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At least 505 records · Page 28

Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering

Enzymes can be engineered at the level of their amino acid sequences to optimize key properties such as expression, stability, substrate range, and catalytic efficiency or even to unlock new catalytic activities not found in nature. Because the search space of possible proteins is vast, enzyme engineering usually involves discovering an enzyme starting point that has some level of the desired activity followed by directed evolution to improve its “fitness” for a desired application. Recently, machine learning (ML) has emerged as a powerful tool to complement this empirical process. ML models can contribute to (1) starting point discovery by functional annotation of known protein sequences or generating novel protein sequences with desired functions and (2) navigating protein fitness landscapes for fitness optimization by learning mappings between protein sequences and their associated fitness values. In this Outlook, we explain how ML complements enzyme engineering and discuss its future potential to unlock improved engineering outcomes.

60 APPLIED LIFE SCIENCES↗

Optimizing the shape of photometric redshift distributions with clustering cross-correlations

We present an optimization method for the assignment of photometric galaxies to a chosen set of redshift bins. This is achieved by combining simulated annealing, an optimization algorithm inspired by solid-state physics, with an unsupervised machine learning method, a self-organizing map (SOM) of the observed colours of galaxies. Starting with a sample of galaxies that is divided into redshift bins based on a photometric redshift point estimate, the simulated annealing algorithm repeatedly reassigns SOM-selected subsamples of galaxies, which are close in colour, to alternative redshift bins. We optimize the clustering cross-correlation signal between photometric galaxies and a reference sample of galaxies with well-calibrated redshifts. Depending on the effect on the clustering signal, the reassignment is either accepted or rejected. By dynamically increasing the resolution of the SOM, the algorithm eventually converges to a solution that minimizes the number of mismatched galaxies in each tomographic redshift bin and thus improves the compactness of their corresponding redshift distribution. This method is demonstrated on the synthetic Legacy Survey of Space and Time cosmoDC2 catalogue. We find a significant decrease in the fraction of catastrophic outliers in the redshift distribution in all tomographic bins, most notably in the highest redshift bin with a decrease in the outlier fraction from 57 percent to 16 percent.

79 ASTRONOMY AND ASTROPHYSICS↗

maestro

MÆSTRO stands for Multi-fidelity Adaptive Ensemble Stochastic Trust Region Optimization and it is a plug n play derivate fee stochastic optimization solver. The problem being considered in MÆSTRO involves fitting Monte Carlo simulations that describe complex phenomena to experiments. This is done by finding parameters of the resource intensive and noisy simulation that yield the least squares objective function value to the noisy experimental data. This problem is solved using a stochastic trust-region optimization algorithm where in each iteration, a local approximation of the simulation signal and of the simulation noise is constructed over data, which is obtained by running the simulation at strategically placed design points within the trust-region around the current iterate. Then the simulation components of the objective are replaced by their approximations and this analytical and closed-form optimization problem is solved to find the next iterate within the trust-region. Then the trust region is moved and the iterations continue until a satisfactory convergence criteria is met.

KRISHNAMOORTHY, MOHAN↗

Sensitivity-based voltage constraints for optimal power flow in low-voltage distribution feeders

The optimal power flow (OPF) problem for distribution systems can include network details down to the low-voltage (LV) points of interconnection of individual customers. This paper addresses the implementation of voltage magnitude constraints, and sets forth a practicable approach for capturing the effects on voltage from the switching behavior of loads (e.g., heat pumps, air conditioners, water heaters, or pool pumps) and from the variability of renewable generation (e.g., rooftop solar). The proposed method adjusts the OPF voltage constraints based on forecasts of load and generation upper and lower bounds, in conjunction with sensitivity factors derived from the power flow equations. An illustrative OPF formulation is also provided, which incorporates transformer models that include core loss. We demonstrate that accurate modeling of these LV network components is critical to avoid voltage violations at customer points of interconnection. Furthermore, the ideas are validated through numerical case studies on a realistic distribution feeder.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Methods and Results for Quantum Optimal Pulse Control on Superconducting Qubit Systems

The effective use of current Noisy Intermediate-Scale Quantum (NISQ) devices is often limited by the noise which is caused by interaction with the environment and affects the fidelity of quantum gates. In transmon qubit systems, the quantum gate fidelity can be improved by applying control pulses that can minimize the effects of the environmental noise. In this work, we employ physics-guided quantum optimal control strategies to design optimal pulses driving quantum gates on superconducting qubit systems. We test our results by conducting experiments on the IBM quantum hardware using their OpenPulse API. We compare the performance of our pulse-optimized quantum gates against the default quantum gates and show that the optimized pulses improve the fidelity of the quantum gates, in particular the single-qubit gates. Here we discuss the challenges we encountered in our work and point to possible future improvements.

97 MATHEMATICS AND COMPUTING↗

CCAMP: OpenMP and OpenACC Interoperable Framework

Heterogeneous systems have become a staple of the HPC environment. Several directive-based solutions, such as OpenMP and OpenACC, have been developed to alleviate the challenges of programming heterogeneous systems, and these standards strive to provide a single portable programming solution across heterogeneous environments. However, in many ways this goal has yet to be realized due to device-specific implementations and different levels of language support across compilers. In this framework we aim to analyze and address the different levels of optimization and compatibility between OpenACC and OpenMP programs and device compilers. We introduce the CCAMP framework, built on the OpenARC compiler, which implements language translation between OpenACC and OpenMP, with the goal of exploiting the maturity of different device-specific compilers to maximize performance for a given architecture. We show that CCAMP allows us to generate code for a specific device-compiler combination given a device-agnostic OpenMP or OpenACC program, allowing compilation and execution of programs with specific directives on otherwise incompatible devices. CCAMP also provides a starting point for a more advanced interoperable framework that can effectively provide directive translation and device, compiler, and application specific optimizations.

Lambert, Jacob↗

A second-order distributed memory parallel fast sweeping method for the Eikonal equation

The Eikonal equation is used to calculate wave propagation and distance fields, and due to its complexity requires numerical treatment for its solution. In this work, we present a second-order distributed memory parallel fast sweeping method. The second-order solution switches on a two-point stencil when two upwind points are available, and reverts to first-order otherwise. In all examples, the second-order method improves the solution over the first-order, allowing for significant savings in memory while achieving the same accuracy. Parallelization over distributed memory saw good weak scaling with optimal convergence. The computational time for second-order was approximately 2.5 times slower than first-order, where the largest amount of mesh points ran on 144 cores (512 GB) was ≈20 billion. The savings in memory from the second-order method combined with the distributed memory algorithm result in the ability to solve problems much larger than are possible with the serial first-order method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Efficient optimization method for finding minimum energy paths of magnetic transitions

Here, efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line search can, therefore, not be performed, the use of limited memory Broyden–Fletcher–Goldfarb–Shanno (LBFGS) and conjugate gradient algorithms in conjunction with orthogonal spin optimization (OSO) approach is shown to greatly outperform the previously used velocity projection and dissipative Landau–Lifschitz dynamics optimization methods. The implementation makes use of energy weighted springs for the distribution of the discretization points along the path and this is found to improve performance significantly. The various methods are applied to several test problems using a Heisenberg-type Hamiltonian, extended in some cases to include Dzyaloshinskii–Moriya and exchange interactions beyond nearest neighbours. Minimum energy paths are found for magnetization reversals in a nano-island, collapse of skyrmions in two-dimensional layers and annihilation of a chiral bobber near the surface of a three-dimensional magnet. The LBFGS-OSO method is found to outperform the dynamics based approaches by up to a factor of 8 in some cases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Weak phonon coupling to nematic quantum critical mode in BaFe 2 ⁢(As 1−𝑥 ⁢P 𝑥 ) 2

Here, in this work, we investigate the softening of the in-plane transverse acoustic phonon driven by electronic nematicity in BaFe 2 ⁢(As 1−𝑥 ⁢P 𝑥 ) 2 using inelastic x-ray scattering, with a focus on the optimally doped sample (𝑥 = 0.31) sample—a system exhibiting signatures of a putative nematic quantum critical point and minimal disorder among iron pnictides. We observe only a modest softening of the phonon frequency and no evidence of critical damping, suggesting that the nematic quantum critical fluctuations couple only weakly to the lattice from our quantum critical model. Given the close proximity of the structural and magnetic transition temperatures in the underdoped sample—which implies that spin-nematic fluctuations couple strongly to the lattice—we conjecture that the quantum critical nematic fluctuations are predominantly orbital in origin.

Wu, S. [University of California, Berkeley, CA (Un↗

Thermal transport properties of IrSbSe

Here we report a thermal transport study of IrSbSe, which crystallizes in a noncentrosymmetric cubic structure with the P2 1 3 space group and shows a narrow-gap semiconducting behavior. The large discrepancy between the activation energy for conductivity [E ρ = 128(2) meV] and for thermopower [E S = 17.7 (9) meV] from 200 to 300 K indicates a polaronic transport mechanism. The electrical resistivity varies as exp (T 0 /T) 1/4 and thermopower varies as T 1/2 at low temperatures, indicating that it evolves into Mott variable-range hopping dominant conduction with decreasing temperature. IrSbSe shows a relatively low value of thermal conductivity (~1.65 W/Km) and thermopower of about 0.24 mV/K around 100 K, yet poor electrical conductivity. On the other hand, a high vacancy defect concentration on both Ir and Sb atomic sites of up to 15% suggests a high defect tolerance and points to the possibility of a future improvement of carrier density by chemical substitution or defect optimization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Resonant Metamaterial Line Array for Ultrasound Compressive Imaging

Abstract Acoustic metamaterials have been proposed for numerous applications including subwavelength imaging, impedance matching, and lensing. Yet, their application in compressive sensing and imaging has not been fully investigated. When metamaterials are used as resonators at certain frequencies, they can generate random radiation patterns in the transmitted waves from the transducers and received waves from a target. Compressive sensing favors such randomness inasmuch as it can increase incoherence by decreasing the amount of mutual information between any two different measurements. This study aims at assessing whether the use of resonating metamaterial unit cells in a single-layered non-optimized array between a number of ultrasound transceivers and targets can improve the sensing capacity, point-spread function of the sensing array (their beam focusing ability), and imaging performance in point-like target detection. The theoretical results are promising and can open the way for more efficient metamaterial designs with the aim of enhancing ultrasound imaging with lower number of transceivers compared to the regular systems.

Acoustics↗

High energy yield bifacial spectrum-splitting photovoltaic system

In this paper a photovoltaic system is proposed that achieves high energy yield by integrating bifacial silicon cells into a spectrum-splitting module. Spectrum splitting is accomplished using volume holographic optical elements to spectrally divide sunlight onto an array of photovoltaic cells with different bandgap energies. Light that is reflected from the ground surface onto the rear side of the module is converted by the bifacial silicon cells. The energy yield of the system is optimized by tuning the volume holographic element parameters, such as film thickness, index modulation, and construction point source positions. An example is presented for utility-scale illumination parameters in Tucson, Arizona, that attains an energy yield of 1010 k w ⋅ <#comment/> h r y r ⋅ <#comment/> m 2 , which is 32.8% of the incident solar insolation.

Chrysler, Benjamin D. (ORCID:0000000186250147)↗

Final cooling with thick wedges for a muon collider

In the final cooling stages for a muon collider, the transverse emittances are reduced while the longitudinal emittance is allowed to increase. In previous studies, Final 4-D cooling used absorbers within very high field solenoids to cool low-momentum muons. Simulations of the systems did not reach the desired cooling design goals. In this study, we develop and optimize a different conceptual design for the final 4D cooling channel, which is based on using dense wedge absorbers. We used G4Beamline to simulate the channel and Python to generate and analyze particle distributions. We optimized the design parameters of the cooling channel and produced conceptual designs (corresponding to possible starting points for the input beam) which achieve transverse cooling in both x and y by a factor of ~3.5. These channels achieve a lower transverse and longitudinal emittance than the best design previously published.

43 PARTICLE ACCELERATORS↗

Dispatch Manager for NEML2 Constitutive Model Calculations Embedded in MOOSE

This report describes the extended capabilities of the NEML2 constitutive modeling library, including a flexible and efficient work dispatching system designed to leverage both CPU and GPU resources. This enhancement addresses one of the primary computational challenges in large-scale simulations: the ability to distribute and execute batches of material model evaluations across heterogeneous computing devices. The new dispatch system introduces a modular set of dispatcher and scheduler classes that coordinate the flow of data and execution between devices. The dispatcher is responsible for efficiently packaging work, managing device-specific memory operations, and synchronizing results. This modularity allows for extensibility, making it straightforward to integrate additional computing backends in the future. From an implementation standpoint, the dispatcher system interfaces seamlessly with NEML2's existing models. They handle device-aware tensor operations, optimize memory transfers, and support asynchronous execution when applicable. This design ensures that batches of material points can be evaluated concurrently, substantially improving throughput compared to previous single-device or serial implementations. These improvements not only enhance the raw performance of NEML2 but also improve its usability in multiscale and high-fidelity simulations, where the simultaneous evaluation of large material point batches is critical. Benchmarks included in the report demonstrate the system’s scalability, highlighting its effectiveness when leveraging modern GPU architectures.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Technical Performance of Refractory Liners for Molten Chloride Salt Thermal Energy Storage Systems

A chloride-based molten-salt system that uses a ternary blend of MgCl2/KCl/NaCl is investigated to provide higher temperature thermal energy storage capability. Despite higher thermal stability, molten chlorides present several unique challenges, including the design of internal refractory-ceramic liners to prevent the corrosion and thermal stress of alloy tank shells. This work discusses issues and potential solutions related to containment of molten chloride salt, specifically the optimization of the refractory material at the molten salt interface (hot face). The down-selected hot face candidate limits permeation of salt through the material and forms a highly stable secondary surface phase in equilibrium with the molten salt. A mortar is created using the corrosion resistant hot face brick. Brick and mortar composite are subjected to mechanical stress/strain analysis, in order to calculate composite material properties and better inform thermomechanical models. The U.S. Department of Energy Generation 3 (DOE Gen3) program seeks to develop higher efficiency CSP plants that can provide cost-competitive, flexible power in the U.S. electric grid. The proposed Gen3 Liquid Pathway CSP plant closely resembles the configuration of current nitrate salt power towers with two-tank storage (Gen2). The differences between Gen2 and Gen3 include the types of compatible materials used in salt storage tank construction. Stainless steel loses strength at Gen3 temperatures, and although nickel superalloys would be capable of withstanding sustained high temperatures, these materials are prohibitively expensive at scale. Uninsulated tank shells also pose a significant risk as common steels are highly susceptible to chemical attack from molten chloride salt. To address these concerns, refractory-ceramic based containment materials are proposed to line the inside of the hot and cold storage tanks. In doing so, stainless or carbon steel shells may be used in construction depending on the level of insulation provided. The composition of the internal liner requires careful consideration to maximize the efficacy of multiple parameters including corrosion resistance, strength at operating temperature, durability, and cost. This is particularly true for the material at the interface with the salt, known as the "hot face", which is responsible for protecting the insulating layers between the tank shell and the hot face brick layer. The molten salt in this system is superheated over 300 °C above its freeze temperature. Therefore, unlike other industrial processes which use refractory-lined vessels, it is not expected that a freeze plane will develop in the hot face. Therefore, the hot face must be designed to withstand chemical corrosion and inhibit permeation of molten salt into the insulating layers. A down selection was performed to identify a hot face candidate best equipped to maintain thermal, mechanical, and chemical integrity when exposed to molten salt over extended periods of time. Long-duration chemical capability experiments were conducted with the down selected hot face refractory fully immersed in molten chloride salt for up to 3000 hours. The average salt penetration does not exceed 100 microns. When extrapolated to 20 and 30 years of continuous exposure, the expected salt penetration depth is approximately 2.0 mm and 2.9 mm, respectively. A magnesium-rich secondary phases develops at the salt/refractory interface. X-ray diffraction identifies the material as forsterite (Mg2SiO4), which is reported to form synthetically in molten chloride salt solutions. These results suggest the selected hot face will adequately inhibit salt permeation. While there is optimism that the hot face brick will inhibit salt permeation, mortar joints are typically the weakest point of a refractory brick liner. From a thermochemical perspective, differing thermal expansion coefficients may result in the mortar and brick to grow independent of each other, creating gaps through which molten salt can penetrate. To address this issue, NREL has developed an in-house mortar composed of the down selected hot face brick that has been shown to be compatible with the salt. Compressive stress/strain analyses have been performed on the brick/ mortar composites to generate stress/strain curves. Modulus of elasticity and Poisson's ratio of the composite may be calculated from the stress/strain curves, in order to provide more representative data to finite element mechanical models for accurate approximation of stress on the tank shell and the amount of thermal expansion expected within the tank liner.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Designing a parallel Feel-the-Way clustering algorithm on HPC systems

This paper introduces a new parallel clustering algorithm, named Feel-the-Way clustering algorithm, that provides better or equivalent convergence rate than the traditional clustering methods by optimizing the synchronization and communication costs. Our algorithm design centers on how to optimize three factors simultaneously: reduced synchronizations, improved convergence rate, and retained same or comparable optimization cost. To compare the optimization cost, we use the Sum of Square Error (SSE) cost as the metric, which is the sum of the square distance between each data point and its assigned clusters. Compared with the traditional MPI k-means algorithm, the new Feel-the-Way algorithm requires less communications among participating processes. As for the convergence rate, the new algorithm requires fewer number of iterations to converge. As for the optimization cost, it obtains the SSE costs that are close to the k-means algorithm. In the paper, we first design the full-step Feel-the-Way k-means clustering algorithm that can significantly reduce the number of iterations that are required by the original k-means clustering method. Next, we improve the performance of the full-step algorithm by adopting an optimized sampling-based approach, named reassignment-history-aware sampling. Our experimental results show that the optimized sampling-based Feel-the-Way method is significantly faster than the widely used k-means clustering method, and can provide comparable optimization costs. More extensive experiments with several synthetic datasets and real-world datasets (e.g., MNIST, CIFAR-10, ENRON, and PLACES-2) show that the new parallel algorithm can outperform the open source MPI k-means library by up to 110% on a high-performance computing system using 4,096 CPU cores. In addition, the new algorithm can take up to 51% fewer iterations to converge than the k-means clustering algorithm.

97 MATHEMATICS AND COMPUTING↗