Search results for "molecular dynamics"

Molecular Simulation of Polymer Melts and Blends: Methods, Phase Behavior, Interfaces, and Surfaces

2016

Topology-Sensitive Microfluidic Filter for Polymers of Varying Stiffness

2017

The separation of polymers based on their size, rigidity, and topology is an essential but also highly challenging task for nanoscience and engineering. Using hybrid molecular dynamics simulations that correctly take into account hydrodynamics, we have designed microfluidic channels for separating linear from ring polymers in dilute solutions. We establish that the transport velocity of the polymers is independent of their topology and rigidity when the channel walls are smooth and repulsive. However, when the walls are decorated with attractive spots arranged on lines parallel to the flow, ring polymers exhibit an order of magnitude higher transport velocity compared to linear chains. The …

Reduction of the glass transition temperature in polymer films: A molecular-dynamics study

2001

We present results of molecular dynamics (MD) simulations for a non-entangled polymer melt confined between two completely smooth and repulsive walls, interacting with inner particles via the potential $U_{\rm wall}\myeq (\sigma/z)^9$, where $z \myeq |z_{\rm particle}-z_{\rm wall}|$ and $\sigma$ is (roughly) the monomer diameter. The influence of this confinement on the dynamic behavior of the melt is studied for various film thicknesses (wall-to-wall separations) $D$, ranging from about 3 to about 14 times the bulk radius of gyration. A comparison of the mean-square displacements in the film and in the bulk shows an acceleration of the dynamics due to the presence of the walls. %Consistent…

Relaxation processes and glass transition of confined polymer melts: A molecular dynamics simulation of 1,4-polybutadiene between graphite walls.

2017

Molecular dynamics simulations of a chemically realistic model for 1,4-polybutadiene in a thin film geometry confined by two graphite walls are presented. Previous work on melts in the bulk has shown that the model faithfully reproduces static and dynamic properties of the real material over a wide temperature range. The present work studies how these properties change due to nano-confinement. The focus is on orientational correlations observable in nuclear magnetic resonance experiments and on the local intermediate incoherent neutron scattering function, Fs(qz, z, t), for distances z from the graphite walls in the range of a few nanometers. Temperatures from about 2Tg down to about 1.15Tg…

Structure of bottle-brush brushes under good solvent conditions: a molecular dynamics study.

2011

We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are performed. We consider a broad range of parameters and present numerical results for the monomer density profile, density of the untethered ends of the grafted flexible backbones and the correlation function describing the range that neighboring grafted bottle-brushes are affected by the presence of the others due to the excluded volume interactions. The end beads of the flexible backbones of the grafted bottle-brushes do not access the region close to the rigid…

Friction between Polymer Brushes in Good Solvent Conditions:  Steady-State Sliding versus Transient Behavior

2003

Previous molecular dynamics simulations of friction between polymer brushes in relative sliding motion [Kreer, T.; Muser, M. H.; Binder, K.; Klein, J. Langmuir 2001, 17, 7804] are extended beyond steady-state conditions. We study two different protocols:  (i) stop and return and (ii) stop and go. In protocol (i), the relative, lateral motion between the two surfaces is stopped abruptly and reimposed opposite to the initial direction after the system could relax for some time. Protocol (ii) is similar except that the sliding direction is maintained. In the constant-velocity steady state, the average lateral extension lc of the polymers is found to be a power law of the sliding velocity v, na…

Coil-Globule Collapse of Polystyrene Chains in Tetrahydrofuran-Water Mixtures.

2018

We study the coil and globule states of a single polymer chain in solution by performing molecular dynamics simulations with a united atom model. Specifically, we characterize the structural properties of atactic polystyrene chains with N = 20–150 monomers in tetrahydrofuran–water mixtures at varying mixing ratios. We find that the hydrophobic polymers form rather open coils when the mole fraction of water, XW, is roughly below 0.25, whereas the chains collapse into globules when XW ≳ 0.75. We confirm the theoretically expected scaling laws for the radius of gyration, Rg, in these regimes, i.e., Rg ∝ N3/5 and Rg ∝ N1/3 for good and poor solvent conditions, respectively. For poor solvent con…

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…

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…

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…