Molecular model

Summary

A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected. The electronic structure is often also omitted unless it is necessary in illustrating the function of the molecule being modeled. Molecular models may be created for several reasons – as pedagogic tools for students or those unfamiliar with atomistic structures; as objects to generate or test theories (e.g., the structure of DNA); as analogue computers (e.g., for measuring distances and angles in flexible systems); or as ae

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https://en.wikipedia.org/wiki/Molecular_model

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Approche expérimentale du comportement mécanique des polymères en sollicitation rapide

In the more recent applications of technical polymers, they are frequently submitted to high strain rates. Being viscoelastic by nature, their mechanical properties are rate dependent. It is therefore important to investigate their properties over a wide range of strain rates. The aims of this study are twofold: i) to propose an experimental technique applicable to a large domain of strain rates, included those covering impact tests, and ii) to apply this technique to the study of the rate dependence of the mechanical properties of some technical polymers. In the first section, the deformation mechanisms of polymers, and the way in which they are influenced by strain rate, are reviewed. Some basics of fracture mechanics are also briefly presented. A detailed study of our original approach to the high rates tests then follows. This technique is based on the reduction of dynamic effects which often affect the measurements at high loading rates. Rather than impact tests, our technique is a quasi-static tests at high rates. This results from the use of a damper as coupling element between the servohydraulic piston and the specimen, together with the specific design of load and displacement detectors. The transient acceleration, responsible for the dynamic effects is decreased, but the high loading rates are maintained. The second section is devoted to the investigation of the rate effect on the tensile and rupture properties of polyoxymethylene (POM) and impact modified polymethylmethacrylate (PMMA). It is shown that high molecular weight POM is less sensitive to the increase of the loading rates than for lower molecular weights. The physical structure, which depends on the processing conditions, plays an important role as well. Results show greater embrittlement by increasing the loading rate than by lowering the temperature. Finally, a molecular model of fracture is proposed. PMMA modified by different fractions and morphologies of the rubbery phase are submitted to tensile and fracture tests at room temperature. Several stages in the micromechanisms of deformation are identified by transmission electron microscopy. The progressive disappearance of some of these stages leads to ductile to brittle transitions in some of the materials studied. The velocity at which these transitions occur depends on the fraction and on the morphology of the modifying phase. It is also shown that a spherical morphology of the rubbery phase is not necessarily required to improve the toughness, but that this latter depends on the interactions between the phases.

EPFL1996

Molecular dynamics simulations of the intrinsically disordered protein amelogenin

Alessandra Apicella, Vincenzo Colangelo, Matteo Gregorio Modesto Marascio, John Christopher Plummer

Amelogenin refers to a class of intrinsically disordered proteins that are the major constituents of enamel matrix derivative (EMD), an extract of porcine fetal teeth used in regenerative periodontal therapy. Modifications in molecular conformation induced by external stresses, such as changes in temperature or pH, are known to reduce the effectiveness of EMD. However, detailed descriptions of the conformational behavior of native amelogenin are lacking in the open literature. In the present work, a molecular model for the secondary and tertiary structure of the full-length major porcine amelogenin P173 was constructed from its primary sequence by replica exchange molecular dynamics (REMD) simulations. The REMD results for isolated amelogenin molecules at different temperatures were shown to be consistent with the available spectroscopic data. They therefore represent an important first step toward the simulation of the intra- and intermolecular interactions that mediate self-organization in amelogenin and its behavior in the presence of other EMD components under conditions representative of its therapeutic application.

Taylor & Francis Inc2017

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Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction center of Photosystem II through resonant energy transfer mechanisms. In the special pair of chlorophylls of the reaction center the charge separation occurs, eventually leading to the oxidation of water molecules into protons, electrons and molecular oxygen. The adsorption properties of the antenna chlorophylls are ad hoc modulated by the protein environment to guarantee fast energy transfer and minimize side and back reactions. At the same time these properties are influenced by the molecular fluctuations occurring at physiological temperature. In the present work, combining classical "molecular dynamics simulations with the Charge Density Coupling method, we estimated the impact of the thermal fluctuations on the site energy shift of the chlorophylls embedded in the Photosystem II complex. Our results show how the effect of the molecular fluctuations is not homogeneous throughout the complex, although the symmetry of the homodimer is maintained. Many peripheral chromophores undergo fluctuations larger then 10 kJ/mol around the average values. Possible physiological roles of such fluctuations are discussed.

Elsevier Science Bv2017

Approche expérimentale du comportement mécanique des polymères en sollicitation rapide

EPFL1996