BINA

Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges …

Transition metal phosphides (TMPs) are promising anode materials for sodium ion battery, thanks to their high theoretical specific capacities. Nevertheless, they suffer from large volume change and from poor conductivity during prolonged cycling. Here we systematically investigate the role of different kinds of single/multi‐wall carbon nanotubes (SWCNTs/MWCNTs) as additives in order to stabilize copper phosphide particles (CuP2) as anode materials in sodium ion batteries (SIBs). All composites show enhancement in the overall capacity and cycling stability compared to the pristine CuP2 due to the well‐connected CNTs on and between the CuP2 particles. At a high currency density of 1 A g−1, CuP2@SWCNTs composite with 13 wt.% SWCNTs can deliver a specific capacity over 400 mAh g−1 for more than 60 cycles, much better than conventional hard carbon materials. The CNTs enhance the …

Enhanced catalytic activity of oxygen evolution reaction (OER) catalysts is necessary to lower the cost of green hydrogen production. This study focuses on the use of a simple strategy of heat treatment to enhance the catalytic activity of NiFeOOH-based aerogels. The study shows that heat treatment of this aerogel at 150 °C leads to significant improvement in its catalytic activity, as evident in the staircase voltammetry results. To understand how heat treatment improves the catalytic activity, a DFT+U calculation was carried out on heat-treated and non-heat-treated catalysts. The calculation shows that the overpotential for OER decreases with heat treatment, which is related to the relative stability of the intermediates in heat-treated and non-heat-treated catalysts. Also, it has been found that heat treatment decreases work function, which might improve charge transfer and, thus, catalytic activity. Our calculations are in …

In the current work, we analyzed the origin of difference in stabilities among the germacrene A and hedycaryol-derived carbocations. This study focused on twelve hydrocarbons derived from germacrene A and twelve from hedycaryol, which can be divided into three groups: four molecules containing 6-6 bicyclic rings, four 5-7 bicyclic compounds with the carbocation being on the seven-membered ring and the remaining four 5-7 bicyclic compounds with the carbocation on the five-membered ring. The variations in energy within the groups of carbocations (ie, 6-6 and two kinds of 5-7 bicyclic carbocations) can be ascribed to intramolecular repulsion interactions, as seen from non-covalent interactions plots. Despite the structural similarities between germacrene A and hedycaryol cations, they possess a somewhat different stability trend. These differences are attributed to C+··· OH intramolecular interactions present in some hedycaryol cations, which are absent in the carbocations derived from germecrene A.

The COVID-19 pandemic highlighted the necessity of fast, sensitive, and efficient methods to test large populations for respiratory viruses. The “gold standard” molecular assays for detecting respiratory viruses, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), rely on invasive swab samples and require time-consuming and labor-intensive extraction processes. Moreover, the turnaround time for RT-qPCR-based assays is too lengthy for rapid screening. Extraction-free saliva-based methods provide a non-invasive sampling process with a fast turnaround time and are suitable for high-throughput applications. However, when used with a standard RT-qPCR system, the absence of extraction significantly reduces the assays’ sensitivity. Here, using a novel optical modulation biosensing (OMB) platform, we developed a rapid and highly sensitive extraction-free saliva …

Transition metal phosphides (TMPs) are promising anode materials for sodium ion battery, thanks to their high theoretical specific capacities. Nevertheless, they suffer from large volume change and from poor conductivity during prolonged cycling. Here we systematically investigate the role of different kinds of single/multi‐wall carbon nanotubes (SWCNTs/MWCNTs) as additives in order to stabilize copper phosphide particles (CuP2) as anode materials in sodium ion batteries (SIBs). All composites show enhancement in the overall capacity and cycling stability compared to the pristine CuP2 due to the well‐connected CNTs on and between the CuP2 particles. At a high currency density of 1 A g−1, CuP2@SWCNTs composite with 13 wt.% SWCNTs can deliver a specific capacity over 400 mAh g−1 for more than 60 cycles, much better than conventional hard carbon materials. The CNTs enhance the …

In recent years, steady progress has been made in synthesizing and characterizing engineered nanoparticles, resulting in several approved drugs and multiple promising candidates in clinical trials. Regulatory agencies such as the Food and Drug Administration and the European Medicines Agency released important guidance documents facilitating nanoparticle-based drug product development, particularly in the context of liposomes and lipid-based carriers. Even with the progress achieved, it is clear that many barriers must still be overcome to accelerate translation into the clinic. At the recent conference workshop “Mechanisms and Barriers in Nanomedicine” in May 2023 in Colorado, U.S.A., leading experts discussed the formulation, physiological, immunological, regulatory, clinical, and educational barriers. This position paper invites open, unrestricted, nonproprietary discussion among senior faculty, young …

The Kirkwood-Dirac quasiprobability distribution emerges from the quantum correlation function of two observables measured at distinct times and is therefore relevant for fundamental physics and quantum technologies. These quasiprobabilities follow all but one of Kolmogorov axioms for joint probability distributions: they can take non-positive values. Their experimental reconstruction becomes challenging when expectation values of incompatible observables are involved. Previous strategies aimed to reconstruct them using weak measurements or combining strong measurements. Here, we use a more direct approach, an interferometric scheme aided by an auxiliary system, to reconstruct the Kirkwood-Dirac quasiprobability distribution. We experimentally demonstrate the interferometric scheme in an electron-nuclear spin system associated with a nitrogen-vacancy center in diamond. By measuring the characteristic function, we reconstruct the quasiprobability distribution of the work and analyze the behavior of the first and second moments of work. Our results clarify the physical meaning of the work quasiprobability distribution in the context of quantum thermodynamics. Finally, having measured the real and imaginary parts of the Kirkwood-Dirac quasiprobability of work, we are also able to study the uncertainty of measuring the Hamiltonian of the system at two times, via the Robertson-Schr{\"o}dinger uncertainty relation, for different initial states.

Chiral induction of chiral crystals attracts significant attention due to its implications for developing chiral materials and understanding mechanisms of symmetry breaking enantioselective crystallization of naturally chiral inorganic crystals and their potential use in chiral discrimination, which are, however, largely unexplored. Here, we investigate the chiral induction during the crystallization of naturally chiral Ag2CO3 crystals using arginine amino acid as the chiral inducer. The chiral nature of Ag2CO3 was evaluated using various techniques. Chiral crystals exhibited chiral selective binding toward different amino acid enantiomers. The significant selectivity in adsorption was confirmed by circular dichroism, high-performance liquid chromatography, and isothermal titration calorimetry. Understanding chiral induction in crystal growth may open avenues for the controlled assembly of chiral materials and the development …

Carbonaceous materials are the most common catalyst supports in proton exchange membrane fuel cell (PEMFCs), yet their corrosion is one of the limiting factors in achieving high durability. Herein, we doped carbon supports with boron (B) to increase the corrosion-resistance of the support. Two types of B-doped carbons were synthesized and studied as platinum support materials. They varied in their morphologies, surface areas, and the types of boron species. The durability of Pt/B-doped carbon catalysts was investigated using the US-DOE catalysts’ supports accelerated stress test (AST) and a mass-spectrometer connected to the fuel cell effluent stream to quantify the mass of corroded carbon support in operando. The addition of boron to the carbon increased the stability of Pt catalysts in long-term usage of PEMFC. After 4,000 AST cycles, more than 50% of initial current density was preserved for the boron …

Magnetic field-induced changes in the electrical resistance of materials reveal insights into the fundamental properties governing their electronic and magnetic behavior. Various classes of magnetoresistance have been realized, including giant, colossal, and extraordinary magnetoresistance, each with distinct physical origins. In recent years, extreme magnetoresistance (XMR) has been observed in topological and non-topological materials displaying a non-saturating magnetoresistance reaching 103−108% in magnetic fields up to 60 T. XMR is often intimately linked to a gapless band structure with steep bands and charge compensation. Here, we show that a linear XMR of 80,000% at 15 T and 2 K emerges at the high-mobility interface between the large band-gap oxides γ-Al2O3 and SrTiO3. Despite the chemically and electronically very dissimilar environment, the temperature/field phase diagrams of γ-Al2O …

Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency …

Magnetic sensors based on the planar Hall effect (PHE) are attractive for applications where sub nano-Tesla field resolution is required. Here we present detailed noise study of PHE sensors made of two crossing masnetic ellipses that measure two axes of the magnetic field in the sensor plane with equivalent magnetic noise level better than 350 at 10 Hz in exactly the same region while keeping the size and noise level of a single axis sensor.

We showcase the application of a 2-dimensional detector for observing energy and momentum-correlated x-ray pairs. This detector introduces novel possibilities for applications in quantum x-ray optics.

The Adaptive Immune Receptor Repertoire Knowledge Commons (AKC) is a publicly accessible repository of data and knowledge about 1) adaptive immune receptors (AIRs) and AIR repertoires, 2) the complex genomic loci encoding AIR genes, and 3) the antigens and epitopes bound by AIR. It empowers research questions that require the integration of data across these three domains to evaluate their interplay and relative contributions across a broad range of health and disease states. The AKC is being established by merging data from existing, community-backed repositories and applying existing and novel, cross-cutting knowledge-generation algorithms to the integrated data. The AKC currently includes 1) data from the AIRR Data Commons, which contains~ 10,000 repertoires with billions of AIRs, integrated with 2) AIR germline allele, genotype, haplotype, and population genetic data from the OGRDB and …

Several decades after the invention of the flow Zn-Br2 systems persistent attempts have been made to develop stationary Zn-Br2 batteries. Such development should increase the energy density of the system simultaneously significantly reducing their cost and opening new challenges associated with the cell design and its performance. One of the major concerns is the rapid self-discharge of stationary systems leading to spontaneous charge loss during battery storage time. While self-discharge in flow cells is generally attributed to the chemical oxidation of the Zn anode, we show that the origin of self-discharge in a static configuration is completely different. By systematic investigations of activated carbon with different surface areas under varied charging conditions, mechanistic insights into this phenomenon were provided. Based on this understanding, we proposed herein an effective way to suppress the cathode …

Recent advancements in thin-film lithium niobate (TFLN) photonics have led to a new generation of high-performance electro-optic devices, including modulators, frequency combs, and microwave-to-optical transducers. However, the broader adoption of TFLN-based devices that rely on all-optical nonlinearities have been limited by the sensitivity of quasi-phase matching (QPM), realized via ferroelectric poling, to fabrication tolerances. Here, we propose a scalable fabrication process aimed at improving the wavelength-accuracy of optical frequency mixers in TFLN. In contrast to the conventional pole-before-etch approach, we first define the waveguide in TFLN and then perform ferroelectric poling. This sequence allows for precise metrology before and after waveguide definition to fully capture the geometry imperfections. Systematic errors can also be calibrated by measuring a subset of devices to fine-tune the QPM design for remaining devices on the wafer. Using this method, we fabricated a large number of second harmonic generation devices aimed at generating 737 nm light, with 73% operating within 5 nm of the target wavelength. Furthermore, we also demonstrate thermo-optic tuning and trimming of the devices via cladding deposition, with the former bringing ~96% of tested devices to the target wavelength. Our technique enables the rapid growth of integrated quantum frequency converters, photon pair sources, and optical parametric amplifiers, thus facilitating the integration of TFLN-based nonlinear frequency mixers into more complex and functional photonic systems.

The Anderson localization transition in quantum graphs has garnered significant recent attention due to its relevance to many-body localization studies. Typically, graphs are constructed using top-down methods. Here, we explore a bottom-up approach, employing a simple local rewriting rule to construct the graph. Through the use of ratio statistics for the energy spectrum and Kullback-Leibler divergence correlations for the eigenstates, numerical analysis demonstrates that slight adjustments to the rewriting rule can induce a transition from a localized to an extended quantum phase. This extended state exhibits non-ergodic behavior, akin to the non-ergodic extended phase observed in the Porter-Rosenzweig model and suggested for many-body localization. Thus, by adapting straightforward local rewriting rules, it becomes feasible to assemble complex graphs from which desired global quantum phases emerge. This approach holds promise for numerical investigations and could be implemented in building optical realizations of complex networks using optical fibers and beam splitters.

Nuclear forward scattering (NFS) is a synchrotron-based technique relying on the recoil-free nuclear resonance effect similar to Mössbauer spectroscopy. In this work, we introduce NFS for in situ and operando measurements during electrocatalytic reactions. The technique enables faster data acquisition and better discrimination of certain iron sites in comparison to Mössbauer spectroscopy. It is directly accessible at various synchrotrons to a broad community of researchers and is applicable to multiple metal isotopes. We demonstrate the power of this technique with the hydrogen evolution mechanism of an immobilized iron porphyrin supported on carbon. Such catalysts are often considered as model systems for iron–nitrogen-carbon (FeNC) catalysts. Using in situ and operando NFS in combination with theoretical predictions of spectroscopic data enables the identification of the intermediate that is formed prior …