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At least 1,711 records · Page 95

Extended Lagrangian Born–Oppenheimer molecular dynamics using a Krylov subspace approximation

It is shown how the electronic equations of motion in extended Lagrangian Born–Oppenheimer molecular dynamics simulations can be integrated using low-rank approximations of the inverse Jacobian kernel. This kernel determines the metric tensor in the harmonic oscillator extension of the Lagrangian that drives the evolution of the electronic degrees of freedom. The proposed kernel approximation is derived from a pseudoinverse of a low-rank estimate of the Jacobian, which is expressed in terms of a generalized set of directional derivatives with directions that are given from a Krylov subspace approximation. The approach allows a tunable and adaptive approximation that can take advantage of efficient preconditioning techniques. The proposed kernel approximation for the integration of the electronic equations of motion makes it possible to apply extended Lagrangian first-principles molecular dynamics simulations to a broader range of problems, including reactive chemical systems with numerically sensitive and unsteady charge solutions. This can be achieved without requiring exact full calculations of the inverse Jacobian kernel in each time step or relying on iterative non-linear self-consistent field optimization of the electronic ground state prior to the force evaluations as in regular direct Born–Oppenheimer molecular dynamics. We note the low-rank approximation of the Jacobian is directly related to Broyden’s class of quasi-Newton algorithms and Jacobian-free Newton–Krylov methods and provides a complementary formulation for the solution of nonlinear systems of equations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Radiation Mapping for an Unmanned Aerial Vehicle: Development and Simulated Testing of Algorithms for Source Mapping and Navigation Path Generation

Image reconstruction algorithms were developed for radiation source mapping and used for generating the search path of a moving radiation detector, such as one onboard an unmanned aerial vehicle. Simulations consisted of first assuming radioactive sources of varying complexity and estimating the radiation fields that would then be produced by that source distribution. Next, the "measurements" that would result from a pair of adjacent spatial locations were computed. A crude estimate of the source distribution likely to have produced such "measurements" was reconstructed based upon the limited measurements. Location of the next "measurement" was then determined as halfway between the location of the estimated source and the current "measurement." With each additional sample, improved source distribution reconstructions were made and used to inform the immediate direction of detector motion. Source reconstruction or mapping was formulated as an inverse problem solved with either maximum a posteriori or least squares (LS) regression deconvolution methods. Different amounts of noise were added to the simulated "measurements," allowing evaluation of the methods' performances as functions of signal-to-noise ratio of the measured map. As expected, methods that promote sparsity were better suited in reconstructing point sources. Reliable prior information of the source distribution also improved the reconstruction results, especially with distributed sources. With a non-negative least square algorithm and the suggested paths it generated, location of sources was successfully estimated to an accuracy of 0.014 m within nine iterations in a single-source scenario and 12 iterations in a two-source scenario, given a 10% error on the integrated counts and a Poisson distribution of the noise associated with the measured counts.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

SU-F-T-201: Acceleration of Dose Optimization Process Using Dual-Loop Optimization Technique for Spot Scanning Proton Therapy

Purpose: The purpose was to demonstrate a developed acceleration technique of dose optimization and to investigate its applicability to the optimization process in a treatment planning system (TPS) for proton therapy. Methods: In the developed technique, the dose matrix is divided into two parts, main and halo, based on beam sizes. The boundary of the two parts is varied depending on the beam energy and water equivalent depth by utilizing the beam size as a singular threshold parameter. The optimization is executed with two levels of iterations. In the inner loop, doses from the main part are updated, whereas doses from the halo part remain constant. In the outer loop, the doses from the halo part are recalculated. We implemented this technique to the optimization process in the TPS and investigated the dependence on the target volume of the speedup effect and applicability to the worst-case optimization (WCO) in benchmarks. Results: We created irradiation plans for various cubic targets and measured the optimization time varying the target volume. The speedup effect was improved as the target volume increased, and the calculation speed increased by a factor of six for a 1000 cm3 target. An IMPT plan for the RTOG benchmark phantom was created in consideration of ±3.5% range uncertainties using the WCO. Beams were irradiated at 0, 45, and 315 degrees. The target’s prescribed dose and OAR’s Dmax were set to 3 Gy and 1.5 Gy, respectively. Using the developed technique, the calculation speed increased by a factor of 1.5. Meanwhile, no significant difference in the calculated DVHs was found before and after incorporating the technique into the WCO. Conclusion: The developed technique could be adapted to the TPS’s optimization. The technique was effective particularly for large target cases.

60 APPLIED LIFE SCIENCES↗

Developing an Active Learning algorithm for learning Bayesian classifiers under the Multiple Instance Learning scenario

In the Multiple Instance Learning scenario, the training data consists of instances grouped into bags, and each bag is labelled with whether it is positive, i.e. contains at least one positive instance. First, Active Learning, in which additional labels can be iteratively requested, has the potential to allow more accurate classifiers to be learned with less labels. Active Learning has been applied to the Multiple Instance Learning under two settings: when bag labels of unlabelled bags can be requested, and when instance labels within bags known to be positive can be requested. Second, Bayesian Active learning methods have the potential to learn accurate classifiers with few labels, because they explicitly track the classifier uncertainty and can thus address its knowledge gaps. Yet, there does not exist any Bayesian Active Learning method for the Multiple Instance Learning Scenario. In this work, we develop the first such method. We develop a Bayesian classifier for the Multiple Instance Learning scenario, show how it can be efficiently used for Bayesian Active Learning, and perform experiments assessing its performance. While its performance exceeds that when no Active Learning is used, it is sometimes better, sometimes worse than the naive baseline of uncertainty sampling, depending on the situation. This suggests future work: building more customizable Bayesian Active Learning methods for the Multiple Instance Scenario, customizable to whether bag or instance label accuracy is targeted, and the labeling budget.

97 MATHEMATICS AND COMPUTING↗

High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering

Electroporation-mediated gene delivery is a cornerstone of synthetic biology, offering several advantages over other methods: higher efficiencies, broader applicability, and simpler sample preparation. Yet, electroporation protocols are often challenging to integrate into highly multiplexed workflows, owing to limitations in their scalability and tunability. These challenges ultimately increase the time and cost per transformation. As a result, rapidly screening genetic libraries, exploring combinatorial designs, or optimizing electroporation parameters requires extensive iterations, consuming large quantities of expensive custom-made DNA and cell lines or primary cells. To address these limitations, we have developed a High-Throughput Microfluidic Electroporation (HTME) platform that includes a 384-well electroporation plate (E-Plate) and control electronics capable of rapidly electroporating all wells in under a minute with individual control of each well. Fabricated using scalable and cost-effective printed-circuit-board (PCB) technology, the E-Plate significantly reduces consumable costs and reagent consumption by operating on nano to microliter volumes. Furthermore, individually addressable wells facilitate rapid exploration of large sets of experimental conditions to optimize electroporation for different cell types and plasmid concentrations/types. Use of the standard 384-well footprint makes the platform easily integrable into automated workflows, thereby enabling end-to-end automation. We demonstrate transformation of E. coli with pUC19 to validate the HTME's core functionality, achieving at least a single colony forming unit in more than 99% of wells and confirming the platform's ability to rapidly perform hundreds of electroporations with customizable conditions. This work highlights the HTME's potential to significantly accelerate synthetic biology Design-Build-Test-Learn (DBTL) cycles by mitigating the transformation/transfection bottleneck.

Gaillard, William R↗

Automatic method of material identification for computed tomography

A method is provided for isolating and labeling discrete features in a spectral radiographic image recorded as a set of images in different energy channels. The disclosed method involves creating a profile for each of at least some pixels in the spectral radiographic image. The profiles are sequences of pixel values, in which each pixel value is a photon count or a similar radiographic exposure value indicative of the attenuation of a portion of the scanning beam in a respective energy channel. Iterative hierarchical clustering is used to cluster the pixels on the basis of their respective profiles. Labels are assigned to one or more of the resulting clusters. In implementations, each label can be associated with an inferred material composition or with an inference that the material composition is unknown.

Jimenez, Jr., Edward Steven↗

A hybrid calibration approach to Hertz-type contact parameters for discrete element models

This study aims at providing a hybrid calibration framework to estimate Hertz-type contact parameters (particle-scale shear modulus and Poisson ratio) for both two-dimensional and three-dimensional discrete element modelling (DEM). On the basis of statistically isotropic granular packings, a set of analytical formulae between macroscopic material parameters (Young modulus and Poisson ratio) and particle-scale Hertz-type contact parameters for granular systems are derived under small-strain isotropic stress conditions. However, the derived analytical solutions are only estimated values for general models. By viewing each DEM modelling as an implicit mathematical function taking the particle-level parameters as independent variables and employing the derived analytical solutions as the initial input parameters, an automatic iterative scheme is proposed to obtain the calibrated parameters with higher accuracies. Considering highly nonlinear features and discontinuities of the macro-micro relationship in Hertz-based discrete element models, the adaptive moment estimation algorithm is adopted in this study because of its capacity of dealing with noise gradients of cost functions. Here, the proposed method is validated with several numerical cases including randomly distributed monodisperse and polydisperse packings. Noticeable improvements in terms of calibration efficiency and accuracy have been made.

Constitutive law↗

Modeling the effect of nitrogen recycling on the erosion and leakage of tungsten impurities from the SAS-VW divertor in DIII-D during nitrogen gas injection

The new SAS-VW divertor in DIII-D has tungsten-coated components to enable the study of tungsten erosion and leakage from a closed, slot-like divertor. A proposed method of actively managing the tungsten impurities is to inject low-Z impurities, such as nitrogen, into the Scrape-off-Layer (SOL) to modify the conditions in the plasma boundary and in turn manipulate both the erosion and subsequent transport of tungsten. Nitrogen injection from the SOL crown has been modeled using SOLPS-ITER to calculate the background plasma including the intrinsic carbon and the injected nitrogen impurities, and subsequently DIVIMP has been used to calculate the tungsten erosion and transport on top of the background plasma solution. This workflow has been used to model scenarios at a variety of nitrogen injection rates with different assumptions about the nitrogen recycling at the target. In the scenario modeled here, an optimal nitrogen injection rate around 3-4 x 10 20 N/s is found to reduce the amount of tungsten reaching the core by a factor of about 2.4. However, when the nitrogen recycling rate at the divertor targets is high, the nitrogen redistributes within the slot leading to increased tungsten sputtering, and the range of injection rates resulting in tungsten mitigation becomes narrower.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Coherent correlation imaging for resolving fluctuating states of matter

Fluctuations and stochastic transitions are ubiquitous in nanometre-scale systems, especially in the presence of disorder. However, their direct observation has so far been impeded by a seemingly fundamental, signal-limited compromise between spatial and temporal resolution. Here we develop coherent correlation imaging (CCI) to overcome this dilemma. Our method begins by classifying recorded camera frames in Fourier space. Contrast and spatial resolution emerge by averaging selectively over same-state frames. Temporal resolution down to the acquisition time of a single frame arises independently from an exceptionally low misclassification rate, which we achieve by combining a correlation-based similarity metric with a modified, iterative hierarchical clustering algorithm. We apply CCI to study previously inaccessible magnetic fluctuations in a highly degenerate magnetic stripe domain state with nanometre-scale resolution. We uncover an intricate network of transitions between more than 30 discrete states. Our spatiotemporal data enable us to reconstruct the pinning energy landscape and to thereby explain the dynamics observed on a microscopic level. CCI massively expands the potential of emerging high-coherence X-ray sources and paves the way for addressing large fundamental questions such as the contribution of pinning and topology in phase transitions and the role of spin and charge order fluctuations in high-temperature superconductivity.

36 MATERIALS SCIENCE↗

Driven similarity renormalization group for excited states: A state-averaged perturbation theory

The multireference driven similarity renormalization group (MRDSRG) approach [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)] is generalized to treat quasi-degenerate electronic excited states. The new scheme, termed state-averaged (SA) MRDSRG, is a state-universal approach that considers an ensemble of quasi-degenerate states on an equal footing. Using the SA-MRDSRG framework, we implement second- (SA-DSRG-PT2) and third-order (SA-DSRG-PT3) perturbation theories. These perturbation theories can treat a manifold of near-degenerate states at the cost of a single state-specific computation. At the same time, they have several desirable properties: (1) they are intruder-free and size-extensive, (2) their energy expressions can be evaluated non-iteratively and require at most the three-body density cumulant of the reference states, and (3) the reference states are allowed to relax in the presence of dynamical correlation effects. Numerical benchmarks on the potential energy surfaces of lithium fluoride, ammonia, and the penta-2,4-dieniminium cation reveal that the SA-DSRG-PT2 method yields results with accuracy similar to that of other second-order quasi-degenerate perturbation theories. The SA-DSRG-PT3 results are instead consistent with those from multireference configuration interaction with singles and doubles (MRCISD). Finally, we compute the vertical excitation energies of (E,E)-1,3,5,7-octatetraene. As a result, the ordering of the lowest three states is predicted to be 2 1 A – g <1 1 B + u <1 1 B – u by both SA-DSRG-PT2 and SA-DSRG-PT3, in accordance with MRCISD plus Davidson correction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ptychographic phase retrieval by proximal algorithms

We derive a set of ptychography phase-retrieval iterative engines based on proximal algorithms originally developed in convex optimization theory, and discuss their connections with existing ones. The use of proximal operator creates a simple frame work that allows us to incorporate the effect of noise from a maximum-likelihood (ML) principle. We focus on three particular algorithms, namely proximal minimization, alternating direction method of multiplier and accelerated proximal gradient (APG). We benchmark their performance with numerical simulations, and discuss their optimal conditions for convergence and accuracy. An experimental dataset is used to demonstrate their effectiveness as well, in which case an array of cubic Au nanoparticles with a size of 50 nm is imaged. We show that with the presence of Poisson noise, a dataset with photon counts up to 10 4 at one detector pixel already requires ML-based methods to achieve a stable convergence. Among the three algorithms derived in this work, APG method is reported first time for its application in ptychographic reconstruction and shows superior performance in terms of both accuracy and convergence rate with a noisy dataset.

36 MATERIALS SCIENCE↗

BioTransformer 3.0 – A Web Server for Accurately Predicting Metabolic Transformation Products

BioTransformer 3.0 is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively viewable/sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes a few seconds. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0, uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human and/or environmental biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, much less prone to combinatorial “explosions” and far more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.

59 BASIC BIOLOGICAL SCIENCES↗

CMB-S4: Forecasting Constraints on Primordial Gravitational Waves

CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.

79 ASTRONOMY AND ASTROPHYSICS↗

A deterministic method for PWR loading pattern optimization

A new deterministic approach to core loading optimization is presented. Selection of fuel enrichment and burnable poison (BP) arrangement in a pressurized water reactor (PWR) core are optimally determined subject to power peaking factor (PF) constraints. The deterministic approach is based on the method of Lagrange multipliers and the direct adjoining approach for the inequality power PF constraint. The optimality conditions are derived using calculus of variations resulting in the presence of jump conditions and a linear control Hamiltonian. The optimal control problems are addressed by simultaneously minimizing the Hamiltonian using the gradient method and performing Newton's method in different regions of the core to produce viable solutions for the controls. Without active control of the power profile in PWRs during depletion, our methodology is able to satisfy the power PF constraint at all times by proper loading selection at the beginning of cycle (BOC). This is achieved by promoting the proper burnup path forward in time during the calculation of the forward optimality conditions. Here this information is utilized in the adjoint burnup calculation, which acts to propagate the optimal control path back to the BOC during the calculation of the adjoint optimality conditions. The methodology has been developed into a new code DMCO (Deterministic Multi-Control Optimization) which can produce two-dimensional two-group depletion results in approximately seven minutes per optimization iteration on a personal computer. No application of heuristics is required and the code is capable of finding solutions from initial control distributions. A preliminary case study is presented for the Westinghouse AP600 first cycle fuel loading design which achieved an extended fuel cycle while satisfying power PF constraints.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

A multiplexed bacterial two-hybrid for rapid characterization of protein–protein interactions and iterative protein design

Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs.

59 BASIC BIOLOGICAL SCIENCES↗

A Large Bore Conduction Cooled Superconducting Magnet for the Princeton Axion Search

Princeton University (PU) is designing and building a new experiment, called the Princeton Axion Search (PXS), that aims to discover (or exclude) Quantum Chromodynamics (QCD) axions in the 0.8–2 μeV mass range that are the cosmological dark matter. Core elements of the experiment are new, and in particular new to the search for axion dark matter. An essential component of the experiment is a 5 T superconducting magnet with a total bore volume of ~500 L. The Princeton Plasma Physics Laboratory (PPPL), a Department of Energy (DOE) Laboratory managed by Princeton University, has the unique expertise and experimental facilities to design and construct such a solenoid magnet assembled with the cavity resonator for PXS. To support this, PPPL utilizes legacy ITER-Nb3Sn conductors, along with its experimental facilities and expertises to design, build and test low-cost conduction-cooled superconducting solenoid magnets to be integrated into the axion detector. This paper discusses the various coil design and integration challenges in the large bore conduction cooled magnet in support of PXS. In conclusion, the proposed instrumental methods will help optimize the path to future and more ambitious axion searches at lower masses.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Physical vapor deposition simulator by graphical processor unit ray casting

This paper presents fast, accurate software for modeling physical vapor deposition systems over irregular surfaces. The model is implemented using graphics processing unit (GPU) ray casting. Applied models are viewed as a cross section of the area of interest. Given evaporation rate, time, and angular profiles in a vacuum system, an iterative time-step approach for calculating deposition profiles is calculated in the GPU architecture following a ballistic modeling approach. Thin-film technologies for the electronics industry will require evaporations on complex surfaces. Depending on the nature of the surface, a uniform thin film across the topology is wanted for various device parameters. The ray casting method is tested against various profiles. The code is freely distributed on GitHub (see https://github.com/adam-r-thomas/PVDS).

Engineering↗