Search results for "dynamics"

No-flow temperature and solidification in injection molding simulation

2011

The no‐flow temperature (NFT) is a parameter representing the rheological solidification temperature of a polymer. A polymer, during injection molding filling stage, can stop its flow because of its high viscosity, although it is not yet fully solidified by means of glass transition or crystallization. The NFT is used in most of injection molding simulation packages: with this simple parameter it is possible to reduce the errors deriving from viscosity extrapolation at relatively low temperatures. The viscosity measurements for polymers are usually carried out at high temperatures, and the viscosity models can fail in prediction at temperatures close to the glass transition or crystallizati…

Glassy dynamics of simulated polymer melts: Coherent scattering and van Hove correlation functions

2001

Whereas the first part of this paper dealt with the relaxation in the β-regime, this part investigates the final relaxation (α-relaxation) of a simulated polymer melt consisting of short non-entangled chains in the supercooled state above the critical temperature of ideal mode-coupling theory (MCT). The temperature range covers the onset of a two-step relaxation behaviour down to a temperature merely 2% above . We monitor the incoherent intermediate scattering function as well as the coherent intermediate scattering function of both a single chain and the melt over a wide range of wave numbers q. Upon approaching the coherent α-relaxation time of the melt increases strongly close to the max…

Monte Carlo and molecular dynamics simulation of the glass transition of polymers

1998

Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by dynamic Monte Carlo methods, and a bead-spring model in the continuum with a Lennard-Jones potential between the beads is treated by Molecular Dynamics. While the dynamics of both models differ for short length scales and associated time scales, on mesoscopic spatial and temporal scales both models behave similarly. In particular, the mode coupling theory of the glass transition can be used to interpret the slowing down of the undercooled polymer melt. For the…

Mesoscopic gel at low agarose concentration in water: a dynamic light scattering study

1995

Previous work in our laboratory has shown that at very low agarose concentration in water gelation still occurs within mutually disconnected, high concentration regions generated by spinodal demixing. The freely diffusing particles obtained in these conditions are studied in the present work by depolarized dynamic light scattering and probe diffusion experiments. These particles are found to behave as large (in fact, mesoscopic) polymer fibers entangled in a continuously rearranged mesh with scaling parameters typical of partially flexible, neutral chains. The present results allow specifying the notion of mesoscopic gelation. They also reveal that the same symmetry-breaking mechanism that …

Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations.

2007

Decapping is a central step in eukaryotic mRNA turnover and in gene expression regulation. The human scavenger decapping enzyme, DcpS, catalyses cap hydrolysis following mRNA degradation. DcpS is a dimeric enzyme, with two active sites. Crystal structures suggest that DcpS must undergo significant conformational changes upon ligand binding, but the mechanism of this transition is unknown. Here, we report two long timescale (20 ns) molecular dynamics simulations of the apo-form of DcpS. The dimer is observed to undergo a strikingly cooperative motion, with one active site closing while the other opens. The amplitude of the conformational change is 6–21 A and the apparent timescale is 4–13 ns…

1988

Phase diagrams were calculated for flowing solutions of polystyrene in trans-decahydronaphthalene assuming that the energy (Es) stored in the sheared state has to be added to the Gibbs energy of mixing; Es is computed from viscometric data (flow curves). The resulting phase diagrams exhibit two maxima in most of the cases instead of only one for the stagnant solutions. A comparison with experimental data (Part 1) shows that the calculated demixing behaviour agrees well for moderate shear rates and concentrations of the polymer. Deviations in the semidilute region, particularly for higher values, are a consequence of the fact that so far no reliable theoretical relation has been given for th…

Structure-based statistical analysis of transmembrane helices

2012

Recent advances in determination of the high-resolution structure of membrane proteins now enable analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in water-soluble helices. In this work, we conducted a large-scale analysis of the prevalent locations of amino acids by using a data set of 170 structures of integral membrane proteins obtained from the MPtopo database and 930 structures of water-soluble helical proteins obtained from the protein data bank. Large hydrophobic amino acids (Leu, Val, Ile, and Phe) plus Gly were clearly prevalent in TM helices whereas polar amino acids (Glu, Lys, Asp, Arg, and Gln) were less frequent in this …

Orientation and Dynamics of Peptides in Membranes Calculated from 2H-NMR Data

2009

Solid-state (2)H-NMR is routinely used to determine the alignment of membrane-bound peptides. Here we demonstrate that it can also provide a quantitative measure of the fluctuations around the distinct molecular axes. Using several dynamic models with increasing complexity, we reanalyzed published (2)H-NMR data on two representative alpha-helical peptides: 1), the amphiphilic antimicrobial peptide PGLa, which permeabilizes membranes by going from a monomeric surface-bound to a dimeric tilted state and finally inserting as an oligomeric pore; and 2), the hydrophobic WALP23, which is a typical transmembrane segment, although previous analysis had yielded helix tilt angles much smaller than ex…

(Co-)solvent selection for single-wall carbon nanotubes: best solvents, acids, superacids and guest-host inclusion complexes.

2011

Analysis of 1-octanol-water, cyclohexane-water and chloroform (CHCl(3))-water partition coefficients P(o-ch-cf) allows calculation of molecular lipophilicity patterns, which show that for a given atom log P(o-ch-cf) is sensitive to the presence of functional groups. Program CDHI does not properly differentiate between non-equivalent atoms. The most abundant single-wall carbon nanotube (SWNT), (10,10), presents a relatively small aqueous solubility and large elementary polarizability, P(o-ch-cf) and kinetic stability. The SWNT solubility is studied in various solvents, finding a class of non-hydrogen-bonding Lewis bases with good solubility. Solvents group into three classes. The SWNTs in so…

The dynamic orientation of membrane-bound peptides: bridging simulations and experiments.

2007

AbstractThe structural organization in a peptide/membrane supramolecular complex is best described by knowledge of the peptide orientation plus its time-dependent and spatial fluctuations. The static orientation, defined by the peptide tilt and a rotation about its molecular axis, is accessible through a number of spectroscopic methods. However, peptide dynamics, although relevant to understand the functionality of these systems, remains largely unexplored. Here, we describe the orientation and dynamics of Trp-flanked and Lys-flanked hydrophobic peptides in a lipid bilayer from molecular dynamics simulations. A novel view is revealed, where collective nontrivial distributions of time-evolvi…