethylene Analog

Abstract An atomic‐level understanding of radiation‐induced damage in simple polymers like polyethylene is essential for determining how these chemical changes can alter the physical and mechanical properties of important technological materials such as plastics. Ensembles of quantum simulations of radiation damage in a polyethylene analog are performed using the Density Functional Tight Binding method to help bind its radiolysis and subsequent degradation as a function of radiation dose. Chemical degradation products are categorized with a graph theory approach, and occurrence rates of unsaturated carbon bond formation, crosslinking, cycle formation, chain scission reactions, and out‐gassing products are computed. Statistical correlations between product pairs show significant correlations between chain scission reactions, unsaturated carbon bond formation, and out‐gassing products, though these correlations decrease with increasing atom recoil energy. The results present relatively simple chemical descriptors as possible indications of network rearrangements in the middle range of excitation energies. Ultimately, the work provides a computational framework for determining the coupling between nonequilibrium chemistry in polymers and potential changes to macro‐scale properties that can aid in the interpretation of future radiation damage experiments on plastic materials.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Remote effects of Tibetan Plateau spring land temperature on global subseasonal to seasonal precipitation prediction and comparison with effects of sea surface temperature: the GEWEX/LS4P Phase I experiment

The prediction skill for precipitation anomalies in late spring and summer months—a significant component of extreme climate events—has remained stubbornly low for years. This paper presents a new idea that utilizes information on boreal spring land surface temperature/subsurface temperature (LST/SUBT) anomalies over the Tibetan Plateau (TP) to improve prediction of subsequent summer droughts/floods over several regions over the world, East Asia and North America in particular. The work was performed in the framework of the GEWEX/LS4P Phase I (LS4P-I) experiment, which focused on whether the TP LST/SUBT provides an additional source for subseasonal-to-seasonal (S2S) predictability. The summer 2003, when there were severe drought/flood over the southern/northern part of the Yangtze River basin, respectively, has been selected as the focus case. With the newly developed LST/SUBT initialization method, the observed surface temperature anomaly over the TP has been partially produced by the LS4P-I model ensemble mean, and 8 hotspot regions in the world were identified where June precipitation is significantly associated with anomalies of May TP land temperature. Consideration of the TP LST/SUBT effect has produced about 25–50% of observed precipitation anomalies in most hotspot regions. The multiple models have shown more consistency in the hotspot regions along the Tibetan Plateau-Rocky Mountain Circumglobal (TRC) wave train. The mechanisms for the LST/SUBT effect on the 2003 drought over the southern part of the Yangtze River Basin are discussed. For comparison, the global SST effect has also been tested and 6 regions with significant SST effects were identified in the 2003 case, explaining about 25–50% of precipitation anomalies over most of these regions. This study suggests that the TP LST/SUBT effect is a first-order source of S2S precipitation predictability, and hence it is comparable to that of the SST effect. With the completion of the LS4P-I, the LS4P-II has been launched and the LS4P-II protocol is briefly presented.

54 ENVIRONMENTAL SCIENCES↗

Liquid-free covalent reinforcement of carbon nanotube dry-spun yarns and free-standing sheets

Carbon nanotubes (CNTs) possess exceptional mechanical properties, surpassing stiffness and strength metrics of common materials such as steel alloys by 100× at the nanoscale. However, when myriads of individual CNTs are bundled together into macroscopic ensembles like fibers or sheets, the result is a 100-fold drop in strength compared to its individual components. Here we present a general strategy aimed to close this gap in property scaling. By using vapor-phase polymerization of a crosslinkable polymer, we reinforced the weak interlinkages among individual CNTs within both yarns and sheets to promote a better transference of mechanical load across the structure. Furthermore, after the treatment, dry-spun, low-density 2.3 μm thin yarns increased their elastic moduli by at least 300%, and free-standing CNT sheets exhibited a 10× boost. In-situ synchrotron small-angle X-ray scattering revealed that polymer-reinforced yarns undergo limited CNT bundle rearrangement when subjected to tensile loads compared to pristine yarns. This evidence supports the hypothesis that the polymer hinders CNTs slippage, the root cause of the poor scaling of mechanical properties in these materials. While we demonstrated this reinforcement method for CNT structures, it is not specific to CNTs and could be used in a wide variety of other hierarchical nanostructured ensembles.

36 MATERIALS SCIENCE↗

Kinetic theory of particle-in-cell simulation plasma and the ensemble averaging technique

Abstract We derive the kinetic theory of fluctuations in physically and numerically stable particle-in-cell (PIC) simulations of electrostatic plasmas. The starting point is the single-time correlation at the start of the simulation between the statistical fluctuations of the weighted densities of macroparticle centers in the plasma particle phase-space. The fluctuations are associated with different initial conditions, typically due to the random initial conditions (in velocity space) of the macroparticles/simulation plasma, assigned according to their initial distribution of probability. The single-time correlations at all time steps and in each spatial grid cell are then determined from the Laplace–Fourier transforms of the discretized Klimontovich-like equation for the macroparticles and Maxwell’s equations for the fields, as computed by modern PIC codes. We recover the expressions for the electrostatic field and the plasma particle density fluctuation autocorrelation spectra as well as the kinetic equations describing the average evolution of PIC-simulated plasma particles, first derived by Langdon (1970b Proc. 4th Conf. Numerical Simulation of Plasmas ) using a test macroparticle approach perturbing a discretized Vlasovian plasma and then averaging the obtained physical quantity over the initial macroparticle velocity distribution. We generalize and extend these results to the modern algorithms in PIC codes using arbitrary macroparticle weights. Analytical estimates of statistical fluctuation amplitudes are derived as a function of the plasma simulation parameters, using the central limit theorem in the limit of a large number of macroparticles per cell. The theory is then used to analyze the ensemble averaging technique of PIC simulations where statistical averages are performed over ensembles of PIC simulations, modeling the same plasma physics problem but using different statistical realizations of the initial distribution functions of the macroparticles. This method is illustrated by linear Landau damping uncovering (from noise, which is usually considered numerical) the physical fluctuations driven by a single small amplitude electrostatic wave perturbing a PIC simulation plasma in equilibrium.

fluctuations correlations↗

Optimizers for stabilizing likelihood-free inference

A growing number of applications in particle physics and beyond use neural networks as unbinned likelihood ratio estimators applied to real or simulated data. Precision requirements on the inference tasks demand a high-level of stability from these networks, which are affected by the stochastic nature of training. We show how physics concepts can be used to stabilize network training through a physics-inspired optimizer. In particular, the energy conserving descent (ECD) optimization framework uses classical Hamiltonian dynamics on the space of network parameters to reduce the dependence on the initial conditions while also stabilizing the result near the minimum of the loss function. We develop a version of this optimizer known as , which has few free hyperparameters with limited ranges guided by physical reasoning. We apply to representative likelihood-ratio estimation tasks in particle physics and find on average that it out-performs the widely used Adam optimizer. We expect that ECD will be a useful tool for wide array of data-limited problems, where it is computationally expensive to exhaustively optimize hyperparameters and mitigate fluctuations with ensembling.

Monte Carlo methods↗