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DOE OSTI2022

Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning

Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Mass of 101 Sn and Bayesian extrapolations to the proton drip line

The favorable energy configurations of nuclei at magic numbers of 𝑁 neutrons and 𝑍 protons are fundamental for understanding the evolution of nuclear structure. The 𝑍 = 50 (tin) isotopic chain is a frontier for such studies, with particular interest at and around the doubly magic 100 Sn isotope, for which the mass is a topic of debate. Precise mass values for neutron-deficient isotopes provide necessary anchor points for mass models to test extrapolations near the proton drip line, where experimental studies remain out of reach. In this work, we report a Penning trap mass measurement of 101 Sn . The determined mass excess of −59889.89⁢(96) keV for 101 Sn represents a factor-of-300 improvement over the current precision and indicates that 101 Sn is less bound than previously thought. Mass predictions from a recently developed Bayesian model combination framework employing statistical machine learning and nuclear masses computed within seven global models based on nuclear density functional theory agree within 1⁢𝜎 with experimental masses from the 48 ≤ 𝑍 ≤ 52 isotopic chains. The framework's resilience to new mass data gave confidence in the extrapolation of tin masses down to 𝑁 = 46. Our calculations suggest that 96 Sn is a two-proton drip line nucleus and predict a mass excess of −58090⁢(800) keV for 100 Sn , showing a preference within 1⁢𝜎 for the mass of 100 Sn derived from the 𝛽-delayed 𝑄 value measured at GSI.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Generating Protein Structures for Pathway Discovery Using Deep Learning

Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Accelerating Solvent Selection for Type II Porous Liquids

Type II porous liquids, comprising intrinsically porous molecules dissolved in a liquid solvent, potentially combine the adsorption properties of porous adsorbents with the handling advantages of liquids. Previously, discovery of appropriate solvents to make porous liquids had been limited to direct experimental tests. We demonstrate an efficient screening approach for this task that uses COSMO-RS calculations, predictions of solvent pK a values from a machine-learning model, and several other features and apply this approach to select solvents from a library of more than 11,000 compounds. Additionally, this method is shown to give qualitative agreement with experimental observations for two molecular cages, CC13 and TG-TFB-CHEDA, identifying solvents with higher solubility for these molecules than had previously been known. Ultimately, the algorithm streamlines the downselection of suitable solvents for porous organic cages to enable more rapid discovery of Type II porous liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Continuous-variable quantum Boltzmann machine

Here, we propose a continuous-variable quantum Boltzmann machine (CVQBM) using a powerful energy-based neural network. It can be realized experimentally on a continuous-variable (CV) photonic quantum computer. We used a CV quantum imaginary time evolution (QITE) algorithm to prepare the essential thermal state and then designed the CVQBM to proficiently generate continuous probability distributions. We applied our method to both classical and quantum data. Using real-world classical data, such as synthetic-aperture radar (SAR) images, we generated probability distributions. For quantum data, we used the output of CV quantum circuits. We obtained high fidelity and low Kullback–Leibler (KL) divergence showing that our CVQBM learns distributions from given data well and generates data sampling from that distribution efficiently. We also discussed the experimental feasibility of our proposed CVQBM. Our method can be applied to a wide range of real-world problems by choosing an appropriate target distribution (corresponding to, e.g., SAR images, medical images, and risk management in finance). Moreover, our CVQBM is versatile and could be programmed to perform tasks beyond generation, such as anomaly detection.

SAR images↗

DOE OSTI2021

Co-design Center for Exascale Machine Learning Technologies (ExaLearn)

We report rapid growth in data, computational methods, and computing power is driving a remarkable revolution in what variously is termed machine learning (ML), statistical learning, computational learning, and artificial intelligence. In addition to highly visible successes in machine-based natural language translation, playing the game Go, and self-driving cars, these new technologies also have profound implications for computational and experimental science and engineering, as well as for the exascale computing systems that the Department of Energy (DOE) is developing to support those disciplines. Not only do these learning technologies open up exciting opportunities for scientific discovery on exascale systems, they also appear poised to have important implications for the design and use of exascale computers themselves, including high-performance computing (HPC) for ML and ML for HPC. The overarching goal of the ExaLearn co-design project is to provide exascale ML software for use by Exascale Computing Project (ECP) applications, other ECP co-design centers, and DOE experimental facilities and leadership class computing facilities.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2019

Shockwave/Boundary-Layer Interaction Studies Performed in the NASA Langley 20-Inch Mach 6 Air Tunnel

This paper highlights results from a collaborative study performed by The University of Tennessee Space Institute (UTSI) and NASA Langley Research Center on the Shockwave/Boundary-Layer Interaction (SWBLI) generated by a cylindrical protuberance on a flat plate in a Mach 6 flow. The study was performed in the 20-Inch Mach 6 Air Tunnel at NASA Langley Research Center and consisted of two separate entries. In the first entry, simultaneous high-speed schlieren and high-speed pressure-sensitive paint (PSP) imaging – which was performed for the first time in the 20-Inch Mach 6 facility at NASA Langley – were performed as well as simultaneous high-speed schlieren and oil-flow imaging. In the second entry, the model configuration was modified to increase the size of the interaction region. High-speed schlieren and infrared thermography (IR) surface imaging were performed in this second entry. The goal of these tests was to characterize the SBLI in the presence of a laminar, transitional, and turbulent boundary layer using high-speed optical imaging techniques. AoA = sting angle-of-attack (°) dcylinder = cylinder diameter (mm) dtrip = cylindrical tripping element diameter (mm) Δshock = shock stand-off distance (mm) hcylinder = cylinder height (mm) htrip = cylindrical tripping element height (mm) HSS = high-speed schlieren M∞ = freestream Mach number PSP = pressure-sensitive paint Re∞ = freestream unit Reynolds number (m-1) SWBLI = shockwave/boundary-layer interaction θplate = model plate angle (°) Introduction his paper highlights two experimental entries performed in the 20-Inch Mach 6 Air Blowdown Tunnel at NASA Langley Research Center in collaboration with The University of Tennessee Space Institute (UTSI). The purpose of these entries was to characterize the dynamic shockwave/boundary-layer interaction (SWBLI) between a vertical cylinder on a flat plate and laminar, transitional (XSWBLI), and turbulent (SWTBLI) boundary layers with a freestream Mach number of 6 using non-intrusive optical diagnostics. Experiments performed by Murphree et al.1,2 were among the first to specifically characterize XSWBLI induced by a vertical cylinder on a flat plate geometry using several optical measurement techniques. Recent optical studies of XSWBLI phenomenon have been performed by UTSI at Mach 2 in their low-enthalpy blow wind tunnel3-8 and by Texas A&M University and UTSI at Mach numbers of 6 and 7 in their Adjustable Contour Expansion wind tunnel.9 The experiments described in this paper were intended to complement previous studies by expanding the freestream unit Reynolds number range, Re∞, over which the XSWBLI phenomena has been observed. Additionally these experiments, made possible under NASA’s new facility funding model under the Aeronautics Evaluation and Test Capabilities (AETC) project, promoted collaboration between university and NASA researchers. The initial entry in the 20-Inch Mach 6 Air Tunnel at NASA Langley occurred in December of 2016. Originally, testing was to occur in November of 2016 in the 31-Inch Mach 10 Air Tunnel at NASA Langley. This facility was chosen so that the XSWBLI phenomenon could be observed at much higher Mach numbers than had previously been attempted in ground test experiments. The model selected for this experiment, a 10° half-angle wedge with a sharp leading edge (described in detail in section II.B), had previously been used by Danehy et al. [10] for boundary layer transition studies using the nitric oxide planar laser-induced fluorescence (NO PLIF) flow visualization technique. In that work, it was determined that transition could be induced downstream of a single htrip = 1-mm tall, dtrip = 4-mm diameter cylindrical tripping element and that the streamwise location of the transition could be changed for a single Re∞ by changing the model angle-of-attack (AoA) (see Fig. A3 in Ref. [10] for more details). Based on the findings of that work, a decision was made to use the wedge model with the cylindrical tripping element to trip the boundary layer flow ahead of a cylindrical protuberance in order to achieve a XSWBLI. Unfortunately, the 31-Inch Mach 10 facility had been taken offline for repairs in October of 2016 and a decision was made to move the test to the 20-Inch Mach 6 facility. Since the behavior of the boundary layer with the chosen model configuration had not been studied before in that facility and the available test time was limited, the entry was considered to be exploratory and was used to collect spatially-resolved and time-resolved flow and surface visualization data that would be used to inform a second entry. Test techniques included simultaneous high-speed schlieren (HSS) captured at 160 kHz and high-speed pressure sensitive paint captured at 10 kHz as well as oil flow visualization, captured at 750 Hz. The second entry in the 20-Inch Mach 6 facility occurred in June and July of 2017. In this follow-on test, modifications to the wind tunnel model were made based on observations made during the first entry and included removing the cylindrical tripping element, increasing the size of the cylinder used to induce the SWBLI to increase the size of the interaction while simultaneously improving spatial resolution, and using a swept ramp array, similar to that described in Ref. [11], to trip the flow to turbulence. Simultaneous HSS (captured at 140 kHz, 100 kHz, and 40 kHz) and conventional IR thermography (captured at 30 Hz) imaging were performed simultaneously in this follow-on entry. This paper is intended to serve as a summary of the work performed during these two entries, to detail lessons learned from each entry, and to highlight some of the datasets acquired. Details on the experimental setup, model configuration, and techniques used are provided. Papers providing a more rigorous analysis of data acquired during the second entry, including statistical, spectral, and modal decomposition methods, can be found in Refs. [12,13]. An entry examining XSWBLI in the 31-Inch Mach 10 Blowdown Wind Tunnel facility is currently planned for mid-to-late calendar year 2019, pending the success of facility repairs. The work performed and described in this paper and the upcoming entry in the 31-Inch Mach 10 facility at NASA Langley have been made possible by NASA’s new facility funding model under the Aeronautics Evaluation and Test Capabilities (AETC) project. Wind Tunnel Facility All experiments discussed in this paper were performed in the 20-Inch Mach 6 Air Tunnel at NASA Langley Research Center. Specific details pertaining to this facility can be found in Refs. [14,15], with only a brief description of the facility provided here. For both entries, the nominal freestream unit Reynolds number was varied between 1.8×106 m-1 (0.5×106 ft-1) and 26.3×106 m-1 (8×106 ft-1). The nominal stagnation pressure was varied between 0.21 MPa and 3.33 MPa and the nominal stagnation temperature was varied between 480 K and 520 K to achieve the desired Re∞ condition. For all runs, the nominal freestream Mach number was 6. The nearly square test section is 520.7-mm (20.5-inches) wide by 508-mm (20-inches) high. Two 431.8-mm (17-inch) diameter windows made of Corning 7940, Grade 5F schlieren-quality glass serve as the side walls of the tunnel and provide optical access for the high-speed schlieren measurements. A rectangular window made of the same material as the side windows served as the top wall of the test section and provided optical access for the high-speed PSP and oil flow measurements. For the second entry, this top window was replaced with a Zinc Selenide (ZnSe) window with an anti-reflection coating capable of passing IR wavelengths between 8μm and 12μm with greater than 98% transmittance. The model was sting supported by a strut attached to a hydraulic system that allows for the model pitch angle to be adjusted between -5° to +55°. For the first entry, an initial pitch/pause sweep of the model AoA was performed to observe the resulting SWBLI. Ultimately, however, the sting pitch angle for this entry was fixed at +10.0° so that the angle of the top surface of the wedge relative to the streamwise axis of the tunnel (referred to herein as the plate angle, θplate), was θplate = 0°. For the second entry, θplate = 0° and θplate = -13.25° were initially tested with the swept ramp array (discussed in the following section) to determine which orientation produced conditions most favorable for XSWBLI to occur based on the heating signatures observed over the top surface of the model in the IR thermography images. Based on these initial tests, θplate = -13.25° was set for the remainder of the runs in the second entry. For both entries, any model changes were performed in a housing located beneath the closed test section. Prior to performing a run of the tunnel, the housing was sealed and the tunnel started. Once the appropriate freestream conditions were achieved, the model was injected into the test section using a hydraulic injection system. B. Model Geometry For all runs, a 10° half-angle (20° full-angle) wedge model with a sharp leading edge was used. The model is described in detail in Refs. [10,16]. The top surface of the sharp leading edge of the model extended 47.8 mm from its upstream-most edge to a junction with the upstream edge of a stainless steel top plate that then extended an (a) (c) (b) Fig. 1 (a) Schematic of top surface of wedge model with gas seeding insert, (b) perspective view of the model in the 20-Inch Mach 6 tunnel with centerline pressure orifices on sharp leading edge, and (c) a perspective view of the model with stainless steel (top) and SLA middle insert (bottom) during the first entry. Flow occurs from left to right.

Bathel, Brett F.↗

NASA NTRSDate not supplied

Artificial Neural Networks to Predict Cognitive Impairment of Rodents Subjected to Space Radiation

INTRODUCTION We use artificial neural networks (ANNs) as an example machine learning (ML) tool to predict the cognitive performance impairment of rats induced by irradiation. The experimental data in the analyses is attentional set-shifting (ATSET) test scores from a rodent model exposed to ≤15 cGy of individual galactic cosmic radiation (GCR) ions: 4He, 28Si, or 56Fe, expected for a Lunar or Mars mission [1]. This work investigates rats at a subject-based level and uses applied dose and performance scores taken before irradiation to predict whether a rat will be impaired when irradiated. The results of this study are significant to crewed space missions as they support the potential of predicting an astronaut’s impairment in a specific task before spaceflight through the implementation of appropriately trained ML tools. METHODS Data used in this work are scores from the ATSET, a multi-stage constrained cognitive flexibility test [2]. Our computational model utilizes the number of attempts to reach the criterion to pass a stage as a behavioral performance measure for rats. We use the post-irradiation scores, generate thresholds from cumulative distribution plots of non-irradiated rats, and calculate the percent of irradiated rats whose scores fall below the threshold to infer how each radiation type/dose affects a population. Rats scoring above the threshold are labeled impaired while the others are non-impaired. We then employ ANNs as a typical ML technique, and use each subject’s individual scores taken before radiation along with the applied dose, to predict their personal susceptibility to cognitive impairment due to space radiation exposure. RESULTS AND CONCLUSION A significant finding is the exhibition of a dose-dependent increasing probability of impairment for 1 to 10 cGy of 28Si or 56Fe in the simple discrimination (SD) stage of the ATSET, and for 1 to 10 cGy of 56Fe in the compound discrimination (CD) stage. On a subject-based level, implementing ML classifiers such as ANNs identifies rats that have a higher tendency for impairment after GCR exposure [1]. The receiver operating characteristic (ROC) and the precision-recall (PR) curves of the ML models show a better prediction of impairment when 56Fe is the ion in question in both SD (Figure 1) and CD stages. They, however, do not depict impairment due to 4He in SD (Figure 1) and 28Si in CD, suggesting no dose-dependent impairment response in these cases. In this work, “good” prediction pertains to “better-than-random-chance”, due to the limited sample size and the high inter- and intra-individual variabilities in response to brain stimulation paradigms, as applicable to both animals and humans. More behavioral tests and biomarkers should be investigated on the same subjects, to be fed to the ML models to capture the agents responsible for performance alterations of some individuals versus others.

machine learning↗

NASA NTRSDate not supplied

Machine Learning Models to Predict Cognitive Impairment of Rodents Subjected to Space Radiation

machine learning↗

DOE OSTI2021

Fully Convolutional Spatio-Temporal Models for Representation Learning in Plasma Science

We have trained a fully convolutional spatio-temporal model for fast and accurate representation learning in the challenging exemplar application area of fusion energy plasma science. The onset of major disruptions is a critically important fusion energy science issue that must be resolved for advanced tokamak plasmas such as the $25B burning plasma international thermonuclear experimental reactor (ITER) experiment. While a variety of statistical methods have been used to address the problem of tokamak disruption prediction and control, recent approaches based on deep learning have proven particularly compelling. In the present paper, we introduce further improvements to the fusion recurrent neural network (FRNN) software suite, which delivered cross-machine disruption predictions with unprecedented accuracy using a large database of experimental signals from two major tokamaks. Up to now, FRNN was based on the long short-term memory (LSTM) variant of recurrent neural networks to leverage the temporal information in the data. Here, we implement and apply the "temporal convolutional neural network (TCN)" architecture to the time-dependent input signals. Furthermore, this allows highly optimized convolution operations to carry the majority of the computational load of training, thus enabling a reduction in training time, and the effective use of high-performance computing resources for hyperparameter tuning. At the same time, the TCN-based architecture achieves better predictive performance when compared with the LSTM architecture for various tasks for a representative fusion database.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Predictive model for real-time energy disaggregation using long short-term memory

To provide affordable energy-saving solutions for the small and medium-sized manufacturers (SMMs), we propose a unified framework for generating predictive models that support real-time disaggregation of power consumption from combined inputs, enabling automatic machine state identification simultaneously for joint analysis of energy usage patterns. Further, the proposed framework transforms raw power consumption into a time series with look-back and bootstrap capabilities for historical pattern detection, while a learning architecture utilizes the stacked long short-term memory (LSTM) layers as encoders for embedding generation with sequential awareness. Experimental results demonstrate 93.65% minimum accuracy in ideal case of real-time energy usage and machine state prediction.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Optimal Adsorbents for Low-Cost Storage of Natural Gas and Hyd: Computational Identification, Experimental Demonstration, and System-Level Projection

This research program will develop best-in-class natural gas (NG) and hydrogen adsorbents based on metal-organic frameworks (MOFs). More specifically, high-throughput computational screening coupled to machine learning will be used to identify MOFs that simultaneously achieve high usable gravimetric and volumetric capacities for methane and hydrogen. The most promising materials pinpointed by computation will be synthesized and characterized experimentally. In addition, the final stage of the project will critically evaluate the use of methane as a model for NG and consider which structural features are most important in making a viable NG storage system.

03 NATURAL GAS↗

DOE OSTI2021

Benchmarking Coordination Number Prediction Algorithms on Inorganic Crystal Structures

Coordination numbers and geometries form a theoretical framework for understanding and predicting materials properties. Algorithms to determine coordination numbers automatically are increasingly used for machine learning and automatic structural analysis. In this work, we introduce MaterialsCoord, a benchmark suite containing 56 experimentally-derived crystal structures (spanning elements, binaries, and ternary compounds) and their corresponding coordination environments as described in the research literature. We also describe CrystalNN, a novel algorithm for determining near neighbors. We compare CrystalNN against 7 existing near-neighbor algorithms on the MaterialsCoord benchmark, finding CrystalNN to perform similarly to several well-established algorithms. For each algorithm, we also assess computational demand and sensitivity towards small perturbations that mimic thermal motion. Finally, we investigate the similarity between bonding algorithms when applied to the Materials Project database. Finally, we expect that this work will aid the development of coordination prediction algorithms as well as improve structural descriptors for machine learning and other applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Utilization of machine learning to accelerate colloidal synthesis and discovery

Machine learning techniques are seeing increased usage for predicting new materials with targeted properties. However, widespread adoption of these techniques is hindered by the relatively greater experimental efforts required to test the predictions. Furthermore, because failed synthesis pathways are rarely communicated, it is difficult to find prior datasets that are sufficient for modeling. This work presents a closed-loop machine learning-based strategy for colloidal synthesis of nanoparticles, assuming no prior knowledge of the synthetic process, in order to show that synthetic discovery can be accelerated despite limited data availability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Combining High-Throughput Experiments and Active Learning to Characterize Deep Eutectic Solvents

The high tunability of deep eutectic solvents (DESs) stems from the ease of changing their precursors and relative compositions. However, measuring the physicochemical properties across large composition and temperature ranges, necessary to properly design target-specific DESs, is tedious and error-prone and represents a bottleneck in the advancement and scalability of DES-based applications. As such, active learning (AL) methodologies based on Gaussian processes (GPs) were developed in this work to minimize the experimental effort necessary to characterize DESs. Owing to its importance for large-scale applications, the reduction of DES viscosity through the addition of a low-molecular-weight solvent was explored as a case study. A high-throughput experimental screening was initially performed on nine different ternary DESs. Then, GPs were successfully trained to predict DES viscosity from its composition and temperature, showcasing the ability of these stochastic, nonparametric models to accurately describe the physicochemical properties of complex mixtures. Finally, the ability of GPs to provide estimates of their own uncertainty was leveraged through an AL framework to minimize the number of data points necessary to obtain accurate viscosity modes. This led to a significant reduction in data requirements, with many systems requiring only five independent viscosity data points to be properly described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2008

Automated Assume-Guarantee Reasoning by Abstraction Refinement

Current automated approaches for compositional model checking in the assume-guarantee style are based on learning of assumptions as deterministic automata. We propose an alternative approach based on abstraction refinement. Our new method computes the assumptions for the assume-guarantee rules as conservative and not necessarily deterministic abstractions of some of the components, and refines those abstractions using counter-examples obtained from model checking them together with the other components. Our approach also exploits the alphabets of the interfaces between components and performs iterative refinement of those alphabets as well as of the abstractions. We show experimentally that our preliminary implementation of the proposed alternative achieves similar or better performance than a previous learning-based implementation.

Pasareanu, Corina S.↗

DOE OSTI2022

Understanding, discovery, and synthesis of 2D materials enabled by machine learning

Machine learning (ML) is becoming an effective tool for studying 2D materials. Taking as input computed or experimental materials data, ML algorithms predict the structural, electronic, mechanical, and chemical properties of 2D materials that have yet to be discovered. Such predictions expand investigations on how to synthesize 2D materials and use them in various applications, as well as greatly reduce the time and cost to discover and understand 2D materials. This tutorial review focuses on the understanding, discovery, and synthesis of 2D materials enabled by or benefiting from various ML techniques. Here, we introduce the most recent efforts to adopt ML in various fields of study regarding 2D materials and provide an outlook for future research opportunities. The adoption of ML is anticipated to accelerate and transform the study of 2D materials and their heterostructures.

2D Materials↗

DOE OSTI2025

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗