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At least 1,315 records · Page 73

Methodology for Good Machine Learning with Multi‐Omics Data

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4‐year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio‐genomics‐based prognostic and predictive factors for HR+/HER− metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi‐omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as “maintaining effective communication” and “following good data science practices,” followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

Pharmacology & Pharmacy↗

The homogeneous mixing of MgO and H 2 O at extreme conditions

Investigating water worlds presents a unique opportunity to understand the fundamental processes of planetary formation and evolution. One key aspect is characterizing the interactions between water and rock under the pressures and temperatures present within these worlds. Investigating the conditions for the homogeneous mixing of these materials is imperative to characterizing bulk properties and evolution of water-rich exoplanets. Here, in this study, we use density functional molecular dynamics simulations to study MgO-H 2 O mixtures at high pressure–temperature conditions where H 2 O occurs in solid, superionic, or liquid form. MgO, the representative rocky material, can be either solid or liquid. We start from 500 K at 120 GPa, increasing the temperature step by step up to 8000 K. By inspection, we determine the temperature at which MgO-HO homogeneously mix in our simulations. At 6000 K and 174 GPa is when we find the system to homogeneously mix. This heat-until-it-mixes approach provides us with an upper bound on the temperature for the mixing of MgO and H 2 O. We find that homogeneous mixing occurs at sufficiently low temperatures to be relevant for the collisional growth of a water-rich planet.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Upcycling Polyethylene Waste into Hybrid Graphitic Porous Carbon Materials Used in High‐Performance Zinc‐Ion Hybrid Capacitors

Polyethylene (PE) waste is a challenge to upcycle into useful materials because this plastic tends to decompose into volatile compounds when heated at relatively low temperatures. In this work, mixtures of PE wastes into a hybrid graphitic porous carbon (HGPC) by a thermal oxidation pretreatment step, with assistance of an inert solid additive (KCl), to functionalize, crosslink, and stabilize the PE waste followed by carbonization and catalytic graphitization steps with a potassium carbonate catalyst, are upcycled. The PE waste‐derived HGPC (PW‐HGPC) has a hybrid structure composed of graphene‐like carbon nanosheets grown on the surface of carbon particles, high porosity with specific surface area, up to 1,763 m 2 g −1 , and good graphitic degree with average Raman I 2D / I G ratios of 0.53. When used as cathode material for zinc‐ion hybrid capacitors, this PW‐HGPC exhibits an excellent specific capacity, up to 126.7 mAh g −1 , at high mass loading of 10 mg cm −2 . Moreover, PW‐HGPC exhibits remarkable cycling stability with capacity retention of >94% after 10 000 cycles. Additionally, the KCl is recycled and reused over five times. This method provides a new solution for upcycling PE wastes into high value‐added carbon materials, not only for zinc‐ion hybrid capacitors but also for other electrochemical energy storage device applications.

hybrid graphitic porous carbon↗

A simplified protocol for the automated production of 2‐[ 18 F]fluoro‐3‐[2‐((S)‐3‐pyrrolinyl)methoxy]pyridine ([ 18 F]nifene) on an IBA Synthera® module

The α4β2 nicotinic acetylcholine receptor (nAChR) ligand 2‐[18F]fluoro‐3‐[2‐((S)‐3‐pyrrolinyl)methoxy]pyridine ([18F]nifene) has been synthesized in 10% decay‐corrected radiochemical yield using the IBA Synthera® platform (IBA Cyclotron Solutions, Louvain‐la‐Neuve, Belgium) with an integrated fluidic processor (IFP). Boc‐nitronifene served as the precursor, and 20% trifluoroacetic acid (TFA) was used to deprotect the Boc‐group after radiolabeling. By omitting the solvent extraction step after radiolabeling, the process was simplified to a single step with no manual intervention. [18F]Nifene was obtained in decay‐corrected radiochemical yields of 10 ± 2% (n = 20) and radiochemical purity >99%. Typical specific radioactivities of 2700–4865 mCi/μmole (100–180 GBq/μmol) were measured at the end of synthesis; total synthesis times were about 1 h 40 min.

IBA Synthera®↗

Reaction mechanisms of a cyclic ether intermediate: Ethyloxirane

Oxiranes are a class of cyclic ethers formed in abundance during low-temperature combustion of hydrocarbons and biofuels, either via chain-propagating steps that occur from unimolecular decomposition of β -hydroperoxyalkyl radicals ( β -˙QOOH) or from reactions of HOÓ with alkenes. Ethyloxirane is one of four alkyl-substituted cyclic ether isomers produced as an intermediate from n -butane oxidation. While rate coefficients for β -˙QOOH → ethyloxirane + ÓH are reported extensively, subsequent reaction mechanisms of the cyclic ether are not. As a result, chemical kinetics mechanisms commonly adopt simplified chemistry to describe ethyloxirane consumption by convoluting several elementary reactions into a single step, which may introduce mechanism truncation error—uncertainty derived from missing or incomplete chemistry. Here we provide fundamental insight on reaction mechanisms of ethyloxirane in support of ongoing efforts to minimize mechanism truncation error. Reaction mechanisms are inferred from the detection of products during chlorine atom-initiated oxidation experiments using multiplexed photoionization mass spectrometry conducted at 10 Torr and temperatures of 650 K and 800 K. To complement the experiments, calculations of stationary point energies were conducted using the ccCA-PS3 composite method on ˙R + O 2 potential energy surfaces for the four ethyloxiranyl radical isomers, which produced barrier heights for 24 reaction pathways. In addition to products from ˙QOOH → cyclic ether + ÓH and ˙R + O 2 → conjugate alkene + HOÓ, both of which were significant pathways and are prototypical to alkane oxidation, other species were identified from ring-opening of both ethyloxiranyl and ˙QOOH radicals. The latter occurs when the unpaired electron is localized on the ether group, causing the initial ˙QOOH structure to ring-open and form a resonance-stabilized ketohydroperoxide-type radical. The present work provides the first analysis of ethyloxirane oxidation chemistry, which reveals that consumption pathways are complex and may require an expansion of submechanisms to increase the fidelity of chemical kinetics mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Isomer-Dependent Reaction Mechanisms of Cyclic Ether Intermediates: cis -23-Dimethyloxirane and trans -23-Dimethyloxirane.

Oxiranes are a class of cyclic ethers formed in abundance during low-temperature combustion of hydrocarbons and biofuels, either via chain-propagating steps that occur from unimolecular decomposition of β-hydroperoxyalkyl radicals (β-˙QOOH) or from reactions of HÒO with alkenes. The cis- and trans-isomers of 2,3-dimethyloxirane are intermediates of n-butane oxidation, and while rate coefficients for β-˙QOOH → 2,3-dimethyloxirane + OH are reported extensively, subsequent reaction mechanisms of the cyclic ethers are not. As a result, chemical kinetics mechanisms commonly adopt simplified chemistry to describe the consumption of 2,3-dimethyloxirane by convoluting several elementary reactions into a single step, which may introduce mechanism truncation error—uncertainty derived from missing or incomplete chemistry. The present research examines the isomerdependence of 2,3-dimethyloxirane reaction mechanisms in support of ongoing efforts to minimize mechanism truncation error. Reaction mechanisms are inferred via the detection of products from Cl-initiated oxidation of both cis-2,3-dimethyloxirane and trans-2,3-dimethyloxirane using multiplexed photoionization mass spectrometry (MPIMS). The experiments were conducted at 10 Torr and temperatures of 650 K and 800 K. To complement the experiments, the enthalpies of stationary points on the ˙R + O 2 surfaces were computed at the ccCA-PS3 level of theory. In total, 28 barrier heights were computed on the 2,3-dimethyloxiranylperoxy surfaces. Two notable aspects are low-lying pathways that form resonance-stabilized ketohydroperoxide-type radicals caused by ˙QOOH ring-opening when the unpaired electron is localized adjacent to the ether group, and cis-trans isomerization of ˙R and ˙QOOH radicals, via inversion, which enable reaction pathways otherwise restricted by stereochemistry. Several species were identified in the MPIMS experiments from ring opening of 2,3-dimethyloxiranyl radicals. Neither of the two conjugate alkene isomers prototypical of ˙R + O 2 reactions were detected. Products were also identified from decomposition of ketohydroperoxide-type radicals. The present work provides the first analysis of 2,3-dimethyloxirane oxidation chemistry and reveals that consumption pathways are complex and require the expansion of submechanisms in chemical kinetics mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Weighted relaxation for multigrid reduction in time

Current trends in computer architectures now mean that faster computation speed must come primarily from increased concurrency, not faster clock speeds, which are stagnating. Thus, this situation creates bottlenecks for serial algorithms, including the well-known bottleneck for sequential time-integration, where each individual time-value (i.e., time-step) is computed sequentially. One approach to alleviate this and achieve parallelism in time is with multigrid. Here, in this work, we consider multigrid-reduction-in-time (MGRIT), a multilevel method applied to the time dimension that computes multiple time-steps in parallel. Like all multigrid methods, MGRIT relies on the complementary relationship between relaxation on a fine-grid and a correction from the coarse grid to solve the problem. All current MGRIT implementations are based on unweighted-Jacobi relaxation; here we introduce the concept of weighted relaxation to MGRIT. We derive new convergence bounds for weighted relaxation, and use this analysis to guide the selection of relaxation weights. Numerical results then demonstrate that by choosing appropriate non-unitary relaxation weights, one can achieve faster convergence rates and lower iteration counts for MGRIT when compared with unweighted relaxation. In most cases, weighted relaxation yields a 10%–20% saving in iterations, which is significant when using large high-performance computers. For A-stable integration schemes, results also illustrate that under-relaxation can restore convergence in some cases where unweighted relaxation is not convergent.

97 MATHEMATICS AND COMPUTING↗

An extended/generalized phase-field finite element method for crack growth with global-local enrichment

In this paper, an extended/generalized finite element method (XFEM/GFEM) for simulating quasistatic crack growth based on a phase-field method is presented. The method relies on approximations to solutions associated with two different scales: a global scale, that is, structural and discretized with a coarse mesh, and a local scale encapsulating the fractured region, that is, discretized with a fine mesh. A stable XFEM/GFEM is employed to embed the displacement and damage fields at the global scale. The proposed method accommodates approximation spaces that evolve between load steps, while preserving a fixed background mesh for the structural problem. In addition, a prediction-correction algorithm is employed to facilitate the dynamic evolution of the confined crack regions within a load step. Several numerical examples of benchmark problems in two- and three-dimensional quasistatic fracture are provided to demonstrate the approach.

multiscale↗

A moving morphable component‐based topology optimization approach considering transient structural dynamic responses

Abstract A novel approach is developed under the moving morphable component (MMC) framework to solve topology optimization problems considering transient structural dynamic responses, where the structure for optimization is constructed with a collection of structural components, and the structural layout can be described explicitly via only a small number of design variables characterizing the positions and geometries of the components. The transient dynamic response of the structure and corresponding sensitivities are computed via step‐by‐step numerical integration and mode reduction technique is also employed to enhance the computational efficiency. Compared with existing works, the numerical instabilities induced by localized vibration modes can be substantially alleviated and the computational effort for direct sensitivity analysis is significantly reduced in the proposed approach. Two and three‐dimensional numerical examples considering the cases of nonproportional damping mechanism and time‐varying mass are also provided to manifest the validity of the proposed approach.

Li, Jialin↗

Stress‐constrained topology optimization of structures subjected to nonproportional loading

Abstract This work considers the topology optimization of hyperelastic structures for maximum stiffness (minimum compliance) subject to constraints on their volume and maximum stress. In contrast to almost all previous works, we subject the structures to nonproportional loading, wherein the maximum stress does not necessarily occur at the final load step. As such, the stress is constrained at each load step. The augmented Lagrangian method is used to formulate the optimization problem with its many constraints. In numerical examples, we investigate different load trajectories for the same terminal load and compare the optimized designs and their performances. The results show the importance of considering the entire load trajectory as the load history significantly influences the optimized designs.

42 ENGINEERING↗

A large deformation multiphase continuum mechanics model for shock loading of soft porous materials

A large deformation, coupled finite-element (FE) model is developed to simulate the multiphase response of soft porous materials subjected to high strain-rate loading. The approach is based on the theory of porous media (TPM) at large deformations. Simplifications to the one-dimensional regime studied in the numerical simulations follow. An overview of several different time integration schemes is presented for the purpose of solving the nonlinear dynamic coupled balance of momenta (mixture and fluid) and balance of mass of the mixture equations. Numerical examples are presented for (i) verification against closed-form analytical solutions assuming small loads, (ii) demonstrating large deformation effects at high strain-rate, and (iii) showing differences in deformations between a single-phase elastodynamics model with occluded compressible pore fluid and a multiphase poroelastodynamics model at high strain-rate. The multiphase model shows that the relative motion of the pore fluid significantly dampens the deformation response of the solid skeleton as compared to the single-phase model, and makes it possible to extract quantitative values for the stresses of the different constituents, thereby allowing one to form preliminary conclusions about the onset of damage in the solid skeleton. The novelty of the current work is developing a multiphase, large deformation, mixture theory numerical model for high strain-rate loading of soft porous materials. It was discovered that explicit, adaptive time-stepping Runge–Kutta schemes offer high accuracy at relatively low cost when compared to traditional implicit or explicit central difference time-stepping schemes for shock-like loadings. Here, shock viscosity is added to the mixture momentum balance equation to regularize the shock front, and a stabilization term is added to the mixture mass balance equation to stabilize equal order interpolation finite elements for the coupled finite element solution of multiphase materials.

Engineering↗

Convergence analysis of single rate and multirate fixed stress split iterative coupling schemes in heterogeneous poroelastic media

Recently, the accurate modeling of flow–structure interactions has gained more attention and importance for both petroleum and environmental engineering applications. Of particular interest is the coupling between subsurface flow and reservoir geomechanics. Different single rate and multirate iterative and explicit coupling schemes have been proposed and analyzed in the past. In addition, Banach fixed point contraction results were obtained for iterative coupling schemes, and conditionally stable results were obtained for explicit coupling schemes. In this work, we will consider the mathematical analysis of the single rate and multirate fixed stress split iterative coupling schemes for spatially heterogeneous poroelastic media. We will re–establish the contractivity for both schemes in the localized case, and we will show that heterogeneities come at the expense of imposing more restricted conditions on the number of fine flow time steps that can be taken within one coarse mechanics time step in the multirate case. Our mathematical analysis is supplemented by numerical simulations validating our derived upper bounds. Finally, to the best of our knowledge, this is the first rigorous mathematical analysis of the multirate fixed–stress split iterative coupling scheme in heterogeneous poroelastic media.

97 MATHEMATICS AND COMPUTING↗

Nonlinear multiobjective and dynamic real-time predictive optimization for optimal operation of baseload power plants under variable renewable energy

Considering the increase of disruptive variable renewable energy penetration into the power grid, this article focuses on the investigation of a multiobjective and dynamic real-time optimization framework to address the cycling of large-scale power plants under renewable penetration. In this framework, a parallelized particle swarm optimization step is first performed to generate feasible initial points. Then, a multiobjective and dynamic real-time optimization formulation generates optimal trajectories. Further, the benefit of predictive capability is investigated for the dynamic component, which introduces the novel nonlinear multiobjective and dynamic real-time predictive optimization approach. Two multiobjective formulations to obtain Pareto front optimal in real time are explored: the modified Tchebycheff-based weighted metric and ϵ-constraint methods. Economic and environmental objectives are considered in this study. A novel topical discussion on the intersection of dynamic real-time optimization with model predictive control is also presented. The developed framework is successfully applied to a baseload coal-fired power plant with postcombustion CO 2 capture. Results indicate that the approach can be deployed for a large-scale system if automatic differentiation, model reduction, and parallelization are adopted to improve computational tractability, with computational improvement up to 120-folds after performing these steps. Finally, market and carbon policies showed an impact on the optimal compromise between the objectives with an additional 63 ton of CO 2 captured under favorable market conditions.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus to thylakoid subdomains in Arabidopsis

Abstract Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark‐adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark‐adapted plants and illuminated plants and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes and reveal the curvature fraction to be a focal point of early photosystem biogenesis.

Chotewutmontri, Prakitchai↗

New Synthetic Route to 4,6‐Diamino‐5,7‐dinitro‐benzo‐furazan, Important Decomposition Product of 1,3,5‐Triamino‐2,4,6‐trinitrobenzene

The important 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) decomposition byproduct, 4,6-diamino-5,7-dinitro-benzo-furazan (F 1 ), was prepared in a four-step reaction sequence starting with commercially available materials through a key intermediate, 4,6-dichloro-5,7-dinitro-benzo-furazan. The introduction of azido to 4,6-dichloro-benzo-furazan, followed by nitration and amination gave F 1 in good yield. This new method showed a greatly improved yield and ease of purification than previous methods (the total yield was 30%–40% in seven steps). F 1 is a stable yellow solid with a melting point of 308.7°C and a thermal decomposing temperature of 310.3°C (differential scanning calorimetry at 10°C/min heating rate). The solid-state structure was solved by single-crystal X-ray analyses at low temperatures (100 K). The compound crystallizes in a P 2 1 c space group with the formula C 6 H 4 N 6 O 5 •H 2 O with 12 molecules of F 1 /H 2 O in the unit cell. This compound has eluded complete characterization for almost 50 years. With this information, more advanced decomposition models can be created to further improve critical safety margins in handling the energetic material, TATB.

decomposition↗

Identification of 2,2-dinitropropanol, a Hydrolyzed Product of Aged Eutectic Bis(2,2-dinitropropyl) Acetal – Bis(2,2-dinitropropyl) Formal Mixture

Eutectic bis(2,2-dinitropropyl) acetal - bis(2,2-dinitropropyl) formal mixture, nitroplasticizer (herein called NP) has historically been produced by either the ter Meer or oxidative nitration synthesis process, wherein 2,2-dinitropropanol (DNPOH) is produced as an intermediate step in both processes. Therefore that DNPOH, could be present in NP either as a production or hydrolysis degradation product is worth investigation. Here, we synthesized DNPOH, validated the synthesis using NMR, and identified DNPOH in aged NP using liquid chromatography tandem time of flight – quadrupole mass spectrometry (LC-QTOF). Using these results, for the first time we positively identify that DNPOH is absent from NP after its production, but is present as a degradation product through hydrolysis from a thermo-chemical aging profile of NP. To hydrolyze NP, prerequisite is the presence of both water and acid. Despite the presence of water in NP, DNPOH is only generated in the late stage of the aging process, when acid concentration is sufficiently high. It has been previously shown both theoretically and experimentally that a primary step of NP degradation is HONO elimination followed by decomposition, wherein nitric acid, nitrous acid, and water are produced (NP→NP’+2HONO and 2HONO→NO+NO 2 +H 2 O). It is shown from this reaction series that water slows HONO decomposition and therefore in small quantities, 100 s of ppm, water actually stabilizes NP against hydrolysis by equilibrium and reducing acidity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the scaling limitations of the variational quantum eigensolver with the bond dissociation of hydride diatomic molecules

Abstract Materials simulations involving strongly correlated electrons pose fundamental challenges to state‐of‐the‐art electronic structure methods but are hypothesized to be the ideal use case for quantum computing algorithms. To date, no quantum computer has simulated a molecule of a size and complexity relevant to real‐world applications, despite the fact that the variational quantum eigensolver (VQE) algorithm can predict chemically accurate total energies. Nevertheless, because of the many applications of moderately sized, strongly correlated systems, such as molecular catalysts, the successful use of the VQE stands as an important waypoint in the advancement toward useful chemical modeling on near‐term quantum processors. In this paper, we take a significant step in this direction. We lay out the steps, write, and run parallel code for an (emulated) quantum computer to compute the bond dissociation curves of the TiH, LiH, NaH, and KH diatomic hydride molecules using the VQE. TiH was chosen as a relatively simple chemical system that incorporates d orbitals and strong electron correlation. Because current VQE implementations on existing quantum hardware are limited by qubit error rates, the number of qubits available, and the allowable gate depth, recent studies using it have focused on chemical systems involving s and p block elements. Through VQE + UCCSD calculations of TiH, we evaluate the near‐term feasibility of modeling a molecule with d‐orbitals on real quantum hardware. We demonstrate that the inclusion of d‐orbitals and the use of the UCCSD ansatz, which are both necessary to capture the correct TiH physics, dramatically increase the cost of this problem. We estimate the approximate error rates necessary to model TiH on current quantum computing hardware using VQE + UCCSD and show them to likely be prohibitive until significant improvements in hardware and error correction algorithms are available.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗