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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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29 records · Page 2

D–MOPH–25: diverse MOF–molecule pairs for Henry’s constants prediction

Computational methods like grand-canonical Monte Carlo simulations and machine learning (ML) have accelerated metal–organic frameworks (MOF) exploration but are typically limited to a narrow range of adsorbates due to data availability and force field constraints. In this study, we introduce a dataset of diverse MOF–molecule pairs for Henry’s constant prediction, D–MOPH–25, which systematically explores a diverse chemical space by combining 113 molecular adsorbates with over 5000 MOF structures through an active learning process. D–MOPH–25 constitutes the most diverse adsorbate dataset used in any ML study of molecular adsorption in MOFs to date. Our workflow builds a benchmark for predicting Henry’s constants at 300 K, leveraging conformal prediction for uncertainty quantification. Assessment through Shannon entropy and uniform manifold approximation and projection confirms the comprehensiveness of D–MOPH–25 while highlighting the importance of robust classification to filter out unphysical data points in regression tasks. Although future enhancements in model architecture and sampling criteria could improve predictive performance, our dataset already spans the target space using only 2.31% of total possibilities. This comprehensive dataset facilitates assessment of model generalizability across adsorbate species and can establish a foundation for high-throughput MOF screening and ML-driven separation processes.

active learning↗

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↗

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

HOD-dependent systematics in Emission Line Galaxies for the DESI 2024 BAO analysis

The Dark Energy Spectroscopic Instrument (DESI) will provide precise measurements of Baryon Acoustic Oscillations (BAO) to constrain the expansion history of the Universe and set stringent constraints on dark energy. Therefore, precise control of the global error budget due to various systematic effects is required for the DESI 2024 BAO analysis. In this work, we estimate the level of systematics induced in the DESI BAO analysis due the assumed Halo Occupation Distribution (HOD) model for the Emission Line Galaxy (ELG) tracer. We make use of mock galaxy catalogs constructed by fitting various HOD models to early DESI data, namely the One-Percent survey data. Our analysis includes typical HOD models for the ELG tracer used in the literature as well as extensions to the baseline models. Among the extensions, we consider various recipes for galactic conformity and assembly bias. We use 25 AbacusSummit simulations under the ΛCDM cosmology for each HOD model and perform independent analyses in Fourier space and in configuration space. To recover the BAO signal from our mocks we perform BAO reconstruction and apply the control variates technique to reduce sample variance noise. Our BAO analyses can recover the isotropic BAO parameter α iso within 0.1% and the Alcock Paczynski parameter α AP within 0.3%. Overall, we find that the systematic error due to the HOD dependence is below 0.17%, with the Fourier space analysis being more robust against the HOD systematics. We conclude that our analysis pipeline is robust enough against the HOD systematics for the ELG tracer in the DESI 2024 BAO analysis, for the assumptions made.

79 ASTRONOMY AND ASTROPHYSICS↗

An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions

Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the “feature importance” approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.

Chemistry↗

Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes

Biological macromolecular machines occupy a continuum of structural conformations to perform cellular tasks. Mapping this conformational space provides an insight into its functionality. While the cryo-electron microscopy resolution revolution has expanded our ability to characterize the conformational continuums, there are obstacles in structurally characterizing regions of high flexibility. These technical barriers have impeded characterization of flexible ribosomal proteins when the ribosome is interacting with mRNA stem-loop structures such as a frameshifting stimulatory sequence (FSS). Small-angle neutron/X-ray scattering and electron microscopy were used to study ribosomal samples and compared structural differences between a ribosome that is bound to an FSS stem-loop compared to a ribosome bound to linear mRNA. This comparison shows that a large protein stalk elongates by 22% when the 70S interacts with an mRNA stem-loop. Finally, our results suggest that ribosomal proteins have extensive flexibility and may influence important ribosomal mechanisms, such as those that involve FSS.

36 MATERIALS SCIENCE↗

NXREFINE

NXRefine implements a complete workflow for both data acquisition and reduction of single crystal diffuse x-ray scattering collected as a series of area detector frames during continuous sample rotation. The data are stored in HDF5 files, which conform to the NeXus data format standard. These files contain a comprehensive set of metadata, including the incident wavelength, powder calibration scans used to define detector distances, beam centers, and yaw, pitch, and roll corrections. Automated peak searches of the three-dimensional data arrays define a set of Bragg peaks that are used to define an orientation matrix, defined according to Busing and Levy, which is then used to transform the data from angular coordinates to reciprocal space coordinates using the CCTW program. Multiple rotations at different detector translations and offset rotation axes are combined to ensure that there are no gaps in the reconstructed data, and allow the construction of masks to eliminate detector artifacts due to Compton scattering within the sensor layers. Finally, the data can be transformed into 3D-ΔPDF maps using the punch-and-fill method after symmetrization.

OSBORN, RAYMOND↗

Machine learning-assisted profiling of a kinked ladder polymer structure using scattering

Ladder polymers consisting of fused rings in the backbone have very limited conformational freedom, which results in very different properties from traditional linear polymers. However, accurately determining their size and chain conformations from solution scattering remains a challenge. Their chain conformations of kinked ladder polymers are largely governed by the structures and relative orientations or configurations of the repeat units, unlike conventional polymer chains whose bending angles between repeat units follow a unimodal Gaussian distribution. Meanwhile, traditional scattering models for polymer chains do not account for these unique structural features. This work introduces a novel approach that integrates machine learning with Monte Carlo simulations to construct a model that can describe the geometry of a type of kinked CANAL ladder polymers. We first develop a Monte Carlo simulation model for sampling the configuration space of CANAL ladder polymers, where each repeat unit is modeled as a biaxial segment. Then, we establish a machine learning-assisted scattering analysis framework based on Gaussian Process Regression. Finally, we conduct small-angle neutron scattering experiments on a CANAL ladder polymer solution to apply our approach. Our method uncovers structural features of such ladder polymers that conventional methods fail to capture.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

The confluence of machine learning and multiscale simulations

Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, have promoted advances in virtually every field of science and engineering and are revitalizing the traditional notions of multiscale modeling. Deep learning has found success in various approaches for distilling information from fine-scale models, such as building surrogate models and guiding the development of coarse-grained potentials. However, perhaps its most powerful use in multiscale modeling is in defining latent spaces that enable efficient exploration of conformational space. In conclusion, this confluence of machine learning and multiscale simulation with modern high-performance computing promises a new era of discovery and innovation in structural biology.

59 BASIC BIOLOGICAL SCIENCES↗

ELG×LRG Distribution through Dark Matter Halo Dynamics

We investigate the clustering and halo occupation distribution (HOD) of DESI Y1 emission-line (ELGs) and luminous red (LRGs) galaxies at 0.8 < z < 1.1, including their cross-correlation (ELG×LRG), using the A BACUS S UMMIT suite and a new Halo Occupation Model (H OME ) for galaxy multitracers. This integrates intrahalo dynamics, halo exclusion, and quenching, bridging insights from hydrodynamical, HOD, abundance-matching, and semianalytic studies. Leveraging full phase-space information from the Uchuu N-body simulation, and sampling satellites from dark-matter particle positions via physically motivated prescriptions, Home reproduces the anisotropic clustering down to s = 200 h −1 kpc with unprecedented accuracy. Model parameters are inferred solely from two-point statistics using a two-level Bayesian framework, yielding high-fidelity ELG, LRG, and cross-reference catalogs. We find that satellite ELGs behave as incoherent flows within their parent halos, dominating the clustering below 4 h −1 Mpc. The HOD from the best-fit Home has the following properties: (i) 90.50% (85.91%) of ELGs (LRGs) are central galaxies without satellites, residing in halos of M vir ∼ 6.6 × 10 11 (1.2 × 10 13 ) h −1 M ⊙ ; (ii) the ELG×LRG cross-correlation is governed by central-central pairs and shaped by halo exclusion on 2–5 h −1 Mpc scales; (iii) 9.50% (14.09%) of ELGs (LRGs) are satellites, of which 1.09% (3.52%) inhabit halos with a central galaxy of the same species in a maximally conformal configuration, 7.02% (0.005%) orbit complementary hosts in a minimally conformal state, and 0.58% (10.57%) are orphans. The high sensitivity of Home precisely captures the dynamics of satellites in different host environments, opening a promising avenue for understanding systematics and the dynamical nature of dark matter, potentially distinguishing gravity models.

Favole, Ginevra [Universidad de La Laguna (Spain);↗

Film Thickness and Composition Effects in Symmetric Ternary Block Copolymer/Homopolymer Blend Films: Domain Spacing and Orientation

We report thickness and homopolymer molar mass dependencies in thin film blends of a compositionally symmetric 75 kg/mol lamellar polystyrene-block-poly(methyl methacrylate) diblock copolymer (PS-b-PMMA) with near-equal volume fractions of PS and PMMA homopolymers on “neutral” surfaces that promote a vertical domain orientation. PS and PMMA homopolymers with equal molar masses of 1, 3, and 22 kg/mol are blended in a 1:1 mass ratio. To efficiently explore this parameter space, we prepared combinatorial samples with gradient homopolymer concentrations using electrospray deposition (ESD) and gradient film thicknesses using flow coating; these samples were subsequently characterized by grazing-incidence small-angle X-ray scattering and scanning electron microscopy, respectively. Our results demonstrate that the added homopolymers increase or reduce domain spacings with respect to the neat (unblended) block copolymer depending on their molar masses, in line with previous reports; a simple heuristic to estimate the domain scaling in ternary blends based on the homopolymer molar mass agrees well with data for the thinnest blend films studied here. More surprisingly, we observe that the measured domain spacing in blends also depends on film thickness, with thicker films exhibiting larger domain spacings than thinner films at the same homopolymer concentration. Furthermore, thickness gradients at fixed homopolymer concentrations reveal a change in lamellae orientation from vertical to horizontal as film thickness is increased beyond the nominal lamellar domain spacing. Coarse-grained molecular dynamics simulations indicate that this change in orientation is induced by homopolymer segregation to film surfaces. Finally, tying these effects together, we hypothesize that the observed dependence of domain spacing on film thickness is a consequence of changes in the vertical homopolymer composition profile in thicker films during lamellae reorientation and the conformational asymmetry between PMMA and PS segments.

36 MATERIALS SCIENCE↗