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DOE OSTI2024

Evaluating the Use of Foundational Chemical Language Models in Multimodal Graph Fusion

Rapid and accurate prediction of the physicochemical properties of molecules given their structures remains a key challenge in cheminformatics. Machine learning approaches offer high-throughput options, but the optimality of inductive biases and data representations are up for debate. For example, BERT-based masked language models (MLMs) can be trained in a self-supervised way on hundreds of millions to billions of readily available SMILES strings. Another option is graph neural networks (GNNs), which can operate directly on molecular structures. Yet, generating accurate molecular geometry is computationally expensive, leading to a relative scarcity in data compared to SMILES strings. It is attractive to combine these two paradigms by pre-training an LM on a large corpus of SMILES strings and embedding these representation into a geometric graph neural network. Despite the promise of such an approach, and contrary to previous studies, we find mixed results with the combination of the LMs and GNNs on several molecule datasets. In particular, we found evidence for improvement on the FreeSolv and QM7 benchmarks, but degraded performance on the ESOL, LIPO and QM9 datasets compared to a GNN baseline.

Francel, Collin [University of Alabama]↗

DOE OSTI2021

Double photoionization of atomic oxygen: Feshbach resonances in the two-electron continuum

In this work, we describe a joint experimental and theoretical investigation on oxygen double photoionization—the emission of two electrons from atomic oxygen following single photon absorption. High-resolution experimental measurements were performed at the Advanced Light Source, revealing sharp resonance structure superimposed on the more familiar Wannier-like, nearly-linear background. These resonance features are attributed to ionization-plus-excitation Feshbach resonances embedded in the double ionization continuum, doubly-excited states that lie above the double-ionization threshold. Such features are absent in the double photoionization cross section of He, or other quasi-two-electron systems, for which the doubly-ionized atomic core remains inert. For a corresponding theoretical analysis, the R-matrix with pseudostates (RMPS) method was invoked by calculating final-state, two-electron resonances-plus-continua wavefunctions and corresponding single-photon absorption cross sections. Overall agreement is found in the direct, background double photoionization cross section. However, the RMPS method, using a small basis due to practical computational limitations, was unable to reproduce quantitatively the smooth background or the sharper resonance features observed in the measurements, showing instead large-scale oscillations about the experimental background, and characteristic pseudoresonance jitter, associated with an insufficient convergence of the pseudostate representation to the true two-electron infinite series of Feshbach resonances embedded in the two-electron continuum. The prominent resonance structure observed highlights the need to consider multiple excitation processes in atoms more complex than He or quasi-two-electron systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Power allocation by load aggregator with heterogeneous loads using weighted projection

With the recently increasing adoption of transactive energy markets, the role of a load aggregator is becoming increasingly important. Among the many tasks of an aggregator, the task of managing the electricity consumption among a group of grid-interactive efficient buildings according to the demand on the grid is taken up. Specifically, here, the task of allocating a certain amount of power among the participating customers while respecting their preferences and comfort is considered. Modeling this as an aggregate flexibility, the virtual battery conditions that are employed to verify the feasibility of a candidate power profile are derived. A feasible power profile, when allocated, satisfies specified comfort bands. To determine the ideal power requirement of the loads, the model-free control method is employed. The feasible power profile is allocated by embedding the customers’ preferences through weights, posing the power constraint as a hyperplane, and employing a weighted projection from the ideal power requirements onto the constraint plane to solve the considered task. The proposed method is computationally efficient and scalable to any number of heterogeneous thermostatically controlled loads in buildings.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

SANE: strategic autonomous non-smooth exploration for multiple optima discovery in multi-modal and non-differentiable black-box functions

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and multimodal parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, material structure image spaces, and molecular embedding spaces. Often these systems are black-boxes and time-consuming to evaluate, which resulted in strong interest towards active learning methods such as Bayesian optimization (BO). However, these systems are often noisy which make the black box function severely multi-modal and non-differentiable, where a vanilla BO can get overly focused near a single or faux optimum, deviating from the broader goal of scientific discovery. To address these limitations, here we developed Strategic Autonomous Non-Smooth Exploration (SANE) to facilitate an intelligent Bayesian optimized navigation with a proposed cost-driven probabilistic acquisition function to find multiple global and local optimal regions, avoiding the tendency to becoming trapped in a single optimum. To distinguish between a true and false optimal region due to noisy experimental measurements, a human (domain) knowledge driven dynamic surrogate gate is integrated with SANE. We implemented the gate-SANE into pre-acquired piezoresponse spectroscopy data of a ferroelectric combinatorial library with high noise levels in specific regions, and piezoresponse force microscopy (PFM) hyperspectral data. SANE demonstrated better performance than classical BO to facilitate the exploration of multiple optimal regions and thereby prioritized learning with higher coverage of scientific values in autonomous experiments. Our work showcases the potential application of this method to real-world experiments, where such combined strategic and human intervening approaches can be critical to unlocking new discoveries in autonomous research.

Biswas, Arpan [University of Tennessee, Knoxville,↗

DOE OSTI2021

Normal stability of slow manifolds in nearly periodic Hamiltonian systems

Kruskal [J. Math. Phys. 3, 806 (1962)] showed that each nearly periodic dynamical system admits a formal U(1) symmetry, generated by the so-called roto-rate. We prove that such systems also admit nearly invariant manifolds of each order, near which rapid oscillations are suppressed. We study the nonlinear normal stability of these slow manifolds for nearly periodic Hamiltonian systems on barely symplectic manifolds—manifolds equipped with closed, non-degenerate 2-forms that may be degenerate to leading order. In particular, we establish a sufficient condition for long-term normal stability based on second derivatives of the well-known adiabatic invariant. We use these results to investigate the problem of embedding guiding center dynamics of a magnetized charged particle as a slow manifold in a nearly periodic system. Here, we prove that one previous embedding and two new embeddings enjoy long-term normal stability and thereby strengthen the theoretical justification for these models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Brightest cluster galaxies trace weak lensing mass bias and halo triaxiality in the three hundred project

Galaxy clusters have a triaxial matter distribution. The weak-lensing signal, an important part in cosmological studies, measures the projected mass of all matter along the line of sight, and therefore changes with the orientation of the cluster. Studies suggest that the shape of the brightest cluster galaxy (BCG) in the centre of the cluster traces the underlying halo shape, enabling a method to account for projection effects. We use 324 simulated clusters at four redshifts between 0.1 and 0.6 from ‘The Three Hundred Project’ to quantify correlations between the orientation and shape of the BCG and the halo. We find that haloes and their embedded BCGs are aligned, with an average ~20 degree angle between their major axes. The bias in weak lensing cluster mass estimates correlates with the orientation of both the halo and the BCG. Mimicking observations, we compute the projected shape of the BCG, as a measure of the BCG orientation, and find that it is most strongly correlated to the weak-lensing mass for relaxed clusters. We also test a 2D cluster relaxation proxy measured from BCG mass isocontours. The concentration of stellar mass in the projected BCG core compared to the total stellar mass provides an alternative proxy for the BCG orientation. We find that the concentration does not correlate to the weak-lensing mass bias, but does correlate with the true halo mass. Here, these results indicate that the BCG shape and orientation for large samples of relaxed clusters can provide information to improve weak-lensing mass estimates.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A Verified Optimizer for Quantum Circuits

We present VOQC, the first verified optimizer for quantum circuits, written using the Coq proof assistant. Quantum circuits are expressed as programs in a simple, low-level language called SQIR, a small quantum intermediate representation, which is deeply embedded in Coq. Optimizations and other transformations are expressed as Coq functions, which are proved correct with respect to a semantics of SQIR programs. SQIR programs denote complex-valued matrices, as is standard in quantum computation, but we treat matrices symbolically to reason about programs that use an arbitrary number of quantum bits. SQIR’s careful design and our provided automation make it possible to write and verify a broad range of optimizations in VOQC, including full-circuit transformations from cutting-edge optimizers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Multiscale Modeling of Nanoparticle Precipitation in Oxide Dispersion-Strengthened Steels Produced by Laser Powder Bed Fusion

Laser Powder Bed Fusion (LPBF) enables the efficient production of near-net-shape oxide dispersion-strengthened (ODS) alloys, which possess superior mechanical properties due to oxide nanoparticles (e.g., yttrium oxide, Y-O, and yttrium-titanium oxide, Y-Ti-O) embedded in the alloy matrix. To better understand the precipitation mechanisms of the oxide nanoparticles and predict their size distribution under LPBF conditions, we developed an innovative physics-based multiscale modeling strategy that incorporates multiple computational approaches. These include a finite volume method model (Flow3D) to analyze the temperature field and cooling rate of the melt pool during the LPBF process, a density functional theory model to calculate the binding energy of Y-O particles and the temperature-dependent diffusivities of Y and O in molten 316L stainless steel (SS), and a cluster dynamics model to evaluate the kinetic evolution and size distribution of Y-O nanoparticles in as-fabricated 316L SS ODS alloys. The model-predicted particle sizes exhibit good agreement with experimental measurements across various LPBF process parameters, i.e., laser power (110–220 W) and scanning speed (150–900 mm/s), demonstrating the reliability and predictive power of the modeling approach. The multiscale approach can be used to guide the future design of experimental process parameters to control oxide nanoparticle characteristics in LPBF-manufactured ODS alloys. Additionally, our approach introduces a novel strategy for understanding and modeling the thermodynamics and kinetics of precipitation in high-temperature systems, particularly molten alloys.

Wang, Zhengming (ORCID:0000000241627112)↗

DOE OSTI2024

Development & Experimental Validation of a Generalized Resistance-Capacitance Model for Numerical Simulation of Phase-Change Material Embedded Heat Exchangers

Latent heat thermal energy storage (LHTES) using phase change material (PCM) has attracted increased attention as a viable solution for overcoming the mismatch between energy supply and demand for renewable energy-based systems. PCM-embedded heat exchangers (PCM-HX) have the potential to significantly improve thermal performance due to high storage capacity and low temperature variation during the phase change process. Most models for simulating LHTES heat transfer use Computational Fluid Dynamics (CFD) simulations, which have high computational costs resulting from considering the complex and time-dependent physics relevant to PCM-HXs. In this paper, a Generalized Resistance Capacitance-based Model (GRCM) was developed to predict the thermal performance of arbitrary PCM-HXs in a computationally efficient manner without compromising modeling accuracy. The GRCM is exercised for three case studies: (i) verification for a single-slabbed finned PCM-HX, (ii) verification and validation for a copper foam/paraffin composite PCM-HX, and (iii) validation for a straight tube annular finned PCM-HX. The copper foam PCM-HX uses an electric heater at the top of HX, while the other two configurations utilize water as heat transfer fluid. For the single-slabbed finned PCM-HX melting case, the mean deviation in average PCM temperature predicted by the GRCM compared to the CFD model was between 0.56 – 0.73 K, with maximum temperature deviation of 2.68 K. For the HTF outlet temperature, the validation results showed that GRCM prediction matches very well with experimental data, with mean temperature deviation of 0.24 K during melting case, while for solidification case was 0.34 K. These results showcase the GRCM’s capability for accurately reproducing the thermal characteristics of PCM-HXs with considerably lower computational effort.

42 ENGINEERING↗

DOE OSTI2021

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

Motivation: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%. Results: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Interpretable and flexible non-intrusive reduced-order models using reproducing kernel Hilbert spaces

This paper develops an interpretable, non-intrusive reduced-order modeling technique using regularized kernel interpolation. Existing non-intrusive approaches approximate the dynamics of a reduced-order model (ROM) by solving a data-driven least-squares regression problem for low-dimensional matrix operators. Our approach instead leverages regularized kernel interpolation, which yields an optimal approximation of the ROM dynamics from a user-defined reproducing kernel Hilbert space. We show that our kernel-based approach can produce interpretable ROMs whose structure mirrors full-order model structure by embedding judiciously chosen feature maps into the kernel. The approach is flexible and allows a combination of informed structure through feature maps and closure terms via more general nonlinear terms in the kernel. We also derive a computable a posteriori error bound that combines standard error estimates for intrusive projection-based ROMs and kernel interpolants. In conclusion, the approach is demonstrated in several numerical experiments that include comparisons to operator inference using both proper orthogonal decomposition and quadratic manifold dimension reduction.

Data-driven model reduction↗

DOE OSTI2019

Structure and proton conduction in sulfonated poly(ether ether ketone) semi-permeable membranes: a multi-scale computational approach.

The design of polymeric membranes for proton or ionic exchange highly depends on the fundamental understanding of the physical and molecular mechanisms that control the formation of the conduction channels. There is an inherent relation between the dynamical structure of the polymeric membrane and the electrostatic forces that drive membrane segregation and proton transport. Here, we used a multi-scale computational approach to analyze the morphology of sulfonated poly(ether ether ketone) membranes at the mesoscale. A self-consistent description of the electrostatic phenomenon was adopted, where discrete polymer chains and a continuum proton field were embedded in a continuum fluid. Brownian dynamics was used for the evolution of the suspended polymer molecules, while a convection-diffusion transport equation, including the Nernst-Planck diffusion mechanism, accounted for the dynamics of the proton concentration field. We varied the polymer concentration, the degree of sulfonation and the level of confinement to find relationships between membrane structure and proton conduction. Our results indicate that the reduced mobility of polymer chains, at concentrations above overlap, and a moderate degree of sulfonation -i.e., 30% - are essential elements for membrane segregation and proton domain connectivity. These conditions also ensure that the membrane structure is not affected by size or by potential gradients. Importantly, our analysis shows that membrane conductivity and current are linearly dependent on polymer concentration and quadratically dependent on the degree of sulfonation. We found that the optimal polymeric membrane design requires a polymer concentration above overlap and a degree of sulfonation around 50%. These conditions promote a dynamical membrane morphology with a constant density of proton channels. Our results and measurements agree with previous experimental works, thereby validating our model and observations.

Molina, Jarol↗

DOE OSTI2018

Development of formalisms based on locally coupled open subsystems for calculations in molecular electronic structure and dynamics

Quantum embedding theories model a collection of interacting molecules as a set of subsystems, where each can be treated with a particular electronic structure method (wave function or density functional theory, for example); these theories can lead to computationally efficient and accurate algorithms. Motivated by challenges in the field, we previously described a formalism (that models two subsystems), which we call “locally coupled open subsystems” (LCOS), for the computation of ground-state energies, fractional electron-occupation numbers of the subsystems, and the size-consistent limit of subsystem dissociation. In this work we present the full (nonrelativistic) LCOS theory and the following extensions of our previous work: (i) the framework to study systems composed of multiple subsystems and a procedure to spin-adapt the auxiliary wave function that describes the partitioned system, so that its spin state matches that of the real system of interest; (ii) potential functionals and ideas to employ machine learning for the computation of ground-state densities and energies; (iii) formulation of two LCOS ground-state approaches where the fragments are assigned Kohn-Sham wave functions; and (iv) a time-dependent (TD) extension of these two ground-state formalisms in which the state of the subsystems evolves according to a unitary propagation; from this evolution we can extract TD electron populations of the fragments, for instance. We also discuss potential applications of the TD LCOS theory to linear photoabsorption and Raman spectroscopy. As a result, the developments presented in this work can lead to ground-state and TD electronic structure calculations where the computational scaling can be controlled, depending on the level of theory and the accuracy desired to model each one of the subsystems and their coupling.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

The Extended Embedded Self-Shielding Method in SCALE 6.3/Polaris

The SCALE transport lattice code, Polaris, has been previously developed to generate few-group homogenized cross sections for whole-core nodal diffusion simulators in which the embedded self-shielding method (ESSM) is used for resonance self-shielding calculations to process cross sections. Although the ESSM capability has been very successful in light-water reactor analysis, it may require enhancements in computational efficiency; treatment of spatially dependent resonance self-shielding effects; and handling of interrelated resonance effects among fuel, cladding, and control rod materials. Therefore, this study focuses on improving computational efficiency by using a Dancoff-based Wigner–Seitz approximation combined with a material-based resonance categorization, through which a spatially dependent ESSM capability is developed to accurately estimate self-shielded cross sections inside the fuel. Benchmark results show that the new capability significantly enhances computational efficiency and accuracy for spatially dependent local zones within the fuel and through depletion.

ESSM↗

DOE OSTI2026

An efficient explicit implementation of a near-optimal quantum algorithm for simulating linear dissipative differential equations

We propose an efficient block-encoding technique for the implementation of the Linear Combination of Hamiltonian Simulations (LCHS) for simulating dissipative initial-value problems. This algorithm approximates a target nonunitary operator as a weighted sum of Hamiltonian evolutions, thereby emulating a dissipative problem by mixing various time scales. We introduce an efficient encoding of the LCHS into a quantum circuit based on a simple coordinate transformation that turns the dependence on the summation index into a trigonometric function. Classically, this method is equivalent to the use of a highly accurate Fejér-Clenshaw-Curtis quadrature formula. Quantumly, this significantly simplifies block-encoding of a dissipative problem and allows one to perform an exponential number of Hamiltonian simulations by a single Quantum Signal Processing (QSP) circuit. The resulting LCHS circuit has high success probability and the selector scales logarithmically with the number of terms in the LCHS sum and linearly with time. Careful analysis of error convergence proves that this method is more efficient than other LCHS circuits that have recently appeared in the literature. We verify the quantum circuit and its scaling by simulating it on a digital emulator of fault-tolerant quantum computers and, as a test problem, solve the advection-diffusion equation. The proposed algorithm can be used for simulating a wide class of nonunitary initial-value problems including the Liouville equation with added dissipation and linear embeddings of nonlinear systems, such as the Koopman-von Neumann and Carleman embeddings.

Novikau, I [Lawrence Livermore National Laboratory↗

DOE OSTI2025

Active-noise-induced dynamic clustering of passive colloidal particles

Active fluids generate spontaneous, often chaotic mesoscale flows. Harnessing these flows to drive soft materials embedded within an active fluid into structures with controlled length scales and lifetimes is a key challenge at the interface between the fields of active matter and nonequilibrium self-assembly. Here, we present a simple and efficient computational approach to model soft materials advected by active fluids, by simulating particles moving in a spatiotemporally correlated noise field. To illustrate our approach, we simulate the dynamical self-organization of repulsive colloids within such an active noise field. The colloids form structures whose sizes and dynamics can be tuned by the correlation time and length of the active fluid, and range from small rotating droplets to clusters with internal flows and system-spanning sizes that vastly exceed the active correlation length. Our results explain how the interplay between active fluid time and length scales and emergent driven assembly can be used to rationally design functional assemblies. More broadly, our approach can be used to efficiently simulate diverse active fluids and other systems with spatiotemporally correlated noise.

Brownian dynamics↗

DOE OSTI2023

Quantum computing for fusion energy science applications

This is a review of recent research exploring and extending present-day quantum computing capabilities for fusion energy science applications. We begin with a brief tutorial on both ideal and open quantum dynamics, universal quantum computation, and quantum algorithms. Then, we explore the topic of using quantum computers to simulate both linear and nonlinear dynamics in greater detail. Because quantum computers can only efficiently perform linear operations on the quantum state, it is challenging to perform nonlinear operations that are generically required to describe the nonlinear differential equations of interest. In this work, we extend previous results on embedding nonlinear systems within linear systems by explicitly deriving the connection between the Koopman evolution operator, the Perron–Frobenius evolution operator, and the Koopman–von Neumann evolution (KvN) operator. We also explicitly derive the connection between the Koopman and Carleman approaches to embedding. Extension of the KvN framework to the complex-analytic setting relevant to Carleman embedding, and the proof that different choices of complex analytic reproducing kernel Hilbert spaces depend on the choice of Hilbert space metric are covered in the appendixes. Finally, we conclude with a review of recent quantum hardware implementations of algorithms on present-day quantum hardware platforms that may one day be accelerated through Hamiltonian simulation. We discuss the simulation of toy models of wave–particle interactions through the simulation of quantum maps and of wave–wave interactions important in nonlinear plasma dynamics.

Joseph, I. (ORCID:0000000255400840)↗

DOE OSTI2019

Creating Training Data for Scientific Named Entity Recognition with Minimal Human Effort

Scientific Named Entity Referent Extraction is often more complicated than traditional Named Entity Recognition (NER). For example, in polymer science, chemical structure may be encoded in a variety of nonstandard naming conventions, and authors may refer to polymers with conventional names, commonly used names, labels (in lieu of longer names), synonyms, and acronyms. As a result, accurate scientific NER methods are often based on task-specific rules, which are difficult to develop and maintain, and are not easily generalized to other tasks and fields. Machine learning models require substantial expert-annotated data for training. Here we propose polyNER: a semi-automated system for efficient identification of scientific entities in text. PolyNER applies word embedding models to generate entity-rich corpora for productive expert labeling, and then uses the resulting labeled data to bootstrap a context-based word vector classifier. Evaluation on materials science publications shows that the polyNER approach enables improved precision or recall relative to a state-of-the-art chemical entity extraction system at a dramatically lower cost: it required just two hours of expert time, rather than extensive and expensive rule engineering, to achieve that result. This result highlights the potential for human-computer partnership for constructing domain-specific scientific NER systems.

Crowdsourcing↗