Search results for " Simulation"
showing 10 items of 4034 documents
Prediction of tyrosinase inhibition activity using atom-based bilinear indices.
2007
A set of novel atom-based molecular fingerprints is proposed based on a bilinear map similar to that defined in linear algebra. These molecular descriptors (MDs) are proposed as a new means of molecular parametrization easily calculated from 2D molecular information. The nonstochastic and stochastic molecular indices match molecular structure provided by molecular topology by using the kth nonstochastic and stochastic graph-theoretical electronic-density matrices, M(k) and S(k), respectively. Thus, the kth nonstochastic and stochastic bilinear indices are calculated using M(k) and S(k) as matrix operators of bilinear transformations. Chemical information is coded by using different pair com…
Fragment- and negative image-based screening of phosphodiesterase 10A inhibitors.
2019
A novel virtual screening methodology called fragment- and negative image-based (F-NiB) screening is introduced and tested experimentally using phosphodiesterase 10A (PDE10A) as a case study. Potent PDE10A-specific small-molecule inhibitors are actively sought after for their antipsychotic and neuroprotective effects. The F-NiB combines features from both fragment-based drug discovery and negative image-based (NIB) screening methodologies to facilitate rational drug discovery. The selected structural parts of protein-bound ligand(s) are seamlessly combined with the negative image of the target's ligand-binding cavity. This cavity- and fragment-based hybrid model, namely its shape and electr…
From capillary condensation to interface localization transitions in colloid-polymer mixtures confined in thin-film geometry.
2008
Monte Carlo simulations of the Asakura-Oosawa (AO) model for colloid-polymer mixtures confined between two parallel repulsive structureless walls are presented and analyzed in the light of current theories on capillary condensation and interface localization transitions. Choosing a polymer to colloid size ratio of q=0.8 and studying ultrathin films in the range of D=3 to D=10 colloid diameters thickness, grand canonical Monte Carlo methods are used; phase transitions are analyzed via finite size scaling, as in previous work on bulk systems and under confinement between identical types of walls. Unlike the latter work, inequivalent walls are used here: while the left wall has a hard-core rep…
Statistical and systematic errors in Monte Carlo sampling
1991
We have studied the statistical and systematic errors which arise in Monte Carlo simulations and how the magnitude of these errors depends on the size of the system being examined when a fixed amount of computer time is used. We find that, depending on the degree of self-averaging exhibited by the quantities measured, the statistical errors can increase, decrease, or stay the same as the system size is increased. The systematic underestimation of response functions due to the finite number of measurements made is also studied. We develop a scaling formalism to describe the size dependence of these errors, as well as their dependence on the “bin length” (size of the statistical sample), both…
Optimized analysis of the critical behavior in polymer mixtures from Monte Carlo simulations
1992
A complete outline is given for how to determine the critical properties of polymer mixtures with extrapolation methods similar to the Ferrenberg-Swendsen techniques recently devised for spin systems. By measuring not only averages but the whole distribution of the quantities of interest, it is possible to extrapolate the data obtained in only a few simulations nearT c over the entire critical region, thereby saving at least 90% of the computer time normally needed to locate susceptibility peaks or cumulant intersections and still getting more precise results. A complete picture of the critical properties of polymer mixtures in the thermodynamic limit is then obtained with finite-size scali…
Mobilization upon Cooling
2021
Abstract Phase transitions between different aggregate states are omnipresent in nature and technology. Conventionally, a crystalline phase melts upon heating as we use ice to cool a drink. Already in 1903, Gustav Tammann speculated about the opposite process, namely melting upon cooling. So far, evidence for such “inverse” transitions in real materials is rare and limited to few systems or extreme conditions. Here, we demonstrate an inverse phase transition for molecules adsorbed on a surface. Molybdenum tetraacetate on copper(111) forms an ordered structure at room temperature, which dissolves upon cooling. This transition is mediated by molecules becoming mobile, i.e., by mobilization up…
Confinement effects on phase behavior of soft matter systems.
2008
When systems that can undergo phase separation between two coexisting phases in the bulk are confined in thin film geometry between parallel walls, the phase behavior can be profoundly modified. These phenomena shall be described and exemplified by computer simulations of the Asakura-Oosawa model for colloid-polymer mixtures, but applications to other soft matter systems (e.g. confined polymer blends) will also be mentioned. Typically a wall will prefer one of the phases, and hence the composition of the system in the direction perpendicular to the walls will not be homogeneous. If both walls are of the same kind, this effect leads to a distortion of the phase diagram of the system in thin …
The impact of thermophysical properties and hysteresis effects on the energy performance simulation of PCM wallboards: Experimental studies, modellin…
2020
Abstract This paper presents a combined experimental and numerical procedure, developed to test the thermophysical behaviour of a real scale PCM wallboard, aiming at providing reliable data for the validation of building energy performance simulation tools. Data obtained from two experimental tests, conducted on real building elements integrating PCM undergoing complete and incomplete phase change, are considered for assessing the impact of thermal properties and hysteresis. A comprehensive comparative numerical analysis, performed by means of an in-house developed simulation tool, called DETECt, is carried out to investigate the reliability of several modelling and simulation approaches av…
Spectroscopic ellipsometry applied to phase transitions in solids: possibilities and limitations
2009
The possibilities of in situ spectroscopic ellipsometry applied to phase transitions investigation in oxide thin films and crystals are examined in this work, along with the use of various parameters calculated from ellipsometric data (band gap energy Eg, refractive index n and surface roughness) together with the directly measured main ellipsometric angles psi and Delta, for the detection of phase transitions. The efficiency of spectroscopic ellipsometry on "surface" phase transition and its sensitivity to surface defects are also demonstrated.
Water-Hydrophobic Zeolite Systems
2012
Water intrusion-extrusion in hydrophobic microporous AFI, IFR, MTW and TON pure silica zeolites (zeosils) has been investigated through molecular dynamics (MD) simulations. It was found that intruded water volumes correlate with the free volume of the zeosil unit cells. Calculated adsorption isotherms allowed us to estimate the amounts of water intruded, and deviations from experiments (lower experimental with respect to calculated intrusion pressures) have been;explained in terms of connectivity defects in the synthesized materials. Water phase transitions in defectless zeosils occur in a narrow range at high pressure. On the basis of a simple model, we derived a thermodynamic equation tha…