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At least 685 records · Page 38

Increase in the effective viscosity of polyethylene under extreme nanoconfinement

Understanding polymer transport in nanopores is crucial for optimizing heterogeneously catalyzed processes in polymer upcycling and fabricating high-performance nanocomposite films and membranes. Although confined polymer dynamics have been extensively studied, the behavior of polyethylene (PE)—the most widely used commodity polymer—in pores smaller than 20 nm remains largely unexplored. We investigate the effects of extreme nanoconfinement on PE transport using capillary rise infiltration in silica nanoparticle packings with average pore radii ranging from ~1 to ~9 nm. Using in situ ellipsometry and the Lucas–Washburn model, we discover a previously unknown inverse relationship between effective viscosity (η eff ) and average pore radius (R pore ). Additonally, we determine that PE transport under these extreme conditions is primarily governed by physical confinement, rather than pore surface chemistry. We refine an existing theory to provide a generalized formalism to describe the polymer transport dynamics over a wide range of pore radii (from 1 nm and larger). Our results offer valuable insights for optimizing catalyst supports in polymer upcycling and improving infiltration processes for nanocomposite fabrication.

36 MATERIALS SCIENCE↗

Data Science Shows that Entropy Correlates with Accelerated Zeolite Crystallization in Monte Carlo Simulations

We have performed a data science study of Monte Carlo simulation trajectories to understand factors that can accelerate formation of zeolite nanoporous crystals, a process that can take days or even weeks. In previous work, Monte Carlo simulations predicted and experiments confirmed that using a secondary organic structure-directing agent (OSDA) accelerates crystallization of all-silica LTA zeolite, with experiments finding a three-fold speedup [PCCP 24, 142-148 (2022)]. However, it remains unclear what physical factors cause the speed-up. Here, we apply data science to analyze the simulation trajectories to discover what drives accelerated zeolite crystallization in Monte Carlo going from a one-OSDA synthesis (1OSDA) to a two-OSDA version (2OSDA). We encoded simulation snapshots using the Smooth Overlap of Atomic Positions approach, which represents all 2- and 3-body correlations within a given cutoff distance. Principal component analyses failed to discriminate datasets of structures from 1OSDA and 2OSDA simulations, while the Support Vector Machine (SVM) approach succeeded at classifying such structures with an area-under-curve (AUC) score of 0.99 (where AUC = 1 is a perfect classification) with all 3-body correlations, and as high as 0.94 with only 2-body correlations. SVM decision functions reveal relatively broad / narrow histograms for 1OSDA / 2OSDA datasets, suggesting that the two simulations differ strongly in information heterogeneity. Informed by these results, we performed pair (2-body) entropy calculations during crystallization, resulting in entropy differences that semi-quantitatively account for the speedup observed in the previous Monte Carlo simulations. We conclude that altering synthesis conditions in ways that substantially changes the entropy of labile silica networks may accelerate zeolite crystallization, and we discuss possible approaches for achieving such acceleration.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Lipid sponge droplets as programmable synthetic organelles

Living cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here, we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and nonionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the colocalization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and self-assembling spatial organization with biochemical reaction systems.

59 BASIC BIOLOGICAL SCIENCES↗

Interfacial dynamics and catalytic behavior of single Ni atom site

Single-atom catalysts (SACs) have garnered significant interest due to their ability to reduce metal particles to the atomic scale, enabling finely tunable local environments and enhanced catalytic properties in terms of reactivity and selectivity. Despite this potential, their application has largely been confined to small-molecule transformations as metal-catalyzed reaction. Here, in this study, we present a diverse single-atom nickel (Ni) catalyst established via a nanoporous carbon (NPC) supported practice. This catalyst represents a breakthrough by achieving the bond formation between carbon and nitrogen and interfacial dynamics in the SAC. The present first principle-based density functional simulations establish the reaction dynamics and catalytic behaviour of such SAC. This dynamic nature comprises an exclusive nitrogen intercalated site showing excellent base effects. This base quickly tunes the interfacial atmosphere, enabling dynamic movement of adatoms into the NPC species, significantly changing the reaction path in Ni SACs due to superior steric effects. The research demonstrates that SACs can extend the capabilities of catalytic systems to include a wider range of complex reactions, offering substantial promise for the development of new, efficient synthetic methods for creating value-added molecular products.

36 MATERIALS SCIENCE↗

End-to-end AI framework for interpretable prediction of molecular and crystal properties

We introduce an end-to-end computational framework that allows for hyperparameter optimization using the DeepHyper library, accelerated model training, and interpretable AI inference. The framework is based on state-of-the-art AI models including CGCNN, PhysNet, SchNet, MPNN, MPNN-transformer, and TorchMD-NET. We employ these AI models along with the benchmark QM9, hMOF, and MD17 datasets to showcase how the models can predict user-specified material properties within modern computing environments. We demonstrate transferable applications in the modeling of small molecules, inorganic crystals and nanoporous metal organic frameworks with a unified, standalone framework. We have deployed and tested this framework in the ThetaGPU supercomputer at the Argonne Leadership Computing Facility, and in the Delta supercomputer at the National Center for Supercomputing Applications to provide researchers with modern tools to conduct accelerated AI-driven discovery in leadership-class computing environments. We release these digital assets as open source scientific software in GitLab, and ready-to-use Jupyter notebooks in Google Colab.

36 MATERIALS SCIENCE↗

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with “place” and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai‘i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16A T , of the new species (DSM 112479 T = NCTC 14602 T ). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61 T , of the new species (DSM 116657 T = LMG = 33184 T ), and Hawai‘i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16E T , of the new species (DSM 112478 T = NCTC 14603 T ).

59 BASIC BIOLOGICAL SCIENCES↗

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

Abstract Summary Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. Availability and implementation https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species

The widespread Pseudomonas genus comprises a collection of related species with remarkable abilities to degrade plastics and polluted wastes and to produce a broad set of valuable compounds, ranging from bulk chemicals to pharmaceuticals. Pseudomonas possess characteristics of tolerance and stress resistance making them valuable hosts for industrial and environmental biotechnology. However, efficient and high-throughput genetic engineering tools have limited metabolic engineering efforts and applications. To improve their genome editing capabilities, we first employed a computational biology workflow to generate a genus-specific library of potential single-stranded DNA-annealing proteins (SSAPs). Assessment of the library was performed in different Pseudomonas using a high-throughput pooled recombinase screen followed by Oxford Nanopore NGS analysis. Among different active variants with variable levels of allelic replacement frequency (ARF), efficient SSAPs were found and characterized for mediating recombineering in the four tested species. New variants yielded higher ARFs than existing ones in Pseudomonas putida and Pseudomonas aeruginosa, and expanded the field of recombineering in Pseudomonas taiwanensisand Pseudomonas fluorescens. These findings will enhance the mutagenesis capabilities of these members of the Pseudomonas genus, increasing the possibilities for biotransformation and enhancing their potential for synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗

Langevin and Fokker-Planck analyses for diffusion-mediated passing of circular and discorectangular species in two-dimensional channels

The propensity for pairs of diffusing species to pass each other within narrow channels or pores is of basic interest as a first-passage-type problem. It is also of relevance for solution-phase transport in nanoporous materials, and in particular for catalytic conversion reactions where high yield requires that product species can efficiently pass reactant species to exit the pores. Here, we analyze a two-dimensional model with nonoverlapping circular and discorectangular species confined to a rectangular channel, and where passing is mediated by Brownian dynamics in an implicit solvent. For narrower channels where passing is still possible, the discorectangle must align with the channel to pass the circular species. Behavior of the passing propensity, 𝑃, can be assessed by strongly damped Langevin simulations, or within an equivalent Fokker-Planck equation (FPE) formalism. The latter corresponds to a diffusion problem in a “higher-dimensional channel” with a constriction. We assess the variation of the passing propensity, 𝑃, for a broad range of channel width including its scaling just above the threshold where passing is sterically blocked. Analysis of 𝑃 versus the rotational diffusion coefficient 𝐷 𝑟 of the discorectangle reveals a significant decrease in 𝑃 for lower 𝐷 𝑟 for moderate channel width. This prompts a direct analysis of the regime where 𝐷 𝑟 → 0 , for which the FPE can be reduced to a three-dimensional diffusion problem, precise analysis of which is facilitated by adaptive-mesh finite element methods. The dependence of 𝑃 on the aspect ratio of the discorectangle is also assessed.

Rahman, Md Khaledur [Ames Laboratory (AMES), Ames,↗

Effect of interfacial vibrational coupling on surface wettability and water transport

Here, we report that the atomic-scale vibrational coupling at the solid-fluid interface can substantially alter the interfacial properties such as wettability and fluid slip. The wettability of water droplets on substrates subjected to various vibrational frequencies is studied using molecular dynamics simulation. The contact angle increases (i.e., becomes more hydrophobic) when the oscillation frequency of the substrate matches the intermolecular bending frequency of liquid water. We investigate the underlying mechanism by examining the dynamics of water molecules at the interface and find that the temporal contact between the solid and fluid is shorter when the frequencies match, resulting in weak solid-fluid adsorption. We further report that the vibrational match at the interface reduces wall-fluid friction and enhances water transport through the nanopore. Our findings demonstrate the importance of the atomic-scale vibrational coupling at the solid-fluid interface on the physicochemical behavior of nanodevices and biological nanochannels.

74 ATOMIC AND MOLECULAR PHYSICS↗

Effect of transport mechanism on the coarsening of bicontinuous structures: A comparison between bulk and surface diffusion

Here, coarsening of bicontinuous microstructures is observed in a variety of systems, such as nanoporous metals and mixtures that have undergone spinodal decomposition. To better understand the morphological evolution of these structures during coarsening, we compare the morphologies resulting from two different coarsening mechanisms, surface and bulk diffusion. We perform phase-field simulations of coarsening via each mechanism in a two-phase mixture at nominal volume fractions of 50%-50% and 36%-64%, and the simulated structures are characterized in terms of topology (genus density), the interfacial shape distribution, structure factor, and autocorrelations of phase and mean curvature. We observe self-similar evolution of morphology and topology and agreement with the expected power laws for dynamic scaling, in which the characteristic length scale increases over time proportionally to t 1/4 for surface diffusion and t 1/3 for bulk diffusion. While we observe the expected difference in the coarsening kinetics, we find that differences in self-similar morphology due to coarsening mechanism are relatively small, although typically they are larger at 36% volume fraction than at 50% volume fraction. In particular, we find that bicontinuous structures coarsened via surface diffusion have lower scaled genus densities than structures coarsened via bulk diffusion. We also compare the self-similar morphologies to those in literature and to two model bicontinuous structures, namely, constant-mean-curvature surfaces based on the Schoen G minimal surface and random leveled-wave structures. The average scaled mean curvatures of these model structures agree reasonably with those of the coarsened structures at both 36% and 50%, but we find substantial disagreements in the scaled genus densities and the standard deviations of mean curvature.

36 MATERIALS SCIENCE↗

An 860 MHz Wireless Surface Acoustic Wave Sensor with a Metal-Organic Framework Sensing Layer for CO2 and CH4

Wireless and passive surface acoustic wave (SAW) devices with nanoporous metal-organic framework (MOF) sensing layers are attractive gas sensors for applications in many fields such as energy industries and air pollution control. Here, we report on enhancing the sensitivity and detection limit of zeolitic imidazolate framework-8 (ZIF-8) MOF-coated SAW reflective delay line mass sensors by increasing the operating frequency for sensitive detection of carbon dioxide (CO2) and methane (CH4) at ambient conditions. In particular, we show at least four times higher sensitivity of an 860 MHz (4-μm periodicity) SAW reflective delay line coated with a 240 nm thick ZIF-8 compared to the sensitivity of a 430 MHz (8-μm periodicity) otherwise identical sensor device to the targeted gases. The detection limits of the higher frequency wireless devices for CO2 and CH4 were estimated to be 0.91 vol-% and 7.01 vol-%, respectively. The enhanced sensitivity for higher frequency devices is explained in terms of the frequency dependent acoustic wave energy confinement.

Devkota, Jagannath↗

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗

Techno-Economic Analysis of a Cryogenic Flux Capacitor for Grid Storage

Abstract The Cryogenic Flux Capacitor (CFC) is a cold, dense fluid storage core with integrated design features that afford the designer flexibility and provide new possibilities for the storage and discharge of energy. The stored energy, in this case, is represented by hydrogen physically bonded within the nanoscale pores within the aerogel composite blanket material, and the process of bonding or debonding is governed by principles of physical adsorption (physisorption) and thermodynamics. The large surface area afforded by the nanoporous aerogel (∼1,000 m2/g) allows for storage densities close to, or in some cases exceeding, that of normal boiling point liquids. Its performance easily exceeds what can be achieved via ambient temperature, high-pressure gas storage for an equivalent volume. CFC storage is predicted to be easily scalable, is constructed from readily available commercial materials, lends itself to a range of pressure applications, and is geometry insensitive. The high energy density of CFC-stored hydrogen allows long durations of storage, such as daily to monthly cycling, which corresponds to approximately 10 to 100 hours of duration, respectively. The techno-economic analysis examines different types of hydrogen storage for commercial viability. The assessment includes the use of hydrogen blended with natural gas in a combined cycle gas turbine. The study provides results for a range of blends from 100% natural gas to 100% hydrogen. The required fuel usages are estimated for the intended application in a grid scenario that features large amounts of renewable penetration, 10 hours, and as a baseload, 100 hours. The study presents preliminary estimates of the capital cost of storage and operating cost of storage. In addition, the cost of firing natural gas and capturing the carbon dioxide (CO2) in a carbon capture and sequestration (CCS) system is assessed. Based on the study, it is shown that CFC can competitively meet performance and cost needs for grid-based energy storage.

08 HYDROGEN↗

Techno-Economic Analysis of Green Hydrogen Energy Storage in a Cryogenic Flux Capacitor

Abstract The Cryogenic Flux Capacitor (CFC) is a cold, dense energy storage core that is being studied in the cryo-compressed, about 300 bar and 80K, region of gaseous hydrogen (GH2) storage and liquid hydrogen (LH2) region near the normal boiling point. Hydrogen storage is improved by physically bonding the molecules within the nanoscale pores of the aerogel composite blanket material. The process of bonding or debonding is governed by principles of physical adsorption (physisorption) and thermodynamics. The large surface area afforded by the nanoporous aerogel (∼1,000 m2/g) allows its storage performance to easily exceed capacities of high-pressure GH2 storage for an equivalent volume. With the integrated aerogel, subscale tests have shown that storage is increased by about 36% over a simple tank filled with GH2 at the same operating temperature and pressure. For LH2 conditions, the CFC is shown to operate at improved densities, but testing is ongoing. For the techno-economic analysis (TEA), the source of hydrogen is compared between onsite steam methane reforming (SMR) and onsite solar photovoltaic (PV) panels providing power to electrolyzers to produce green GH2. The TEA compares pure hydrogen produced at a small scale for a 25 MW power system and at a large scale in a 500 MW power system. The system allowed for hydrogen imports and exports at a set price with a tank sized for 10 hours of power production. The two power producing technologies are a combined cycle gas turbine (CCGT) and hydrogen fuel cells. The SMR system uses natural gas as an input and includes a carbon capture and storage (CCS) system. The levelized cost of electricity (LCOE), levelized cost of hydrogen (LCOH), and levelized cost of storage (LCOS) are developed based on the capital cost and operating cost of the systems. The results are shown for current costs using a 2021 benchmark and DOE projections for cost improvements by 2030. The TEA showed that onsite hydrogen generation from SMR has an LCOH of about 1.4 to 2 USD per kg over the life of the plant and the PV hydrogen production LCOH is about 5.2 to 5.5 USD per kg. The LCOS of conventional GH2 systems is estimated to be $210/MWh and cost of storage for LH2 systems is $205/MWh for fuel cell systems and $249/MWh for CCGT systems. CFC improved the LCOS of all these systems to $198/MWh, $191/MWh and $233/MWh respectively. The LCOE also improved with conventional systems between $171/MWh and $228/MWh improved by CFC to between $167/MWh and $212/MWh. Using projections for improvement in costs following DOE’s goals by 2030, green hydrogen improved to as low as $78/MWh LCOS and LCOE for conventional cases. CFC improved over conventional storage with the lowest LCOS being $62/MWh and the lowest LCOE being $73/MWh. These results correspond to an LCOH of $2/kg. Finally, the TEA shows how LCOE is improved for hydrogen conditioning and storage over conventional systems and caverns in the 10 to 50 hour range.

08 HYDROGEN↗

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗

Top-down design of protein architectures with reinforcement learning

As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a “top-down” reinforcement learning–based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo–electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design.

Science & Technology - Other Topics↗