Search results for "molecular dynamics"
showing 10 items of 1075 documents
Internal dynamics and energy transfer in dansylated POPAM dendrimers and their eosin complexes.
2010
Internal dynamics of dansylated poly(propyleneamine) dendrimers (POPAM, G1-G4) in solution and excitation energy transfer from dansyls to eosin in POPAM-eosin complexes have been studied by time-resolved fluorescence spectroscopy and molecular dynamics (MD) simulations. Combining the results from fluorescence anisotropy and the MD simulation studies suggests three time domains for the internal dynamics of the G3 and G4 generations, about 60 ps for motions of the outer-sphere dansyls, 500-1000 ps for restricted motions of back-folded dansyls, and 1500-2600 ps for the overall rotation. For the smaller generations, the contribution from the restricted motions was not entirely evident. Eosin bi…
Experimental IR study and ab initio modelling of ethylene adsorption in a MFI - type host zeolite.
2009
International audience; Different ab initio methods and experimental results are used to investigate the effect of the adsorption of one ethylene molecule on silicalite-1, a MFI type zeolite. We used simplified models to simulate a portion of a straight or sinusoidal channel of silicalite-1 at a quantum level. The calculated absorption spectra of the models are qualitatively in good agreement with the experimental FTIR spectrum of silicalite-1. Additionally we simulate the FTIR spectrum of the isolated ethylene molecule and that of an ethylene molecule in interaction with the above-mentioned zeolite models. Results are discussed depending on the method and specific basis set and compared wi…
Water adsorption on amorphous silica surfaces: A Car-Parrinello simulation study
2005
A combination of classical molecular dynamics (MD) and ab initio Car-Parrinello molecular dynamics (CPMD) simulations is used to investigate the adsorption of water on a free amorphous silica surface. From the classical MD SiO_2 configurations with a free surface are generated which are then used as starting configurations for the CPMD.We study the reaction of a water molecule with a two-membered ring at the temperature T=300K. We show that the result of this reaction is the formation of two silanol groups on the surface. The activation energy of the reaction is estimated and it is shown that the reaction is exothermic.
Study of the reactive dynamics of nanometric metallic multilayers using Molecular Dynamics: the Al−Ni system
2012
A molecular dynamics study of a layered Ni-Al-Ni system is developed using an embedded atom method potential. The specific geometry is designed to model a Ni-Al nanometric metallic multilayer. The system is initially thermalized at the fixed temperature of 600 K. We first observe the interdiffusion of Ni and Al at the interfaces, which is followed by the spontaneous phase formation of B2-NiAl in the Al layer. The solid-state reaction is associated with a rapid system's heating which further enhances the diffusion processes. NiAl phase is organized in small regions separated by grain boundaries. This study confirms the hypothesis of a layer-by-layer development of the new phase. For longer t…
Quantum mechanics-molecular dynamics approach to the interpretation of x-ray absorption spectra.
2009
The quantum mechanics-molecular dynamics approach to the simulation of configuration-averaged EXAFS spectra is proposed, and its application is discussed for the example of the Ti K-edge EXAFS spectrum in cubic perovskite SrTiO(3). Proper use of ab initio quantum mechanics allows a number of empirical parameters, used in the molecular dynamics simulation, to be reduced, whereas the molecular dynamics allows us to account for temperature effects. All together, the approach provides a way of accounting for static and dynamic disorder in EXAFS signals from the coordination shells above the first one, where many-atom (multiple-scattering) effects are often important.
Interpretation of the Co K-edge EXAFS in LaCoO3 using molecular dynamics simulations
2011
Abstract Temperature dependent (180–400 K) Co K-edge EXAFS spectra from perovskite-type rhombohedral ( R 3 ¯ c ) LaCoO 3 have been successfully interpreted using a combination of classical NVT molecular dynamics (MD) and ab initio multiple-scattering (MS) theory. The method allowed us to account entirely for thermal disorder and to interpret reliably the contribution from the coordination shells beyond the first one into the total EXAFS spectrum taking into account many-body effects. The best agreement between experimental and configuration-averaged EXAFS spectra was obtained for pure ionic La 3+ and partially ionic Co 1.35+ and O 1.45− charges indicating the mixed ionic-covalent character …
Optical Imaging of Coherent Molecular Rotors
2020
International audience; Short laser pulses are widely used for controlling molecular rotational degrees of freedom and inducing molecular alignment, orientation, unidirectional rotation and other types of coherent rotational motion. To follow the ultra-fast rotational dynamics in real time, several techniques for producing molecular movies have been proposed based on the Coulomb explosion of rotating molecules, or recovering molecular orientation from the angular distribution of high-harmonics. The present work offers and demonstrates a novel non-destructive optical method for direct visualization and recording of movies of coherent rotational dynamics in a molecular gas. The technique is b…
Characterization of Locally Excited and Charge-Transfer States of the Anticancer Drug Lapatinib by Ultrafast Spectroscopy and Computational Studies
2020
[EN] Lapatinib (LAP) is an anticancer drug, which is metabolized to theN- and O-dealkylated products (N-LAP andO-LAP, respectively). In view of the photosensitizing potential of related drugs, a complete experimental and theoretical study has been performed on LAP,N-LAP andO-LAP, both in solution and upon complexation with human serum albumin (HSA). In organic solvents, coplanar locally excited (LE) emissive states are generated; they rapidly evolve towards twisted intramolecular charge-transfer (ICT) states. By contrast, within HSA only LE states are detected. Accordingly, femtosecond transient absorption reveals a very fast switching (ca. 2 ps) from LE (lambda(max)=550 nm) to ICT states (…
Non-syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A
2018
International audience; Filamin A (FLNa), expressed in endocardial endothelia during fetal valve morphogenesis, is key in cardiac development. Missense mutations in FLNa cause non-syndromic mitral valve dysplasia (FLNA-MVD). Here, we aimed to reveal the currently unknown underlying molecular mechanism behind FLNA-MVD caused by the FLNa P637Q mutation. The solved crystal structure of the FLNa3-5 P637Q revealed that this mutation causes only minor structural changes close to mutation site. These changes were observed to significantly affect FLNa's ability to transmit cellular force and to interact with its binding partner. The performed steered molecular dynamics simulations showed that signi…
Study of nickel corrosion processes by molecular dynamics with reactive potential ReaxFF
2012
Understanding of corrosion processes is important for the study of the durability of materials in aggressive environment. The objective is to provide new lights on the corrosion processes of nickel in aqueous condition with molecular dynamics simulation using a reactive force field "ReaxFF."We are particularly interested by the reaction between water molecules and mono-crystalline surfaces of nickel. No dissociation of water was showed on the surfaces. Moreover, an adsorption of molecules in bilayer was observed, reflecting the mutual polarization between water and nickel, which confirms the charge calculation. The metal surface is positively charged and the first water layer charged negati…