Search results for "Simulation."
showing 10 items of 4779 documents
Surface waves on cylindrical solids: numerical and experimental study.
2013
The use of Rayleigh waves enables the solution of several important inspection problems. Propagation of surface waves along straight boundaries has been properly studied but investigations about their propagation on cylindrical surfaces are not sufficient, despite they can be still of interest for NDE applications. It has been proved experimentally that a surface wave pulse suffers a phase shift during its propagation along a cylindrical surface. A numerical approach has been developed to efficiently study these effects for different materials, curvatures and frequencies. This study can help the scientific community to better understand the phenomenon, quite complex and not yet fully explor…
Approximation of Continuous Media Models for Granular Systems Using Cellular Automata
2004
In this paper a new cellular automata model suitable for granular systems simulation is presented. The proposed model is shown to be equivalent to a particularization of the well known BCRE model of granular systems and a correspondence between the parameters of the presented model and the BCRE model is also set, allowing to fit these parameters for a given system. The model has the advantage over other cellular automata models of being more realistic in the behavior of the surface of heaps and slopes. The dynamics of the CA is analyzed in order to confirm that it also has one of the most important features of these systems, 1/f noise.
Quantifying the limits of transition state theory in enzymatic catalysis
2017
Significance Transition state theory (TST) is the most popular theory to calculate the rates of enzymatic reactions. However, in some cases TST could fail due to the violation of the nonrecrossing hypothesis at the transition state. In the present work we show that even for one of the most controversial enzymatic reactions—the hydride transfer catalyzed by dihydrofolate reductase—the error associated to TST represents only a minor correction to the reaction rate. Moreover, this error is actually larger for the reaction in solution than in the enzymatic active site. Based on this finding and on previous studies we propose an “enzymatic shielding” hypothesis which encompasses various aspects …
Experimental and theoretical evidence of overcharging of calcium silicate hydrate
2007
International audience; Electrokinetic measurements such as electrophoresis may show an inversion of the effective surface charge of colloidal particle called overcharging. This phenomenon has been studied by various theoretical approaches but up to now very few attempts of confrontation between theory and experiment have been conducted. In this work we report electrophoretic measurements as well as Monte Carlo simulations of the electrokinetic potential for the surface of calcium silicate hydrate (Csingle bondSsingle bondH), which is the major constituent of hydrated cement. In the simulations, the surface charge of Csingle bondSsingle bondH nanoparticles in equilibrium with the ionic solu…
2D dynamical arrest transition in a mixed nanoparticle-phospholipid layer studied in real and momentum spaces
2015
AbstractWe investigate the interfacial dynamics of a 2D self-organized mixed layer made of silica nanoparticles interacting with phospholipid (DPPC) monolayers at the air/water interface. This system has biological relevance, allowing investigation of toxicological effects of nanoparticles on model membranes and lung surfactants. It might also provide bio-inspired technological solutions, exploiting the self-organization of DPPC to produce a non-trivial 2D structuration of nanoparticles. The characterization of interfacial dynamics yields information on the effects of NPs on the mechanical properties, important to improve performances of systems such as colloidosomes, foams, creams. For thi…
Surface-exposed Amino Acid Residues of HPV16 L1 Protein Mediating Interaction with Cell Surface Heparan Sulfate
2007
Efficient infection of cells by human papillomaviruses (HPVs) and pseudovirions requires primary interaction with cell surface proteoglycans with apparent preference for species carrying heparan sulfate (HS) side chains. To identify residues contributing to virus/cell interaction, we performed point mutational analysis of the HPV16 major capsid protein, L1, targeting surface-exposed amino acid residues. Replacement of lysine residues 278, 356, or 361 for alanine reduced cell binding and infectivity of pseudovirions. Various combinations of these amino acid exchanges further decreased cell attachment and infectivity with residual infectivity of less than 5% for the triple mutant, suggesting …
The coupling of the electrostatic potential with the transport and adsorption mechanisms in ion-exchange chromatography systems: Theory and experimen…
2005
The coupling of the constitutive expression for the electrostatic potential as specified through Poisson's equation together with the constitutive equations for the mechanisms of convection, diffusion, electrophoretic migration, and adsorption provides the necessary set of constitutive expressions to be employed in the material balance equations of ion-exchange chromatography systems to construct macroscopic continuum models that could be used to design and simulate the dynamic behavior of systems involving a single charged adsorbate or multiple charged adsorbates. A physically relevant and consistent macroscopic continuum model that can predict, as has been observed experimentally by UV co…
Anomalous surface diffusion of protons on lipid membranes.
2014
AbstractThe cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive re…
A mesoscopic mechanical model of the surface tension and some simulation results
2019
Abstract Drops of mercury do not spread on a surface. A metal paper clip can float on water. These phenomena are macroscopic manifestations of molecular interactions and can be explained in terms of surface tension. In this study, we discuss a simple mesoscopic mechanical model of the surface tension and the results of numerical fluid dynamics simulations implemented on the basis of it. We study the droplet formation without and with gravity when it can drop from a narrow hole like a trickling tap and finally the behaviour of free surface liquid in a vessel. Teachers and students can be able to study the surface tension by using the computer simulation as a “tool” for analysing and discussi…
Computer simulations to approach surface tension by means of a simple mesoscopic mechanical model
2019
A small insect can stand or walk on water surface, drops of mercury do not spread on a solid surface, and a meniscus is formed at the free surface of a liquid contained in a thin vessel. These phenomena can be seen as macroscopic manifestations of molecular interactions and can be explained macroscopically in terms of surface tension. In this study, we deal with an approach to surface tension from a mechanical point of view, presenting a simple mesoscopic mechanical model of surface tension and the results of its implementation in numerical fluid dynamics simulations. Particularly, phenomena like droplet formation without gravity and with gravity when it can drop from a narrow hole like a t…