Search results for "molecular dynamics"
showing 10 items of 1075 documents
Intramolecular caging in polybutadiene due to rotational barriers
2003
We present molecular dynamics simulations of a chemically realistic model of 1,4-polybutadiene and a freely rotating chain model derived from the first model by neglecting all dihedral potentials. We show that the presence of energy barriers hindering dihedral rotation leads to an intermediate plateau regime in the tagged particle mean-squared displacement reminiscent of the cage effect underlying the mode-coupling description of the liquid-glass transition. This intramolecular caging, however, occurs already at temperatures well above the glass transition regime. Because of its different physical origin, it also does not comply with the theoretical predictions of the mode-coupling theory. …
Spinodal decomposition of polymer solutions: molecular dynamics simulations of the two-dimensional case.
2012
As a generic model system for phase separation in polymer solutions, a coarse-grained model for hexadecane/carbon dioxide mixtures has been studied in two-dimensional geometry. Both the phase diagram in equilibrium (obtained from a finite size scaling analysis of Monte Carlo data) and the kinetics of state changes caused by pressure jumps (studied by large scale molecular dynamics simulations) are presented. The results are compared to previous work where the same model was studied in three-dimensional geometry and under confinement in slit geometry. For deep quenches the characteristic length scale ℓ(t) of the formed domains grows with time t according to a power law close to [Formula: see…
Computer Simulations for Polymer Dynamics
1991
In this paper we review recent work on the dynamics of polymeric systems using computer simulation methods. For a two-dimensional polymer melt, we show that the chains segregate and the dynamics can be described very well by the Rouse model. This simulation was carried out using the bond fluctuation Monte Carlo method. For three-dimensional (3d) melts and for the study of hydrodynamic effects, we use a molecular dynamics simulation. For 3d melts our results strongly support the concept of reptation. A detailed comparison to experiment shows that we can predict the time and length scales for the onset of reptation for a variety of polymeric liquids. For a single chain, we find the expected h…
Anomalous diffusion of polymers in supercooled melts near the glass transition
2007
Two coarse-grained models for polymer chains in dense melts near the glass transition are investigated: the bond fluctuation lattice model, where long bonds are energetically favored, is studied by dynamic Monte Carlo simulation, and an off-lattice bead-spring model with Lennard-Jones forces between the beads is treated by Molecular Dynamics. We compare the time-dependence of the mean square displacements of both models, and show that they become very similar on mesoscopic scales (i.e., displacements larger than a bond length). The slowing down of motions near the glass transition is discussed in terms of the mode coupling theory and other concepts.
Computer Simulations and Coarse-Grained Molecular Models Predicting the Equation of State of Polymer Solutions
2010
Monte Carlo and molecular dynamics simulations are, in principle, powerful tools for carrying out the basic task of statistical thermodynamics, namely the prediction of macroscopic properties of matter from suitable models of effective interactions between atoms and molecules. The state of the art of this approach is reviewed, with an emphasis on solutions of rather short polymer chains (such as alkanes) in various solvents. Several methods of constructing coarse-grained models of the simple bead–spring type will be mentioned, using input either from atomistic models (considering polybutadiene as an example) or from experiment. Also, the need to have corresponding coarse-grained models of t…
Density functional study of amorphous, liquid and crystalline Ge(2)Sb(2)Te(5): homopolar bonds and/or AB alternation?
2008
The amorphous, liquid and crystalline phases of the phase change material Ge(2)Sb(2)Te(5) (GST) have been studied by means of density functional/molecular dynamics simulations. The large sample (460 atoms and 52 vacancies in the unit cell) and long simulations (hundreds of picoseconds) provide much new information. Here we extend our original analysis (2007 Phys. Rev. B 76 235201) in important ways: partial coordination numbers and radial distribution functions, bond angle distributions, new local order parameters, vibration frequencies, and the charges on atoms and vacancies. The valence band densities of states in amorphous and crystalline GST are compared with ones from x-ray photoemissi…
β-process of supercooled o-terphenyl: a comparison of dielectrical and NMR data guided by mode-coupling theory
1990
Abstract According to predictions of mode-coupling theory of the liquid-glass transition, a Cole-Cole dynamical susceptibility is applied to the β-relaxation of supercooled o -terphenyl as studied by 2 H NMR spin-lattice relaxation and by dielectrical relaxation. A temperature-dependent amplitude (1- f ) is assumed for the β-process which yields a description of the NMR data consistent with the dielectrical data. The plateau value f separating the α- and β-processes in the two-step correlation function reveals a similar temperature dependence as compared to the Debye-Waller factor.
Self-assembly in surfactant-based liquid mixtures: Octanoic acid/Bis(2-ethylhexyl)amine systems
2012
Abstract The physico-chemical properties of Bis(2-ethylhexyl)amine (BEEA) plus octanoic acid (OA) mixtures have been investigated by IR, SAXS, WAXS, viscosimetry, and AC complex impedance spectroscopy in the whole composition range. Mainly driven by proton transfer from the acidic OA to the basic BEEA, the formation of stoichiometrically well-defined adducts takes place in the mixtures. This causes the slowing down of molecular dynamics and the increase in charge carrier number density. Interestingly, while the pure components possess no significant conductivity (about 10−12 S cm−1 at 25 °C), their mixtures show a composition-dependent enhanced conductivity (up to about 10−5 S cm−1), i.e., …
The Study of Carbamoyl Phosphate Synthetase 1 Deficiency Sheds Light on the Mechanism for Switching On/Off the Urea Cycle
2015
12 páginas, 4 figuras, 2 tablas.
Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.
2013
ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp…