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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Computational approaches to model X-ray photon correlation spectroscopy from molecular dynamics

X-ray photon correlation spectroscopy (XPCS) allows for the resolution of dynamic processes within a material across a wide range of length and time scales. X-ray speckle visibility spectroscopy (XSVS) is a related method that uses a single diffraction pattern to probe ultrafast dynamics. Interpretation of the XPCS and XSVS data in terms of underlying physical processes is necessary to establish the connection between the macroscopic responses and the microstructural dynamics. To aid the interpretation of the XPCS and XSVS data, we present a computational framework to model these experiments by computing the X-ray scattering intensity directly from the atomic positions obtained from molecular dynamics simulations. We compare the efficiency and accuracy of two alternative computational methods: the direct method computing the intensity at each diffraction vector separately, and a method based on fast Fourier transform that computes the intensities at all diffraction vectors at once. Furthermore, the computed X-ray speckle patterns capture the density fluctuations over a range of length and time scales and are shown to reproduce the known properties and relations of experimental XPCS and XSVS for liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2016

INTEGRATION OF PANDA WORKLOAD MANAGEMENT SYSTEM WITH SUPERCOMPUTERS

Abstract The Large Hadron Collider (LHC), operating at the international CERN Laboratory in Geneva, Switzerland, is leading Big Data driven scientific explorations. Experiments at the LHC explore the funda- mental nature of matter and the basic forces that shape our universe, and were recently credited for the dis- covery of a Higgs boson. ATLAS, one of the largest collaborations ever assembled in the sciences, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System for managing the workflow for all data processing on over 140 data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data cen- ters are physically scattered all over the world. While PanDA currently uses more than 250000 cores with a peak performance of 0.3+ petaFLOPS, next LHC data taking runs will require more resources than Grid computing can possibly provide. To alleviate these challenges, LHC experiments are engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with supercomputers in United States, Europe and Russia (in particular with Titan supercomputer at Oak Ridge Leadership Com- puting Facility (OLCF), Supercomputer at the National Research Center Kurchatov Institute , IT4 in Ostrava, and others). The current approach utilizes a modified PanDA pilot framework for job submission to the supercomputers batch queues and local data management, with light-weight MPI wrappers to run single- threaded workloads in parallel on Titan s multi-core worker nodes. This implementation was tested with a variety of Monte-Carlo workloads on several supercomputing platforms. We will present our current accom- plishments in running PanDA WMS at supercomputers and demonstrate our ability to use PanDA as a portal independent of the computing facility s infrastructure for High Energy and Nuclear Physics, as well as other data-intensive science applications, such as bioinformatics and astro-particle physics.

De, K↗
DOE OSTI2011

On the Origin of Ultra High Energy Cosmic Rays II

We show that accretion disks around Active Galactic Nuclei (AGNs) could account for the enormous power in observed ultra high energy cosmic rays {approx}10{sup 20} eV (UHEs). In our model, cosmic rays are produced by quasi-steady acceleration of ions in magnetic structures previously proposed to explain jets around Active Galactic Nuclei with supermassive black holes. Steady acceleration requires that an AGN accretion disk act as a dynamo, which we show to follow from a modified Standard Model in which the magnetic torque of the dynamo replaces viscosity as the dominant mechanism accounting for angular momentum conservation during accretion. A black hole of mass M{sub BH} produces a steady dynamo voltage V {proportional_to} {radical}M{sub BH} giving V {approx} 10{sup 20} volts for M{sub BH} {approx} 10{sup 8} solar masses. The voltage V reappears as an inductive electric field at the advancing nose of a dynamo-driven jet, where plasma instability inherent in collisionless runaway acceleration allows ions to be steadily accelerated to energies {approx} V, finally ejected as cosmic rays. Transient events can produce much higher energies. The predicted disk radiation is similar to the Standard Model. Unique predictions concern the remarkable collimation of jets and emissions from the jet/radiolobe structure. Given MBH and the accretion rate, the model makes 7 predictions roughly consistent with data: (1) the jet length; (2) the jet radius; (3) the steady-state cosmic ray energy spectrum; (4) the maximum energy in this spectrum; (5) the UHE cosmic ray intensity on Earth; (6) electron synchrotron wavelengths; and (7) the power in synchrotron radiation. These qualitative successes motivate new computer simulations, experiments and data analysis to provide a quantitative verification of the model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Models, data, and scripts associated with “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning”

This data package is associated with the publication “Prediction of Distributed River Sediment Respiration Rates using Community-Generated Data and Machine Learning’’ submitted to the Journal of Geophysical Research: Machine Learning and Computation (Scheibe et al. 2024). River sediment respiration observations are expensive and labor intensive to obtain and there is no physical model for predicting this quantity. The Worldwide Hydrobiogeochemisty Observation Network for Dynamic River Systems (WHONDRS) observational data set (Goldman et al.; 2020) is used to train machine learning (ML) models to predict respiration rates at unsampled sites. This repository archives training data, ML models, predictions, and model evaluation results for the purposes of reproducibility of the results in the associated manuscript and community reuse of the ML models trained in this project. One of the key challenges in this work was to find an optimum configuration for machine learning models to work with this feature-rich (i.e. 100+ possible input variables) data set. Here, we used a two-tiered approach to managing the analysis of this complex data set: 1) a stacked ensemble of ML models that can automatically optimize hyperparameters to accelerate the process of model selection and tuning and 2) feature permutation importance to iteratively select the most important features (i.e. inputs) to the ML models. The major elements of this ML workflow are modular, portable, open, and cloud-based, thus making this implementation a potential template for other applications. This data package is associated with the GitHub repository found at Please see the file level metadata (flmd; “sl-archive-whondrs_flmd.csv”) for a list of all files contained in this data package and descriptions for each. Please see the data dictionary (dd; “sl-archive-whondrs_dd.csv”) for a list of all column headers contained within comma separated value (csv) files in this data package and descriptions for each. The GitHub repository is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning models trained on the data in “input_data”; (3) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; (4) “examples” contains the visualization of the results in this repository including plotting scripts for the manuscript (e.g., model evaluation, FPI results) and scripts for running predictions with the ML models (i.e., reusing the trained ML models); (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. Furthermore, depending on the number of features used to train the ML models, the preprocessing and postprocessing scripts, and their intermediate results, can also be different branch-to-branch. The “main-*” branches are meant to be starting points (i.e. trunks) for each model branch (i.e. sprouts). Please see the Branch Navigation section in the top-level README.md in the GitHub repository for more details. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please the top-level README.md in the GitHub repository for more details on the automation.

13C↗
DOE OSTI2015

Analytic reconstruction algorithms for triple-source CT with horizontal data truncation

Purpose: This paper explores a triple-source imaging method with horizontal data truncation to enlarge the field of view (FOV) for big objects. Methods: The study is conducted by using theoretical analysis, mathematical deduction, and numerical simulations. The proposed algorithms are implemented in c + + and MATLAB. While the basic platform is constructed in MATLAB, the computationally intensive segments are coded in c + +, which are linked via a MEX interface. Results: A triple-source circular scanning configuration with horizontal data truncation is developed, where three pairs of x-ray sources and detectors are unevenly distributed on the same circle to cover the whole imaging object. For this triple-source configuration, a fan-beam filtered backprojection-type algorithm is derived for truncated full-scan projections without data rebinning. The algorithm is also extended for horizontally truncated half-scan projections and cone-beam projections in a Feldkamp-type framework. Using their method, the FOV is enlarged twofold to threefold to scan bigger objects with high speed and quality. The numerical simulation results confirm the correctness and effectiveness of the developed algorithms. Conclusions: The triple-source scanning configuration with horizontal data truncation cannot only keep most of the advantages of a traditional multisource system but also cover a larger FOV for big imaging objects. In addition, because the filtering is shift-invariant, the proposed algorithms are very fast and easily parallelized on graphic processing units.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

cuZ-Checker: A GPU-Based Ultra-Fast Assessment System for Lossy Compressions

Lossy compression is becoming an indispensable technique for the success of today's extreme-scale high-performance computing projects that produce vast volumes of data during scientific simulations or instrument data acquisitions. Comprehensively understanding the compression quality and performance of different lossy compressors is critical to selecting the best-fit compressors and using them properly and efficiently in practice. A few lossy compression assessment tools (e.g., Z-checker) have been developed, but none of them support the execution in a GPU environment. This is a significant gap because many recent extreme-scale applications and lossy compressors (e.g., cuSZ) can run entirely within GPUs. In this work, we develop an efficient lossy compression measuring system (called cuZ-Checker) on the GPU platform, which aims to perform the lossy compression quality and performance assessment completely within the GPU environment. Our contribution is threefold. (1) We develop a novel GPU-based lossy compression measuring framework using a computation pattern-based design approach. This approach classifies the computing-intensive metrics into three categories based on their patterns which creates large opportunities for kernel fusion and data reuse. (2) For each pattern in cuZ-Checker, we develop a CUDA kernel and provide fine-grained optimizations to boost its performance. (3) We thoroughly evaluate our cuZ-checker on a V100 GPU using four real-world scientific application datasets. Experiments show that cuZ-Checker can significantly accelerate the overall lossy compression assessment performance by 23X similar to 31X compared with the OpenMP-based multithreading CPU performance. To the best of our knowledge, this is the first lossy compression measuring system designed for GPU devices.

GPU↗
DOE OSTI2019

Learning nonlinear level sets for dimensionality reduction in function approximation

We developed a Nonlinear Level-set Learning (NLL) method for dimensionality reduction in high-dimensional function approximation with small data. This work is motivated by a variety of design tasks in real-world engineering applications, where practitioners would replace their computationally intensive physical models (e.g., high-resolution fluid simulators) with fast-to-evaluate predictive machine learning models, so as to accelerate the engineering design processes. There are two major challenges in constructing such predictive models: (a) high-dimensional inputs (e.g., many independent design parameters) and (b) small training data, generated by running extremely time-consuming simulations. Thus, reducing the input dimension is critical to alleviate the over-fitting issue caused by data insufficiency. Existing methods, including sliced inverse regression and active subspace approaches, reduce the input dimension by learning a linear coordinate transformation; our main contribution is to extend the transformation approach to a nonlinear regime. Specifically, we exploit reversible networks (RevNets) to learn nonlinear level sets of a high-dimensional function and parameterize its level sets in low-dimensional spaces. A new loss function was designed to utilize samples of the target functions' gradient to encourage the transformed function to be sensitive to only a few transformed coordinates. The NLL approach is demonstrated by applying it to three 2D functions and two 20D functions for showing the improved approximation accuracy with the use of nonlinear transformation, as well as to an 8D composite material design problem for optimizing the buckling-resistance performance of composite shells of rocket inter-stages.

Zhang, Guannan↗
DOE OSTI2018

Machine Learning Algorithms for Matching Theories, Simulations, and Observations in Cosmology (Final Project)

The search for simple and elegant equations to explain and predict observable natural phenomena has been a driving force in scientific theory for several centuries. The great successes of Newton's laws, Maxwell's equations, the Schrodinger equation, and the theory of General Relativity have encouraged this perspective, and perhaps a beautiful equation comprising a “theory of everything” remains to be discovered. But now scientists are grappling with systems of ever-increasing complexity, fraught with nonlinearity, and with the quantities of interest often only indirectly observed. Nature may resist a simple description, and the most important discoveries of the next century may be complex theories with countless variables and parameters. The era of big data opens up a promising new approach to scientific discovery in this setting. The predictions of modern theories, even if complex or nonlinear, can be examined through detailed and computationally-intensive simulations that take days or weeks to run and fill petabytes of disk space. The upcoming generation of scientific instruments will provide petabytes of observations at unprecedented resolution and depth. The challenge is to compare data to simulations so as to test theories and identify those that best match the observations. The data are numerous and rich but are subject to noise and various systematic biases. The simulations are large and detailed but are so costly that the effective sample size is small. Moreover, the mapping from data to simulation to the parameters of interest is typically complicated and ill-conditioned. Although these challenges, and the solutions we propose, apply across the sciences, we will ground our efforts by focusing on cosmology. Here, we are truly entering the era of big data in several senses. Ever larger experiments survey larger and larger cosmological volumes, resulting in enormous amounts of pixel data to process and extract the information of cosmological interest. These include large imaging surveys, which collect all the light in broad wavelength ranges over significant fractions of the sky, and spectroscopic surveys, which measure the light as a function of wavelength to map out 3D distances. These experiments are designed to shed light on the big unanswered questions in cosmology. Distilling the petabytes of data into observed quantities for comparison with theory is a daunting task. But these large experiments do not only result in large amounts of data to analyze: if we wish to compare to theories of physics, then we need increasingly extensive predictions for the observed quantities as well, which requires ever-larger cosmological simulations that take substantial -- and at times prohibitive -- computational resources to produce. Our goal is to develop statistical and machine learning methods for using observed and simulated data to advance machine learning with applications cosmology. In particular, we focus our research efforts on the following tasks: The challenge for automated science is that it is computationally impossible and statistically dangerous to consider every possible model in order to find the best one. We will develop Bayesian Optimization based active-learning methods that accelerate both the execution of the simulations and the search for best-fitting parameters. The key idea is to make the simulations adaptive -- across resolutions, time, and parameters -- using the data to search as the simulation runs; Most ML methods operate on simple finite dimensional feature vectors. However, many cosmology and other science applications require ML methods that can operate on more complex objects as inputs or outputs such as functions, distributions, or sets and point clouds. Our goal is to develop efficient ML methods for this problem and demonstrate their applicability in Cosmology, Astrophysics, and other science problems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Differentiable Earth mover’s distance for data compression at the high-luminosity LHC

Abstract The Earth mover’s distance (EMD) is a useful metric for image recognition and classification, but its usual implementations are not differentiable or too slow to be used as a loss function for training other algorithms via gradient descent. In this paper, we train a convolutional neural network (CNN) to learn a differentiable, fast approximation of the EMD and demonstrate that it can be used as a substitute for computing-intensive EMD implementations. We apply this differentiable approximation in the training of an autoencoder-inspired neural network (encoder NN) for data compression at the high-luminosity LHC at CERN The goal of this encoder NN is to compress the data while preserving the information related to the distribution of energy deposits in particle detectors. We demonstrate that the performance of our encoder NN trained using the differentiable EMD CNN surpasses that of training with loss functions based on mean squared error.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Validation and Calibration of Energy Models with Real Vehicle Data from Chassis Dynamometer Experiments

Accurate estimation of vehicle fuel consumption typically requires detailed modeling of complex internal powertrain dynamics, often resulting in computationally intensive simulations. However, many transportation applications-such as traffic flow modeling, optimization, and control-require simplified models that are fast, interpretable, and easy to implement, while still maintaining fidelity to physical energy behavior. This work builds upon a recently developed model reduction pipeline that derives physics-like energy models from high-fidelity Autonomie vehicle simulations. These reduced models preserve essential vehicle dynamics, enabling realistic fuel consumption estimation with minimal computational overhead. While the reduced models have demonstrated strong agreement with their Autonomie counterparts, previous validation efforts have been confined to simulation environments. This study extends the validation by comparing the reduced energy model's outputs against real-world vehicle data. Focusing on the MidSUV category, we tune the baseline Autonomie model to closely replicate the characteristics of a Toyota RAV4. We then assess the accuracy of the resulting reduced model in estimating fuel consumption under actual drive conditions. Our findings suggest that, when the reference Autonomie model is properly calibrated, the simplified model produced by the reduction pipeline can provide reliable, semi-principled fuel rate estimates suitable for large-scale transportation applications.

42 ENGINEERING↗
DOE OSTI2023

Using Data-Driven Prediction of Downstream 1D River Flow to Overcome the Challenges of Hydrologic River Modeling

Methods for downstream river flow prediction can be categorized into physics-based and empirical approaches. Although based on well-studied physical relationships, physics-based models rely on numerous hydrologic variables characteristic of the specific river system that can be costly to acquire. Moreover, simulation is often computationally intensive. Conversely, empirical models require less information about the system being modeled and can capture a system’s interactions based on a smaller set of observed data. This article introduces two empirical methods to predict downstream hydraulic variables based on observed stream data: a linear programming (LP) model, and a convolutional neural network (CNN). We apply both empirical models within the Colorado River system to a site located on the Green River, downstream of the Yampa River confluence and Flaming Gorge Dam, and compare it to the physics-based model Streamflow Synthesis and Reservoir Regulation (SSARR) currently used by federal agencies. Results show that both proposed models significantly outperform the SSARR model. Moreover, the CNN model outperforms the LP model for hourly predictions whereas both perform similarly for daily predictions. Although less accurate than the CNN model at finer temporal resolution, the LP model is ideal for linear water scheduling tools.

13 HYDRO ENERGY↗
DOE OSTI2026

Autoregressive long-horizon prediction of plasma edge dynamics *

Accurate modeling of scrape-off layer (SOL) and divertor-edge dynamics is vital for designing plasma-facing components in fusion devices. High-fidelity edge fluid/neutral codes such as SOLPS-ITER capture SOL physics with high accuracy, but their computational cost limits broad parameter scans and long transient studies. We present transformer-based, autoregressive surrogates for efficient prediction of 2D, time-dependent plasma edge state fields. Trained on SOLPS-ITER spatiotemporal data for the KSTAR tokamak, the surrogates forecast electron temperature, electron density, and radiated power over extended horizons. We evaluate model variants trained with increasing autoregressive horizons (1–100 steps) on short- and long-horizon prediction tasks. Longer-horizon training systematically improves rollout stability and mitigates error accumulation, enabling stable predictions over hundreds to thousands of steps and reproducing key dynamical features such as the motion of high-radiation regions. Measured end-to-end wall-clock times show the surrogate is orders of magnitude faster than SOLPS-ITER, enabling rapid parameter exploration. Prediction accuracy degrades when the surrogate enters physical regimes not represented in the training dataset, motivating future work on data enrichment and physics-informed constraints. Overall, this approach provides a fast, accurate surrogate for computationally intensive plasma edge simulations, supporting rapid scenario exploration, control-oriented studies, and progress toward real-time applications in fusion devices.

autoregressive deep learning↗
DOE OSTI2015

A Surrogate-based Adaptive Sampling Approach for History Matching and Uncertainty Quantification

A critical procedure in reservoir simulations is history matching (or data assimilation in a broader sense), which calibrates model parameters such that the simulation results are consistent with field measurements, and hence improves the credibility of the predictions given by the simulations. Often there exist non-unique combinations of parameter values that all yield the simulation results matching the measurements. For such ill-posed history matching problems, Bayesian theorem provides a theoretical foundation to represent different solutions and to quantify the uncertainty with the posterior PDF. Lacking an analytical solution in most situations, the posterior PDF may be characterized with a sample of realizations, each representing a possible scenario. A novel sampling algorithm is presented here for the Bayesian solutions to history matching problems. We aim to deal with two commonly encountered issues: 1) as a result of the nonlinear input-output relationship in a reservoir model, the posterior distribution could be in a complex form, such as multimodal, which violates the Gaussian assumption required by most of the commonly used data assimilation approaches; 2) a typical sampling method requires intensive model evaluations and hence may cause unaffordable computational cost. In the developed algorithm, we use a Gaussian mixture model as the proposal distribution in the sampling process, which is simple but also flexible to approximate non-Gaussian distributions and is particularly efficient when the posterior is multimodal. Also, a Gaussian process is utilized as a surrogate model to speed up the sampling process. Furthermore, an iterative scheme of adaptive surrogate refinement and re-sampling ensures sampling accuracy while keeping the computational cost at a minimum level. The developed approach is demonstrated with an illustrative example and shows its capability in handling the above-mentioned issues. Multimodal posterior of the history matching problem is captured and are used to give a reliable production prediction with uncertainty quantification. The new algorithm reveals a great improvement in terms of computational efficiency comparing previously studied approaches for the sample problem.

Li, Weixuan↗
DOE OSTI2017

High Performance Data Transfer for Distributed Data Intensive Sciences

We report on the development of ZX software providing high performance data transfer and encryption. The design scales in: computation power, network interfaces, and IOPS while carefully balancing the available resources. Two U.S. patent-pending algorithms help tackle data sets containing lots of small files and very large files, and provide insensitivity to network latency. It has a cluster-oriented architecture, using peer-to-peer technologies to ease deployment, operation, usage, and resource discovery. Its unique optimizations enable effective use of flash memory. Using a pair of existing data transfer nodes at SLAC and NERSC, we compared its performance to that of bbcp and GridFTP and determined that they were comparable. With a proof of concept created using two four-node clusters with multiple distributed multi-core CPUs, network interfaces and flash memory, we achieved 155Gbps memory-to-memory over a 2x100Gbps link aggregated channel and 70Gbps file-to-file with encryption over a 5000 mile 100Gbps link.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

High-Accuracy Module Emulators from Physically-Constrained AI Algorithms

Focal Area(s): How do we use AI tools to integrate observations, simulated data and physical and chemical fundamentals (Focal Area 3) into model components (Focal Area 2) that have high accuracy and stability and low computational burden to improve Earth System Predictability? Science Challenge: Earth system modeling of the hydrological cycle involves compute-intensive modules representing complex chemical and physical process. Recently, AI tools that are far less compute intensive have been developed that emulate these modules, but many of these efforts are not yet sufficiently accurate or even stable. We know a lot about the physics and chemistry of earth system processes. The Science Challenge is developing AI tools that not only incorporate observations and simulated data, but also incorporate the physics and chemistry of the process, while still maintaining the compute efficiency.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Toward Large-Scale Image Segmentation on Summit

Semantic segmentation of images is an important computer vision task that emerges in a variety of application domains such as medical imaging, robotic vision and autonomous vehicles to name a few. While these domain-specific image analysis tasks involve relatively small image sizes (~ 10 2 × 10 2 ), there are many applications that need to train machine learning models on image data with extents that are orders of magnitude larger (~10 4 × 10 4 ). Training deep neural network (DNN) models on large extent images is extremely memory-intensive and often exceeds the memory limitations of a single graphical processing unit, a hardware accelerator of choice for computer vision workloads. Here, an efficient, sample parallel approach to train U-Net models on large extent image data sets is presented. Its advantages and limitations are analyzed and near-linear strong-scaling speedup demonstrated on 256 nodes (1536 GPUs) of the Summit supercomputer. Using a single node of the Summit supercomputer, an early evaluation of a recently released model parallel framework called GPipe is demonstrated to deliver ~ 2X speedup in executing a U-Net model with an order of magnitude larger number of trainable parameters than reported before. Performance bottlenecks for pipelined training of U-Net models are identified and mitigation strategies to improve the speedups are discussed. Together, these results open up the possibility of combining both approaches into a unified scalable pipelined and data parallel algorithm to efficiently train U-Net models with very large receptive fields on data sets of ultra-large extent images.

Seal, Sudip↗
DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗