Metal-water interface formation: Thermodynamics from ab initio molecular dynamics simulations.

Metal-water interfaces are central to many electrochemical, (electro)catalytic, and materials science processes and systems. However, our current understanding of their thermodynamic properties is limited by the scarcity of accurate experimental and computational data and procedures. In this work, thermodynamic quantities for metal-water interface formation are computed for a range of FCC(111) surfaces (Pd, Pt, Au, Ag, Rh, and PdAu) through extensive density functional theory based molecular dynamics and the two-phase entropy model.

Unbiased plasma profiling using pre-selected RNA aptamer pools predicts mortality in COVID-19 and identifies protein risk factors.

The impact of the COVID-19 pandemic demands effective prognostic tools for precise risk evaluation and timely intervention. This study utilized the APTASHAPE technology to profile plasma proteins in COVID-19 patient samples. Employing a highly diverse 2'-fluoro-protected RNA aptamer pool enriched toward proteins in the plasma samples from COVID-19 patients, we performed a single round of parallel selection on the derivation cohort and identified 93 discriminatory aptamers capable of distinguishing COVID-19 and healthy plasma samples.

MicroRNAs as Bile-based biomarkers in pancreaticobiliary cancers (MIRABILE): a cohort study.

Background: Biliary obstruction can be due to both malignant and benign pancreaticobiliary disease. Currently, there are no biomarkers that can accurately help make this distinction. MicroRNAs (miRNAs) are stable molecules in tissue and biofluids that are commonly deregulated in cancer.

circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.

Circular RNAs represent a class of endogenous RNAs that regulate gene expression and influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Using time-course depletion of circHIPK3 and specific candidate RNA-binding proteins, we identify several perturbed genes by RNA sequencing analyses.

Do All Paths Lead to Rome? How Reliable is Umbrella Sampling Along a Single Path?

Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free energies of protein-ligand and protein-protein complexes. A routinely used method for binding free energy calculations with MD is umbrella sampling (US), which calculates the potential of mean force (PMF) along a single reaction coordinate. Surprisingly, in spite of its widespread use, few validation studies have focused on the convergence of the free energy computed along a single path for specific cases, not addressing the reproducibility of such calculations in general.

Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application.

Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules.

Aliphatic Ketone Claisen Rearrangement: Troubleshooting the Transetherification Step by Identifying a Stable Acid Catalyst.

After optimization for retention of catalytic activity, 4-chlorobenzoic acid emerged as the optimal catalyst for the aliphatic ketone Claisen rearrangement. The optimal catalyst enables a one-pot, metal-free, catalytic protocol from allylic alcohols to γ,δ-unsaturated ketones. The optimized process tolerates a range of substrates, including substituents with acid-labile protecting groups.

Insights into the nucleation and growth of BiOCl nanoparticles by X-ray pair distribution function analysis and liquid cell TEM.

The synthesis of bismuth oxyhalides as defined nanostructures is hindered by their fast nucleation and growth in aqueous solutions. Using our recently developed single-source precursor, the formation of bismuth oxychloride in such solutions can be slowed significantly. As reported herein, this advance enables BiOCl formation to be investigated by X-ray total scattering and liquid cell transmission electron microscopy.

Advances in block copolymer-phospholipid hybrid vesicles: from physical-chemical properties to applications.

Hybrid vesicles, made of lipids and amphiphilic block copolymers, have become increasingly popular thanks to their versatile properties that enable the construction of intricate membranes mimicking cellular structures. This tutorial review gives an overview over the different hybrid vesicle designs, and provides a detailed analysis of their properties, including their composition, membrane fluidity, membrane homogeneity, permeability, stability. The review puts emphasis on the application of these hybrid vesicles in bottom-up synthetic biology and aims to offer an overview of design guidelines, particularly focusing on composition, to eventually realize the intended applications of these hybrid vesicles.

Impact of MoS Monolayers on the Thermoelastic Response of Silicon Heterostructures.

Understanding the thermoelastic response of a nanostructure is crucial for the choice of materials and interfaces in electronic devices with improved and tailored transport properties at the nanoscale. Here, we show how the deposition of a MoS monolayer can strongly modify the nanoscale thermoelastic dynamics of silicon substrates close to their interface. We demonstrate this by creating a transient grating with extreme ultraviolet light, using ultrashort free-electron laser pulses, whose ≈84 nm period is comparable to the size of elements typically used in nanodevices, such as electric contacts and nanowires.

Metal-ligand bond in group-11 complexes and nanoclusters.

Density functional theory is used to study geometric, energetic, and electronic properties of metal-ligand bonds in a series of group-11 metal complexes and ligand-protected metal clusters. We study complexes as the forms of M-L (L = SCH, SCH, PPh, NHC, NHC, NHC, NHC, CCMe, CCPh) and L-M-L (L = NHC, PPh, and L = CCPh). Furthermore, we study clusters denoted as [MLBr] (L = PPh, NHC, NHC, NHC, NHC).

Identification and Suppression of Point Defects in Bromide Perovskite Single Crystals Enabling Gamma-Ray Spectroscopy.

Methylammonium lead tribromide (MAPbBr) stands out as the most easily grown wide-band-gap metal halide perovskite. It is a promising semiconductor for room-temperature gamma-ray (γ-ray) spectroscopic detectors, but no operational devices are realized. This can be largely attributed to a lack of understanding of point defects and their influence on detector performance.

Development of Focused Ultrasound-Assisted Nanoplexes for RNA Delivery.

RNA-based therapeutics, including siRNA, have obtained recognition in recent years due to their potential to treat various chronic and rare diseases. However, there are still limitations to lipid-based drug delivery systems in the clinical use of RNA therapeutics due to the need for optimization in the design and the preparation process. In this study, we propose adaptive focused ultrasound (AFU) as a drug loading technique to protect RNA from degradation by encapsulating small RNA in nanoliposomes, which we term nanoplexes.

Magnetic motors in interphases: Motion control and integration in soft robots.

Magnetic motors are a class of out-of-equilibrium particles that exhibit controlled and fast motion overcoming Brownian fluctuations by harnessing external magnetic fields. The advances in this field resulted in motors that have been used for different applications, such as biomedicine or environmental remediation. In this Perspective, an overview of the recent advancements of magnetic motors is provided, with a special focus on controlled motion.

Gold-Thiolate Nanocluster Dynamics and Intercluster Reactions Enabled by a Machine Learned Interatomic Potential.

Monolayer protected metal clusters comprise a rich class of molecular systems and are promising candidate materials for a variety of applications. While a growing number of protected nanoclusters have been synthesized and characterized in crystalline forms, their dynamical behavior in solution, including prenucleation cluster formation, is not well understood due to limitations both in characterization and first-principles modeling techniques. Recent advancements in machine-learned interatomic potentials are rapidly enabling the study of complex interactions such as dynamical behavior and reactivity on the nanoscale.

Electroluminescence Rectification and High Harmonic Generation in Molecular Junctions.

The field of molecular electronics has emerged from efforts to understand electron propagation through single molecules and to use them in electronic circuits. Serving as a testbed for advanced theoretical methods, it reveals a significant discrepancy between the operational time scales of experiments (static to GHz frequencies) and theoretical models (femtoseconds). Utilizing a recently developed time-linear nonequilibrium Green function formalism, we model molecular junctions on experimentally accessible time scales.

Specific inhibition of α-synuclein oligomer generation and toxicity by the chaperone domain Bri2 BRICHOS.

Protein misfolding and aggregation are involved in several neurodegenerative disorders, such as α-synuclein (αSyn) implicated in Parkinson's disease, where new therapeutic approaches remain essential to combat these devastating diseases. Elucidating the microscopic nucleation mechanisms has opened new opportunities to develop therapeutics against toxic mechanisms and species. Here, we show that naturally occurring molecular chaperones, represented by the anti-amyloid Bri2 BRICHOS domain, can be used to target αSyn-associated nucleation processes and structural species related to neurotoxicity.

Engineering the Cellular Microenvironment: Integrating Three-Dimensional Nontopographical and Two-Dimensional Biochemical Cues for Precise Control of Cellular Behavior.

The development of biomaterials capable of regulating cellular processes and guiding cell fate decisions has broad implications in tissue engineering, regenerative medicine, and cell-based assays for drug development and disease modeling. Recent studies have shown that three-dimensional (3D) nanoscale physical cues such as nanotopography can modulate various cellular processes like adhesion and endocytosis by inducing nanoscale curvature on the plasma and nuclear membranes. Two-dimensional (2D) biochemical cues such as protein micropatterns can also regulate cell function and fate by controlling cellular geometries.

Unlocking the diagnostic power of plasma extracellular vesicle miR-200 family in pancreatic ductal adenocarcinoma.

Background: Distinguishing benign from malignant pancreaticobiliary disease is challenging because of the absence of reliable biomarkers. Circulating extracellular vesicles (EVs) have emerged as functional mediators between cells. Their cargos, including microRNAs (miRNAs), are increasingly acknowledged as an important source of potential biomarkers.

Building better habitats: Spatiotemporal signaling cues in 3D biointerfaces for tailored cellular functionality.

A promising research direction in the field of biological engineering is the design and functional programming of three-dimensional (3D) biointerfaces designed to support living cell functionality and growth in vitro, offering a route to precisely regulate cellular behaviors and phenotypes for addressing therapeutic challenges. While traditional two-dimensional (2D) biointerfaces have provided valuable insights, incorporating specific signaling cues into a 3D biointeractive microenvironment at the right locations and time is now recognized as crucial for accurately programming cellular decision-making and communication processes. This approach aims to engineer cell-centric microenvironments with the potential to recapitulate complex biological functions into a finite set of growing cellular organizations.

Unveiling the mechanism of triphos-Ru catalysed C-O bond disconnections in polymers.

Ruthenium complexes with facially coordinating tripodal phosphine ligands are privileged catalysts for a broad range of (de-)hydrogenation-based transformations. Among these, C-O bond hydrogenolysis holds potential for the depolymerisation of both the biopolymer lignin and epoxy resins applied in wind turbine blades, aircrafts and more. However, this methodology is poorly understood in mechanistic terms.

Integrative network analysis of miRNA-mRNA expression profiles during epileptogenesis in rats reveals therapeutic targets after emergence of first spontaneous seizure.

Epileptogenesis is the process by which a normal brain becomes hyperexcitable and capable of generating spontaneous recurrent seizures. The extensive dysregulation of gene expression associated with epileptogenesis is shaped, in part, by microRNAs (miRNAs) - short, non-coding RNAs that negatively regulate protein levels. Functional miRNA-mediated regulation can, however, be difficult to elucidate due to the complexity of miRNA-mRNA interactions.