BINA

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters─Ser8(Cl–)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl–. For the latter of these clusters, the correct …

Acoustic-directed assembly is a modular and flexible bottom-up technique with the potential to pattern a wide range of materials. Standing acoustic waves have been previously employed for patterning preformed metal particles, however, direct patterning of metallic structures from precursors remains unexplored. Here, we investigate utilization of standing waves to exert control over chemical reaction products, while also exploring their potential in the formation of multi-layered and composite micro-structures. Periodic metallic micro-structures were formed in a single step, simplifying microstructure fabrication. Concentric structures were obtained by introducing a metal precursor salt and a reducing agent into a cylindrical piezoelectric resonator that also served as a reservoir. In addition, we introduce an innovative approach to directly fabricate metallic multi-layer and composite structures by reducing different metal ions or adding nanoparticles during the reduction step. Fewer steps are needed, compared with other methods, and there is no need to stabilize the nanoparticles or to ensure chemical affinity between the metallic matrix and inorganic nanoparticles. This innovative approach is promising for production of complex microstructures with enhanced functionality and controlled properties.

The state‐of‐the‐art Platinum group metal (PGM)‐free oxygen reduction reaction (ORR) catalysts have been synthesized using the pyrolysis of iron, nitrogen, and carbon precursors, and result in highly active ORR catalysts, but their undefined structure limits their further development. Since the inspiration for these catalysts came from well‐defined structures of transition metal complexes, it is important to understand the various parameters that govern the reaction potential, selectivity, and the stability with well‐defined catalysts and try to extrapolate them to the pyrolyzed catalysts. In this chapter, we give an overview of the parameters that influence the catalysis of ORR with well‐defined ORR catalysts. These can later be used to further enhance the performance of the state‐of‐the‐art PGM‐free ORR catalysts.

In article number 2200029, Vasily Astratov and colleagues representing 27 research teams worldwide created a roadmap on label-free super-resolution imaging. Its scope spans from diffraction-limited interference detection techniques to methods allowing to overcome classical diffraction limit without using fluorescent markers, which are based on information science; structured illumination; near-field, nonlinear, and transformation optics; and advanced superlens designs. Cover images are provided by Aydogan Ozcan and Nikolay Zheludev participating in this Roadmap.

Millions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: −26 nt for ADAR2 and −35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2 …

Surface characterization is essential for understanding chemical and electrochemical transformations occurring on surfaces or at interfaces. Battery electrode aging processes, biofilm growth, crystallization, and transport/signaling across cellular membranes are only a few examples of such phenomena. This special issue delves into applied electrochemistry and nonlinear optical techniques applicable to surface characterization.

This paper revisits the geometric foundations of electromagnetic theory, by studying Faraday's concept of field lines. We introduce "covariant electromagnetic field lines," a novel construct that extends traditional field line concepts to a covariant framework. Our work includes the derivation of a closed-form formula for the field line curvature in proximity to a moving electric charge, showcasing the curvature is always non-singular, including nearby a point charge. Our geometric framework leads to a geometric derivation of the Lorentz force equation and its first-order corrections, circumventing the challenges of self-force singularities and providing insights into the problem of radiation-reaction. This study not only provides a fresh geometric perspective on electromagnetic field lines but also opens avenues for future research in fields like quantum electrodynamics, gravitational field theory, and beyond.

The ability to control neuronal mobility and organization is of great importance in developing neuronal interfaces and novel therapeutic approaches. An emerging promising method is the manipulation of neuronal cells from afar via magnetic forces. Nevertheless, using magnetic iron oxide nanoparticles as internal actuators may lead to biotoxicity, adverse influence on intracellular processes, and thus requires prerequisite considerations for therapeutic approaches. Magnetizing the cells via the incorporation of magnetic particles that can be applied extracellularly is advantageous. Herein, we have developed a magnetic system based on streptavidin–biotin interaction to decorate cellular membrane with magnetic elements. In this model, superparamagnetic microparticles, coated with streptavidin, were specifically bound to biotinylated PC12 cells. We demonstrated that cell movement can be directed remotely by the forces produced by pre-designed magnetic fields. First, using time lapse imaging, we analyzed the kinetics of cell migration towards the higher flux zone. Next, to form organized networks of cells we designed and fabricated micro-patterned magnetic devices. The fabricated devices were composed of a variety of ferromagnetic shapes, sputter-deposited onto glass substrates. Cells that were conjugated to the magnetic particles were plated atop the micro-patterned substrates, attracted to the magnetic actuators and became fixed onto the magnetic patterns. In all, our study presents a novel system based on a well-known molecular technology combined with nanotechnology that may well lead to the expansion of implantable magnetic …

Tissue-integrated micro-electronic devices for neural stimulation hold great potential in restoring the functionality of degenerated organs, specifically, retinal prostheses, which are aimed at vision restoration. The fabrication process of 3D polymer-metal devices with high resolution and a high aspect-ratio (AR) is very complex and faces many challenges that impair its functionality. Here we describe the optimization of the fabrication process of a bio-functionalized 3D high-resolution 1mm circular subretinal implant composed of SU-8 polymer integrated with dense gold microelectrodes (23μm pitch) passivated with 3D micro-well-like structures (20μm diameter, 3μm resolution). The main challenges were overcome by step-by-step planning and optimization while utilizing a two-step bi-layer lift-off process; bio-functionalization was carried out by N2 plasma treatment and the addition of a bio-adhesion molecule. In-vitro and in-vivo investigations, including SEM and FIB cross section examinations, revealed a good structural design, as well as a good long-term integration of the device in the rat sub-retinal space and cell migration into the wells. Moreover, the feasibility of subretinal neural stimulation using the fabricated device was demonstrated in-vitro by electrical activation of rat’s retina. The reported process and optimization steps described here in detail can aid in designing and fabricating retinal prosthetic devices or similar neural implants.

The process of aging refers to physiological changes that occur to an organism as time progresses and involves changes to DNA, proteins, metabolism, cells, and organs. Like the rest of the cells in the body, gametes age, and it is well established that there is a decline in reproductive capabilities in females and males with aging. One of the major pathways known to be involved in aging is epigenetic changes. The epigenome is the multitude of chemical modifications performed on DNA and chromatin that affect the ability of chromatin to be transcribed. In this review, we explore the effects of aging on female and male gametes with a focus on the epigenetic changes that occur in gametes throughout aging. Quality decline in oocytes occurs at a relatively early age. Epigenetic changes constitute an important part of oocyte aging. DNA methylation is reduced with age, along with reduced expression of DNA …

Maintaining protein homeostasis is critical for cellular function, as disruptions can result in accumulation of misfolded proteins associated with various diseases. RNA editing, particularly deamination by base-editing enzymes like ADAR, can modify the transcriptome, potentially influencing amino acid sequences and protein diversity. We hypothesize that irregular RNA editing, leading to a more complex proteome, may generate defective proteins, triggering cellular toxicity. Using an editing-naïve yeast system expressing a robust ADAR enzyme, we demonstrated that extensive RNA editing results in non-synonymous protein changes, correlated with increased protein ubiquitination and reliance on quality control pathways. This suggests that extensive editing in yeast produces abnormal proteins prone to misfolding and degradation. While mouse and human genomes are well-adapted to the ADAR enzymes, introduction of base editors into human cells is found to increase activity in proteotoxic-stress-related pathways due to off-target editing. Signs of proteotoxic stress are also observed in human samples exhibiting elevated activity of endogenous ADARs. These findings emphasize the detrimental impact of dysregulated RNA editing on protein balance and suggest a potential role for aberrant editing in disease onset and progression.

The state‐of‐the‐art Platinum group metal (PGM)‐free oxygen reduction reaction (ORR) catalysts have been synthesized using the pyrolysis of iron, nitrogen, and carbon precursors, and result in highly active ORR catalysts, but their undefined structure limits their further development. Since the inspiration for these catalysts came from well‐defined structures of transition metal complexes, it is important to understand the various parameters that govern the reaction potential, selectivity, and the stability with well‐defined catalysts and try to extrapolate them to the pyrolyzed catalysts. In this chapter, we give an overview of the parameters that influence the catalysis of ORR with well‐defined ORR catalysts. These can later be used to further enhance the performance of the state‐of‐the‐art PGM‐free ORR catalysts.

X ray fluorescence ghost imaging (XRF-GI) was recently demonstrated for x ray lab sources. It has the potential to reduce the acquisition time and deposited dose by choosing their trade-off with a spatial resolution while alleviating the focusing constraints of the probing beam. Here, we demonstrate the realization of synchrotron-based XRF-GI: we present both an adapted experimental setup and its corresponding required computational technique to process the data. This extends the above-mentioned potential advantages of GI to synchrotron XRF imaging. In addition, it enables new strategies to improve resilience against drifts at all scales and the study of previously inaccessible samples, such as liquids.

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters─Ser8(Cl–)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl–. For the latter of these clusters, the correct …

Iron–nitrogen–carbon (FeNC) catalysts are a viable alternative to platinum, but still lack the necessary performance. Now, pyrolysis under forming gas is found as a path to boosting their site density, activity and durability.

Imaging speed and spatial resolution are key factors in optical diffraction tomography (ODT), while they are mutually exclusive in 3D refractive index imaging. This paper presents a multi-harmonic structured illumination-based optical diffraction tomography (MHSI-ODT) to acquire 3D refractive index (RI) maps of transparent samples. MHSI-ODT utilizes a digital micromirror device (DMD) to generate structured illumination containing multiple harmonics. For each structured illumination orientation, four spherical spectral crowns are solved from five phase-shifted holograms, meaning that the acquisition of each spectral crown costs 1.25 raw images. Compared to conventional SI-ODT, which retrieves two spectral crowns from three phase-shifted raw images, MHSI-ODT enhances the imaging speed by 16.7% in 3D RI imaging. Meanwhile, MHSI-ODT exploits both the 1st-order and the 2nd-order harmonics; therefore, it …

The seawater electrolysis is an economically favorable approach for water splitting application because seawater is one of the plentiful abundant natural resources on our earth. In water splitting pathway, the anodic half-cell reaction from seawater stills a challenging task due to anodic corrosion and the competitive chloride oxidation process. In the current study, we prepared flower-shaped porous nanorods of iron doped cobalt nickel layered double hydroxide supported on nickel foam (Fe0.05 CoNi LDH/NF), which require very less oxygen evolution reaction (OER) overpotential in 1M KOH (212mV) and alkaline seawater (287mV) to deliver 10 mAcm−2 current density and exhibited remarkable 14h durability. At the same time, post treated sample reveals the better OER activity after chronopotentiometry analysis, because of superior conductivity and corrosion-resistance of the electrocatalyst. The doping of Fe cation …

Atopic dermatitis (AD) is associated with dysregulated type 1 interferon (IFN)–mediated responses, in parallel with the dominant type 2 inflammation. However, the pathophysiology of this dysregulation is largely unknown. Adenosine-to-inosine (A-to-I) RNA editing plays a critical role in immune regulation by preventing double-stranded (ds) RNA recognition by MDA5 and IFN activation. We studied global A-to-I editing in AD in order to elucidate the role played by altered editing in the pathophysiology of this disease.Analysis of three RNA sequencing (RNA-seq) datasets of AD skin samples revealed reduced levels of A-to-I RNA editing in AD. This reduction was seen globally throughout Alu repeats, as well as in coding genes and in specific pre-mRNA loci expected to create long dsRNA, the main substrate of MDA5 leading to type I IFN activation. Consistently, IFN signature genes (ISG) were upregulated. In contrast …

Recent studies have underscored the pivotal role of adenosine-to-inosine RNA editing, catalyzed by ADAR1, in suppressing innate immune interferon responses triggered by cellular double-stranded RNA (dsRNA). However, the specific ADAR1 editing targets crucial for this regulatory function remain elusive. We review analyses of transcriptome-wide ADAR1 editing patterns and their evolutionary dynamics, which offer valuable insights into this unresolved query. The growing appreciation of the significance of immunogenic dsRNAs and their editing in inflammatory and autoimmune diseases and cancer calls for a more comprehensive understanding of dsRNA immunogenicity, which may promote our understanding of these diseases and open doors to therapeutic avenues.