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At least 415 records · Page 23

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. In this paper, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.

59 BASIC BIOLOGICAL SCIENCES↗

Long-term strength retrogression of silica-enriched oil well cement: A comprehensive multi-approach analysis

The strength retrogression of a Class G cement enriched by adding 60–80% silica cured under the condition of 200 °C and 50 MPa were investigated by multiple different analysis methods. Short-term strength analysis suggests sonic strength testing is a poor indicator of real mechanical strength at such curing condition. Long-term testing up to 142 d shows all designed systems experiences dramatic deterioration in physical and mechanical properties, such as compressive strength, Young's modulus, water permeability and gas permeability. Further testing was conducted using X-ray diffraction, thermal gravimetric analysis, mercury intrusion and scanning electron microscope. The study reveals that the set cement experiences significant microstructure coarsening with increasing curing time, especially after 30 d curing. The strength retrogression and microstructure coarsening seem to be accompanied with the continued consumption of silica, and are likely caused by the gradual conversion of semi-crystalline C-S-H into crystalline tobermorite and xonolite over the long-term curing.

36 MATERIALS SCIENCE↗

Comprehensive parametric study of CO 2 sequestration in deep saline aquifers

Carbon dioxide injection in deep saline aquifers is a key method for permanently sequestering anthropogenic CO 2 . Here this study employs a reactive transport model to explore mineral precipitation/dissolution and its impact on reservoir properties in deep saline aquifers. We also assess capillary pressure and relative permeability hysteresis on various CO 2 trapping mechanisms. Results from this study reveal the significant influence of initial brine composition on mineral precipitation/dissolution. The dissolution and precipitation of minerals have different effects around the wellbores compared to the overall reservoir. Additionally, salt concentration (Ca ++ and Mg ++ ) and quartz surface area affect CO 2 mineralization, while Na + impacts halite precipitation, altering flow properties. The effect of capillary pressure is significant, as including the capillary pressure in the simulation case resulted in significantly improved CO 2 trapping, achieving almost total dissolution of the injected CO 2 in around 300 years. This study offers novel insights into the interactions of reservoir minerals, brine properties, and the injected CO 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Plastic additives in the ocean: Use of a comprehensive dataset for meta-analysis and method development

In excess of 13,000 chemicals are added to plastics (‘additives’) to improve performance, durability, and production of plastic products. They are categorized into numerous chemical classes including flame retardants, light stabilizers, antioxidants, and plasticizers. While research on plastic additives in the marine environment has increased over the past decade, there is a lack of methodological standardization. To direct future measurement of plastic additives, we compiled a first-of-its-kind dataset of literature assessing plastic additives in marine environments, delineated by sample type (plastic debris, seawater, sediment, biota). Using this dataset, we performed a meta-analysis to summarize the state of the science. Currently, our dataset includes 217 publications published between 1978 and May 2023. The majority of publications analyzed plastic additives in biota collected from Europe and Asia. Analyses concentrated on plasticizers, brominated flame retardants, and bisphenols. Common sample preparation techniques included Solvent - Agitation extraction for plastic, sediment, and biota samples, and Solid Phase Extraction for seawater samples with dichloromethane and solvent mixtures including dichloromethane as the organic extraction solvent. Finally, most analyses were performed utilizing gas chromatography/mass spectrometry. There are a variety of data gaps illuminated by this meta-analysis, most notably the small number of compounds that have been targeted for detection compared to the large number of additives used in plastic production. The provided dataset facilitates future investigation of trends in plastic additive concentration data in the marine environment (allowing for comparison to toxicity thresholds) and acts as a starting point for optimizing and harmonizing plastic additive analytical methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A comprehensive and fair comparison of two neural operators (with practical extensions) based on $\mathrm{FAIR}$ data

Neural operators can learn nonlinear mappings between function spaces and offer a new simulation paradigm for real-time prediction of complex dynamics for realistic diverse applications as well as for system identification in science and engineering. Herein, we investigate the performance of two neural operators, which have shown promising results so far, and we develop new practical extensions that will make them more accurate and robust and importantly more suitable for industrial-complexity applications. The first neural operator, DeepONet, was published in 2019 (Lu et al., 2019), and its original architecture was based on the universal approximation theorem of Chen & Chen (1995). The second one, named Fourier Neural Operator or FNO, was published in 2020, and it is based on parameterizing the integral kernel in the Fourier space. DeepONet is represented by a summation of products of neural networks (NNs), corresponding to the branch NN for the input function and the trunk NN for the output function; both NNs are general architectures, e.g., the branch NN can be replaced with a CNN or a ResNet. According to Kovachki et al. (2021), FNO in its continuous form can be viewed conceptually as a DeepONet with a specific architecture of the branch NN and a trunk NN represented by a trigonometric basis. In order to compare FNO with DeepONet computationally for realistic setups, we develop several extensions of FNO that can deal with complex geometric domains as well as mappings where the input and output function spaces are of different dimensions. We also develop an extended DeepONet with special features that provide inductive bias and accelerate training, and we present a faster implementation of DeepONet with cost comparable to the computational cost of FNO, which is based on the Fast Fourier Transform. Here we consider 16 different benchmarks to demonstrate the relative performance of the two neural operators, including instability wave analysis in hypersonic boundary layers, prediction of the vorticity field of a flapping airfoil, porous media simulations in complex-geometry domains, etc. We follow the guiding principles of FAIR (Findability, Accessibility, Interoperability, and Reusability) for scientific data management and stewardship. The performance of DeepONet and FNO is comparable for relatively simple settings, but for complex geometries the performance of FNO deteriorates greatly. We also compare theoretically the two neural operators and obtain similar error estimates for DeepONet and FNO under the same regularity assumptions.

42 ENGINEERING↗

Autoignition and preliminary heat release of gasoline surrogates and their blends with ethanol at engine-relevant conditions: Experiments and comprehensive kinetic modeling

This work utilizes a rapid compression machine (RCM) to experimentally quantify autoignition and preliminary heat release characteristics for blends of 0 to 30% ethanol by volume into two surrogates (FGF-LLNL and FGF-KAUST) that represent a full boiling range gasoline (FACE-F). Experimental conditions cover pressures from 15 to 100 bar, temperatures from 700 to 1000 K, and diluted/stoichiometric and undiluted/lean fuel loading conditions representative of boosted spark-ignition and advanced compression ignition engines, respectively. Direct comparison is made with previously reported results for FACE-F/E0–E30 blends. Here, a detailed gasoline surrogate chemistry model is also proposed, and chemical kinetic modeling is undertaken using the proposed model to generate chemical insights into the compositional effects and ethanol blending effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A comprehensive experimental and kinetic modeling study of di-isobutylene isomers: Part 2

A wide variety of high temperature experimental data obtained in this study complement the data on the oxidation of the two di-isobutylene isomers presented in Part I and offers a basis for an extensive validation of the kinetic model developed in this study. Due to the increasing importance of unimolecular decomposition reactions in high-temperature combustion, we have investigated the di-isobutylene isomers in high dilution utilizing a pyrolysis microflow reactor and detected radical intermediates and stable products using vacuum ultraviolet (VUV) synchrotron radiation and photoelectron photoion coincidence (PEPICO) spectroscopy. Additional speciation data at oxidative conditions were also recorded utilizing a plug flow reactor at atmospheric pressure in the temperature range 725-1150 K at equivalence ratios of 1.0 and 3.0 and at residence times of 0.35 s and 0.22 s, respectively. Combustion products were analyzed using gas chromatography (GC) and mass spectrometry (MS). Ignition delay time measurements for di-isobutylene were performed at pressures of 15 and 30 bar at equivalence ratios of 0.5, 1.0, and 2.0 diluted in 'air' in the temperature range 900-1400 K using a high-pressure shock-tube facility. New measurements of the laminar burning velocities of di-isobutylene/air flames are also presented. The experiments were performed using the heat flux method at atmospheric pressure and initial temperatures of 298-358 K. Moreover, data consistency was assessed with the help of analysis of the temperature and pressure dependencies of laminar burning velocity measurements, which was interpreted using an empirical power-law expression. Electronic structure calculations were performed to compute the energy barriers to the formation of many of the product species formed. The predictions of the present mechanism were found to be in adequate agreement with the wide variety of experimental measurements performed.

09 BIOMASS FUELS↗

A comprehensive model to capture electrical discharge and spark channel evolution during spark-ignition processes

Emissions reduction through engine efficiency improvements is a priority for automakers who have turned to unconventional engine operation such as highly dilute, boosted, and stratified charge. Given its importance to flame initiation and sustained turbulent flame propagation, reliable and accurate spark ignition models are necessary to design ignition systems that reduce cyclic indicated mean effective pressure (IMEP) variability and increase engine efficiency in these operation modes. In this paper, secondary electric circuit, short-circuit, blowout, and re-strike sub-models are added to the Lagrangian-Eulerian spark ignition (LESI) model to simulate electrical discharge and spark channel elongation in an inert cross-flow combustion vessel. First, the physics of the underlying sub-models are described and the governing equations discussed with the spark channel voltage expression playing a critical role. Then, the experimental and simulations setups are presented. The results section begins with the derivation of spark channel voltage from experimental results. Then, electrical discharge and spark channel elongation simulations in inert flows are carried out using LESI and compared against experimental results. Finally, the results validate the model's ability to accurately predict spark channel elongation, as well as the occurrence of short-circuits, blowouts, re-strikes, and end of discharge.

42 ENGINEERING↗

Autoignition of cyclohexane at low-to-intermediate temperatures: Rapid compression machine experiments and improved comprehensive chemical kinetic model

Cycloalkanes are an important class of hydrocarbons found in conventional and alternative transportation fuels. Being one of the simplest practical cycloalkanes, cyclohexane is often used as a surrogate in studies to understand the oxidation, ignition, and sooting characteristics of cycloalkanes more broadly. Although cyclohexane has been extensively studied, very limited datasets for cyclohexane oxidation at low-to-intermediate temperatures are available in the literature. Moreover, the literature autoignition data from rapid compression machines (RCMs) did not provide information on volume histories or experimental heat transfer characteristics which can significantly impact model predictions, thereby hindering the detailed validation of chemical kinetic models. It has also been observed that the cyclohexane kinetic models developed so far are not able to predict the literature data across a wide range of operating and mixture conditions. Hence, further studies are recommended to understand and improve model predictions for cyclohexane oxidation. In this study, RCM experiments were conducted using cyclohexane/air mixtures at varying compressed pressures (P C =15, 20, and 30 bar), equivalence ratios (ϕ=0.5, 1.0, and 2.0), and compressed temperatures (T C =670–960 K). The current RCM results of cyclohexane were found to complement well with the literature data, with the first-stage IDTs at high pressures and volume histories at all test conditions being first reported for better development and validation of chemical kinetic models. Additionally, a detailed chemical kinetic model for the cyclohexane oxidation has been developed and validated using both newly acquired experimental IDTs in this study and literature experimental studies (IDTs in RCMs and STs, species profiles in jet-stirred reactors, and laminar burning velocities). Unlike literature models, the proposed model was observed to provide an overall better prediction for experimental results over a wide range of conditions. Chemical kinetic analysis of the developed model was further conducted to identify the reaction pathways controlling the autoignition of cyclohexane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Point defect energetics in gallium arsenide, a comprehensive density functional theory study

In materials, point defects often control or modify functional properties. To predict the performance of materials intended for application in optoelectronic devices, it is imperative to understand the properties of those point defects. For the first time, all six intrinsic defects of GaAs, a key optoelectronics material, and their charge transition levels are calculated using density functional theory with the HSE06 functional. For comparison, both PBE and r 2 SCAN calculations are also carried out. The HSE06 results are found to be in better agreement with experimental data than previous calculations. In conclusion, the importance of using the exact electron exchange present in hybrid functionals and larger supercells to accurately determine defect levels and ground state defect configurations is demonstrated.

36 MATERIALS SCIENCE↗

Simulators for quantum network modeling: A comprehensive review

Quantum network research is exploring new networking protocols, physics-based hardware and novel experiments to demonstrate how quantum distribution will work over large distances. Current work explores much of these concepts in simulations, that are developed to understand how quantum networking will be set up and researchers can experiment virtually. Exposing flaws in network designs, like unsustainable topologies, or develop protocols that efficiently utilize network resources, simulators can also help assess whether workloads are balanced across virtual machines in the network. However, much of these simulation models come without reliable verification methods, for testing performance in real deployments. Here, in this paper, we present a review of, to the best of our knowledge, currently used toolkits for modeling quantum networks. With these toolkits and standardized validation techniques, we can lay down the foundations for more accurate and reliable quantum network simulators.

97 MATHEMATICS AND COMPUTING↗

Using hydrogen and ammonia for renewable energy storage: A geographically comprehensive techno-economic study

Hydrogen and, more recently, ammonia have received worldwide attention as energy storage media. In this work we investigate the economics of using each of these chemicals as well as the two in combination for islanded renewable energy supply systems in 15 American cities representing different climate regions throughout the country. We use an optimal combined capacity planning and scheduling model which minimizes the levelized cost of energy (LCOE) by determining optimal unit selection and size along with unit commitments, production rates, and storage inventories for each period of system operation. These periods are aggregated from full year hourly resolution data via a consecutive temporal clustering algorithm. Ammonia is generally more economical than hydrogen as a single method of energy storage. Additionally, systems which use both hydrogen and ammonia outperform those which use only one storage option and have LCOE between $\$ 0.17$/kWh and $\$ 0.28$/kWh, including full investment in renewable generation infrastructure.

25 ENERGY STORAGE↗

Comprehensive assessment of deep reinforcement learning approaches for economic dispatch in nuclear-driven microgrids

As the electrical grid integrates more variable renewable energy sources such as wind and solar, the demand for distributed and flexible systems to address this increased variability becomes critical. Nuclear-driven microgrids provide a promising solution by offering stable generation to complement intermittent renewables, ensuring grid reliability and operating efficiency. This paper proposes a recurrent deep reinforcement learning framework for optimal economic dispatch in a nuclear-powered microgrid integrating renewable energy sources, small modular reactors, battery storage systems, and balance-of-plant dynamics. A three-agent control architecture is developed, where demand and renewable energy agents act as forecasters, and a reinforcement learning-based dispatch agent performs real-time energy allocation. A nonlinear programming formulation is first used to generate an optimal baseline for benchmarking. The proposed dispatch controller, based on Proximal Policy Optimization enhanced with Long Short-Term Memory networks, exploits temporal correlations in system dynamics by taking advantage of the time series used as inputs to improve policy robustness under uncertainty. Comparative analysis against established deep reinforcement learning methods, including Proximal Policy Optimization with a feedforward architecture, Soft Actor-Critic, and Twin Delayed Deep Deterministic Policy Gradient, demonstrates superior performance. Numerical results indicate that the proposed controller achieves a 0.39% cost reduction relative to the nonlinear programming benchmark and outperforms other learning-based methods by generating additional revenue of up to 0.35%. All reinforcement learning controllers compute dispatch actions in less than 0.3 s, resulting in a computational speedup of more than three orders of magnitude over the nonlinear programming baseline. The findings of this paper highlight their applicability for real-time operation and control in nuclear-integrated microgrids under volatile operating conditions.

24 POWER TRANSMISSION AND DISTRIBUTION↗