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DOE OSTI2022

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Hydration structure and water exchange kinetics at xenotime–water interfaces: implications for rare earth minerals separation

Hydration of surface ions gives rise to structural heterogeneity and variable exchange kinetics of water at complex mineral–water interfaces. In this work, we employ ab initio molecular dynamics (AIMD) simulations and water adsorption calorimetry to examine the aqueous interfaces of xenotime, a phosphate mineral that contains predominantly Y 3+ and heavy rare earth elements. Consistent with natural crystal morphology, xenotime is predicted to have a tetragonal prismatic shape, dominated by the {100} surface. Hydration of this surface induces multilayer interfacial water structures with distinct OH orientations, which agrees with recent crystal truncation rod measurements. The exchange kinetics between two adjacent water layers exhibits a wide range of underlying timescales (5–180 picoseconds), dictated by ion–water electrostatics. Adsorption of a bidentate hydroxamate ligand reveals that {100} xenotime surface can only accommodate monodentate coordination with water exchange kinetics strongly depending on specific ligand orientation, prompting us to reconsider traditional strategies for selective separation of rare-earth minerals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Molecular concentration field design using closed-form steady-state solutions

Control over spatial concentration fields represents a fundamental challenge in designing synthetic biological systems and programmable soft materials. While nature creates morphogen gradients that orchestrate complex developmental processes, synthetic approaches have largely relied on empirical optimization and computationally intensive simulations. Here, we present an analytical framework for steady-state concentration fields generated by finite-sized localized sources in diffusion–degradation systems and derive closed-form solutions for one-, two-, and three-dimensional geometries. By expressing these solutions in dimensionless form, we show that gradient steepness and spatial structure are organized by the Thiele modulus, which captures the competition between diffusion and degradation length scales. The analysis reveals distinct design regimes: in degradation-dominated systems, gradient shape is governed by exponential decay and becomes dimension-independent, whereas in diffusion-dominated systems, gradient magnitude and extent follow dimension-dependent power-law scaling. Building on these results, we introduce a quantitative design strategy that uses threshold-based criteria to program concentration ranges by tuning physically accessible parameters, most directly the production rate, while holding transport and degradation properties fixed. Comparisons with numerical solutions and reported experimental systems demonstrate consistency with the predicted scaling behavior. Together, this work provides a generalizable and physically transparent framework for designing steady-state concentration fields in synthetic biological and soft matter systems, enabling predictive control of gradient-mediated organization without reliance on extensive numerical optimization.

Kim, Dong Woo [Johns Hopkins University, Baltimore↗

DOE OSTI2021

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

crystal structures↗

DOE OSTI2021

Anthropogenic aerosols prolong fog lifetime in China

Investigation of aerosol effects on fog with long-term measurements has generally focused on fog occurrence frequency and intensity; here we examine the effects on fog lifetime, fog formation, and fog dissipation. From analysis of 52 years (1960–2011) of data collected at 404 stations in China, it is found that fog lifetime exhibits a clear increasing trend with time, and the increased lifetime is mainly attributable to delayed fog dissipation. Increased aerosol levels and global warming affect fog lifetime in opposite ways; increased aerosol levels serve to prolong fog lifetime by primarily delaying fog dissipation, whereas warming decreases fog lifetime by primarily delaying fog formation. The overall aerosol effect on fog lifetime in China is shown to predominate, especially in the highly polluted region of Eastern China. The observational findings are confirmed by a suite of WRF-Chem simulations that reveal the influences of both increased aerosol levels and temperatures through a complex chain of interactions among microphysical, dynamical, thermodynamic, and radiative processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Advancing set-conditional set generation: Diffusion models for fast simulation of reconstructed particles

The computational intensity of detector simulation and event reconstruction poses a significant difficulty for data analysis in collider experiments. This challenge inspires the continued development of machine learning techniques to serve as efficient surrogate models. We propose a fast emulation approach that combines simulation and reconstruction. In other words, a neural network generates a set of reconstructed objects conditioned on input particle sets. To make this possible, we advance set-conditional set generation with diffusion models. Using a realistic, generic, and public detector simulation and reconstruction package (COCOA), we show how diffusion models can accurately model the complex spectrum of reconstructed particles inside jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Entanglement Structure of Non-Gaussian States and How to Measure It

Rapidly growing capabilities of quantum simulators to probe quantum many-body phenomena require new methods to characterize increasingly complex states. Here, we present a protocol that constrains quantum states using experimentally measured correlation functions. This method enables measurement of a quantum state’s entanglement structure, opening a new route to study entanglement-related phenomena. Our approach extends Gaussian state parameterizations by systematically incorporating higher-order correlations. We show the protocol’s usefulness in conjunction with current and forthcoming experimental capabilities, focusing on weakly interacting fermions as a proof of concept. Here, the lowest nontrivial expansion quantitatively predicts early time thermalization dynamics, including signaling the onset of quantum chaos indicated by the entanglement Hamiltonian.

Fermi gases↗

DOE OSTI2024

Benchmarking Optimizers for Qumode State Preparation with Variational Quantum Algorithms

Quantum state preparation involves preparing a target state from an initial system, a process integral to applications such as quantum machine learning and solving systems of linear equations. Recently, there has been a growing interest in qumodes due to advancements in the field and their potential applications. However there is a notable gap in the literature specifically addressing this area. This paper aims to bridge this gap by providing performance benchmarks of various optimizers used in state preparation with Variational Quantum Algorithms. We conducted extensive testing across multiple scenarios, including different target states, both ideal and sampling simulations, and varying numbers of basis gate layers. Our evaluations offer insights into the complexity of learning each type of target state and demonstrate that some optimizers perform better than others in this context. Notably, the Powell optimizer was found to be exceptionally robust against sampling errors, making it a preferred choice in scenarios prone to such inaccuracies. Additionally, the Simultaneous Perturbation Stochastic Approximation optimizer was distinguished for its efficiency and ability to handle increased parameter dimensionality effectively.

Kan, Shuwen [Fordham University]↗

DOE OSTI2024

Global Pathway Selection with Zero-RK

Global Pathway Selection (GPS) is an algorithm to effectively generates reduced (skeletal) chemistry mechanisms, which speeds up simulations and can be used as a systematic analytics tool to extract insights from complex reacting system. This release is an extension of the original code to run in parallel and to use LLNL's Zero-RK solver for fast solution of chemical problems.

Whitesides, RussellA↗

DOE OSTI2025

Global Pathway Selection with Zero-RK v0.5

Whitesides, RussellA [Lawrence Livermore National ↗

DOE OSTI2025

Convection-Permitting Ensembles of an Isolated Mountain Thunderstorm during RELAMPAGO/CACTI

Abstract The north–south-oriented Sierras de Córdoba (SDC) ridge in central Argentina is noted for initiating thunderstorms that may grow into intense mesoscale convective systems (MCSs). It also initiates more isolated, shorter-lived cells under weaker synoptic forcing. These cells are less impactful than MCSs but may be difficult to predict in convective-scale numerical weather prediction (NWP) due to their strong sensitivities to subgrid and partially resolved processes. To study the mechanisms and predictability of such cells, convection-permitting ensemble simulations were conducted of an isolated, diurnally forced SDC thunderstorm during Cloud, Aerosol, and Complex Terrain Interactions (CACTI)/Remote Sensing of Electrification, Lightning, and Mesoscale/Microscale Processes with Adaptive Ground Observations (RELAMPAGO). The rich observational data facilitated detailed ensemble verification, where dry biases in the surface energy balance and soil moisture were identified. These biases promoted rapid removal of convective inhibition and an early onset of precipitating cells over the SDC that were shallower and weaker than the observed cell. Correction, and then overcorrection, of the soil moisture bias in two successive ensembles was required to rectify the surface energy balance and improve the representation of the SDC cell. Nevertheless, substantial ensemble variability in convective precipitation was found, with some members producing more widespread convection than observed and others producing no deep convection at all. This variability was largely explained by a combination of thermodynamic and dynamic mechanisms, dominated by a positive sensitivity of convective precipitation to preconvective moist instability over the ridge. Secondary sensitivities were found to low-level upward mass flux and midlevel cross-barrier winds, the latter of which caused gravity waves with elevated downdrafts that tended to suppress incipient clouds.

Lopez, Andres [Department of Atmospheric and Ocean↗

DOE OSTI2024

Tethys: A Spatiotemporal Downscaling Model for Global Water Demand

Humans use water for many important tasks, such as drinking, growing food, and cooling power plants. Since future water demands depend on complex global interactions between economic sectors (e.g., demand for wheat in one country causing demand for water to grow that wheat in another country), it is often modeled at coarse spatial and temporal scales as part of models that account for complex, multi-sector system dynamics. However, models that project future water availability typically simulate physical processes at much finer scales. Tethys enables integration between these kinds of models by downscaling region-scale water demand projections using sector-specific proxies and formulas.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Closures and Simulation for Thermal Radiation Transport in Stochastic Media with Nonlinear Temperature Dependence

Because of the practical challenge of rendering very complex realistic spatial structures for numerical work, it is common practice to resort to characterizing such media as stochastic mixtures of materials, ideally parametrized with low order statistics such as the mean, variance, and correlation functions of the now random material properties. This enables realizations of the medium to be repeatedly generated and radiation transport computations to, in principle, be performed for a large ensemble of these realizations to obtain a statistically well-characterized radiation field. Statistical post-processing yields desired quantities such as conditional and unconditional mean radiation flux and probability distributions of transmitted radiation. However, such computations prove expensive for all but the simplest stochastic geometries and are most suited for benchmarking approximate models. The most common approximations lead to homogenized media so that transport computations are required only on a single medium realization but by construct provide only limited statistical information on the radiation field. Almost all approximate approaches to this problem attempt to develop equations for low order moments of the radiation intensity (mean, second moment, correlation function) but inevitably encounter a closure problem: the equation for any statistical moment will contain terms depending on unknown higher-order moments. Thus, the challenge shifts to one of developing closure relations that relate the unknown moments to the lower order moments. Under very special conditions, an exact closure can be derived but in general closures are heuristically stated constitutive relations. Also, closure approaches depend on whether the mixing statistics are spatially and/or temporally continuous as in fluctuating turbulent fields, or discontinuous as in randomly mixed solid chunks of material. Thus, unconditional averaging is generally applied in the former case but conditional averaging is more appropriate when the mixing is discontinuous. In this work, the emphasis is on binary statistical mixtures of immiscible fluids as as such the quantities of interest are averages (flux, temperature) conditioned on the material type.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Orbital-Free Quantum Simulation Methods for Application to Warm Dense Matter (Final Technical Report)

Predictive simulations for prediction of condensed system behavior in state conditions far from ambient is increasingly crucial to DOE priorities. Warm dense matter (WDM) is the paradigm: temperature T > 1-15 eV, pressures P to 1 Mbar or greater. Experiments under such state conditions are difficult and costly. We summarize work driven by the need and opportunity to make free-energy density functional theory (DFT) as powerful a tool for ab initio simulation of matter under such extreme conditions as ground state DFT is for ordinary matter Advancing orbital-free DFT (OF-DFT) to eliminate the Kohn-Sham (KS) scaling bottleneck in such simulations is the other priority. The concurrent challenge for both goals is the intrinsic complexity of WDM. We summarize 15 years of successes and major progress on (1) free energy exchange-correlation functionals; (2) non-interacting free energy functionals (counterpart to T=0 Kohn-Sham kinetic energy density functionals); (3) rigorous results and constraints for free-energy DFT; (4) software for free energy DFT calculations in both conventional Kohn-Sham and OF-DFT form; (5) de-orbitalization of advanced orbital-dependent ground state functionals for use in OF-DFT; (6) demonstration calculations; (7) ancillary achievements (e.g. major review articles, secondary explorations motivated by primary goals).

36 MATERIALS SCIENCE↗

DOE OSTI2024

High-Temperature Gas-Cooled Pebble-Bed Reactors Running In And Transient Modeling Capabilities Demonstration

This study presents a comprehensive benchmarking and verification effort of several thermal-hydraulic and multiphysics capabilities for high-temperature gas-cooled reactor (HTGR) applications. The first part of this effort focuses on the running-in verification of Griffin's multiphysics capabilities, specifically for simulating the evolution of Pebble Bed reactor cores from startup to equilibrium. In the absence of validation data, code-to-code comparisons are conducted with Kugelpy, showing good agreement for key quantities like maximum power density and fresh core k-eigenvalue predictions. However, discrepancies in equilibrium core predictions suggest potential issues with cross sections, underscoring the need for further refinement and evaluation. The HTTF system analysis code benchmark involves RELAP5-3D, SAM, and GAMMA+ to assess their predictive capabilities for HTTF behavior under both normal operation and pressurized conduction cooldown (PCC) transient conditions. While there is good agreement in predicting major parameters such as coolant temperature, solid temperature, and flow distribution, discrepancies in transient behavior highlight differences in modeling approaches, nodalizations, and heat transfer models. The HTTF lower plenum CFD benchmark employs nekRS to simulate flow mixing phenomena, successfully capturing relevant flow physics and demonstrating mesh independence in complex geometries. Preliminary results suggest a relatively uniform temperature field but significant unsteadiness in the flow, requiring time-averaging analyses. The GPBR200 system analysis code benchmark uses SAM's core channel and porous media models, incorporating an RCCS loop for decay heat removal. During steady-state and transient conditions, including protected de-pressurized and pressurized loss of forced cooling (DLOFC and PLOFC), both models show good agreement in predicting temperature profiles and key parameters. Notably, while the core channel model underpredicts convective heat transfer effects, both models maintain temperatures well below the TRISO fuel safety limit. These benchmarking efforts collectively enhance the predictive capabilities of the tools used in HTGR design and safety analysis, guiding developments to improve their accuracy and applicability.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Learning the factors controlling mineral dissolution in three-dimensional fracture networks: applications in geologic carbon sequestration

We perform a set of high-fidelity simulations of geochemical reactions within three-dimensional discrete fracture networks (DFN) and use various machine learning techniques to determine the primary factors controlling mineral dissolution. The DFN are partially filled with quartz that gradually dissolves until quasi-steady state conditions are reached. At this point, we measure the quartz remaining in each fracture within the domain as our primary quantity of interest. We observe that a primary sub-network of fractures exists, where the quartz has been fully dissolved out. This reduction in resistance to flow leads to increased flow channelization and reduced solute travel times. However, depending on the DFN topology and the rate of dissolution, we observe substantial variability in the volume of quartz remaining within fractures outside of the primary subnetwork. This variability indicates an interplay between the fracture network structure and geochemical reactions. We characterize the features controlling these processes by developing a machine learning framework to extract their relevant impact. Specifically, we use a combination of high-fidelity simulations with a graph-based approach to study geochemical reactive transport in a complex fracture network to determine the key features that control dissolution. We consider topological, geometric and hydrological features of the fracture network to predict the remaining quartz in quasi-steady state. We found that the dissolution reaction rate constant of quartz and the distance to the primary sub-network in the fracture network are the two most important features controlling the amount of quartz remaining. This study is a first step towards characterizing the parameters that control carbon mineralization using an approach with integrates computational physics and machine learning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Wilkins: HPC in situ workflows made easy

In situ approaches can accelerate the pace of scientific discoveries by allowing scientists to perform data analysis at simulation time. Current in situ workflow systems, however, face challenges in handling the growing complexity and diverse computational requirements of scientific tasks. In this work, we present Wilkins, an in situ workflow system that is designed for ease-of-use while providing scalable and efficient execution of workflow tasks. Wilkins provides a flexible workflow description interface, employs a high-performance data transport layer based on HDF5, and supports tasks with disparate data rates by providing a flow control mechanism. Wilkins seamlessly couples scientific tasks that already use HDF5, without requiring task code modifications. We demonstrate the above features using both synthetic benchmarks and two science use cases in materials science and cosmology.

HPC↗

DOE OSTI2026

Energy Partition in Collisionless Counterstreaming Plasmas

Fast, counterstreaming plasma outflows drive magnetic field amplification, plasma heating, and particle acceleration in numerous astrophysical environments, from supernova remnant shocks to active galactic nuclei jets. Understanding how, in the absence of Coulomb collisions, energy is redistributed between the different plasma species remains a fundamental open question. We use three-dimensional, fully kinetic simulations to investigate energy partition in weakly magnetized counterpropagating plasmas. Our results reveal a complex interplay between different processes, where at early times the Weibel instability drives a first stage of magnetic field amplification and at late times the kinking of current filaments drives a second amplification stage via a dynamo-type mechanism. Electrons are heated primarily during the latter phase through magnetic pumping. By the time the flows thermalize, we observe that the final temperature ratio T e /T i and energy partition depend on the ion-to-electron mass ratio. For electron–proton flows, the electron thermal energy only reaches up to a few percent of the initial ion kinetic energy.

Marret, Alexis [SLAC National Accelerator Laborato↗