Search results for "molecular dynamics"
showing 10 items of 1075 documents
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…
Effects of afforestation with four unmixed plant species on the soil–water interactions in a semiarid Mediterranean region (Sicily, Italy)
2012
Purpose An assessment of the effect of plant cover on the properties of four afforested soils in central Sicily was performed with the aim of discriminating among them after 60 years of afforestation. Materials and methods Chemical and biochemical soil analyses were coupled to fast field cycling (FFC) NMR relaxation investigations in order to monitor surface interactions of water in water-saturated soils. Results and discussion The traditional soil analyses revealed that the most stable soil properties such as soil texture and pH are not affected by 60 years of afforestation. Soils developed under eucalyptus trees showed larger amounts of hydrophilic organic matter as compared to the soils …
Prediction of structural and thermodynamic properties of zinc-blende AlN: molecular dynamics simulation
2004
Abstract Structural and elastic properties of AlN are investigated by using a molecular dynamics simulation based on the Tersoff empirical interatomic potential. Both of zinc-blende and rock-salt structures are discussed. The calculated bulk properties and elastic constants agree well with the available experimental and theoretical data. The Thermodynamic properties in zinc-blende structure are also predicted including the Debye temperature, melting temperature, heat capacity, linear thermal coefficient. This study is helpful to understand the bahviour of physical properties of AlN when the temperature varies.
The superlattice model of lateral organization of membranes and its implications on membrane lipid homeostasis.
2008
AbstractMost biological membranes are extremely complex structures consisting of hundreds of different lipid and protein molecules. According to the famous fluid-mosaic model lipids and many proteins are free to diffuse very rapidly in the plane of the membrane. While such fast diffusion implies that different membrane lipids would be laterally randomly distributed, accumulating evidence indicates that in model and natural membranes the lipid components tend to adopt regular (superlattice-like) distributions. The superlattice model, put forward based on such evidence, is intriguing because it predicts that 1) there is a limited number of allowed compositions representing local minima in mem…
Lipid carbonyl groups terminate the hydrogen bond network of membrane-bound water.
2015
We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the …
Evidence of thin-film precursors formation in hydrokinetic and atomistic simulations of nano-channel capillary filling
2008
We present hydrokinetic Lattice Boltzmann and Molecular Dynamics simulations of capillary filling of high-wetting fluids in nano-channels, which provide clear evidence of the formation of thin precursor films, moving ahead of the main capillary front. The dynamics of the precursor films is found to obey the Lucas-Washburn law as the main capillary front, z2(t) proportional to t, although with a larger prefactor, which we find to take the same value for both geometries under inspection. Both hydrokinetic and Molecular Dynamics approaches indicate a precursor film thickness of the order of one tenth of the capillary diameter. The quantitative agreement between the hydrokinetic and atomistic m…