Losses in plasmonics: from mitigating energy dissipation to embracing loss-enabled functionalities
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Boriskina, Svetlana V. (ORCID:0000000167988082)↗
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Light-Driven C(sp 3 )–C(sp 3 ) Bond Functionalizations Enabled by the PCET Activation of Alcohol O–H Bonds
Methods that enable the selective functionalization of C–C bonds offer unique opportunities for the skeletal diversification of complex molecules and provide access to unique structures without the need for de novo synthesis. While considerable advances have been made in transition-metal-based approaches, much recent work has focused on alternative strategies for C–C bond cleavage enabled by transient free radicals. In particular, alkoxy radicals derived from simple alcohols are known to significantly destabilize adjacent C–C bonds, enabling spontaneous cleavage to eject a carbon-centered radical and afford carbonyl products via β-fragmentation. Here, while this reactivity has long been recognized, its applications in synthesis have been limited, in part, by the challenges associated with generating the key alkoxy radical intermediates.
Alcohols↗
Differential programming enabled functional imaging with Lorentz transmission electron microscopy
Abstract Lorentz transmission electron microscopy is an advanced characterization technique that enables the simultaneous imaging of both the microstructure and functional properties of materials. Information such as magnetization and electric potentials is carried by the phase of the electron wave, and is lost during image acquisition. Various methods have been proposed to retrieve the phase of the electron wavefunction using intensities of the acquired images, most of which work only in the small defocus limit. Imaging at strong defoci not only carries more quantitative phase information, but is essential to the study of weak magnetic and electrostatic fields at the nanoscale. In this work we develop a method based on differentiable programming to solve the inverse problem of phase retrieval. We show that our method maintains a high spatial resolution and robustness against noise even at the upper defocus limit of the microscope. More importantly, our proposed method can go beyond recovering just the phase information. We demonstrate this by retrieving the electron-optical parameters of the contrast transfer function alongside the electron exit wavefunction.
97 MATHEMATICS AND COMPUTING↗
Leveraging Sequential Doping of Semiconducting Polymers to Enable Functionally Graded Materials for Organic Thermoelectrics
With the ability to modulate electronic properties through molecular doping coupled with ease in processability, semiconducting polymers are at the forefront in enabling organic thermoelectric devices for thermal energy management. In contrast to uniform thermoelectric material properties, an alternative route focuses on functionally graded materials (FGMs) where one spatially controls and optimizes transport properties across the length of a thermoelectric material. While primarily studied in the context of inorganic materials, the concept of FGMs for organic thermoelectrics has not been explored. Herein, we introduce how molecular doping of semiconducting polymers enables spatial compositional control of thin-film FGMs. Specifically, we utilize sequential vapor doping of poly[2,5-bis(3-tetradecylthiophen-2-yl) thieno [3,2-b]thiophene] (PBTTT) with the small molecule acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) to fabricate the simplest form of FGMs – double- segmented thin films. The two thin-film segments are of equal length (7.5 mm), but each set to different doping levels. Our study focuses on understanding the thermoelectric properties (Seebeck coefficient, α, and electronic conductivity, σ) and structural properties (through X-ray scattering, UV-vis-NIR spectroscopy, and Raman spectroscopy) within and across the two segments. We observe the presence of a small diffuse interfacial region of 0.5 – 1 mm between the two segments where the doping level and transport properties vary continuously. Despite the diffuse interface, the measured effective Seebeck coefficient (αeff) across the two segments is simply the average of α within each segment. Importantly, this experimental result is consistent with reported mathematical models describing αeff in graded thermoelectric materials. Finally, our results demonstrate the facile fabrication and characterization of functionally graded organic thermoelectric materials, providing guidelines for further development on more complex FGMs.
36 MATERIALS SCIENCE↗
The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species
Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources.
97 MATHEMATICS AND COMPUTING↗
Nanowire Array Structures for Photocatalytic Energy Conversion and Utilization: A Review of Design Concepts, Assembly and Integration, and Function Enabling
The increasing human demand for clean and renewable energy and a cleaner environment has stimulated various materials related research and development for efficient solar energy conversion and utilization, photocatalytic environmental remediation, and photoassisted selective conversion of organic compounds. Among the various candidate solutions to improving the efficiency of these processes, semiconductor nanowire (NW) and nanorod (NR) array structures have been offering a unique tool box combining desirable characteristics in structure, function, and applicability. Efficient photocatalytic energy conversion requires excellent light absorption, readily charge separation, transport, and collection, as well as fast kinetics of interfacial reactions and mass transport of reactants. The long axis of the NW enables adequate light absorption, while the radical axis provides short electron–hole separation distance. Additionally, the NW arrays have relatively high surface area to facilitate interfacial kinetics while their open pore structure allows good mass transport properties. This study reviews the current status of research on NW and NR array structures of some most popular semiconducting materials for photocatalytic energy conversion and utilization including photocatalytic water splitting and CO 2 reduction/fixation, dye/quantum dot sensitized solar cells, and other photoassisted reactive applications such as pollutant degradation, selective conversion of organic compounds, and biological disinfection.
Hoang, Son↗
Colloidal Gelation in Liquid Metals Enables Functional Nanocomposites of 2D Metal Carbides (MXenes) and Lightweight Metals
Nanomaterials dispersed in different media, such as liquids or polymers, generate a variety of functional composites with synergistic properties. In this work, we discuss liquid metals as the nanomaterials' dispersion media. For example, 2D transition-metal carbides and nitrides (MXenes) can be efficiently dispersed in liquid Ga and lightweight alloys of Al, Mg, and Li. We show that the Lifshitz theory predicts strong van der Waals attraction between nanoscale objects interacting through liquid metals. However, a uniform distribution of MXenes in liquid metals can be achieved through colloidal gelation, where particles form self-supporting networks stable against macroscopic phase segregation. This network acts as a reinforcement boosting mechanical properties of the resulting metal-matrix composite. By choosing Mg-Li alloy as an example of ultralightweight metal matrix and Ti 3 C 2 T x MXene as a nanoscale reinforcement, we apply a liquid metal gelation technique to fabricate functional nanocomposites with an up to 57% increase in the specific yield strength without compromising the matrix alloy's plasticity. MXenes largely retain their phase and 2D morphology after processing in liquid Mg-Li alloy at 700 degrees C. The 2D morphology enables formation of a strong semicoherent interface between MXene and metal matrix, manifested by biaxial strain of the MXene lattice inside the metal matrix. Finally, this work expands applications for MXenes and shows the potential for developing MXene-reinforced metal matrix composites for structural alloys and other emerging applications with metal-MXene interfaces, such as batteries and supercapacitors.
36 MATERIALS SCIENCE↗
Monolayer Molecular Functionalization Enabled by Acid–Base Interaction for High-Performance Photochemical CO 2 Reduction
We report the development of a hybrid catalyst consisting of carbon nitride (CN x ) and cobalt phthalocyanine tetracarboxylic acid (CoPc-COOH), which converts CO 2 to CO with high reaction rate (1067 μmol/g·h) and high selectivity (over 98%), under simulated solar irradiation. The carboxylic acid substituents on the phthalocyanine ligands play a critical role as they bind to the amine groups of CN x to enable nearly ideal monolayer coverage of the molecular co-catalyst on the semiconductor surface and promote catalytic activity from the molecular complex. Specifically, the CN x /CoPc-COOH hybrid material achieves a reaction rate 16 times higher than a CN x material containing unsubstituted CoPc molecules. We further show that activation and deactivation of the CN x /CoPc-COOH composite, which are associated with the reduction and decomposition of CoPc-COOH, respectively, both proceed at a nearly constant rate regardless of the CO 2 reduction reaction rate. Here, the decoupling of charge carrier injection and CO 2 reduction catalysis has important mechanistic implications for future performance optimization and materials design of photocatalysts for CO 2 reduction.
14 SOLAR ENERGY↗
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d
Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.
59 BASIC BIOLOGICAL SCIENCES↗
Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy
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Autophagy↗
Automated Detection of Qubit Structures on Quantum Chips
In this study, YOLO (You Only Look Once), a well-known object detection and image segmentation model, is used to detect qubits on a quantum chip. The model is trained by exposing it to various images of objects of interest and by tweaking various training parameters to allow the model to learn from a limited and highly specialized dataset of SEM imagery. The model was provided with numerous images of qubits and various prominent features of note located on a qubit. These detections were then integrated into a simple GUI, allowing for real-time feedback alongside SEM usage. This will allow us to create various functions enabling automated functions like chip-wide scanning, auto-focusing, and image correction.
Perjuste, Ruth [Wellesley Coll.]↗
Function-based Taxonomy Implementation
Function-based taxonomies are relational mapping tools used to clearly illustrate how an organization delivers Critical Functions by using various people, processes, technologies, information, and infrastructure (PPTII). Critical Functions are the actions or activities that make up the organization’s primary purpose. Enabling Functions are the combination of PPTII used by the organization to deliver their Critical Functions. A function-based taxonomy provides a framework to categorize information and related artifacts that document an organization’s unique implementation of PPTII for Critical Function delivery. The ideal state of a function-based taxonomy is to organize the existing knowledge the organization already has throughout their numerous systems, policies, people, procedures, and configurations. A well-organized taxonomy helps organizations to effectively leverage their knowledge by clearly identifying dependencies and connections. This document is the result of combined engineering and analytical experience and describes a repeatable method for producing function-based taxonomies.
42 ENGINEERING↗
Petascale Orbital-Free Density Functional Theory Enabled by Small-Box Algorithms
Orbital-free density functional theory (OFDFT) is a quantum-mechanics-based method that utilizes electron density as its sole variable. The main computational cost in OFDFT is the ubiquitous use of the fast Fourier transform (FFT), which is mainly adopted to evaluate the kinetic energy density functional (KEDF) and electron–electron Coulomb interaction terms. We design and implement a small-box FFT (SBFFT) algorithm to overcome the parallelization limitations of conventional FFT algorithms. We also propose real-space truncation of the nonlocal Wang–Teter KEDF kernel. The scalability of the SBFFT is demonstrated by efficiently simulating one full optimization step (electron density, energies, forces, and stresses) of 1,024,000 lithium (Li) atoms on up to 65,536 cores. We perform other tests using Li as a test material, including calculations of physical properties of different phases of bulk Li, geometry optimizations of nanocrystalline Li, and molecular dynamics simulations of liquid Li. All of the tests yield excellent agreement with the original OFDFT results, suggesting that the OFDFT-SBFFT algorithm opens the door to efficient first-principles simulations of materials containing millions of atoms.
Chemistry↗
How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties
Background. Much of the structure-based mechanistic understandings of the function of SLC6A neurotransmitter transporters emerged from the study of their bacterial LeuT-fold homologs. It has become evident, however, that structural differences such as the long N- and C-termini of the eukaryotic neurotransmitter transporters are involved in an expanded set of functional properties to the eukaryotic transporters. These functional properties are not shared by the bacterial homologs, which lack the structural elements that appeared later in evolution. However, mechanistic insights into some of the measured functional properties of the eukaryotic transporters that have been suggested to involve these structural elements are sparse or merely descriptive. Results. To learn how the structural elements added in evolution enable mechanisms of the eukaryotic transporters in ways not shared with their bacterial LeuT-like homologs, we focused on the human dopamine transporter (hDAT) as a prototype. We present the results of a study employing large-scale molecular dynamics simulations and comparative Markov state model analysis of experimentally determined properties of the wild-type and mutant hDAT constructs. These offer a quantitative outline of mechanisms in which a rich spectrum of interactions of the hDAT N-terminus and C-terminus contribute to the regulation of transporter function (e.g., by phosphorylation) and/or to entirely new phenotypes (e.g., reverse uptake (efflux)) that were added in evolution. Conclusions. The findings are consistent with the proposal that the size of eukaryotic neurotransmitter transporter termini increased during evolution to enable more functions (e.g., efflux) not shared with the bacterial homologs. The mechanistic explanations for the experimental findings about the modulation of function in DAT, the serotonin transporter, and other eukaryotic transporters reveal separate roles for the distal and proximal segments of the much larger N-terminus in eukaryotic transporters compared to the bacterial ones. The involvement of the proximal and distal segments — such as the role of the proximal segment in sustaining transport in phosphatidylinositol 4,5-bisphosphate-depleted membranes and of the distal segment in modulating efflux — may represent an evolutionary adaptation required for the function of eukaryotic transporters expressed in various cell types of the same organism that differ in the lipid composition and protein complement of their membrane environment.
59 BASIC BIOLOGICAL SCIENCES↗
Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica
Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.
59 BASIC BIOLOGICAL SCIENCES↗
Carboxyl-functionalized perovskite enables ALD growth of a compact and uniform ion migration barrier
Mixed-halide wide-band-gap perovskites are critical components of highly efficient tandem cells, but their operating stability is limited by halide migration. Metal oxides deposited via atomic layer deposition (ALD) have been shown to block halide migration; however, previously pursued methods result in inhomogeneous nucleation and growth. We hypothesized that functionalizing the perovskite surface with ALD-active carboxyl groups could promote nucleation and enable higher-temperature metal oxide growth. We find that 5-ammonium valeric acid iodide (5-AVAI) facilitates the formation of a compact and uniform aluminum oxide (Al 2 O 3 ) layer and allows growth at 100°C compared with the previous limit of 75°C. We demonstrate that halide migration into the C 60 electron transport layer is reduced by a factor of 10 compared with the reference case. Finally, Al 2 O 3 -capped perovskite solar cells with a band gap of 1.78 eV retain 90% of their initial power conversion efficiency after 1,000 h of continuous operation under 1-sun illumination at 55°C.
Al2O3↗
Virus-induced gene editing of stomatal regulators in Nicotiana benthamiana enables rapid functional genomics
Virus-induced gene editing (VIGE) holds promise as a rapid and scalable approach for functional genomics in plants. Here, we apply a tobacco rattle virus (TRV)-based single-guide RNA (sgRNA) delivery system to target key regulators of stomatal development in Nicotiana benthamiana using transgenic Cas9-expressing lines. sgRNAs fused to a mobile RNA element and co-delivered with TRV enabled both somatic and heritable genome editing across orthologs of STOMAGEN, EPF2, YODA, and SPEECHLESS. Somatic editing frequencies reached up to 95%, and heritable tetra-allelic mutations were recovered in multiple target genes. Mutants exhibited significant, gene-specific changes in stomatal density, with corresponding effects on leaf temperature indicative of altered evaporative cooling. Additionally, sgRNAs fused to an AmCyan reporter enabled visualization of virus-infected tissues, allowing stomatal phenotyping in edited M0 sectors. This TRV-based platform facilitates functional assessment of genes influencing stomatal patterning and offers a powerful tool for dissecting gene function in a developmentally and physiologically relevant context.
60 APPLIED LIFE SCIENCES↗