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At least 1,603 records · Page 89

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

59 BASIC BIOLOGICAL SCIENCES↗

Frequency-domain full-waveform inversion with non-linear descent directions

Full-waveform inversion (FWI) is a highly non-linear inverse problem, normally solved iteratively, with each iteration involving an update constructed through linear operations on the residuals. Incorporating a flexible degree of non-linearity within each update may have important consequences for convergence rates, determination of low model wavenumbers and discrimination of parameters. In this study, we examine one approach for doing so, wherein higher order scattering terms are included within the sensitivity kernel during the construction of the descent direction, adjusting it away from that of the standard Gauss–Newton approach. These scattering terms are naturally admitted when we construct the sensitivity kernel by varying not the current but the to-be-updated model at each iteration. Linear and/or non-linear inverse scattering methodologies allow these additional sensitivity contributions to be computed from the current data residuals within any given update. We show that in the presence of pre-critical reflection data, the error in a second-order non-linear update to a background of s 0 is, in our scheme, proportional to at most (Δs/s 0 ) 3 in the actual parameter jump Δs causing the reflection. In contrast, the error in a standard Gauss–Newton FWI update is proportional to (Δs/s 0 ) 2 . For numerical implementation of more complex cases, we introduce a non-linear frequency-domain scheme, with an inner and an outer loop. A perturbation is determined from the data residuals within the inner loop, and a descent direction based on the resulting non-linear sensitivity kernel is computed in the outer loop. We examine the response of this non-linear FWI using acoustic single-parameter synthetics derived from the Marmousi model. Lastly, the inverted results vary depending on data frequency ranges and initial models, but we conclude that the non-linear FWI has the capability to generate high-resolution model estimates in both shallow and deep regions, and to converge rapidly, relative to a benchmark FWI approach involving the standard gradient.

58 GEOSCIENCES↗

Computation of pseudospectral abscissa for large-scale nonlinear eigenvalue problems

We present an algorithm to compute the pseudospectral abscissa for a nonlinear eigenvalue problem. The algorithm relies on global under-estimator and over-estimator functions for the eigenvalue and singular value functions involved. These global models follow from eigenvalue perturbation theory. The algorithm has three particular features. First, it converges to the globally rightmost point of the pseudospectrum, and it is immune to nonsmoothness. The global convergence assertion is under the assumption that a global lower bound is available for the second derivative of a singular value function depending on one parameter. It may not be easy to deduce such a lower bound analytically, but assigning large negative values works robustly in practice. Second, it is applicable to large-scale problems since the dominant cost per iteration stems from computing the smallest singular value and associated singular vectors, for which efficient iterative solvers can be used. Furthermore, a significant increase in computational efficiency can be obtained by subspace acceleration, that is, by restricting the domains of the linear maps associated with the matrices involved to small but suitable subspaces, and solving the resulting reduced problems. Occasional restarts of these subspaces further enhance the efficiency for large-scale problems. Finally, in contrast to existing iterative approaches based on constructing low-rank perturbations and rightmost eigenvalue computations, the algorithm relies on computing only singular values of complex matrices. Hence, the algorithm does not require solutions of nonlinear eigenvalue problems, thereby further increasing efficiency and reliability. This work is accompanied by a robust implementation of the algorithm that is publicly available.

97 MATHEMATICS AND COMPUTING↗

Analytic Evolution of Singular Distribution Amplitudes in QCD

We describe a method of analytic evolution of distribution amplitudes (DA) that have singularities, such as non-zero values at the end-points of the support region, jumps at some points inside the support region and cusps. We illustrate the method by applying it to the evolution of a flat (constant) DA, anti-symmetric at DA and then use it for evolution of the two-photon generalized distribution amplitude. Our approach has advantages over the standard method of expansion in Gegenbauer polynomials, which requires infinite number of terms in order to accurately reproduce functions in the vicinity of singular points, and over a straightforward iteration of an initial distribution with evolution kernel. The latter produces logarithmically divergent terms at each iteration, while in our method the logarithmic singularities are summed from the start, which immediately produces a continuous curve, with only one or two iterations needed afterwards in order to get rather precise results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Optimal constraints on primordial gravitational waves from the lensed CMB

We demonstrate how to obtain optimal constraints on a primordial gravitational wave component in lensed Cosmic Microwave Background (CMB) data under ideal conditions. We first derive an estimator of the tensorto- scalar ratio, r, by using an error-controlled close approximation to the exact posterior, under the assumption of Gaussian primordial CMB and lensing deflection potential. This combines fast internal iterative lensing reconstruction with optimal recovery of the unlensed CMB. We evaluate its performance on simulated lownoise polarization data targeted at the recombination peak. We carefully demonstrate our r-posterior estimate is optimal and shows no significant bias, making it the most powerful estimator of primordial gravitational waves from the CMB. We compare these constraints to those obtained from B-mode band-power likelihood analyses on the same simulated data, before and after map-level quadratic estimator delensing, and iterative delensing. Internally, iteratively delensed band powers are only slightly less powerful on average (by less than 10%), promising close-to-optimal constraints from a stage IV CMB experiment.

79 ASTRONOMY AND ASTROPHYSICS↗

Solving the parquet equations for the Hubbard model beyond weak coupling

We find that imposing crossing symmetry in the iteration process considerably extends the range of convergence for solutions of the parquet equations for the Hubbard model. When crossing symmetry is not imposed, the convergence of both simple iteration and more complicated continuous loading (homotopy) methods is limited to high temperatures and weak interactions. We modify the algorithm to impose the crossing symmetry without increasing the computational complexity. We also imposed time reversal and a subset of the point group symmetries, but they did not further improve the convergence. We elaborate the details of the latency hiding scheme which can significantly improve the performance in the computational implementation. With these modifications, stable solutions for the parquet equations can be obtained by iteration more quickly even for values of the interaction that are a significant fraction of the bandwidth and for temperatures that are much smaller than the bandwidth. This may represent a crucial step towards the solution of two-particle field theories for correlated electron models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

TETRIS-ADAPT-VQE: An adaptive algorithm that yields shallower, denser circuit Ansätze

Adaptive quantum variational algorithms are particularly promising for simulating strongly correlated systems on near-term quantum hardware, but they are not yet viable due, in large part, to the severe coherence time limitations on current devices. In this paper, we introduce an algorithm called TETRIS-ADAPT-VQE (tiling efficient trial circuits with rotations implemented simultaneously adaptive derivative-assembled problem-tailored variational quantum eigensolver), which iteratively builds up variational a few operators at a time in a way dictated by the problem being simulated. This algorithm is a modified version of the ADAPT-VQE algorithm, in which the one-operator-at-a-time rule is lifted to allow for the addition of multiple operators with disjoint supports in each iteration. TETRIS-ADAPT-VQE results in denser but significantly shallower circuits, without increasing the number of controlled- gates or variational parameters. Its advantage over the original algorithm in terms of circuit depths increases with the system size. Moreover, the expensive step of measuring the energy gradient with respect to each candidate unitary at each iteration is performed only a fraction of the time compared with ADAPT-VQE. These improvements bring us closer to the goal of demonstrating a practical quantum advantage on quantum hardware. Published by the American Physical Society 2024

Anastasiou, Panagiotis G. (ORCID:0000000256601791)↗

A direct approach to estimate the anisotropy of protein structures from small-angle X-ray scattering

In the field of small-angle X-ray scattering (SAXS), the task of estimating the size of particles in solution is usually synonymous with the Guinier plot. The approximation behind this plot, developed by Guinier in 1939, provides a simple yet accurate characterization of the scattering behavior of particles at low scattering angle or momentum transfer q , together with a computationally efficient way of inferring their radii of gyration R G . Moreover, this approximation is valid beyond spherical scatterers, making its use ubiquitous in the SAXS world. However, when it is important to estimate further particle characteristics, such as the anisotropy of the scatterer's shape, no similar or extended approximations are available. Existing tools to characterize the shape of scatterers rely either on prior knowledge of the scatterers' geometry or on iterative procedures to infer the particle shape ab initio . In this work, a low-angle approximation of the scattering intensity I ( q ) for ellipsoids of revolution is developed and it is shown how the size and anisotropy information can be extracted from the parameters of that approximation. The goal of the approximation is not to estimate a particle's full structure in detail, and thus this approach will be less accurate than well known iterative and ab initio reconstruction tools available in the literature. However, it can be considered as an extension of the Guinier approximation and used to generate initial estimates for the aforementioned iterative techniques, which usually rely on R G and D max for initialization. This formulation also demonstrates that nonlinearity in the Guinier plot can arise from anisotropy in the scattering particles. Beyond ideal ellipsoids of revolution, it is shown that this approximation can be used to estimate the size and shape of molecules in solution, in both computational and experimental scenarios. The limits of the approach are discussed and the impact of a particle's anisotropy in the Guinier estimate of R G is assessed.

catalysis (homogeneous), catalysis (heterogeneous)↗

Enhancing Photosynthesis Simulation Performance in ESMs with Machine Learning-Assisted Solvers

When simulating vegetation dynamics, photosynthesis accounts for a large fraction of the computational cost in most Earth System Models (ESMs). This is largely since photosynthesis is represented as a system of nonlinear equations, and the solution requires the use of an initial guess followed by many iterations of the numerical solver to obtain a solution. We use machine learning (ML) to replicate the response surface of the model’s numerical solver to improve the choice of initial guess, therefore requiring fewer iterations to obtain a final solution. We implemented this test on the leaf-level calculations as well as at the canopy scale, and for both we observed fewer iterations of the photosynthesis solver when a ML-based initial guess was implemented. The model tested here is the Energy Exascale Earth System Model - Land Model (ELM). The ML-based algorithms used here are trained on simulations from the model itself and used only to improve the initial guess for the solver; therefore, the model maintains its own set of physics to obtain the final solution. This work shows novel ways to utilize ML-based methods to improve the performance of numerical solvers in ESMs.

Massoud, Elias [ORNL] (ORCID:0000000217725361)↗

SymProp: Scaling Sparse Symmetric Tucker Decomposition via Symmetry Propagation

Sparse symmetric tensors are an important class of tensors, and their decompositions serve as powerful tools for revealing low-rank structures. This paper introduces SymProp, a novel approach for scaling sparse symmetric Tucker decomposition by propagating symmetry through intermediate computations. SymProp optimizes two key computational kernels: Sparse Symmetric Tensor Times Same Matrix chain (S3 TTMc) for Higher-Order Orthogonal Iteration (HOOI) and Sparse Symmetric Tensor Times Same Matrix chain Times Core (S3 TTMcTC) for Higher-Order QR Iteration (HOQRI). Our method employs a metaprogramming-based index iteration approach to efficiently handle the upper triangular parts of intermediate dense symmetric tensors. SymProp achieves up to 50.9× speedup over SPLATT and up to 360.8× over Compressed Sparse Symmetric (CSS) format on the S3 TTMc operation. Moreover, our S3 TTMc and S3 TTMcTC implementations support tensor orders four levels higher than state-of-the-art methods. Our HOQRI demonstrates superior scalability and up to a 33.6× speedup over optimized HOOI. By enabling more scalable Tucker decompositions for higher orders, decomposition ranks, and dimension sizes, SymProp opens new possibilities for analyzing complex hypergraph structures in fields such as network science, data mining, and machine learning.

Li, Zecheng [North Carolina State University]↗

Learning-Accelerated ADMM for Distributed DC Optimal Power Flow

We suggest a novel data-driven method to accelerate the convergence of Alternating Direction Method of Multipliers (ADMM) for solving distributed DC optimal power flow (DC-OPF) where lines are shared between independent network partitions. Using previous observations of ADMM trajectories for a given system under varying load, the method trains a recurrent neural network (RNN) to predict the converged values of dual and consensus variables. Given a new realization of system load, a small number of initial ADMM iterations is taken as input to infer the converged values and directly inject them into the iteration. We empirically demonstrate that the online injection of these values into the ADMM iteration accelerates convergence by a significant factor for partitioned 14-, 118-and 2848-bus test systems under differing load scenarios. The proposed method has several advantages: it maintains the security of private decision variables inherent in consensus ADMM; inference is fast and so may be used in online settings; RNN-generated predictions can dramatically improve time to convergence but, by construction, can never result in infeasible ADMM subproblems; it can be easily integrated into existing software implementations. While we focus on the ADMM formulation of distributed DC-OPF in this paper, the ideas presented are naturally extended to other distributed optimization problems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Soft Syndrome Decoding of Quantum LDPC Codes for Joint Correction of Data and Syndrome Errors

Quantum errors are primarily detected and corrected using the measurement of syndrome information which itself is an unreliable step in practical error correction implementations. Typically, such faulty or noisy syndrome measurements are modeled as a binary measurement outcome flipped with some probability. However, the measured syndrome is in fact a discretized value of the continuous voltage or current values obtained in the physical implementation of the syndrome extraction. In this paper, we use this "soft" or analog information without the conventional discretization step to benefit the iterative decoders for decoding quantum low-density parity-check (QLDPC) codes. Syndrome-based iterative belief propagation (BP) decoders are modified to utilize the syndrome-soft information to successfully correct both data and syndrome errors simultaneously, without repeated measurements. We demonstrate the advantages of extracting the soft information from the syndrome in our improved decoders, not only in terms of comparison of thresholds and logical error rates for quasi-cyclic lifted-product QLDPC code families, but also for faster convergence of iterative decoders. In particular, the new BP decoder with noisy syndrome performs as good as the standard BP decoder under ideal syndrome.

97 MATHEMATICS AND COMPUTING↗

DIII-D accomplishments and plans in support of fusion next steps

DIII-D is using its flexibility and diagnostics to address the critical science required to enable next step fusion devices. We have adapted operating scenarios for ITER to low torque and are now being optimized for transport. Three ELM mitigation scenarios have been developed to near-ITER parameters. New control techniques are managing the most challenging plasma instabilities. Disruption mitigation tools show promising dissipation strategies for runaway electrons and heat load. An off axis neutral beam upgrade has enabled sustainment of high βN capable steady state regimes. Divertor research is identifying the challenge, physics and candidate solutions for handling the hot plasma exhaust with notable progress in heat flux reduction using the snowflake configuration. Our work is helping optimize design choices and prepare the scientific tools for operation in ITER, and resolve key elements of the plasma configuration and divertor solution for an FNSF.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Recent developments in support of the shattered pellet technique for disruption mitigation

The technology for producing, accelerating, and shattering large pellets (before injection into plasmas) for disruption mitigation has been under development at the Oak Ridge National Laboratory for several years, including a system on DIII-D that has been used to provide some significant experimental results. The original proof-of-principle testing was carried out using a pipe gun injector cooled by a cryogenic refrigerator (temperatures ~8 to 20 K) and equipped with a stainless steel tube to produce 16.5 mm pellets composed of either pure D2, pure Ne, or a dual layer with a thin outer shell of D2 and core of Ne. Recently, significant progress has been made in the laboratory using that same pipe gun and a new injector that is an ITER test apparatus cooled with liquid helium. The new injector operates at ~5 to 8 K, which is similar to temperatures expected with cooling provided by the flow of supercritical helium on ITER. An alternative technique for producing/solidifying large pellets directly from a pre-mixed gas has now been successfully tested in the laboratory. Also, two additional pellet sizes have been tested recently (nominal 24.4 and 34.0 mm diameters). With larger pellets, the number of injectors required for ITER disruption mitigation can be reduced, resulting in less cost and a smaller footprint for the hardware. An attractive option is longer pellets, and 24.4 mm pellets with a length/diameter ratio of ~3 have been successfully tested. Since pellet speed is the key parameter in determining the response time of a shattered pellet system to a plasma disruption event, recent tests have concentrated on documenting the speeds with different hardware configurations and operating parameters; speeds of ~100 to 800 m/s have been recorded. The data and results from laboratory testing are presented and discussed.

neon↗

Aluminum-Based Superconducting Tunnel Junction Sensors for Nuclear Recoil Spectroscopy

The BeEST experiment is searching for sub-MeV sterile neutrinos by measuring nuclear recoil energies from the decay of 7 Be implanted into superconducting tunnel junction (STJ) sensors. The recoil spectra are affected by interactions between the radioactive implants and the sensor materials. We are therefore developing aluminum-based STJs (Al-STJs) as an alternative to existing tantalum devices (Ta-STJs) to investigate how to separate material effects in the recoil spectrum from potential signatures of physics beyond the Standard Model. Three iterations of Al-STJs were fabricated. The first had electrode thicknesses similar to existing Ta-STJs. They had low responsivity and reduced resolution, but were used successfully to measure 7 Be nuclear recoil spectra. The second iteration had STJs suspended on thin SiN membranes by backside etching. These devices had low leakage current, but also low yield. The final iteration was not backside etched, and the Al-STJs had thinner electrodes and thinner tunnel barriers to increase signal amplitudes. These devices achieved 2.96 eV FWHM energy resolution at 50 eV using a pulsed 355 nm (~3.5 eV) laser. These results establish Al-STJs as viable detectors for systematic material studies in the BeEST experiment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Solidification and Acceleration of Large Cryogenic Pellets Relevant for Plasma Disruption Mitigation

The technology for producing, accelerating, and shattering large pellets (before injection into plasmas) for disruption mitigation has been under development at the Oak Ridge National Laboratory for several years, including a system on DIII-D that has been used to provide some significant experimental results. The original proof-of-principle testing was carried out using a pipe gun injector cooled by a cryogenic refrig- erator (temperatures ~8-20 K) and equipped with a stainless steel tube to produce 16.5-mm pellets composed of either pure D 2 , pure Ne, or a dual layer with a thin outer shell of D 2 and core of Ne. Recently, significant progress has been made in the laboratory using that same pipe gun and a new injector that is an ITER test apparatus cooled with liquid helium. The new injector operates at ~5-8 K, which is similar to temperatures expected with cooling provided by the flow of supercritical helium on ITER. An alternative technique for producing/solidifying large pellets directly from a premixed gas has now been successfully tested in the laboratory. Also, two additional pellet sizes have been tested recently (nominal 24.4 and 34.0 mm diameters). With larger pellets, the number of injectors required for ITER disruption mitigation can be reduced, resulting in less cost and a smaller footprint for the hardware. An attractive option is longer pellets, and 24.4-mm pellets with a length/diameter ratio of ~3 have been successfully tested. Since pellet speed is the key parameter in determining the response time of a shattered pellet system to a plasma disruption event, recent tests have concentrated on documenting the speeds with different hardware configurations and operating parameters; speeds of ~100-800 m/s have been recorded. The data and results from laboratory testing are presented and discussed, and a simple model for the pellet solidification process is described.

36 MATERIALS SCIENCE↗

Optimal Decentralized Protocol for Electric Vehicle Charging

We propose a decentralized algorithm to optimally schedule electric vehicle (EV) charging. The algorithm exploits the elasticity of electric vehicle loads to fill the valleys in electric load profiles. We first formulate the EV charging scheduling problem as an optimal control problem, whose objective is to impose a generalized notion of valley-filling, and study properties of optimal charging profiles. We then give a decentralized algorithm to iteratively solve the optimal control problem. In each iteration, EVs update their charging profiles according to the control signal broadcast by the utility company, and the utility company alters the control signal to guide their updates. The algorithm converges to optimal charging profiles (that are as "flat" as they can possibly be) irrespective of the specifications (e.g., maximum charging rate and deadline) of EVs, even if EVs do not necessarily update their charging profiles in every iteration, and use potentially outdated control signal when they update. Moreover, the algorithm only requires each EV solving its local problem, hence its implementation requires low computation capability. We also extend the algorithm to track a given load profile and to real-time implementation.

Gan, LW↗