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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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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease

Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A combined machine learning and density functional theory study of binary Ti-Nb and Ti-Zr alloys: Stability and Young’s modulus

The multicomponent Ti alloys, specifically the -phase, have experienced a strong growth over the last decades, due to their outstanding properties of ultra-high strength and low Young’s modulus. These properties play a significant role in many aerospace and biomedical applications. Selection and optimization of multicomponent alloys is challenging due to the vast chemical and compositional space. Here we investigate the use of machine learning techniques informed by density functional calculations to guide the selection of Nb- and Zr-based Ti binary alloys. From the cubic structures obtained from high throughput calculations and literature, we identify several structures with Young’s moduli below 40 GPa. The multivariant decision tree methods provide efficient surrogate models to identify structure variables have high influences on the energetic stability and Young’s modulus. Furthermore, we implement a workflow of incorporating DFT provided results and machine learning method to explore the chemical and composition space of other binary and multicomponent alloys, to eventually accelerate the material design via taking advantages of identified key variables.

36 MATERIALS SCIENCE↗
DOE OSTI2025

One Pot Synthesis of Cyan Emitting CdZnSSe Quantum Dots for Human Centric Lighting

A one pot synthesis of blue and green emissive CdZnSSe quantum dots (QDs) from thio- and selenoureas and Cd and Zn carboxylates is optimized using high throughput robotic optimization. A large set of spectral data (N = 192) is used to train machine learning models that accurately predict the photoluminescence emission wavelength (λmax) and full-width half-maximum, and the relative photoluminescence quantum yield (PLQY) from the S:Se and Zn:Cd stoichiometries and reaction time. ZnS shells are deposited on the crude QD heterostructures using 4-tert-butylbenzyl mercaptan, a more reactive source of sulfide that enables shell growth below the temperature where ion diffusion in the QD can broaden its optical spectrum (≤275 °C). These optimized procedures provide gram quantities of blue-green emitting QDs (PLQY = 85–99%) in a single reaction vessel. A solid state lighting device (4260 K) that incorporates cyan emissive QDs achieved a higher luminous efficacy of 179 lm/W and melanopic daylight efficiency ratio (0.71) than existing commercial human centric lighting devices.

Jordan, Abraham J↗
DOE OSTI2024

Toward Accelerating Discovery via Physics-Driven and Interactive Multifidelity Bayesian Optimization

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often nondifferentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest toward active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge of the system in the form of partially known physics laws and exploration policies often vary during the experiment. Here, we propose an interactive workflow building on multifidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) structured MFBO (sMFBO), and finally extend it to allow human-in-the-loop interactive interactive MFBO (iMFBO) workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly nonsmooth multifidelity simulation data generated from an Ising model, considering spin–spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real-time human decisions for improved exploration with increased alignment to ground truth. Here, the associated notebooks allow to reproduce the reported analyses and apply them to other systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Machine Learning on a Robotic Platform for the Design of Polymer–Protein Hybrids

Polymer–protein hybrids are intriguing materials that can bolster protein stability in non-native environments, thereby enhancing their utility in diverse medicinal, commercial, and industrial applications. One stabilization strategy involves designing synthetic random copolymers with compositions attuned to the protein surface, but rational design is complicated by the vast chemical and composition space. Here, a strategy is reported to design protein-stabilizing copolymers based on active machine learning, facilitated by automated material synthesis and characterization platforms. The versatility and robustness of the approach is demonstrated by the successful identification of copolymers that preserve, or even enhance, the activity of three chemically distinct enzymes following exposure to thermal denaturing conditions. Although systematic screening results in mixed success, active learning appropriately identifies unique and effective copolymer chemistries for the stabilization of each enzyme. Overall, this work broadens the capabilities to design fit-for-purpose synthetic copolymers that promote or otherwise manipulate protein activity, with extensions toward the design of robust polymer–protein hybrid materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

The structure and migration of twin boundaries in tetragonal β -Sn: An application of machine learning based interatomic potentials

Although atomistic simulations have contributed significantly to our understanding of twin boundary structure and migration in metals and alloys with hexagonal close packed (HCP) crystal structures, few direct atomistic studies of twinning have been conducted for other types of low symmetry materials, in large part due to a lack of reliable interatomic potentials. In this work, we examine twin boundary structure and migration in a tetragonal material, β-Sn, comparing high resolution Transmission Electron Microscopy (TEM) images of deformation twins in β-Sn to the results of direct atomistic simulations using multiple interatomic potentials. ML-based potentials developed in this work are found to give results consistent with our experimental data, revealing faceted twin boundary structures formed by the nucleation and motion of twinning disconnections. We use bicrystallographic methods in combination with atomistic simulations to analyze the structure, energy and shear coupled migration of observed twin facets in β-Sn. In analogy to Prismatic-Basal (PB/BP) interfaces in HCP metals, we discover low energy asymmetric Prismatic-A-plane (PA/AP) interfaces important to twin growth in β-Sn. Finally, a Moment Tensor Potential (MTP) and Rapid Artificial Neural Network (RANN) interatomic potential suitable for studying twinning and phase transformations in Sn are made publicly available as part of this work.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Machine Learning for Additive Manufacturing of Functionally Graded Materials

Additive Manufacturing (AM) is a transformative manufacturing technology enabling direct fabrication of complex parts layer-by-layer from 3D modeling data. Among AM applications, the fabrication of Functionally Graded Materials (FGMs) has significant importance due to the potential to enhance component performance across several industries. FGMs are manufactured with a gradient composition transition between dissimilar materials, enabling the design of new materials with location-dependent mechanical and physical properties. This study presents a comprehensive review of published literature pertaining to the implementation of Machine Learning (ML) techniques in AM, with an emphasis on ML-based methods for optimizing FGMs fabrication processes. Through an extensive survey of the literature, this review article explores the role of ML in addressing the inherent challenges in FGMs fabrication and encompasses parameter optimization, defect detection, and real-time monitoring. The article also provides a discussion of future research directions and challenges in employing ML-based methods in the AM fabrication of FGMs.

36 - MATERIALS SCIENCE↗
DOE OSTI2023

Machine-Learning Assisted Identification of Battery Life Models

Predictive battery life models are commonly utilized to extrapolate degradation trends observed during accelerated aging tests for simulation of degradation in real-world applications. Thus, fitting accelerated aging data as accurately as possible and with low uncertainty is crucial for making believable projections of battery lifetime, but it is challenging to identify algebraic expressions that accurately fit multivariate degradation trends. A review of models published in literature reveal some common expressions for fitting calendar aging data, which is only dependent on temperature and state-of-charge, but no consistency across many models for fitting cycle aging data, indicating the need for a statistically rigorous data driven approach for developing empirical models. This talk will describe a machine-learning assisted method for identification of predictive battery life models utilizing bilevel optimization and symbolic regression. Bilevel optimization with cross-validation is used to statistically determine cell- and stress-dependent model parameters, while symbolic regression identifies both linear and multiplicative candidate expressions to predict stress-dependent degradation rates by selecting low-order subsets of features from a generated feature library. Because model expressions are identified empirically, it is crucial to ensure resulting models behave according to physical expectations, so the stability of models for interpolation or extrapolation is interrogated qualitatively through simulation and quantitatively through cross-validation and uncertainty quantification via bootstrap resampling. This model identification approach substantially improves upon models identified purely using expert judgement in terms of both accuracy and uncertainty. Model simulation and validation is then conducted by deriving a state-equation form of the predictive model, enabling simulation of battery aging under dynamic stresses. This enables validation of the predictive battery model on lab-based tests with varying conditions or on drive-cycle or application-cycle testing protocols. Parameter uncertainty can be carried forward into model simulation, giving lifetime estimates and confidence windows for cell- or system-level lifetime. The financial impact of battery model uncertainty can be estimated by incorporating uncertainty into a technoeconomic model.

battery↗
DOE OSTI2024

Differentiable Multiphysics Codes: A Breakthrough Technology for Simulation and Computing

This document summarizes the findings of a strategic planning exercise commissioned by the Weapons Simulation and Computing, Computational Physics (WSC/CP) program at the Lawrence Livermore National Laboratory (LLNL) in FY24. During the year, the committee met with multiple stakeholder communities to gather input, opinions, suggestions and concerns which have been incorporated throughout this document. The key findings from this exercise are summarized: • The development of multiphysics modelling and simulation (mod/sim) codes and software technologies, their deployment on exascale compute platforms, and their broad adoption across the NNSA is a major success of the Advanced Simulation and Computing (ASC) program and the Exascale Computing Project (ECP). Sustained investment in these core technologies is essential. • Today’s state of the art involves running ensembles of O(100K) simulations to perform uncertainty quantification (UQ) and design studies using multiple statistical methods such as Bayesian optimization to understand sensitivities of our models and explore parameterized design spaces. Even with exascale computing, we are practically limited to O(10) parameters in these studies since the number of simulations required to sample the space scales exponentially with the number of design parameters. • The data from these simulation ensembles is increasingly being used to train machine learned (ML) surrogates (or reduced order models, ROMs) which can then be used for optimization or real time design exploration. However, the trained surrogates are still limited in the number of parameters they can represent due to the sampling limitations previously noted. • Augmenting our suite of integrated multiphysics simulation codes, both current and emerging, with the ability to compute gradients (solution derivatives) of arbitrary simulation outputs with respect to (some or all) simulation inputs would be a breakthrough technology, opening the door to a new era of efficient and automated inverse design based on verified and validated mod/sim capabilities. • This capability, which we refer to as differentiable multiphysics codes (DMCs), would revolutionize both UQ and optimization studies by breaking the curse of dimensionality that presently limits our “gradient-free” ensemble based computing approach. A similar breakthrough occurred in the AI/ML community once the ability to compute gradients of arbitrary loss functions using back-propagation became commonplace. Gradient information from the multiphysics codes can also be used to dramatically improve the efficiency and scale of training of ML/ROM surrogates for rapid assessments. • Achieving this in our suite of codes will be a grand challenge, similar to the amount of effort that was required to transition from CPU to GPU computing. It will require buy-in from the entire WSC/CP program and beyond, including all integrated codes, physics and engineering models, third-party library dependencies and performance portability abstractions. It will also require investment in research and development of numerical methods for computing adjoints of coupled physics across multiple adaptively refined moving meshes and of stochastic (Monte Carlo) and mesh free (SPH) methods. • New software and numerical techniques, largely pioneered by the AI/ML community, make this feasible. Chief among these is automatic differentiation (AD), the ability to employ AD at point-wise locations in a physics calculation (instead of traditional black-box approaches) and the ability to perform “back-propagation in time” (or reverse mode AD) for non-linear partial differential equations (PDEs). Fundamentally, the conclusion of this strategic planning exercise is that the time is right to undertake a large scale effort in WSC, centered on the existing integrated codes, to continue the natural evolution of mod/sim in the age of AI/ML. Instead of attempting to replace mod/sim with purely data driven AI/ML models, we believe the key to success is to integrate AI/ML by building on top of the decades of hard-won knowledge and the verified/validated multiphysics modelling capability that is the hallmark of the ASC program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Dynamic systems modeling of the spallation neutron source cryogenic moderator system to optimize transient control and prepare for power upgrades

Through support of the US Department of Energy's Office of Basic Energy Sciences, Oak Ridge National Laboratory has begun applying machine learning methods to improve accelerator and target performance of the Spallation Neutron Source (SNS). These methods are being applied to the control optimization and power upgrade of the SNS Cryogenic Moderator System (CMS). A numerical model of the CMS has been developed to study these optimizations and system modifications using EcosimPro. This paper compares steady-state and transient numerical results with experimental data. Control optimization studies focused on dampening mass flow, temperature, and pressure fluctuations during sudden losses of accelerator beam power. This analysis was conducted by adjusting five proportional-integral-derivative controllers connected to four flow control valves and one heater. Future efforts include power uprate studies focused on increasing the CMS cooling capacity. The current accelerator power is 1.4 MW; the first target station is being upgraded to 2.0 MW as part of the Proton Power Upgrade effort. The CMS cooling capacity is sufficient for 2.0 MW operation.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Developing multi-gene CRISPRa/i programs to accelerate DBTL cycles in ABF hosts engineered for chemical production

This project developed and implemented a modular CRISPR activation and interference (CRISPRa/i) platform to accelerate strain optimization and pathway development for industrially relevant microbial hosts. By integrating multiplexed transcriptional perturbation tools with data-driven Design–Build–Test–Learn (DBTL) workflows, the team achieved reductions in cycle time and enhanced production of industrial aromatics, particularly 4-aminocinnamic acid (4-ACA), in Pseudomonas putida. Key accomplishments included: ● Development of a robust, tunable CRISPRa/i system in P. putida that enabled efficient multi-target gene regulation via guide RNA (gRNA) programs ● Completion of two full DBTL cycles, guided by machine learning (ML) models trained on transcriptomic and performance data, reducing engineering time by over 30% ● Optimization of multi-gene regulatory programs to balance expression of host and pathway modules, improve 4-ACA titers, and resolve metabolic bottlenecks ● Demonstration of system portability through a limited proof-of-concept extension in Acinetobacter baylyi, underscoring the generalizability of the approach ● Evaluation of strain performance on lignocellulosic biomass-derived substrates, demonstrating the feasibility of converting renewable carbon into aromatic building blocks These results illustrate the feasibility of applying ML-guided CRISPRa/i perturbation strategies to accelerate strain development in complex microbial systems. The resulting tools and datasets contribute to DOE objectives by improving platform predictability, reducing development costs, and enabling broader access to sustainable, economically viable bioproduction technologies.

09 BIOMASS FUELS↗
DOE OSTI2026

SODAs: sparse optimization for the discovery of differential and algebraic equations

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by time-scale separation, conservation laws and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods for DAE systems with unknown constraints and time scales. We introduce sparse optimization for differential-algebraic systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems. It has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves since SODAs is singular numerical stability when handling high correlations between library terms, caused by near-perfect algebraic relationships, by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.

DAE↗
DOE OSTI2022

Photovoltaic System Health-State Architecture for Data-Driven Failure Detection

The timely detection of photovoltaic (PV) system failures is important for maintaining optimal performance and lifetime reliability. A main challenge remains the lack of a unified health-state architecture for the uninterrupted monitoring and predictive performance of PV systems. To this end, existing failure detection models are strongly dependent on the availability and quality of site-specific historic data. The scope of this work is to address these fundamental challenges by presenting a health-state architecture for advanced PV system monitoring. The proposed architecture comprises of a machine learning model for PV performance modeling and accurate failure diagnosis. The predictive model is optimally trained on low amounts of on-site data using minimal features and coupled to functional routines for data quality verification, whereas the classifier is trained under an enhanced supervised learning regime. The results demonstrated high accuracies for the implemented predictive model, exhibiting normalized root mean square errors lower than 3.40% even when trained with low data shares. The classification results provided evidence that fault conditions can be detected with a sensitivity of 83.91% for synthetic power-loss events (power reduction of 5%) and of 97.99% for field-emulated failures in the test-bench PV system. Finally, this work provides insights on how to construct an accurate PV system with predictive and classification models for the timely detection of faults and uninterrupted monitoring of PV systems, regardless of historic data availability and quality. Such guidelines and insights on the development of accurate health-state architectures for PV plants can have positive implications in operation and maintenance and monitoring strategies, thus improving the system’s performance.

photovoltaics↗
DOE OSTI2022

A differentiable approach to the maximum independent set problem using dataless neural networks

The success of machine learning solutions for reasoning about discrete structures has brought attention to its adoption within combinatorial optimization algorithms. Such approaches generally rely on supervised learning by leveraging datasets of the combinatorial structures of interest drawn from some distribution of problem instances. Reinforcement learning has also been employed to find such structures. Here, in this paper, we propose a different approach in that no data is required for training the neural networks that produce the solution. In this sense, what we present is not a machine learning solution, but rather one that is dependent on neural networks and where backpropagation is applied to a loss function defined by the structure of the neural network architecture as opposed to a training dataset. In particular, we reduce the popular combinatorial optimization problem of finding a maximum independent set to a neural network and employ a dataless training scheme to refine the parameters of the network such that those parameters yield the structure of interest. Additionally, we propose a universal graph reduction procedure to handle large-scale graphs. The reduction exploits community detection for graph partitioning and is applicable to any graph type and/or density. Experimental results on both real and synthetic graphs demonstrate that our proposed method performs on par or outperforms state-of-the-art learning-based methods in terms of the size of the found set without requiring any training data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Optimal dimensionality selection for independent component analysis of transcriptomic data

Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Deep learning based x-ray spectrometer for high repetition rate characterization of betatron radiation

Betatron radiation produced from a laser-wakefield accelerator is a broadband, hard x-ray (>1 keV) source that has been used in a variety of applications in medicine, engineering, and fundamental science. Further development and optimization of stable, high repetition rate (HRR) (>1 Hz) betatron sources will provide a means to extend their application base to include single-shot dynamical measurements of ultrafast processes or dense materials. Recent advances in laser technology used in such experiments have enabled increases in shot-rate and system stability, providing improved statistical analysis and detailed parameter scans. However, unique challenges exist at high repetition rate, where data throughput and source optimization are now limited by diagnostic acquisition rates and analysis. Here, we present the development of a machine-learning algorithm for the real-time analysis of betatron radiation. We report on the fielding of this deep learning algorithm for online source characterization at the Institut National de la Recherche Scientifique's Advanced Laser Light Source. By fine-tuning an algorithm originally trained on a fully synthetic dataset using a subset of experimental data, the algorithm can predict the betatron critical energy with a percent error of 7.2 % with a reconstruction time of 1.5 ms, providing a valuable tool for real-time, multi-objective optimization at HRR.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

A machine learning approach targeting parameter estimation for plant functional type coexistence modeling using ELM-FATES (v2.0)

Tropical forest dynamics play a crucial role in the global carbon, water, and energy cycles. However, realistically simulating the dynamics of competition and coexistence between different plant functional types (PFTs) in tropical forests remains a significant challenge. This study aims to improve the modeling of PFT coexistence in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a vegetation demography model implemented in the Energy Exascale Earth System Model (E3SM) land model (ELM), ELM-FATES. Specifically, we explore (1) whether plant trait relationships established from field measurements can constrain ELM-FATES simulations and (2) whether machine learning (ML)-based surrogate models can emulate the complex ELM-FATES model and optimize parameter selections to improve PFT coexistence modeling. We conducted three ensembles of ELM-FATES experiments at a tropical forest site near Manaus, Brazil. By comparing the ensemble experiments without (Exp-CTR) and with (Exp-OBS) consideration of observed trait relationships, we found that accounting for these relationships slightly improves the simulations of water, energy, and carbon variables when compared to observations but degrades the simulation of PFT coexistence. Using ML-based surrogate models trained on Exp-CTR, we optimized the trait parameters in ELM-FATES and conducted another ensemble of experiments (Exp-ML) with these optimized parameters. The proportion of PFT coexistence experiments significantly increased from 21 % in Exp-CTR to 73 % in Exp-ML. After filtering the experiments that allow for PFT coexistence to agree with observations (within 15 % tolerance), 33 % of the Exp-ML experiments were retained, which is a significant improvement compared to the 1.4 % in Exp-CTR. Exp-ML also accurately reproduces the annual means and seasonal variations in water, energy, and carbon fluxes and the field inventory of aboveground biomass. This study represents a reproducible method that utilizes machine learning to identify parameter values that improve model fidelity against observations and PFT coexistence in vegetation demography models for diverse ecosystems. Our study also suggests the need for new mechanisms to enhance the robust simulation of coexisting plants in ELM-FATES and has significant implications for modeling the response and feedbacks of ecosystem dynamics to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗