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Results for “thermodynamics of computing”

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 307 records · Page 17

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DOE OSTI2020

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

tLaSDI: Thermodynamics-informed latent space dynamics identification

Here we propose a latent space dynamics identification method, namely tLaSDI, that embeds the first and second principles of thermodynamics. The latent variables are learned through an autoencoder as a nonlinear dimension reduction model. The latent dynamics are constructed by a neural network-based model that precisely preserves certain structures for the thermodynamic laws through the GENERIC formalism. An abstract error estimate is established, which provides a new loss formulation involving the Jacobian computation of autoencoder. The autoencoder and the latent dynamics are simultaneously trained to minimize the new loss. Computational examples demonstrate the effectiveness of tLaSDI, which exhibits robust generalization ability, even in extrapolation. In addition, an intriguing correlation is empirically observed between a quantity from tLaSDI in the latent space and the behaviors of the full-state solution.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

A systematic analysis of phase stability in refractory high entropy alloys utilizing linear and non-linear cluster expansion models

We report that obtaining surrogate models for various types of materials has long been a goal of computational material scientists and physicists, as they allow the calculation of thermodynamic quantities and properties of interest far more efficiently than DFT. Many surrogate models, including interatomic potentials generated by machine learning algorthims and cluster expansions, rely on incorporating many-body interactions such as three-body or four-body interactions. When utilizing machine learning algorithms for interatomic potentials, it is common to start with two-body interactions and systematically include three- and four-body clusters to improve the fit, stopping when including the additional clusters does not measurably change the predictive power of the model. In cluster expansions for FCC and related lattices, it is often enough to include mostly two-body interactions and a handful of three-body interactions. However, it remains to be seen whether those will be enough in the case of lattices with a lower packing fraction, such as BCC.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Adaptive Conformer Sampling for Property Prediction Using the Conductor-like Screening Model for Real Solvents

The valorization of lignocellulose-derived bioproducts requires effective separation from excessive water. Liquid–liquid extraction is a promising low-energy separation technology, but effective extraction requires solvent selection based on the thermodynamic properties of the bioproduct and solvent components. We propose a computational framework for predicting such properties by developing an adaptive conformer selection approach for use with COSMO-RS (conductor-like screening model for real solvents) calculations. In this framework, molecular dynamics simulations are used to generate many molecular structures (conformers) at representative temperatures in varying solvent environments. Conformers are then clustered based on structural metrics in a low-dimensional space and selected using a mixed-integer quadratic programming problem to iteratively insert a sampled conformer. At each iteration, we determine bioproduct properties using COSMO-RS. Here, we demonstrate the capability of the proposed framework on representative bioproducts to show convergence of the adaptive sampling toward experimentally measured properties with fewer calculations than required by random conformer sampling, enabling the improved screening of solvent systems for liquid-phase separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

X-ray diffraction reveals two structural transitions in szomolnokite

Hydrated sulfates have been identified and studied in a wide variety of environments on Earth, Mars, and the icy satellites of the solar system. The subsurface presence of hydrous sulfur-bearing phases to any extent necessitates a better understanding of their thermodynamic and elastic properties at pressure. End-member experimental and computational data are lacking and are needed to accurately model hydrous, sulfur-bearing planetary interiors. In this work, high-pressure X-ray diffraction (XRD) and synchrotron Fourier-transform infrared (FTIR) measurements were conducted on szomolnokite (FeSO 4 ·H 2 O) up to ~83 and 24 GPa, respectively. This study finds a monoclinic-triclinic (C2/c to P1¯) structural phase transition occurring in szomolnokite between 5.0(1) and 6.6(1) GPa and a previously unknown triclinic-monoclinic (P1¯ to P2 1 ) structural transition occurring between 12.7(3) and 16.8(3) GPa. The high-pressure transition was identified by the appearance of distinct reflections in the XRD patterns that cannot be attributed to a second phase related to the dissociation of the P1¯ phase, and it is further characterized by increased H 2 O bonding within the structure. We fit third-order Birch-Murnaghan equations of state for each of the three phases identified in our data and refit published data to compare the elastic parameters of szomolnokite, kieserite (MgSO 4 ·H 2 O), and blödite (Na 2 Mg(SO 4 ) 2 ·4H 2 O). At ambient pressure, szomolnokite is less compressible than blödite and more than kieserite, but by 7 GPa both szomolnokite and kieserite have approximately the same bulk modulus, while blödite’s remains lower than both phases up to 20 GPa. Furthermore, these results indicate the stability of szomolnokite’s high-pressure monoclinic phase and the retention of water within the structure up to pressures found in planetary deep interiors.

58 GEOSCIENCES↗

DOE OSTI2026

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials

Silicon carbide (SiC) divacancies are attractive candidates for spin-defect qubits possessing long coherence times and optical addressability. The high activation barriers associated with SiC defect formation and motion pose challenges for their study by first-principles molecular dynamics. In this work, we develop and deploy machine learning interatomic potentials (MLIPs) to accelerate defect dynamics simulations while retaining ab initio accuracy. We employ an active learning strategy comprising symmetry-adapted collective variable discovery and enhanced sampling to compile configurationally diverse training data, calculation of energies and forces using density functional theory (DFT), and training of an E(3)-equivariant MLIP based on the Allegro model. Here, the trained MLIP reproduces DFT-level accuracy in defect transition activation free energy barriers, enables the efficient and stable simulation of multidefect 216-atom supercells, and permits an analysis of the temperature dependence of defect thermodynamic stability and formation/annihilation kinetics to propose an optimal annealing temperature to maximally stabilize VV divacancies.

Computer simulations↗

DOE OSTI2021

FY21 Status Report on the Molten Salt Thermal Properties Database (MSTDB) Development

This report describes the thermodynamic assessments for the ZrF 4 -BeF 2 , AlCl 3 -NaCl, AlCl3-KCl and the PuCl 3 -CsCl pseudo-binary subsystems. Calculation results are compared to the inputs used to optimize the adjustable model parameters. The data came from experimental studies reported in the open literature, from the MSR research community, and/or computational results generated within the NEAMS program and from collaborators. The models from the thermodynamic assessment of these salt systems are integrated into the MSTDB-TC (Molten Salt Thermal Properties Database-Thermochemical). A brief description of the companion MSTDB-TP (Molten Salt Thermal Properties Database-Thermophysical) is given along with an overview of the approach for predicting both thermodynamic and thermophysical property behavior of multicomponent systems.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

TROPHY: A Topologically Robust Physics-Informed Tracking Framework for Tropical Cyclones

Tropical cyclones (TCs) are among the most destructive weather systems. Realistically and efficiently detecting and tracking TCs are critical for assessing their impacts and risks. In particular, the eye is a signature feature of a mature TC. Therefore, knowing the eyes’ locations and movements is crucial for both operational weather forecasts and climate risk assessments. Recently, a multilevel robustness framework has been introduced to study the critical points of time-varying vector fields. The framework quantifies the robustness (i.e., structural stability) of critical points across varying neighborhoods. By relating the multilevel robustness with critical point tracking, the framework has demonstrated its potential in cyclone tracking. An advantage is that it identifies cyclonic features using only 2D wind vector fields, which is encouraging as most tracking algorithms require multiple dynamic and thermodynamic variables at different altitudes. A disadvantage is that the framework does not scale well computationally for datasets containing a large number of cyclones. Herein this paper introduces a topologically robust physics-informed tracking framework (TROPHY) for TC tracking. The main idea is to integrate physical knowledge of TC to drastically improve the computational efficiency of multilevel robustness framework for large-scale climate datasets. First, during preprocessing, we propose a physics-informed feature selection strategy to filter 90% of critical points that are short-lived and have low stability, thus preserving good candidates for TC tracking. Second, during in-processing, we impose constraints during the multilevel robustness computation to focus only on physics-informed neighborhoods of TCs. We apply TROPHY to 30 years of 2D wind fields from reanalysis data in ERA5 and generate a number of TC tracks. In comparison with the observed tracks, we demonstrate that TROPHY can capture TC characteristics (e.g., frequency, intensity, duration, latitudes with maximum intensity, and genesis) that are comparable to and sometimes even better than a well-validated TC tracking algorithm that requires multiple dynamic and thermodynamic scalar fields.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

DFTTK: Density Functional Theory ToolKit for high-throughput lattice dynamics calculations

In this work, we present a software package in Python for high-throughput first-principles calculations of thermodynamic properties at finite temperatures, which we refer to as DFTTK (Density Functional Theory ToolKit). DFTTK is based on the atomate package and integrates our experiences in the last decades on the development of theoretical methods and computational softwares. It includes task submissions on all major operating systems and task executions on high-performance computing environments. Furthermore, the distribution of the DFTTK package comes with examples of calculations of phonon density of states, heat capacity, entropy, enthalpy, and free energy under the quasi-harmonic phonon scheme for the stoichiometric phases of Al, Ni, Al 3 Ni, AlNi, AlNi 3 , Al 3 Ni 4 , and Al 3 Ni 5 , and the fcc solution phases treated using the special quasirandom structures at the compositions of Al 3 Ni, AlNi, and AlNi 3 .

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Elastic forces drive nonequilibrium pattern formation in a model of nanocrystal ion exchange

The widely used process of nanocrystal ion exchange operates out of thermodynamic equilibrium and can require mixing components of varying sizes. Here we use theory and computer simulation to study a simple model which captures these two basic features of ion exchange reactions. We show that a strong driving force for exchange among different-sized species creates nonequilibrium patterns within model nanocrystals. We further demonstrate that such patterns can be thermodynamically stable within core/shell nanocrystals. These results help us understand the heterostructures formed in ion-exchanged nanocrystals and suggest strategies for leveraging elasticity to design patterns in nanoscale materials. Chemical transformations, such as ion exchange, are commonly employed to modify nanocrystal compositions. Yet the mechanisms of these transformations, which often operate far from equilibrium and entail mixing diverse chemical species, remain poorly understood. Here we explore an idealized model for ion exchange in which a chemical potential drives compositional defects to accumulate at a crystal’s surface. These impurities subsequently diffuse inward. We find that the nature of interactions between sites in a compositionally impure crystal strongly impacts exchange trajectories. In particular, elastic deformations which accompany lattice-mismatched species promote spatially modulated patterns in the composition. These same patterns can be produced at equilibrium in core/shell nanocrystals, whose structure mimics transient motifs observed in nonequilibrium trajectories. Moreover, the core of such nanocrystals undergoes a phase transition—from modulated to unstructured—as the thickness or stiffness of the shell is decreased. Our results help explain the varied patterns observed in heterostructured nanocrystals produced by ion exchange and suggest principles for the rational design of compositionally patterned nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

EOSPAC User’s Manual: V.6.5

The EOSPAC utility package is a collection of interface routines, which can be used to access the SESAME data library and perform various data adjustments and interpolations on the SESAME data. The SESAME data library contains both thermodynamic (e.g., equation of state) and transport coefficients (e.g., opacity and conductivity). Note, for simplicity, the term EOS (equation of state) used herein includes both thermodynamic variables and transport coefficients. The EOSPAC utility package is designed to be used by physics codes (henceforth "host codes") written in multiple languages and on multiple platforms. The remainder of this manual is organized into several sections.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

New Dimension in Ab Initio Electronic Structure Theory: Temperature, Pressure, and Chemical Potential

Ab initio electronic structure theory has transformed gas-phase molecular science with its predictive ability. In the attempt to bring such predictive ability to macroscopic systems and condensed matter, the theory must integrate quantum mechanics with statistical thermodynamics, so that thermodynamic functions such as free energy, internal energy, entropy, and chemical potentials are computed as functions of temperature in a systematically converging series of approximations. Here, a general, versatile strategy of elevating ab initio electronic structure theory to nonzero temperatures is introduced and discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

First-principles free energies by hybrid thermodynamic integration for phase equilibria and fission product solubility in molten salts

The overarching goal of this research project is quantitative microscopic modeling of phase diagrams and solubility of actinides and lanthanide-fission products in molten salts for molten salt reactors. Application of molten salts as coolants and liquid fuels for next-generation reactors requires quantitative understanding of phase diagrams, equations of state and transport properties of binary and ternary molten salt mixtures, as well as solubility of fuel, fission products and reactor-wall corrosion products, but these remain beyond the reach of current first-principles computational techniques. We will address this fundamental capability gap using a novel hybrid framework for thermodynamic integration to directly predict absolute free energies of solid and molten salts at any specified conditions of composition, temperature and pressure. This framework will combine a hierarchy of first-principles, molecular dynamics and continuum techniques to deliver first-principles-level accuracy at a fraction of the computational cost of conventional ab initio molecular dynamics approaches. In particular, this technique is expected to provide first-principles accuracy, while off-loading most of the computational work on much less expensive classical molecular dynamics and continuum techniques.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Fluid modeling of low-temperature plasmas

Fluid models are essential for understanding and predicting low-temperature plasma (LTP) behavior in various scientific and industrial settings. This paper provides an introductory tutorial on fluid modeling of LTPs, covering model formulation, implementation, and computational simulations. The tutorial focuses on five main components of the formulation of LTP fluid models: fluid flow, energy, chemistry, electromagnetism, and material properties, as well as in essential aspects of model implementations, including multiscale phenomena, multiphysics coupling, and numerical convergence. Designed for students and early-career researchers, this work offers a practical foundation for developing and using fluid models, from in-house computational codes to commercial software, bridging fundamental theory with real-world applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Thermodynamic stability versus kinetic accessibility: Pareto fronts for programmable self-assembly

A challenge in designing self-assembling building blocks is to ensure the target state is both thermodynamically stable and kinetically accessible. These two objectives are known to be typically in competition, but it is not known how to simultaneously optimize them. We consider this problem through the lens of multi-objective optimization theory: we develop a genetic algorithm to compute the Pareto fronts characterizing the tradeoff between equilibrium probability and folding rate, for a model system of small polymers of colloids with tunable short-ranged interaction energies. We use a coarse-grained model for the particles' dynamics that allows us to efficiently search over parameters, for systems small enough to be enumerated. For most target states there is a tradeoff when the number of types of particles is small, with medium-weak bonds favouring fast folding, and strong bonds favouring high equilibrium probability. Additionally, the tradeoff disappears when the number of particle types reaches a value m *, that is usually much less than the total number of particles. This general approach of computing Pareto fronts allows one to identify the minimum number of design parameters to avoid a thermodynamic–kinetic tradeoff. However, we argue, by contrasting our coarse-grained model's predictions with those of Brownian dynamics simulations, that particles with short-ranged isotropic interactions should generically have a tradeoff, and avoiding it in larger systems will require orientation-dependent interactions.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Olefin Coupling Catalyzed by (Pybox)Os Complexes via Osmacyclopentane Intermediates: Comparison with Isoelectronic (Phebox)Ir

(Pybox)Os is found to catalyze alkene hydrovinylation, effecting the dimerization of ethylene, tail-to-tail coupling of propene and 1-butene, and cross-coupling of ethylene with higher α-olefins. This reactivity contrasts with the previously reported dehydrogenative coupling of ethylene to give butadiene catalyzed by the isoelectronic fragment (Phebox)Ir. The reaction mechanism was investigated through computational and experimental means. Both the Os- and Ir-catalyzed reactions proceed through a [2 + 2 + 1] cyclization of the corresponding bis-olefin complex to yield an experimentally observed metallacyclopentane intermediate. In both cases, the metallacyclopentane undergoes β- H elimination, via a dechelated κ 2 -pincer-ligated intermediate, to yield a σ−π-but-3-enyl hydride complex or derivative. Both the greater reactivity and the distinct chemoselectivity of the Os system relative to the Ir system are attributable to C−H reductive elimination by the σ−π-but-3-enyl hydride having a barrier for Os much lower than that for Ir. This lower barrier to C−H elimination for Os is unexpected given that the thermodynamic driving force for elimination is much less for Os than for Ir. Computational studies of model complexes were conducted, comparing (Pybox)Os(L)(CH 3 )(H) with the isoelectronic (Phebox)Ir(L)(CH 3 )(H). The results indicate that the more facile kinetics with Os relative to Ir may be general for C−H elimination from six-coordinate d 6 complexes of the two metals, as well as for the microscopic reverse, i.e., C−H addition to the corresponding four-coordinate d 8 species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Elucidation of Marcus Relationships for Hydride Transfer Reactions Involving Transition Metal Hydrides

The rate of hydride transfer from three Ir hydride complexes of the type Cp*Ir( R bpy)H + (Cp* = C 5 Me 5 ; R bpy = 4,4′-R-2,2′-bipyridine, R = OMe, H, CO 2 Me) to six N-methylacridinium ( R Acr + ) acceptors with electronically different substituents in the 2- or 2,7-positions were measured. Using the thermodynamic hydricity of the donors and the hydride affinity of the acceptors the thermodynamic driving forces for hydride transfer were determined. Brønsted plots, which correlate kinetic and thermodynamic hydricity, demonstrate distinct linear free energy relationships for each complex, with different Brønsted α values. Thus, at the same driving force hydride transfer from Cp*Ir( OMe bpy)H + is faster than for Cp*Ir(bpy)H + or Cp*Ir( CO2Me bpy)H + . Experimental and computational analyses are consistent with a concerted hydride transfer mechanism for all Ir complexes. As the thermodynamic driving force increases an earlier transition state is observed and all transition states also include π-stacking interactions between the donor and acceptor, which likely contribute to the different α values. The experimental data fits well to the Marcus model, enabling the determination of reorganization energies (λ) that range from 58 to 69 kcal mol -1 . These are lower than λ values for hydride transfer reactions involving organic donors and acceptors. This work provides a rare example of the correlation of kinetic and thermodynamic hydricity using only experimental data and shows that hydride transfer reactions involving metal hydrides can follow Marcus theory. Furthermore, the findings offer insight into controlling metal-catalyzed hydride transfer reactions, which is valuable for designing improved systems for a range of transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

PyJMAK: An Open-Source Python Toolkit for Modeling Solid-State Metallurgical Phase Transformations

Accurate prediction of metallurgical phase transformations is an essential basis for autonomous optimization and rapid part qualification. Several methods can be used to estimate the evolution of phase fractions such as JMAK kinetics-based models, phase-field models, thermodynamic models, and data-driven machine learning models. Thermodynamic and phase-field-based methodologies solve multiphysics equations requiring numerous calibration parameters and significant computational resources. As a result, the computation domain is limited to a point or on order of micron-meters. The data-driven models rely on large datasets from experiments and simulations. While the JMAK model only provides information about phase fraction evolution, it can predict this evolution in near real-time using thermal history and thermodynamic data without restriction on the domain. JMAK models have been popularly used by researchers to model phase transformations occuring during additive manufacturing or over arbitrary temperature profiles. Commercial proprietary software such as Abaqus and Ansys or closed-source in-house implementations offer the ability to model JMAK based kinetics to predict phase transformation. However, these software packages are not open-source or freely available for use and development in conjunction with manufacturing machines, sensors, and machine learning algorithms. In addition, the use of the model is restricted by a license token. In contrast, given temperature profiles at multiple points in the domain, this Python-based PyJMAK model can compute phase evolution in parallel due to its stand-alone modular, voxel-based structure, and it can be executed on high-performance computing resources without any license restrictions.

Prabhune, Bhagya [Oak Ridge National Laboratory (O↗