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At least 199 records · Page 11

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E . coli . Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E . coli lifestyles.

59 BASIC BIOLOGICAL SCIENCES↗

Optimized recursion relation for the computation of partition functions in the superconfiguration approach

Partition functions of a canonical ensemble of non-interacting bound electrons are a key ingredient of the super-transition-array approach to the computation of radiative opacity. A few years ago, we published a robust and stable recursion relation for the calculation of such partition functions. In this work, we propose an optimization of the latter method and explain how to implement it in practice. The formalism relies on the evaluation of elementary symmetric polynomials, which opens the way to further improvements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Probing Accuracy-Speedup Tradeoff in Machine Learning Surrogates for Molecular Dynamics Simulations

The performance promise of machine learning surrogates of molecular dynamics simulations of soft materials is significant but generally comes at the cost of acquiring large training datasets to learn the complex relationships between input soft material attributes and output properties. Under the constraint of limited high-performance computing resources, optimizing the size of the training datasets becomes paramount. Using an artificial neural network based surrogate for molecular dynamics simulations of confined electrolytes, we explore the tradeoff between surrogate accuracy and computational gains. Accuracy is assessed by computing the root-mean-square errors between the surrogate predictions and the ground truth results obtained via molecular dynamics simulations. The computational performance is judged by evaluating the speedup which incorporates the training dataset creation time. Improvement in accuracy occurs with a loss of speedup, which scales as the inverse of the training dataset size. Furthermore, the link between surrogate generalizability and the accuracy-speedup tradeoff is assessed by examining the errors incurred in surrogate predictions on unseen, interpolated input variables and developing a net speedup metric to capture the associated gains.

Anions↗

Advocating Feedback Control for Human-Earth System Applications

This paper proposes a feedback control perspective for Human-Earth Systems (HESs) which essentially are complex systems that capture the interactions between humans and nature. Recent attention in HES research has been directed towards devising strategies for climate change mitigation and adaptation, aimed at achieving environmental and societal objectives. However, existing approaches heavily rely on HES models, which inherently suffer from inaccuracies due to the complexity of the system. Moreover, overly detailed models often prove impractical for optimization tasks. We propose a framework inheriting from feedback control strategies the robustness against model errors, because inaccuracies are mitigated using measurements retrieved from the field. The framework comprises two nested control loops. The outer loop computes the optimal inputs to the HES, which are then implemented by actuators controlled in the inner loop. Potential fields of applications are also identified and a numerical example is provided.

biological system modeling↗

Modeling the AC Power Flow Equations with Optimally Compact Neural Networks: Application to Unit Commitment

Nonlinear power flow constraints render a variety of power system optimization problems computationally intractable. Emerging research shows, however, that the nonlinear AC power flow equations can be successfully modeled using neural networks. These neural networks can be exactly transformed into mixed integer linear programs and embedded inside challenging optimization problems, thus replacing nonlinearities that are intractable for many applications with tractable piecewise linear approximations. Such approaches, though, suffer from an explosion of the number of binary variables needed to represent the neural network. Accordingly, this paper develops a technique for training an "optimally compact'' neural network, i.e., one that can represent the power flow equations with a sufficiently high degree of accuracy while still maintaining a tractable number of binary variables. We demonstrate the use of this neural network as an approximator of the nonlinear power flow equations by embedding it in the AC unit commitment problem, transforming the problem from a mixed integer nonlinear program into a more manageable mixed integer linear program. We use the 14-, 57-, and 89-bus networks as test cases and compare the AC-feasibility of commitment decisions resulting from the neural network, DC, and linearized power flow approximations. Our results show that the neural network model outperforms both the DC and linearized power flow approximations when embedded in the unit commitment problem. The neural network formulation most often selects a feasible unit commitment schedule, and furthermore, it only s

AC power flow↗

A large-scale benchmarking of deterministic and stochastic derivative-free optimization algorithms

This presentation summarizes our work in the PrOMMiS project on benchmarking of data-driven optimization algorithms and their applications in self-driving laboratories. This work supports the broader project goal of accelerating the identification of promising separation methods and operating conditions for critical minerals separation processes. We present a systematic benchmarking study of 42 data-driven optimization algorithms on a broad collection of 502 test problems. The results identify BAM, GLCCLUSTER, and MULTIMIN as the most effective optimization solvers, with BAM showing the highest overall performance and solving more than 80% of the benchmark problems. The study also shows that no single solver consistently outperforms the others across all problem types, indicating that our future laboratory applications may benefit from using a small set of strong solvers rather than relying on a single method. The presentation also illustrates an in-silico chemical reactor case study showing that data-driven optimization methods can guide autonomous experimentation in a self-driving laboratory and identify optimal operating conditions within a small number of experiments. Overall, the results provide a basis for selecting efficient optimization methods and demonstrate the practical use of data-driven optimization in self-driving laboratory workflows.

36 MATERIALS SCIENCE↗

Algorithm-guided experimentation for autonomous AI systems in self-driving laboratories

This presentation summarizes our work in the PrOMMiS project on benchmarking of data-driven optimization algorithms and their applications in self-driving laboratories. This work supports the broader project goal of accelerating the identification of promising separation methods and operating conditions for critical minerals separation processes. We present a systematic benchmarking study of 42 data-driven optimization algorithms on a broad collection of 502 test problems. The results identify BAM, GLCCLUSTER, and MULTIMIN as the most effective optimization solvers, with BAM showing the highest overall performance and solving more than 80% of the benchmark problems. The study also shows that no single solver consistently outperforms the others across all problem types, indicating that our future laboratory applications may benefit from using a small set of strong solvers rather than relying on a single method. The presentation also illustrates an in-silico chemical reactor case study showing that data-driven optimization methods can guide autonomous experimentation in a self-driving laboratory and identify optimal operating conditions within a small number of experiments. Overall, the results provide a basis for selecting efficient optimization methods and demonstrate the practical use of data-driven optimization in self-driving laboratory workflows.

36 MATERIALS SCIENCE↗

Cost-optimized Automated Variance Reduction for Highly Angle-dependent Radiation Transport Analyses [Dissertation]

Monte Carlo variance-reduction techniques that directly bias particle direction have historically received limited attention despite being useful for many radiation transport applications such as those in which radiation travels through large regions with a low probability of colliding. One such technique is known as DXTRAN (short for deterministic transport) in the MCNP Monte Carlo radiation transport code. Until now, effectively applying DXTRAN in calculations is largely based on empirical observations of computational performance. Optimal DXTRAN parameters are identified through manual iteration. This work develops new mathematical descriptions of the DXTRAN variance-reduction process and demonstrates a new automated variance-reduction method that applies these mathematical formulations to determine the optimal application of DXTRAN in a given problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Case Study of Using Kokkos and SYCLs Performance-Portable Frameworks for Milc-Dslash Benchmark on NVIDIA, AMD and Intel GPUs

Six of the top ten supercomputers in the TOP500 list from June 2021 rely on NVIDIA GPUs to achieve their peak compute bandwidth. With the announcement of Aurora, Frontier, and El Capitan, Intel and AMD have also entered the domain of providing GPUs for scientific computing. A consequence of the increased diversity in the GPU landscape is the emergence of portable programming models such as Kokkos, SYCL, OpenCL, and OpenMP, which allow application developers to maintain a single-source code across a diverse range of hardware architectures. While the portable frameworks try to optimize the compute resource usage on a given architecture, it is the programmers responsibility to expose parallelism in an application that can take advantage of thousands of processing elements available on GPUs. In this paper, we introduce a GPU-friendly parallel implementation of Milc-Dslash that exposes multiple hierarchies of parallelism in the algorithm. Milc-Dslash was designed to serve as a benchmark with highly optimized matrix-vector multiplications to measure the resource utilization on the GPU systems. The parallel hierarchies in the Milc-Dslash algorithm are mapped onto a target hardware using Kokkos and SYCL programming models. We present the performance achieved by Kokkos and SYCL implementations of Milc-Dslash on NVIDIA A100 GPU, AMD MI100 GPU, and Intel Gen9 GPU. Additionally, we compare the Kokkos and SYCL performances with those obtained from the versions written in CUDA and HIP programming models on NVIDIA A100 GPU and AMD MI100 GPU, respectively.

Dufek, Amanda S↗

Optimal Operation of a Hybrid Hydraulic Electric Architecture (HHEA) for Off-Road Vehicles Over Discrete Operating Decisions

Many off-highway machines including construction and agriculture equipment use hydraulics for power transmission and throttling as a means for control. Trends towards better efficiency and electrification have led to the creation of a novel Hybrid Hydraulic-Electric Architecture (HHEA) which could significantly reduce energy consumption and maintain control performance, even in machines that are too large to be directly electrified. This is achieved by using a set of common pressure rails to transmit the majority of power via power dense hydraulics and modulating the power with small electric motor-drives to achieve precise control. This paper proposes a computationally efficient method for computing the optimal sequence of pressure rail selections for the HHEA over finite drive cycles. This is useful for fairly comparing the novel architecture’s energy performance to existing architectures and for use in iterative optimal design of the architecture. The optimal control technique makes use of a static model of the architecture and losses. Constraints are enforced such that the drive cycle is repeatable. The constrained optimal operation is solved using a Lagrange multiplier technique that transforms the optimization into a small set of sub-problems by considering combinations of active constraints. Each of these sub-problems can be solved efficiently because loss calculations for all time steps can be computed in parallel. A case study of an off-road construction machine demon-strates that the HHEA reduces energy consumption by 2/3 compared to the baseline load sensing architecture.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Precision Computations in Strongly Coupled Conformal Field Theories (Final Technical Report)

Conformal Field Theories (CFTs) are quantum field theories that are invariant under the conformal symmetry group (which includes translations and rotations, but also local rescalings of spacetime). They are building blocks of general quantum field theories, and appear in many areas of physics, including statistical physics, condensed matter physics, particle physics, and quantum gravity. Because of their extra symmetries, the mathematical structure of CFTs is tightly constrained, and this leads to the idea of the ``conformal bootstrap," which is to use these mathematical structures to constrain, and in some cases determine, CFT observables. A new numerical implementation of the conformal bootstrap idea appeared in 2008 with the work of Rattazzi, Rychkov, Tonni, and Vichi. Their observation was that certain bootstrap constraints (conformal symmetry and unitarity) could be combined to yield a convex optimization problem that constraints CFT data. By solving this convex optimization problem on a computer, one could obtain bounds on observables like critical exponents and operator product expansion (OPE) coefficients. Over the course of this award, the PI has improved numerical bootstrap techniques by optimizing known algorithms and finding new ones for performing the required convex optimization computations. The PI has applied these techniques to compute high-precision observables in several important strongly-coupled systems. The PI has also explored both analytical and numerical bootstrap methods for constraining the space of low energy effective field theories of quantum gravity, and developed new analytical techniques for CFT and QFT more broadly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Pseudospectral convex optimization for on-ramp merging control of connected vehicles

It can be a daunting task for human drivers to merge into highways because of the intricate vehicle negotiations and potential risk within limited time and space. Connected vehicle (CV) technologies could be a solution to this problem and offer many benefits to the road safety, traffic mobility, and energy efficiency. However, real-time optimal control of CVs is still an open challenge, due to the nonlinear vehicle dynamics, non-convex fuel consumption model, and highly dynamic uncertain inter-vehicle interactions. To tackle these issues, a novel real-time optimal control approach that balances the computational efficiency and solution optimality is proposed for the purpose of onboard application. To this end, the pseudospectral collocation method is integrated with a sequential convex programming approach to develop two new optimization algorithms, which are implemented within a model predictive control (MPC) framework to allow for real-time generation of optimal merging speed profiles. One algorithm leverages the line search technique to improve convergence, and the other benefits from the trust region method for better computational efficiency. The optimality and convergence process of both proposed algorithms are investigated by comparing their solutions with a popular non-linear solver. Furthermore, simulation results show that the proposed methods outperform the benchmark in terms of computational cost, fuel consumption, and traffic efficiency. In particular, the proposed fuel-economy merging rule can save 57.1% fuel consumption on average on four different traffic volumes. Meanwhile, the proposed optimal control algorithms can reduce 2.2% travel time on average comparing to the “first-in-first-out” merging rule.

33 ADVANCED PROPULSION SYSTEMS↗

Acceleration of Thermochemistry Solves in MOOSE and Pronghorn

This work focuses on the development and implementation of strategies to accelerate thermochemical calculations within MOOSE-based multiphysics simulations, particularly for applications in MSRs. We highlight the inherent complexity of nuclear materials, which require a multiscale approach to accurately model their behavior across various physical domains, including mechanical, chemical, and thermal phenomena. Thermochemical equilibrium calculations are crucial for predicting material properties and enhancing the fidelity of these simulations. The integration of Thermochimica, a Gibbs energy minimizer, into MOOSE allows for the direct minimization of Gibbs energy at every point on the mesh. However, the computational cost of such integration is significant. To address this, we explored acceleration strategies such as multi-threading support and the use of a thermodynamic ValueCache to reduce redundant calculations. Additionally, we investigated modifications to Thermochimica to enable phase constraints and improve its coupling with phase-field models, which are essential for simulating microstructural evolution and corrosion in MSR. These efforts aim to optimize the computational efficiency and accuracy of multiphysics simulations, thereby supporting the development of reliable and efficient nuclear materials for next-generation reactor technologies.

36 - MATERIALS SCIENCE↗

Sum-of-Fractions Methodology for Actinides in Water- and Polyethylene-Moderated and -Reflected Systems

Sum-of-fractions is a method intended to make sure a subcritical margin for aqueous solutions and slurries of fissionable isotopes exists. The method indicates that a system is subcritical if the sum of the ratios of the mass of each isotope (in a mixture) to its individual minimum subcritical mass limit is less than or equal to one. Historically, the basis of the sum-of-fractions has been derived from allowances given in the American National Standards Institute (ANSI)/ American Nuclear Society (ANS)-8.15-1981. However, the allowance was removed in ANSI/ANS-8.15-2014 due to a lack of technical basis. A methodology was developed to assess the validity of using the sum-of-fractions for water- or polyethylene-moderated systems for the following nuclides: 232 U, 233 U, 234 U, 235 U, 237 Np, 236 Pu, 238 Pu, 239 Pu, 240 Pu, 241 Pu, 242 Pu, 241 Am, 242 m Am, 243 Am, 242 Cm, 243 Cm, 244 Cm, 245 Cm, 246 Cm, 247 Cm, 249 Cf, and 251 Cf. The methodology uses available benchmark data for mixtures of 233 U, 235 U, and 239 Pu to establish the calculational margin, and a mass limit reduction to establish the margin of subcriticality. Water- or polyethylene-moderated and -reflected mixtures containing the nuclides are evaluated with the code system, SCALE 6.2.4. Including the calculational margin, subcritical mass limits for each nuclide were computed for optimally water- or polyethylene-moderated and fully reflected systems. These masses were used to create nuclide mixtures in which the sum of the mass to subcritical mass limit ratios is one. The various nuclide mixtures were modeled over a range of moderation and demonstrate the keff does not exceed the calculational margin. For additional assurance of subcriticality, a significant mass reduction is applied to each computed minimum critical mass of the nuclides without adequate benchmark data consistent with the method in ANSI/ANS-8.15-2014.

07 ISOTOPE AND RADIATION SOURCES↗

Evaluation of the Sum-of-Fractions Methodology for Water and Polyethylene Moderated Systems

Sum-of-Fractions is a method intended to assure a subcritical margin for aqueous solutions and slurries of fissionable isotopes. The method indicates that a system is subcritical if the sum of the ratios of the mass of each isotope in a mixture to its individual minimum subcritical mass limit is less than or equal to one. The basis of the Sum-of Fractions has historically been derived from allowances given in ANSI/ANS-8.15-1981. However, the allowance was removed in ANSI/ANS-8.15-2014 due to a lack of technical basis. A methodology was developed to assess the validity of using the Sum-of-Fractions for water or polyethylene moderated systems for the following nuclides: 232 U, 233 U, 234 U, 235 U, 237 Np, 236 Pu, 238 Pu, 239 Pu, 240 Pu, 241 Pu, 242 Pu, 241 Am, 242 mAm, 243 Am, 242 Cm, 243 Cm, 244 Cm, 245 Cm, 246 Cm, 247 Cm, 249 Cf, and 251 Cf. The methodology uses available benchmark data for mixtures of 233 U, 235 U, and 239 Pu to establish the calculational margin, and a mass limit reduction to establish the margin of subcriticality. Water or polyethylene moderated and reflected mixtures containing the nuclides are evaluated with SCALE 6.2.4. Including the calculational margin, subcritical mass limits for each nuclide were computed for optimally water or polyethylene moderated and fully reflected systems. These masses were used to create nuclide mixtures in which the sum of the mass to subcritical mass limit ratios is one. The various nuclide mixtures were modeled over a range of moderation and demonstrate the k eff does not exceed the calculational margin. For additional assurance of subcriticality, a significant mass reduction is applied to each computed minimum critical mass of the nuclides without adequate benchmark data consistent with the method in ANSI/ANS-8.15-2014.

07 ISOTOPE AND RADIATION SOURCES↗

Sum-of-Fractions Method

Sum-of-fractions is a method intended to make sure a subcritical margin for aqueous solutions and slurries of fissionable isotopes exists. The method indicates that a system is subcritical if the sum of the ratios of the mass of each isotope (in a mixture) to its individual minimum subcritical mass limit is less than or equal to one. Historically, the basis of the sum-of-fractions has been derived from allowances given in the American National Standards Institute (ANSI)/ American Nuclear Society (ANS)-8.15-1981. However, the allowance was removed in ANSI/ANS-8.15-2014 due to a lack of technical basis. A methodology was developed to assess the validity of using the sum-of-fractions for water- or polyethylene-moderated systems for the following nuclides: 232U, 233U, 234U, 235U, 237Np, 236Pu, 238Pu, 239Pu, 240Pu, 241Pu, 242Pu, 241Am, 242mAm, 243Am, 242Cm, 243Cm, 244Cm, 245Cm, 246Cm, 247Cm, 249Cf, and 251Cf. The methodology uses available benchmark data for mixtures of 233U, 235U, and 239Pu to establish the calculational margin, and a mass limit reduction to establish the margin of subcriticality. Water- or polyethylene-moderated and -reflected mixtures containing the nuclides are evaluated with the code system, SCALE 6.2.4. Including the calculational margin, subcritical mass limits for each nuclide were computed for optimally water- or polyethylene-moderated and fully reflected systems. These masses were used to create nuclide mixtures in which the sum of the mass to subcritical mass limit ratios is one. The various nuclide mixtures were modeled over a range of moderation and demonstrate the keff does not exceed the calculational margin. For additional assurance of subcriticality, a significant mass reduction is applied to each computed minimum critical mass of the nuclides without adequate benchmark data consistent with the method in ANSI/ANS-8.15-2014.

criticality safety, Actinide↗