Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Mesoscopic structural organization in fluorinated pyrrolidinium-based room temperature ionic liquids
2019
Abstract In this contribution the microscopic and mesoscopic structural organization in a series of fluorinated room temperature ionic liquids, based on N-methyl-N-alkylpyrrolidinium cations and on bis(perfluoroalkylsulfonyl)imide anions, is investigated, using a synergy of experimental (X-ray and neutron scattering) and computational (Molecular Dynamics) techniques. The proposed ionic liquids are of high interest as electrolyte media for lithium battery applications. Together with information on their good ion transport properties in conjunction with low viscosity, we also describe the existence of nm-scale spatial organization induced by the segregation of fluorous moieties into domains. …
Carbon nanotube – Protamine hybrid: Evaluation of DNA cell penetration
2016
International audience; Carbon nanotubes (CNTs) represent a class of nanomaterials with important potential for biomedical and biotechnological applications. CNT based vectorization is an emerging approach to the transport of nucleic acid through cell membrane but limited by detachment of DNA and degradation process. To increase DNA internalization, it was proved that cationic functionalized CNT was essential. In such a way, protamine efficiently used in several transfection processes is a cationic protein which was never associated to CNT.We propose here a novel nanovector based on single-walled carbon nanotubes (SWCNT) functionalized by protamine. Our results based on qPCR methods clearly…
Communication: anion-specific response of mesoscopic organization in ionic liquids upon pressurization
2018
One of the outstanding features of ionic liquids is their inherently hierarchical structural organization at mesoscopic spatial scales. Recently experimental and computational studies showed the fading of this feature when pressurising. Here we use simulations to show that this effect is not general: appropriate anion choice leads to an obstinate resistance against pressurization. Published by AIP Publishing.
H2 Transformations on Graphene Supported Palladium Cluster: DFT-MD Simulations and NEB Calculations
2020
Molecular dynamics simulations based on density functional theory were employed to investigate the fate of a hydrogen molecule shot with different kinetic energy toward a hydrogenated palladium cluster anchored on the vacant site of a defective graphene sheet. Hits resulting in H2 adsorption occur until the cluster is fully saturated. The influence of H content over Pd with respect to atomic hydrogen spillover onto graphene was investigated. Calculated energy barriers of ca. 1.6 eV for H-spillover suggest that the investigated Pd/graphene system is a good candidate for hydrogen storage.
Limits of stability in supported graphene nanoribbons subject to bending
2016
Graphene nanoribbons are prone to in-plane bending even when supported on flat substrates. However, the amount of bending that ribbons can stably withstand remains poorly known. Here, by using molecular dynamics simulations, we study the stability limits of 0.5-1.9 nm wide armchair and zigzag graphene nanoribbons subject to bending. We observe that the limits for maximum stable curvatures are below ~10 deg/nm, in case the bending is externally forced and the limit is caused by buckling instability. Furthermore, it turns out that the limits for maximum stable curvatures are also below ~10 deg/nm, in case the bending is not forced and the limit arises only from the corrugated potential energy…
Structure and dynamics in amorphous tellurium and Te-n clusters: A density functional study
2012
Density functional/molecular dynamics simulations have been performed on amorphous tellurium (a melt-quenched sample of 343 atoms at 300 K) and on Te clusters with up to 16 atoms. The former extend our calculations on liquid Te at 560, 625, 722, and 970 K [Phys. Rev. B 81, 094202 (2010)]. We discuss trends in structures (including those of other group-16 elements), electronic densities of states, and vibration frequencies. Chain structures are common in S and Se, but the chains in amorphous Te are short, and branching sites with threefold-coordinated atoms are common. The energy difference between two- and threefold local coordination depends sensitively on the exchange-correlation function…
Microscopic structural and dynamic features in triphilic room temperature ionic liquids
2019
Here we report a thorough investigation of the microscopic and mesoscopic structural organization in a series of triphilic fluorinated room temperature ionic liquids, namely [1-alkyl, 3-methylimidazolium][(trifluoromethanesulfonyl)(nonafluorobutylsulfonyl)imide], with alkyl=ethyl, butyl, octyl ([C(n)mim][IM14], n = 2, 4, 8), based on the synergic exploitation of X-ray and Neutron Scattering and Molecular Dynamics simulations. This study reveals the strong complementarity between X-ray/neutron scattering in detecting the complex segregated morphology in these systems at mesoscopic spatial scales. The use of MD simulations delivering a very good agreement with experimental data allows us to g…
Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type-αtransfor…
1996
The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168; Bassolino-Klimas D et al., 1996, Protein Sci 5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-alpha transforming growth factor (hTGF alpha). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF a…
Dynamics of a Spreading Nanodroplet: A Molecular Dynamic Simulation
2003
The spreading of polymer nanodroplets upon a sudden change from partial to complete wetting on an ideally flat and structureless solid substrate has been studied by molecular dynamic simulations using a coarse-grained bead-spring model of flexible macromolecules. Tanner's law for the growth of the lateral droplet radius {R(f) t 0.1 } is found to hold as long as the droplet does not disintegrate into individually moving chains. The data for the contact angle θ following from Tanner's law correspond to a dependence on time {θ(t) t -0.3 }. Our analysis of the mean square displacements of the polymer centers of mass reveals several dynamic regimes during the process of spreading. PACS numbers: …
Equilibrating Glassy Systems with Parallel Tempering
2001
We discuss the efficiency of the so-called parallel tempering method to equilibrate glassy systems also at low temperatures. The main focus is on two structural glass models, SiO2 and a Lennard-Jones system, but we also investigate a fully connected 10 state Potts-glass. By calculating the mean squared displacement of a tagged particle and the spin-autocorrelation function, we find that for these three glass-formers the parallel tempering method is indeed able to generate, at low temperatures, new independent configurations at a rate which is O(100) times faster than more traditional algorithms, such as molecular dynamics and single spin flip Monte Carlo dynamics. In addition we find that t…