1,721,010 research outputs found
Tonelli Principle: Finite Reduction and Fixed Energy Molecular Dynamics Trajectories
No full textWe propose a novel theoretical and practical alternative to the Maupertuis functional in the field of molecular dynamics: the Tonelli functional. Our aim is to adapt this technique to the study of rare events where the initial and the final states of a system are known, and we look for transition paths. We reach it with a rigorous mathematical development of the functional and an efficient numerical algorithm. We couple the Tonelli functional with an exact finite dimensional reduction, and we prove error estimates for its implementation. This is not far from a multiscale approach; indeed the reduction will help the study of the high frequencies of the systems: it can be seen as a magnifying glass for atomic trajectories. We test our techniques first on simple models in order to show the details and the main features of these new tools: an harmonic oscillator, a one dimensional double-well potential, the well-tested Mueller potential, and a short oscillatory trajectory of a 4-atom cluster are studied under different points of view. Then we pass to a more demanding test: the isomerization of a Lennard-Jones cluster of 38 interacting atoms
Surface molecular dynamics simulation with two orthogonal surface steps: how to beat the particle conservation problem
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The reaction mechanism of the azide-alkyne Huisgen cycloaddition
No full textThe azide-alkyne Huisgen cycloaddition has a key role in click chemistry and is configured as a powerful tool in pharmaceutical and medicinal chemistry. Although this reaction has already been largely studied, there is an ongoing debate about its mechanism. In this work we study the dynamical aspects of the process using metadynamics computer simulations. We focus on the conformational aspects that determine the course of the reaction and characterize its free energy landscape. To properly capture the thermodynamics of the process we select optimal collective variables using harmonic linear discriminant analysis. The results qualitatively confirm and explain the experimental evidence and give insights into the role of the substituents and the possible transition mechanisms
Islands, craters, and a moving surface step on a hexagonally reconstructed (100) noble metal surface
No full textDeposition/removal of metal atoms on the hex reconstructed (100) surface of Au, Pt and Ir should present intriguing aspects, since a new island implies hex-->square deconstruction of the substrate, and a new crater implies the square-->hex reconstruction of the uncovered layer. To obtain a microscopic understanding of how islands/craters form in these conditions, we have conducted simulations of island and crater growth on Au(100), whose atomistic behavior, including the hex reconstruction on top of the square substrate, is well described by means of classical many-body forces. By increasing/decreasing the Au coverage on Au(100), we find that island/craters will not grow unless they exceed a critical size of about eight to 10 atoms. This value is close to that which explains the non-linear coverage of dependence observed in molecular adsorption on the closely related surface Pt (100). This threshold size is rationalized in terms of a transverse step correlation length, measuring the spatial extent where reconstruction of a given plane is disturbed by the nearby step. (C) 2000 Elsevier Science B.V. All rights reserved
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