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At least 811 records · Page 45

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗

Advances in High-Power Wireless Charging Systems: Overview and Design Considerations

Wireless charging systems are foreseen as an effective solution to improve the convenience and safety of conventional conductive chargers. As this technology has matured, recent broad applications of wireless chargers to electrified transportation have indicated a trend toward higher power, power density, modularity, and scalability of designs. In this article, commercial systems and laboratory prototypes are reviewed, focusing mostly on the advances in high-power wireless charging systems. The recent endeavors in magnetic pad designs, compensation networks, power electronics converters, control strategies, and communication protocols are illustrated. Both stationary and dynamic (in-motion) wireless charging systems are discussed, and critical differences in their designs and applications are emphasized. On that basis, the comparisons among different solutions and design considerations are summarized to present the essential elements and technology roadmap that will be necessary to support large-scale deployment of high-power wireless charging systems. The review is concluded with the discussion of several fundamental challenges and prospects of high-power wireless power transfer (WPT) systems. Foreseen challenges include utilization of advanced materials, electric and electromagnetic field measurement and mitigation, customization, communications, power metering, and cybersecurity.

25 ENERGY STORAGE↗

Civil Procedure for the Anthropocene

Climate considerations must become an element of procedural analysis. Scholars, rule makers, legislators, and judges have historically prioritized procedural values including cost, speed, and accuracy. More recent waves of scholarship—including critical perspectives—have emphasized participation as a further procedural goal. Yet this list has grown stale. Current environmental realities force all areas of law, including civil procedure, to reckon with climate change. In the future, proceduralists will be forced to integrate climate-aware thinking into their analyses, proposals, and discussions. Predictably, minds will disagree on how to accomplish this and the kinds of trade-offs that are warranted. Yet the fundamental point of this article remains: climate change resilience is a procedural concern that has not been recognized but must be. This signals not the genesis of a new branch of procedural scholarship but an opportunity to broaden the discussion for all procedural scholarship. In addition, this Article serves as a guide for rule makers and legislators who have just recently begun to show interest in climate-aware procedures. It directs them to procedural topics that require urgent attention, provides implementation strategies for developing resilient procedures, and considers the attendant costs and benefits of different approaches ranging from laissez-faire to aggressive engagement. Just as civil procedural innovations contributed to the emergence and success of the civil rights movement, our collective response to climate change will also be shaped by civil procedure. This Article prepares for this future and offers a corrective to the field’s failure to anticipate and respond to climate change.

54 ENVIRONMENTAL SCIENCES↗

Multi-fidelity Uncertainty Quantification for Homogenization Problems in Structure-Property Relationships from Crystal Plasticity Finite Elements

Crystal plasticity finite element method (CPFEM) has been an integrated computational materials engineering (ICME) workhorse to study materials behaviors and structure-property relationships for the last few decades. These relations are mappings from the microstructure space to the materials properties space. Due to the stochastic and random nature of microstructures, there is always some uncertainty associated with materials properties, for example, in homogenized stress-strain curves. For critical applications with strong reliability needs, it is often desirable to quantify the microstructure-induced uncertainty in the context of structure-property relationships. However, this uncertainty quantification (UQ) problem often incurs a large computational cost because many statistically equivalent representative volume elements (SERVEs) are needed. In this article, we apply a multi-level Monte Carlo (MLMC) method to CPFEM to study the uncertainty in stress-strain curves, given an ensemble of SERVEs at multiple mesh resolutions. By using the information at coarse meshes, we show that it is possible to approximate the response at fine meshes with a much reduced computational cost. We focus on problems where the model output is multi-dimensional, which requires us to track multiple quantities of interest (QoIs) at the same time. In conclusion, our numerical results show that MLMC can accelerate UQ tasks around 2.23x, compared to the classical Monte Carlo (MC) method, which is widely known as ensemble average in the CPFEM literature.

36 MATERIALS SCIENCE↗

A Multi-scale, Geo-data Science Method for Assessing Unconventional Critical Mineral Resources

Critical minerals (CM) supply raw materials that constitute many of our essential infrastructure, defense, technology, and electrification needs. Currently, production and refinement of these materials from conventional sources is limited to few regions globally, which makes supply of these resources particularly venerable to disruption. To help overcome these risks and meet growing demand, attention has focused on identifying and developing resource potential of unconventional geologic CM sources, such as rare-earth elements in sedimentary systems. However, the unconventional nature of these types of sources means they are often poorly characterized and/or under-explored with respect to conventional counterparts. We present a regional case study for an Unconventional Rare-earth and Critical minerals (URC) assessment method for predicting and identifying REE resource potential and occurrence in unconventional systems in the Central Appalachian Basin (CAB). The method utilizes a geologic and geospatial data-driven approach, informed and guided by knowledge of REE enrichment processes, to systematically predict and identify areas of higher enrichment. Results from the test case indicate locations with potential for different types of coal-REE deposits, demonstrating its utility for reducing the area of exploration and identifying sites for more detailed investigation. Building upon the regional scale assessment capability, ongoing science-based enhancements to the method will allow for finer-scale (e.g., mine-scale) predictions required to support technical and economic assessments.

Creason, Christopher↗

High strain-rate compression behavior of polymeric rod and plate Kelvin lattice structures

The compressive high strain-rate behavior of polymeric Kelvin lattice structures with rod-based or plate-based unit cells was investigated through experimental techniques and finite element simulations. Polymeric lattice structures with 5x5x5 unit cell geometries were manufactured on the millimeter scale using vat polymerization additive manufacturing and tested at low (0.001/s) and high (1000/s) strain-rates. High strain-rate experiments were performed and validated for a viscoelastic split-Hopkinson (Kolsky) pressure bar system (SHPB) coupled with high-speed imaging and digital image correlation (DIC). Experimental results at both low and high strain-rates show the formation of a localized deformation band which was more prevalent in low relative density specimens and low strain-rate experiments. Strain-rate effects of lattice specimens strongly correlate with effects of the base polymer material; both bulk polymer and lattice specimen demonstrated strain-rate hardening, strain-rate stiffening, and decreased fracture strain under dynamic loading. Results show mechanical failure properties and energy absorption depended strongly on the relative density of the lattice specimen and exhibited distinct scaling between relative density and geometry type (rod, plate) and loading rate. High relative density plate-lattices demonstrated inferior mechanical properties to rod-lattices; however, there exists a critical relative density for a given mechanical property (17%- 28%) below which plate-lattices outperform rod-lattices of similar mass. As a result, high strain-rate explicit finite element simulations were performed and showed good agreement with the mechanical failure trends and deformation modes observed in the experiments.

36 MATERIALS SCIENCE↗

Operando synchrotron X-ray analysis of melt pool dynamics in an Al-Sn immiscible alloy

The melt flow in an Al-50vol.% Sn immiscible alloy, produced by single-track laser melting of Al and Sn elemental powders, was studied in real time. High-speed synchrotron X-ray imaging was used to track Al and Sn liquids’ movements, and also to examine elemental distributions in the laser tracks, complimented by electron microscopy after solidification. Key aspects, including melt pool geometry, keyhole instability, and flow dynamics (flow pattern and velocity), were examined using digital image analysis. Relatively deeper melt pools formed at 400 W and 300 mm/s exhibited greater stability, with smooth surfaces, consistent outward flow, and minor vortices near the keyhole. In contrast, shallower pools produced at higher scanning speeds (>500 mm/s) demonstrated greater instability with increased surface waviness, and stronger velocity fluctuations, leading to numerous micro-vortices and increased Al-Sn heterogeneity. Velocity scale estimations, supported by experimental observations, examined the roles of vapour pressure, Marangoni effect, buoyancy, inertial, and surface tension forces in the flow. The results revealed that vapour pressure and mechanical waves dominated at high scanning speeds (shallow pools), while Marangoni forces were equally significant in deep pools at lower speeds (300 mm/s). Buoyancy was found to have minimal impact in both cases. Furthermore, the interaction between inertial and surface tension forces played a critical role in determining the degree of waviness of the pools’ surfaces. These findings offer valuable insights into melt pool dynamics during laser processing of immiscible alloys and other metallic systems using elemental powders, and provide guidance for developing high-fidelity computational fluid dynamics models.

immiscible alloys↗

Active Thermochemical Tables: Enthalpies of Formation of Bromo- and Iodo-Methanes, Ethenes and Ethynes

Here, the thermochemistry of halocarbon species containing iodine and bromine is examined through an extensive interplay between new Feller–Peterson–Dixon (FPD) style composite methods and a detailed analysis of all available experimental and theoretical determinations using the thermochemical network that underlies the Active Thermochemical Tables (ATcT). From the computational viewpoint, a slower convergence of the components of composite thermochemistry methods is observed relative to species that solely contain first row elements, leading to a higher computational expense for achieving comparable levels of accuracy. Potential systematic sources of computational uncertainty are investigated, and, not surprisingly, spin-orbit coupling is found to be a critical component, particularly for iodine containing molecular species. The ATcT analysis of available experimental and theoretical determinations indicates that prior theoretical determinations have significantly larger uncertainties than originally reported, particularly in cases where molecular spin-orbit effects were ignored. Accurate and reliable heats of formation are reported for 38 halogen containing systems, based on combining the current computations with previous experimental and theoretical work via the ATcT approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synchrotron CT imaging of lattice structures with engineered defects

Understanding mechanical failure, crack propagation, and compressive behavior at the micrometer scale is essential for tailoring material properties for structural performance in cellular materials. Typically, modeling of traditional polymer foam materials is clouded by the lack of control in material morphology and its inherent stochastic structure. Additive manufacturing with sub-micrometer resolution provides a direct path for experimenters to specifically tailor structures needed by modelers to explicitly probe mechanical performance. Using laboratory-based 3D X-ray computed tomographic imaging (CT), the examination of deformation and damage provides a critical path to understand how these soft materials behave. Additionally, synchrotron CT yields realistic information at higher strain rates to directly validate the robustness of our finite element modeling. For this study, nanolithographic printing was employed to generate a series of engineered lattices with increasing levels of defects through the random removal of ligaments. These structures were mechanically tested and imaged with laboratory-based microCT. Additionally, synchrotron experiments were conducted in which the structures were imaged in 3D at 14 Hz during compression at a 0.4 s –1 strain rate. These 3D images show the changes in the structure as the ligaments bend, buckle and fracture in real time. This technique provides a robust framework for developing our methodologies and future exploration of engineered structures.

36 MATERIALS SCIENCE↗

Actinide Molten Salts: A Machine-Learning Potential Molecular Dynamics Study

We know that actinide molten salts represent a class of important materials in nuclear energy. Understanding them at a molecular level is critical to proper and optimal design of relevant technological applications. Yet, owing to the complexity of electronic structure due to the 5f orbitals, computational studies of heavy elements in condensed phases using ab initio potentials to study the structure and dynamics of these elements embedded in molten salts are difficult. This lack of efficient computational protocols makes it difficult to obtain information on properties that require extensive statistical sampling like transport. To tackle this problem, we adopted a machine-learning approach to study ThCl 4 -NaCl and UCl 3 -NaCl binary systems. The machine-learning potential, with the density functional theory accuracy, allows us to obtain long molecular dynamics trajectories (ns) for large systems (10 3 atoms) at a considerably low computing cost, thereby efficiently gaining information about their bonding structures, thermodynamics, and dynamics at a range of temperature. We observed a considerable change in the coordination environments of actinide elements and their characteristic coordination-sphere lifetime. Our study also suggests that actinides in molten salts may not follow well known entropy-scaling laws.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

3D Bragg Coherent Diffraction Imaging of Extended Nanowires: Defect Formation in Highly Strained InGaAs Quantum Wells

InGaAs quantum wells embedded in GaAs nanowires can serve as compact near-infrared emitters for direct integration onto Si complementary metal oxide semiconductor technology. While the core–shell geometry in principle allows for a greater tuning of composition and emission, especially farther into the infrared, the practical limits of elastic strain accommodation in quantum wells on multifaceted nanowires have not been established. One barrier to progress is the difficulty of directly comparing the emission characteristics and the precise microstructure of a single nanowire. Here, in this study, we report an approach to correlating quantum well morphology, strain, defects, and emission to understand the limits of elastic strain accommodation in nanowire quantum wells specific to their geometry. We realize full 3D Bragg coherent diffraction imaging (BCDI) of intact quantum wells on vertically oriented epitaxial nanowires, which enables direct correlation with single-nanowire photoluminescence. By growing In 0.2 Ga 0.8 As quantum wells of distinct thicknesses on different facets of the same nanowire, we identified the critical thickness at which defects are nucleated. A correlation with a traditional transmission electron microscopy analysis confirms that BCDI can image the extended structure of defects. Finite element simulations of electron and hole states explain the emission characteristics arising from strained and partially relaxed regions. This approach, imaging the 3D strain and microstructure of intact nanowire core–shell structures with application-relevant dimensions, can aid the development of predictive models that enable the design of new compact infrared emitters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First-principles investigation of structure-property relationships in stable and metastable MXenes

Understanding the structure–property relationships in layered transition-metal carbides or nitrides, known as MXenes, is of critical importance for their rational design, synthesis, and application. However, the vast chemical and structural diversity of MXenes, stemming from their wide range of M and X elements, surface terminations, and different atomic coordination environments, makes it challenging to clearly understand these structure–property relationships. Here, in this work, we perform first-principles density functional theory (DFT) calculations and molecular dynamics (MD) simulations to comprehensively investigate the stability and a variety of physical properties of MXenes with different coordination environments. Using Ti- and Mo-based carbide MXenes as model systems, energetic calculations reveal that Ti-based MXenes are most stable in octahedral coordination, whereas Mo-based MXenes preferentially adopt prismatic coordination. This fundamental difference in preferred atomic coordination gives rise to markedly distinct properties between these two systems as a function of the fraction of octahedral and prismatic sites. For instance, the in-plane stiffness of Ti-based MXenes increases as octahedral coordination becomes dominant, but it decreases in the Mo-based MXenes under the same conditions. Additional stability analyses based on mechanical, lattice-dynamical, and temperature-dependent thermodynamic properties demonstrate that many metastable MXenes not only satisfy the strict stability criteria but can also undergo phase transitions among different structures and even become stabilized at elevated temperatures. Although surface terminations, such as F and O atoms, do not alter the energetic ordering or the overall stiffness trends among stable and metastable MXenes, they influence other material properties. For instance, O termination can induce semiconducting behavior in both stable and metastable Ti 2 ⁢CO 2 MXenes. This study significantly advances the fundamental understanding of structure–property relationships in MXenes and provides valuable guidance for developing coordination-based design principles to precisely engineer MXenes with improved properties.

Oyeniran, Noah [University of Alabama, Tuscaloosa,↗

Williston Basin Carbon Ore, Rare Earth, and Critical Minerals (CORE-CM) Program

The U.S. Department of Energy’s (DOE’s) Office of Fossil Energy awarded 13 Carbon Ore, Rare-Earth and Critical Minerals (CORE-CM) programs as part of the CORE-CM Initiative, designed to develop the technology and upstream and midstream supply chains to extract rare-earth elements (REEs) and CMs from the nation’s coal supplies. The intent is to catalyze regional economic growth and job creation while strengthening the use of domestic resources. The Williston Basin CORE-CM Program aims to drive the expansion and transformation of coal and coal-based resource usage within the Williston Basin to produce REEs, CMs, and nonfuel carbon-based products (CBPs). The work constitutes Phase 1 of a long-term program. The objectives of Phase 1 are to identify the existing knowledge base and gaps and to develop a series of assessments/plans, including an initial basinal assessment; a characterization and data acquisition plan; a waste stream reuse plan; a basinal strategies assessment for infrastructure, industries, and business; a technology assessment, development, and field-testing plan; a technology innovation center plan(s); and a stakeholder outreach and education plan. Originally, the CORE-CM programs were to do little if any sample collection as part of the Phase 1 program. As part of the ongoing interactions with DOE regarding the progress of the 13 CORE-CM programs, DOE has decided to extend Phase 1 with additional funding to allow all of the Phase 1 CORE-CM programs to collect and characterize more samples that have potential to be sources of REEs and CMs. The goal of this project is to initiate the development of a new industry in the resource-rich Williston Basin that will generate economic growth and job creation through a coalition team of private industry; university; and state, local, and federal government entities. A coalition team of nearly 30 private industry; university; and state, local, and federal government partners was formed for this program. Partners include the University of North Dakota Energy & Environmental Research Center, Institute for Energy Studies, and Nistler College; North Dakota State University; Montana Tech University; Pacific Northwest National Laboratory; Critical Materials Institute; North Dakota Geological Survey; South Dakota Geological Survey; U.S. Geological Survey; North American Coal Corporation; BNI Energy; Basin Electric Power Cooperative; Minnkota Power Cooperative; and many more.

Kay, John P.↗

Understanding the effect of refractory metal chemistry on the stacking fault energy and mechanical property of Cantor-based multi-principal element alloys

Multi-principal-element alloys (MPEAs) based on 3d-transition metals show remarkable mechanical properties. In this study, the stacking fault energy (SFE) in face-centered cubic (fcc) alloys is a critical property that controls underlying deformation mechanisms and mechanical response. Here, we present an exhaustive density-functional theory study on refractory- and copper-reinforced Cantor-based systems to ascertain the effects of refractory metal chemistry on SFE. We find that even a small percent change in refractory metal composition significantly changes SFEs, which correlates favorably with features like electronegativity variance, size effect, and heat of fusion. For fcc MPEAs, we also detail the changes in mechanical properties, such as bulk, Young's, and shear moduli, as well as yield strength. A Labusch-type solute-solution-strengthening model was used to evaluate the temperature-dependent yield strength, which, combined with SFE, provides a design guide for high-performance alloys. We also analyzed the electronic structures of two down-selected alloys to reveal the underlying origin of optimal SFE and strength range in refractory-reinforced fcc MPEAs. These new insights on tuning SFEs and modifying composition-structure-property correlation in refractory- and copper-reinforced MPEAs by chemical disorder, provide a chemical route to tune twinning- and transformation-induced plasticity behavior in fcc MPEAs.

36 MATERIALS SCIENCE↗

Synchrotron X‐Ray‐Driven Nitrogen Reduction on an AgCu Thin Film

Abstract Nitrogen (N 2 ) is an essential element for life, but kinetically stable N 2 in the atmosphere needs to be reduced to biologically available forms as a nutrient for organisms. Abiotic nitrogen fixation is critical to the origin of life on the early Earth, which is due to lightning or mineral‐based reduction. Here, synchrotron X‐ray‐induced silver nitrate formation on a silver copper (AgCu) thin‐film is reported. Time‐resolved X‐ray diffraction measurements show that under intense X‐ray exposure, initially formed silver oxides (AgOx) are quickly converted to silver nitrate (AgNO 3 ). Interestingly, AgNO 3 is first formed in its high‐temperature phase with a space group of R3cH , which gradually transforms to the room temperature phase with a space group of Pbca under continuous X‐ray irradiation. The result not only provides a new clue about the abiotic nitrogen reduction prior to life but also demonstrates a novel strategy of materials synthesis using synchrotron X‐rays.

Hui, Jian↗

Understanding the impacts of inorganic species in woody biomass for preprocessing and pyrolysis–A review

Woody biomass represents an abundant resource for sustainable biofuels, biochemicals, and bioproducts. Technologies for converting woody biomass have been established for decades, and research consistently highlights the critical role of inorganic species and ash plays in feedstock handling and conversion processes, including equipment plugging, corrosion, and catalyst deactivation. A thorough understanding of the variability, transport behavior, and downstream impact of inorganic species in woody biomass is essential for defining feedstock quality specifications and developing effective management strategies for conversion processes. This review compiles critical information in five main sections: 1) inorganic species concentration in woody biomass, based on anatomical fractions and their sources of variability; 2) technique features for quantifying inorganic elemental chemical analysis; 3) impacts of inorganic species on biomass preprocessing; 4) impacts of inorganic species on pyrolysis, and 5) mitigation strategies. Additionally, this review explores future challenges and opportunities in addressing the impacts of inorganic species on biomass quality. These insights aim to support the sustainable development of the biomass-to-bioenergy pipeline and ensure high-quality lignocellulosic feedstocks for efficient downstream conversions. The findings offer valuable guidance to policy makers, industry stakeholders, and researchers in developing effective strategies for managing inorganic species in woody biomass and fostering the sustainable processes for lignocellulosic biorefineries.

09 BIOMASS FUELS↗

Environmental influence on cracking and debonding of electrically conductive adhesives

Electrically conductive adhesives (ECAs) are starting to replace metallic solders in recent designs of photovoltaic (PV) modules. This transition represents a significant material change, and a proper understanding of the durability and reliability of the new interconnect needs to be established. This paper presents our continued work on developing a degradation model for ECA interconnects in PV modules. Here, we characterize the fracture mechanics properties of an epoxy-based ECA, for both critical and subcritical, mode I and mode II loading conditions. Emphasis is on the influence of different environmental conditions such as temperature and humidity. We use the Finite Element Method to account for residual stresses, induced by temperature changes and moisture absorption, and correct the apparent fracture toughness. We found that high moisture levels not only can weaken the fracture resistance of the ECA interconnect, but can also promote subcritical debonding at significantly lower driving forces than in dry environments.

42 ENGINEERING↗

A Novel Zwitterionic Chromatography Approach to Separate Lithium from Unconventional Resources

Lithium (Li) is a key element for clean energy technologies, and, accordingly, the global lithium demand has been increasing rapidly. Therefore, to meet the Li demand and maintain supply chain stability, it is critical to develop efficient lithium extraction technologies that allow exploitation of unconventional lithium resources, such as geothermal brines and inland brine streams. However, the recovery of Li from these resources is challenging due to low Li concentration, low ratios of Li/Na, Li/Mg, or Li/Ca, and complex feed compositions. To address this, we introduced a new Direct Lithium Extraction (DLE) process using Zwitterionic Chromatography (ZIC) to separate Li from other salts. Since salts are partitioned on ZIC under water elution, no reagent chemicals are needed, and the Li separation is not limited by the adsorption capacity. We prepared 13 different zwitterionic (ZI) resins to investigate the salt retention on various ZI groups and then screened out promising sorbents for efficient Li separation. It was found that salt retention was synergistically affected by the pore size and ZI configurations. Using carboxybetaine (QAC3CA) sorbents, multicomponent separations showed that Li can be partitioned from divalent salts or Na with selectivities of 1.8 or 1.9, respectively. Although the selectivity is relatively low, in real brine tests, Li was separated from Ca and Mg with 79.2 % yield, showing the potential for a continuous process to achieve high productivity and high yield. Simulation studies suggest the salt elution mechanism is related to the hydration reaction energy and the effective hydrated radius of cations.

critical minerals↗