Infinitely-fast diffusion in Single-File Systems

We have used Dynamic Monte Carlo (DMC) methods and analytical techniques to analyze Single-File Systems for which diffusion is infinitely-fast. We have simplified the Master Equation removing the fast reactions and we have introduced a DMC algorithm for infinitely-fast diffusion. The DMC method for fast diffusion give similar results as the standard DMC with high diffusion rates. We have investigated the influence of characteristic parameters, such as pipe length, adsorption, desorption and conversion rate constants on the steady-state properties of Single-File Systems with a reaction, looking at cases when all the sites are reactive and when only some of them are reactive. We find that the effect of fast diffusion on single-file properties of the system is absent even when diffusion is infinitely-fast. Diffusion is not important in these systems. Smaller systems are less reactive and the occupancy profiles for infinitely-long systems show an exponential behavior.Comment: 8 pages, 5 figure

Mitochondrial Variability as a Source of Extrinsic Cellular Noise

We present a study investigating the role of mitochondrial variability in generating noise in eukaryotic cells. Noise in cellular physiology plays an important role in many fundamental cellular processes, including transcription, translation, stem cell differentiation and response to medication, but the specific random influences that affect these processes have yet to be clearly elucidated. Here we present a mechanism by which variability in mitochondrial volume and functionality, along with cell cycle dynamics, is linked to variability in transcription rate and hence has a profound effect on downstream cellular processes. Our model mechanism is supported by an appreciable volume of recent experimental evidence, and we present the results of several new experiments with which our model is also consistent. We find that noise due to mitochondrial variability can sometimes dominate over other extrinsic noise sources (such as cell cycle asynchronicity) and can significantly affect large-scale observable properties such as cell cycle length and gene expression levels. We also explore two recent regulatory network-based models for stem cell differentiation, and find that extrinsic noise in transcription rate causes appreciable variability in the behaviour of these model systems. These results suggest that mitochondrial and transcriptional variability may be an important mechanism influencing a large variety of cellular processes and properties

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Bonding of hydrogen atoms to iridium tetramer clusters: the effect of magnesium(2+) ions

Local-d.-approxn. calcns. were made of at. H adsorption on tetrahedral Ir4 clusters. The hydrogen atom prefers twofold or threefold coordination. The effect of the presence of a Mg2+ ion next to the Ir4 on the adsorption is studied. It changes the calcd. adsorption energy by less than 10%, but the Ir-H stretch frequencies may change as much as 25%. A comparison with earlier results of H2 adsorption on the same tetrahedral Ir4 clusters supports the hypothesis that polarization of the metal particle by a Mg2+ ion in zeolites promotes H2 dissoc

A computational study of the influence of the ceria surface termination on the mechanism of CO oxidation of isolated Rh atom

The reaction mechanism for CO oxidation by isolated Rh atoms stabilized on CeO2(111), CeO2(110) and CeO2(100) surfaces is investigated by a combination of Density Functional Theory and kinetic Monte Carlo calculations. On Rh/CeO2(111), one adsorbed CO molecule on Rh was found to form a stable intermediate structure with surface O. The reaction cycle cannot be closed because of the strong adsorption of the CO2 complex. The presence of a second adsorbed CO significantly decreases the desorption energy, thus opening a possible reaction path. Formation of the oxygen vacancy is accompanied by reduction of surface cerium. On Rh/CeO2(110), adsorbed CO can easily react with a ceria surface O atom due to the lower Ce–O bond energy. Since surface O atom migration is much more facile on Rh/CeO2(110) than on Rh/CeO2(111), CO2 desorption is also more easy for the former surface. Molecular oxygen will adsorb on the resulting vacancy. After desorption of the second CO2 product molecule by reaction of adsorbed CO with another surface O atom, the adsorbed oxygen molecule migrates spontaneously to the vacancy site and dissociates with negligible barrier. The role of molecular oxygen is to heal the oxygen vacancy rather than being involved in a direct reaction with adsorbed CO. The Rh/CeO2(100) model was found to be inactive for CO oxidation, mainly because of the geometric constraints for the adsorbed CO molecule to react with one of the surface O atoms, despite the low Ce–O bond energy of the CeO2(100) surface. The main reason is the large distance between the C of adsorbed CO and the ceria O surface atoms. The particularities of the CO oxidation mechanism for isolated Rh atoms on these ceria surfaces are in agreement with the experimental activity trends

Lattice-gas modeling of electrochemical Langmuir-Hinshelwood surface reactions

We consider the lattice–gas modeling of simple A+A and A+B electrochemical Langmuir–Hinshelwood surface reactions and compare exact Monte Carlo cyclic voltammograms with those obtained in the mean-field and quasi-chemical or cluster approximations. For A+A reactions, we demonstrate the importance of local correlations between adspecies when a repulsive interaction between neighboring species exists. The mean-field approximation (MFA) cannot account for such local correlations (i.e. ordered adlayers), whereas the quasi-chemical approximation gives results quite close to the Monte Carlo simulations. For the A+B reaction, poor mixing caused by low surface mobility of the adspecies, may result in local correlations (island formation) that cannot be treated satisfactorily by the MFA. A cluster approximation is able to partly bridge the gap between the mean-field and Monte Carlo results

The role of water in silicate oligomerization reaction

The silicate oligomerization reaction is key to sol–gel chemistry and zeolite synthesis. Numerous experimental and theoretical studies have been devoted to investigating the physical chemistry of silicate oligomers in the prenucleation stage of siliceous zeolite formation. Most of the previous quantum chemical computational work has used gas phase models or continuous solvent models for silica oligomerization. Here we apply Car–Parrinello molecular dynamics simulations with explicit inclusion of water molecules to investigate the reaction pathway for the anionic bond formation of siliceous oligomers. The rates of SiO–Si bond formation of linear or ring containing silicate oligomers become substantially enhanced, compared to gas phase results. The formation of 3-ring oligomer is more favorable than the formation of higher branched and ring silica oligomer

Role of Water in Silica Oligomerization

he silicate oligomerization reaction is key to sol-gel chemistry and zeolite synthesis. Numerous experimental and theoretical studies have been devoted to investigating the physical chemistry of silicate oligomers in the prenucleation stage of siliceous zeolite formation. Most of the reported computational studies of silica oligomerization employ a quantum chemical phase model supplemented with a continuum model for the solvent. We report a density-functional theory based molecular dynamics simulation of silica oligomerization in a bulk solution of explicit water molecules. Our study provides thermodynamics, kinetics, and mechanism of the reaction pathway for the anionic bond formation of siliceous oligomers. We reveal that in the water cleavage step a direct and a water mediated proton transfer pathways may occur and show that changing from a continuum to a explicit water model the rates of SiO-Si bond formation of linear and three-ring oligomers are significantly enhanced, whereas the overall thermodynamics becomes less favorable

Ab-initio kinetics of heterogeneous catalysis : NO+N+O/Rh(111)

We show that advances in two fields of computational chemistry, Dynamic Monte Carlo simulations and Density-Functional Theory calculations, are now making it possible to do ab-initio kinetics of realistic surface reactions. We present results of simulations of Temperature-Programmed Desorption experiments of NO reduction to N2 and O2 on the Rh(111) surface. Kinetic parameters were obtained from Density- Functional Theory calculations with the Generalized Gradient Approximation, making this one of the first, and up till now the most complex, example of ab-initio kinetics in heterogeneous catalysis. Top, hcp, and fcc sites are all involved and also lateral interactions are necessary to understand the kinetics of this system