Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6
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Biochemistry & Molecular Biology↗
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Results for “computational optimization”
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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Computational optimal transport for molecular spectra: The fully continuous case
Computational optimal transport is used to analyze the difference between pairs of continuous molecular spectra. It is demonstrated that transport distances which are derived from this approach may be a more appropriate measure of the difference between two continuous spectra than more familiar measures of distance under many common circumstances. Associated with the transport distances is the transport map which provides a detailed analysis of the difference between two molecular spectra and is a key component of our study of quantitative differences between two continuous spectra. The use of optimal transport for comparing molecular spectra is developed in detail here with a set of model spectra, so that the discussion is self-contained. The difference between the transport distance and more common definitions of distance is elucidated for some well-chosen examples and it is shown where transport distances may be very useful alternatives to standard definitions of distance. The transport distance between a theoretical and experimental electronic absorption spectrum for SO 2 is studied and it is shown how the theoretical spectrum can be modified to fit the experimental spectrum better adjusting the theoretical band origin and the resolution of the theoretical spectrum. In conclusion, this analysis includes the calculation of transport maps between the theoretical and experimental spectra suggesting future applications of the methodology.
74 ATOMIC AND MOLECULAR PHYSICS↗
Computational Optimization of Room Temperature Usable Capacity for Hydrogen Storage in MFU-4-Type Metal–Organic Frameworks via Pairwise Metal Substitutions
The efficient storage of hydrogen is a critical challenge in the quest for sustainable energy solutions. Current adsorbent-based methods achieve satisfactory storage densities predominantly under cryogenic temperatures and/or high pressures, which imposes problems with cost-efficient and safe implementation of this technology. Materials that can bind hydrogen gas reversibly at ambient temperatures and more moderate pressures could play a pivotal role in enabling hydrogen-powered technologies. In this study, we use reliable computational modeling to investigate two synthetically feasible paths for tuning the enthalpy of H2 binding in MFU-4-type metal–organic frameworks (MOFs), aiming to maximize usable capacity. This study examines MIM4 IICl3(bta)6 (bta– = benzotriazolate) Kuratowski-type clusters as a model for strong binding sites in MFU-4l frameworks. We systematically evaluate the impact of separately tuning the central MII metal ion (which plays a structural role) and the peripheral MI metal ion (which binds the substrate) on the energetics of H2 binding. Our computational study reveals that H2 binding at an MI site mostly follows the trend AgI < CuI < NiI < CoI < AuI while a larger central MII site generally weakens the H2 binding at a MI site. Importantly, we have identified three new combinations of MI and MII to achieve high fractional usable capacities of the total H2 adsorbed under a pressure swing from 5 to 100 bar at room temperature. Additionally, we examine the nature of the binding interaction between the peripheral metal atom and the hydrogen molecule. While charge transfer predominantly induces this interaction, for several atom combinations, a change in the polarization (associated with variations in the ionic radius of the MI binding atom) is another important factor for adjusting the strength of the interaction. We suggest that the proposed compositions of Kuratowski-type clusters are highly desirable synthetic targets for future laboratory study.
Tkachenko, Nikolay V↗
Computational Optimization of 133m Xe Production via Neutron Irradiation in a TRIGA Reactor
Here, the Comprehensive Nuclear-Test-Ban Treaty bans all nuclear tests worldwide. As part of treaty compliance, the concentration of radioactive nuclides in the atmosphere is monitored to detect nuclear weapons tests. Radioactive noble gas fission products, specifically radioxenon, can vent into the atmosphere after a nuclear weapons test, even if the test is well contained underground or underwater. Radioxenon thus serves as a signal for nuclear weapons tests. All atmospheric monitoring systems require samples of radioxenon isotopes for detector calibration, quality control, and certification. Here, we present a novel, improved method for creating samples of 133m Xe via neutron irradiation of 132 Xe in the Washington State University TRIGA reactor. 132 Xe neutron absorption results in either 133 Xe or 133m Xe—thermal neutron absorption results in 133m Xe 12% of the time, while fast neutron absorption (above ~1 MeV) results in 133m Xe ~50% of the time. To optimize the production of 133m Xe via neutron absorption in 132 Xe in the thermal TRIGA reactor, spectral tuning using an irradiation chamber is required to maximize the fraction of fast neutrons being absorbed and minimize the number of thermal neutrons interacting with the 132 Xe. We used MCNP to tally 132 Xe absorptions with the isotopic tally function, flux tallies and neutron attenuation to estimate the number of neutrons reaching the 132 Xe through the irradiation chamber, and the adjoint importance function to improve the source strength estimate. Additionally, we performed a heat transfer analysis for safety considerations. It was determined that the use of a 96% enriched 10 B boron carbide chamber, placed next to the fuel elements in reactor position D8, increases the 133m Xe/ 133 Xe activity ratio from a baseline value of 0.3 to 1.0, a 233% increase. Additionally, it was determined that the alpha heating produced in the boron does not become an unmanageable problem in the Washington State University reactor.
37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
Computationally Optimized New World Arenavirus Glycoprotein Epigraphs are Displayed and Functional in VSVdG Vectors
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Johnson, Dylan Mac Gregor [Sandia National Laborat↗
Computing an Optimal Entanglement Path with Throughput and Fidelity Considerations
Entanglement distribution is a core function of quantum networks essential for operations including teleportation, distributed quantum sensing, and multisite computation. Entanglement throughput and fidelity are two critical performance measures that depend on the quantum transmission along the links and swapping operations at the repeaters along the path. We study the problem of computing a end-to-end entanglement path that satisfies both fidelity and throughput requirements, leveraging qubit buffers at the nodes and considering the sequential swapping order. We show that the general problem of simultaneously satisfying both metrics to be NP-hard, and develop an algorithm to maximize throughput subject to a given fidelity threshold. We introduce the concepts of entanglement probability distribution and path domination and exploit them in the design of our algorithm. Extensive numerical results show that our algorithm can find optimal solutions in networks with thousands of nodes in less than a second. We also describe practical and possible implementation aspects of this algorithm in terms of devices and architecture support.
Xue, Guoliang [Arizona State University]↗
Unleashed from constrained optimization: quantum computing for quantum chemistry employing generator coordinate inspired method
Hybrid quantum-classical approaches offer potential solutions to quantum chemistry problems, yet they often manifest as constrained optimization problems. Here, we explore the interconnection between constrained optimization and generalized eigenvalue problems through the Unitary Coupled Cluster (UCC) excitation generators. Inspired by the generator coordinate method, we employ these UCC excitation generators to construct non-orthogonal, overcomplete many-body bases, projecting the system Hamiltonian into an effective Hamiltonian, which bypasses issues such as barren plateaus that heuristic numerical minimizers often encountered in standard variational quantum eigensolver (VQE). Diverging from conventional quantum subspace expansion methods, we introduce an adaptive scheme that robustly constructs the many-body basis sets from a pool of the UCC excitation generators. This scheme supports the development of a hierarchical ADAPT quantum-classical strategy, enabling a balanced interplay between subspace expansion and ansatz optimization to address complex, strongly correlated quantum chemical systems cost-effectively, setting the stage for more advanced quantum simulations in chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational Antigen Optimization through Symbolic Optimization and Affinity Maturation Simulation
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Biological and medical sciences, Mathematics and C↗
Dielectric Resonator Design for Low Power and Low Temperature Microwave Plasma
Waveguide-based microwave plasmas generally operate at high temperatures (2000 - 6000K)[1], making it difficult to directly interface solid materials with the plasma without significant thermal damage. Dielectric microwave resonators (DMRs), long studied for wave-based manipulation of electromagnetic radiation for telecom and optics, can focus radiation to extremely small mode volumes, creating intense localized fields with low-power input.[2] This phenomenon can be used for applications ranging from efficient plasma electronics to near-ambient plasma-materials interactions. Such DMR-based plasmas have been demonstrated a handful of times in the literature, but the majority of research towards this utilize the lowest frequency resonance mode.[3], [4], [5] By carefully controlling the geometry of cylindrical resonators, a variety of electromagnetic modes can be excited. In this work, COMSOL Multiphysics simulations are used to study the electric field enhancement and absorption properties of CaTiO3 DMRs as a function of geometry and excitation frequency. Whereas previous studies have utilized the HEM111 resonance frequency to drive low power plasma excitation, we find that higher order resonance frequencies are more effective at field enhancement and result in less power loss within the dielectric material, hence less wasted heating. The effectiveness of these modes is also geometry dependent and can be computationally optimized for plasma generation. Complementing these computational efforts, we demonstrate a new closed-system reactor design built in a WR-650 waveguide and experimentally demonstrate the formation of atmospheric argon microwave plasma using < 30 W input power on DMR dimers. We observe a shifting resonance frequency as the DMRs heat in response to microwave excitation and develop a Python-based lock-in mechanism to effectively track the DMR resonance over time, leading to stable plasma operation. We use infrared thermal imaging to monitor the temperature of the DMR dimers and surrounding quartz chamber, demonstrating thermal temperatures < 60 degreesC. Finally, we utilize optical emission spectroscopy (OES) to probe the plasma properties as a function of the resonance mode.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Explosively driven Richtmyer–Meshkov instability jet suppression and enhancement via coupling machine learning and additive manufacturing
The ability to control the behavior of fluid instabilities at material interfaces, such as the shock-driven Richtmyer–Meshkov instability, is a grand technological challenge with a broad number of applications ranging from inertial confinement fusion experiments to explosively driven shaped charges. In this work, we use a linear-geometry shaped charge as a means of studying methods for controlling material jetting that results from the Richtmyer–Meshkov instability. A shaped charge produces a high-velocity jet by focusing the energy from the detonation of high explosives. The interaction of the resulting detonation wave with a hollowed cavity lined with a thin metal layer produces the unstable jetting effect. By modifying the characteristics of the detonation wave prior to striking the lined cavity, the kinetic energy of the jet can be enhanced or reduced. Modifying the geometry of the liner material can also be used to alter jetting properties. We apply optimization methods to investigate several design parameterizations for both enhancing or suppressing the shaped-charge jet. This is accomplished using 2D and 3D hydrodynamic simulations to investigate the design space that we consider. We also apply new additive manufacturing methods for producing the shaped-charge assemblies, which allow for the experimental testing of complicated design geometries obtained through computational optimization. We present a direct comparison of our optimized designs with experimental results carried out at the High Explosives Application Facility at Lawrence Livermore National Laboratory.
36 MATERIALS SCIENCE↗
Review of multi-fidelity models
Multi-fidelity models provide a framework for integrating computational models of varying complexity, allowing for accurate predictions while optimizing computational resources. These models are especially beneficial when acquiring high-accuracy data is costly or computationally intensive. This review offers a comprehensive analysis of multi-fidelity models, focusing on their applications in scientific and engineering fields, particularly in optimization and uncertainty quantification. It classifies publications on multi-fidelity modeling according to several criteria, including application area, surrogate model selection, types of fidelity, combination methods and year of publication. The study investigates techniques for combining different fidelity levels, with an emphasis on multi-fidelity surrogate models. Here this work discusses reproducibility, open-sourcing methodologies and benchmarking procedures to promote transparency. The manuscript also includes educational toy problems to enhance understanding. Additionally, this paper outlines best practices for presenting multi-fidelity-related savings in a standardized, succinct and yet thorough manner. The review concludes by examining current trends in multi-fidelity modeling, including emerging techniques, recent advancements, and promising research directions.
42 ENGINEERING↗
Generating Euler Diagrams Through Combinatorial Optimization
Abstract Can a given set system be drawn as an Euler diagram? We present the first method that correctly decides this question for arbitrary set systems if the Euler diagram is required to represent each set with a single connected region. If the answer is yes, our method constructs an Euler diagram. If the answer is no, our method yields an Euler diagram for a simplified version of the set system, where a minimum number of set elements have been removed. Further, we integrate known wellformedness criteria for Euler diagrams as additional optimization objectives into our method. Our focus lies on the computation of a planar graph that is embedded in the plane to serve as the dual graph of the Euler diagram. Since even a basic version of this problem is known to be NP‐hard, we choose an approach based on integer linear programming (ILP), which allows us to compute optimal solutions with existing mathematical solvers. For this, we draw upon previous research on computing planar supports of hypergraphs and adapt existing ILP building blocks for contiguity‐constrained spatial unit allocation and the maximum planar subgraph problem. To generate Euler diagrams for large set systems, for which the proposed simplification through element removal becomes indispensable, we also present an efficient heuristic. We report on experiments with data from MovieDB and Twitter. Over all examples, including 850 non‐trivial instances, our exact optimization method failed only for one set system to find a solution without removing a set element. However, with the removal of only a few set elements, the Euler diagrams can be substantially improved with respect to our wellformedness criteria.
Computer Science↗
Renewable electricity capacity planning with uncertainty at multiple scales
Abstract We formulate and compare optimization models of investment in renewable generation using a suite of social planning models that compute optimal generation capacity investments for a hydro-dominated electricity system where inflow uncertainty results in a risk of energy shortage. The models optimize the expected cost of capacity expansion and operation allowing for investments in hydro, geothermal, solar, wind, and thermal plant, as well as battery storage for smoothing load profiles. A novel feature is the integration of uncertain seasonal hydroelectric energy supply and short-term variability in renewable supply in a two-stage stochastic programming framework. The models are applied to data from the New Zealand electricity system and used to estimate the costs of moving to a 100% renewable electricity system by 2035. We also explore the outcomes obtained when applying different forms of CO 2 constraint that limit respectively non-renewable capacity, non-renewable generation, and CO 2 emissions on average, almost surely, or in a chance-constrained setting, and show how our models can be used to investigate the merits of a proposed pumped-hydro scheme in New Zealand’s South Island.
Ferris, Michael C.↗
Intrusive Uncertainty Quantification and Optimal Experiment Design in the Open-Source Pyomo Ecosystem
This contribution describes ParmEst and Pyomo.DoE, two pillars of the open-source Python-based Pyomo ecosystem for computational optimization with (partial differential) algebraic equation mathematical models. Specifically, ParmEst facilitates intrusive frequentist parameter estimation (PE) and uncertainty quantification (UQ) through built-in features, such as covariance matrix estimation, bootstrapping, and likelihood ratio tests. Complementary, Pyomo.DoE enables optimal experiment design by maximizing various metrics of the Fisher information matrix, such as A-optimality (trace), D-optimality (determinant), E-optimality (minimum eigenvalue), and ME-optimality (condition number). ParmEst and Pyomo.DoE can solve high-dimensional optimization problems by leveraging the model structure and exact derivative information. Finally, we will discuss future opportunities to integrate PE and UQ capabilities with optimization under uncertainty, including robust optimization with non-convex models via PyROS.
97 MATHEMATICS AND COMPUTING↗
Universal energy-speed-accuracy trade-offs in driven nonequilibrium systems
The connection between measure theoretic optimal transport and dissipative nonequilibrium dynamics provides a language for quantifying nonequilibrium control costs, leading to a collection of thermodynamic speed limits, which rely on the assumption that the target probability distribution is perfectly realized. This is almost never the case in experiments or numerical simulations, so here we address the situation in which the external controller is imperfect. We obtain a lower bound for the dissipated work in generic nonequilibrium control problems that (1) is asymptotically tight and (2) matches the thermodynamic speed limit in the case of optimal driving. Along with analytically solvable examples, we refine this imperfect driving notion to systems in which the controlled degrees of freedom are slow relative to the nonequilibrium relaxation rate, and identify independent energy contributions from fast and slow degrees of freedom. Furthermore, we develop a strategy for optimizing minimally dissipative protocols based on optimal transport flow matching, a generative machine learning technique. Furthermore, this latter approach ensures the scalability of both the theoretical and computational framework we put forth. Crucially, we demonstrate that we can compute the terms in our bound numerically using efficient algorithms from the computational optimal transport literature and that the protocols we learn saturate the bound.
59 BASIC BIOLOGICAL SCIENCES↗
AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps
Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. Here, we quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.
3D alignment↗
CIRCLEZ : Reliable photometric redshifts for active galactic nuclei computed solely using photometry from Legacy Survey Imaging for DESI
Photometric redshifts for galaxies hosting an accreting supermassive black hole in their center, known as active galactic nuclei (AGNs), are notoriously challenging. At present, they are most optimally computed via spectral energy distribution (SED) fittings, assuming that deep photometry for many wavelengths is available. However, for AGNs detected from all-sky surveys, the photometry is limited and provided by a range of instruments and studies. This makes the task of homogenizing the data challenging, presenting a dramatic drawback for the millions of AGNs that wide surveys such as SRG/eROSITA are poised to detect. This work aims to compute reliable photometric redshifts for X-ray-detected AGNs using only one dataset that covers a large area: the tenth data release of the Imaging Legacy Survey (LS10) for DESI. LS10 provides deep grizW1-W4 forced photometry within various apertures over the footprint of the eROSITA-DE survey, which avoids issues related to the cross-calibration of surveys. We present the results from CIRCLEZ, a machine-learning algorithm based on a fully connected neural network. CIRCLEZ is built on a training sample of 14 000 X-ray-detected AGNs and utilizes multi-aperture photometry, mapping the light distribution of the sources. The accuracy (σNMAD) and the fraction of outliers (η) reached in a test sample of 2913 AGNs are equal to 0.067 and 11.6%, respectively. The results are comparable to (or even better than) what was previously obtained for the same field, but with much less effort in this instance. We further tested the stability of the results by computing the photometric redshifts for the sources detected in CSC2 and Chandra-COSMOS Legacy, reaching a comparable accuracy as in eFEDS when limiting the magnitude of the counterparts to the depth of LS10. The method can be applied to fainter samples of AGNs using deeper optical data from future surveys (for example, LSST, Euclid), granting LS10-like information on the light distribution beyond the morphological type. Along with this paper, we have released an updated version of the photometric redshifts (including errors and probability distribution functions) for eROSITA/eFEDS.
79 ASTRONOMY AND ASTROPHYSICS↗
Role of Computational Parameters on Predicting Self-Consistent Residual Stress and Distortion during Wire Arc Additive Manufacturing
Production of three-dimensional metallic parts through integration of an articulated robot and gas metal arc welding, also known as wire arc additive manufacturing (WAAM), can produce large-scale components with moderate geometrical complexity. This technology is particularly appealing due to its high deposition rates, scalability, and cost-effective feedstock compared to other AM processes. Despite its advantages, WAAM adoption is hindered by challenges in ensuring geometric conformity without extensive distortion, defect-free structures, and consistent mechanical properties. Finite element analysis (FEA) is often used to address the challenge of geometrical conformity. As the size of parts increases, the best practices for mesh size and temporal resolution known in the literature become computationally unviable. This research examined the effects of mesh and time-step resolutions during transient FEA of a large-scale (248 layers) metallic part. The impact of computational parameters on the thermal history, displacement, and residual stress distributions were evaluated. The results showed that predicted distortion was consistent across resolutions, while time-step length significantly affected predicted thermal history, and mesh size influenced residual stress distributions. To investigate this relationship further, directionally biased meshes were considered and analyzed. The results indicated that increasing mesh resolution perpendicular to the welding path yielded stress predictions that aligned closely with higher-resolution models while offering substantial computational savings. In conclusion, the significances of this research are related to verification and validation of WAAM models for widespread industrial adoption and pragmatic guidelines for optimizing computation parameters for balancing computational efficiency and predictive accuracy of residual stress and distortion.
Solsbee, Brandon [Univ. of Tennessee, Knoxville, T↗