Influence of surface diffusion on catalytic reactivity of spatially inhomogeneous surfaces mean field modeling

Kinetics of model catalytic processes proceeding on inhomogeneous surfaces is studied. We employ an extended mean-field model that takes into account surface inhomogeneities. The influence of surface diffusion of adsorbent on the kinetics of the catalytic process is investigated. It is shown that diffusion is responsible for differences in the reaction rate of systems with different arrangements of active sites. The presence of cooperative effects between inactive and active sites is demonstrated and the conditions when these effects are important are discussed. We show that basic catalytic phenomena on nonuniform surfaces can be studied with mean-field modeling methods.Comment: Submitted to Chemical Physics Letters. Includes supporting material in Appendice

Self-Association of Organic Solutes in Solution: A NEXAFS Study of Aqueous Imidazole

N K-edge near-edge X-ray absorption fine-structure (NEXAFS) spectra of imidazole in concentrated aqueous solutions have been acquired. The NEXAFS spectra of the solution species differ significantly from those of imidazole monomers in the gas phase and in the solid state of imidazole, demonstrating the strong sensitivity of NEXAFS to the local chemical and structural environment. In a concentration range from 0.5 to 8.2 mol L−1 the NEXAFS spectrum of aqueous imidazole does not change strongly, confirming previous suggestions that imidazole self-associates are already present at concentrations more dilute than the range investigated here. We show that various types of electronic structure calculations (Gaussian, StoBe, CASTEP) provide a consistent and complete interpretation of all features in the gas phase and solid state spectra based on ground state electronic structure. This suggests that such computational modelling of experimental NEXAFS will permit an incisive analysis of the molecular interactions of organic solutes in solutions. It is confirmed that microhydrated clusters with a single imidazole molecule are poor models of imidazole in aqueous solution. Our analysis indicates that models including both a hydrogen-bonded network of hydrate molecules, and imidazole–imidazole interactions, are necessary to explain the electronic structure evident in the NEXAFS spectra

Functionalization of the Parylene C Surface Enhances the Nucleation of Calcium Phosphate : Combined Experimental and Molecular Dynamics Simulations Approach

Interactions at the solid-body fluid interfaces play a vital role in bone tissue formation at the implant surface. In this study, fully atomistic molecular dynamics (MD) simulations were performed to investigate interactions between the physiological components of body fluids (Ca2+, HPO42-, H2PO4-, Na+, Cl-, and H2O) and functionalized parylene C surface. In comparison to the native parylene C (-Cl surface groups), the introduction of -OH, -CHO, and -COOH surface groups significantly enhances the interactions between body fluid ions and the polymeric surface. The experimentally observed formation of calcium phosphate nanocrystals is discussed in terms of MD simulations of the calcium phosphate clustering. Surface functional groups promote the clustering of calcium and phosphate ions in the following order: -OH > -CHO > -Cl (parent parylene C) approximate to -COO-. This promoting role of surface functional groups is explained as stimulating the number of Ca2+ and HPO42- surface contacts as well as ion chemisorption. The molecular mechanism of calcium phosphate cluster formation at the functionalized parylene C surface is proposed.Peer reviewe

UV absorption spectra of TAMRA and TAMRA labeled peptides : a combined density functional theory and classical molecular dynamics study

This study explores the structural and electronic factors affecting the absorption spectra of 5-carboxy-tetramethylrhodamine (TAMRA) in water, a widely used fluorophore in imaging and molecular labeling in biophysical studies. Through molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we examine TAMRA UV absorption spectra together with TAMRA-labeled peptides $(Arg_{9}, Arg_{4}, Lys_{9})$. We found that DFT calculations with different functionals underestimate TAMRA maximum UV absorption peak by ~100 nm, resulting in the maximum at ca. 450 nm instead of the experimental value of ca. 550 nm. However, incorporating MD simulation snapshots of TAMRA in water, the UV maximum peak shifts and is in close agreement with the experimental results due to the rotation of TAMRA $N(CH_{3})_{2}$ groups, effectively captured in MD simulations. The method is used to estimate the UV absorption spectra of TAMRA-labeled peptides, matching experimental values

Reliable Actors with Retry Orchestration

Enterprise cloud developers have to build applications that are resilient to failures and interruptions. We advocate for, formalize, implement, and evaluate a simple, albeit effective, fault-tolerant programming model for the cloud based on actors, reliable message delivery, and retry orchestration. Our model guarantees that (1) failed actor invocations are retried until success, (2) in a distributed chain of invocations only the last one may be retried, (3) pending synchronous invocations with a failed caller are automatically cancelled. These guarantees make it possible to productively develop fault-tolerant distributed applications ranging from classic problems of concurrency theory to complex enterprise applications. Built as a service mesh, our runtime system can interface application components written in any programming language and scale with the application. We measure overhead relative to reliable message queues. Using an application inspired by a typical enterprise scenario, we assess fault tolerance and the impact of fault recovery on application performance.Comment: 14 pages, 6 figure

Interactions of polar lipids with cholesteryl ester multilayers elucidate tear film lipid layer structure

Purpose: The tear film lipid layer (TFLL) covers the tear film, stabilizing it and providing a protective barrier against the environment. The TFLL is divided into polar and non-polar sublayers, but the interplay between lipid classes in these sublayers and the structure-function relationship of the TFLL remains poorly characterized. This study aims to provide insight into TFLL function by elucidating the interactions between polar and non-polar TFLL lipids at the molecular level. Methods: Mixed films of polar O-acyl-omega-hydroxy fatty acids (OAHFA) or phospholipids and non-polar cholesteryl esters (CE) were used as a model of the TFLL. The organization of the films was studied by using a combination of Brewster angle and fluorescence microscopy in a Langmuir trough system. In addition, the evaporation resistance of the lipid films was evaluated. Results: Phospholipids and OAHFAs induced the formation of a stable multilamellar CE film. The formation of this film was driven by the interdigitation of acyl chains between the monolayer of polar lipids and the CE multilayer lamellae. Surprisingly, the multilayer structure was destabilized by both low and high concentrations of polar lipids. In addition, the CE multilayer was no more effective in resisting the evaporation of water than a polar lipid monolayer. Conclusions: Formation of multilamellar films by major tear film lipids suggest that the TFLL may have a similar structure. Moreover, in contrast to the current understanding, polar TFLL lipids may not mainly act by stabilizing the non-polar TFLL sublayer, but through a direct evaporation resistant effect.Peer reviewe

Unraveling the effect of water and ethanol on ibuprofen nanoparticles formation

In this study, we investigate how water and ethanol affect the formation of ibuprofen sodium salt nanoparticles. Particle sizes were measured with the use of Nanoparticle Tracking Analysis and Transmission Electron Microscopy at concentrations of 30, 50, and 80 mg/mL. In water, nanoparticles had an average size of 93 nm, whereas in ethanol they were significantly smaller, averaging 36 nm. Molecular dynamics simulations revealed that in water, ibuprofen molecules aggregate into clusters of 80–300 molecules. In ethanol, stronger ibuprofen-ethanol interactions lead to the formation of much smaller clusters of 2–3 molecules. Both experimental data and simulations indicate that ethanol is a superior solvent for ibuprofen nanosizing. These findings provide a rational basis for selecting solvents in drug formulation and offer a broader perspective for optimizing drug delivery applications

Tail-Oxidized Cholesterol Enhances Membrane Permeability for Small Solutes

Cholesterol renders mammalian cell membranes more compact by reducing the amount of voids in the membrane structure. Because of this, cholesterol is known to regulate the ability of cell membranes to prevent the permeation of water and water-soluble molecules through the membranes. Meanwhile, it is also known that even seemingly tiny modifications in the chemical structure of cholesterol can lead to notable changes in membrane properties. The question is, how significantly do these small changes in cholesterol structure affect the permeability barrier function of cell membranes? In this work, we applied fluorescence methods as well as atomistic molecular dynamics simulations to characterize changes in lipid membrane permeability induced by cholesterol oxidation. The studied 7 beta-hydroxycholesterol (7 beta-OH-chol) and 27-hydroxycholesterol (27-OH-chol) represent two distinct groups of oxysterols, namely, ring- and tail-oxidized cholesterols, respectively. Our previous research showed that the oxidation of the cholesterol tail has only a marginal effect on the structure of a lipid bilayer; however, oxidation was found to disturb membrane dynamics by introducing a mechanism that allows sterol molecules to move rapidly back and forth across the membranebobbing. Herein, we show that bobbing of 27-OH-chol accelerates fluorescence quenching of NBD-lipid probes in the inner leaflet of liposomes by dithionite added to the liposomal suspension. Systematic experiments using fluorescence quenching spectroscopy and microscopy led to the conclusion that the presence of 27-OH-chol increases membrane permeability to the dithionite anion. Atomistic molecular dynamics simulations demonstrated that 27-OH-chol also facilitates water transport across the membrane. The results support the view that oxysterol bobbing gives rise to successive perturbations to the hydrophobic core of the membrane, and these perturbations promote the permeation of water and small water-soluble molecules through a lipid bilayer. The observed impairment of permeability can have important consequences for eukaryotic organisms. The effects described for 27-OH-chol were not observed for 7 beta-OH-chol which represents ring-oxidized sterols.Peer reviewe

In vitro and in silico studies of functionalized polyurethane surfaces toward understanding biologically relevant interactions

The solid-aqueous boundary formed upon biomaterial implantation provides a playground for most biochemical reactions and physiological processes involved in implant-host interactions. Therefore, for biomaterial development, optimization, and application, it is essential to understand the biomaterial-water interface in depth. In this study, oxygen plasma-functionalized polyurethane surfaces that can be successfully utilized in contact with the tissue of the respiratory system were prepared and investigated. Through experiments, the influence of plasma treatment on the physicochemical properties of polyurethane was investigated by atomic force microscopy, attenuated total reflection infrared spectroscopy, differential thermal analysis, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, and contact angle measurements, supplemented with biological tests using the A549 cell line and two bacteria strains (Staphylococcus aureus and Pseudomonas aeruginosa). The molecular interpretation of the experimental findings was achieved by molecular dynamics simulations employing newly developed, fully atomistic models of unmodified and plasma-functionalized polyurethane materials to characterize the polyurethane-water interfaces at the nanoscale in detail. The experimentally obtained polar and dispersive surface free energies were consistent with the calculated free energies, verifying the adequacy of the developed models. A 20% substitution of the polymeric chain termini by their oxidized variants was observed in the experimentally obtained plasma-modified polyurethane surface, indicating the surface saturation with oxygen-containing functional groups.Peer reviewe