Search results for "molecular dynamics"
showing 10 items of 1075 documents
Bioinspired catechol-terminated self-assembled monolayers with enhanced adhesion properties
2013
The role of the catechol moiety in the adhesive properties of mussel proteins and related synthetic materials has been extensively studied in the last years but still remains elusive. Here, a simplified model approach is presented based on a self-assembled monolayer (SAM) of upward-facing catechols thiol-bound to epitaxial gold substrates. The orientation of the catechol moieties is confirmed by spectroscopy, which also showed lack of significant amounts of interfering o-quinones. Local force-distance curves on the SAM measured by atomic force microscopy (AFM) shows an average adhesion force of 45 nN, stronger than that of a reference polydopamine coating, along with higher reproducibility …
Excess free energy of nanoparticles in a polymer brush
2008
Abstract We present an efficient method for direct determination of the excess free energy Δ F of a nanoparticle inserted into a polymer brush. In contrast to Widom's insertion method, the present approach can be efficiently implemented by Monte Carlo or Molecular Dynamics methods also in a dense environment. In the present investigation the method is used to determine the free energy penalty Δ F ( R , D ) for placing a spherical particle with an arbitrary radius R at different positions D between the grafting plane and the brush surface. Deep inside the brush, or for dense brushes, one finds Δ F ∝ R 3 whereas for shallow nanoclusions Δ F ∝ R 2 , regardless of the particle interaction (…
Molecular Dynamics of a 1,4-Polybutadiene Melt. Comparison of Experiment and Simulation
1999
We have made detailed comparison of the local and chain dynamics of a melt of 1,4-polybutadiene (PBD) as determined from experiment and molecular dynamics simulation at 353 K. The PBD was found to have a random microstructure consisting of 40% cis, 50% trans, and 10% 1,2-vinyl units with a number-average degree of polymerization 〈Xn〉 = 25.4. Local (conformational) dynamics were studied via measurements of the 13C NMR spin−lattice relaxation time T1 and the nuclear Overhauser enhancement (NOE) at a proton resonance of 300 MHz for 12 distinguishable nuclei. Chain dynamics were studied on time scales up to 22 ns via neutron spin−echo (NSE) spectroscopy with momentum transfers ranging from q = …
13C NMR Spin−Lattice Relaxation and Conformational Dynamics in a 1,4-Polybutadiene Melt
2001
We have performed molecular dynamics (MD) simulations of a melt of 1,4-polybutadiene (PBD, 1622 Da) over the temperature range 400-273 K. 13 C NMR spin-lattice relaxation times (T 1 ) and nuclear Overhauser enhancement (NOE) values have been measured from 357 to 272 K for 12 different resonances. The T 1 and NOE values obtained from simulation C-H vector P 2 (t) orientational autocorrelation functions were in good agreement with experiment over the entire temperature range. Analysis of conformational dynamics from MD simulations revealed that T 1 depends much less strongly on the local chain microstructure than does the mean conformational transition time. Spin-lattice relaxation for a give…
Study of the molecular origin of the mechanical and dielectric β relaxation of methyl methacrylate/isopropenyl methyl ketone copolymers
1988
Resultats de l'etude dielectrique, mecanique et par TSC en faveur d'une combinaison d'une barriere intra- et intermoleculaire dans la relaxation beta
Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation
2006
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $\sigma$ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enoug…
The Role of Internal Rotational Barriers in Polymer Melt Chain Dynamics
2002
We present molecular dynamics simulations on 1,4-polybutadiene comparing the dynamics of melt chains between chemically realistic models and a freely rotating chain version of one of the models. These models exhibit the same liquid structure, as measured by the structure factor, and meso- to large-scale chain structure, as measured by the Rouse-mode amplitudes. We show that in this case the Rouse-like chain dynamics as observable in the momentum transfer range of neutron spin-echo experiments is the same for the chains with and without torsion barriers. Our results bear on a recent comparative neutron spin-echo study of the chain dynamics of two polymers with similar chain structure which r…
Single Molecules Probing the Freezing of Polymer Melts: A Molecular Dynamics Study for Various Molecule-Chain Linkages
2010
8 pages; International audience; We present molecular dynamics simulations of coarse-grained model systems of a glassforming polymer matrix containing fluorescent probe molecules. These probe molecules are either dispersed in the matrix or covalently attached to the center or the end of a dilute fraction of the polymer chains. We show that in all cases the translational and rotational relaxation of the probe molecules is a faithful sensor for the glass transition of the matrix as determined from a mode-coupling analysis or Vogel-Fulcher analysis of their R-relaxation behavior. Matrix and dumbbell related relaxation processes show a clear violation of the Stokes-Einstein-Debye laws. In accor…
Conformations, Transverse Fluctuations and Crossover Dynamics of a Semi-Flexible Chain in Two Dimensions
2014
We present a unified scaling description for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence length $\ell_p$ and the case $L\gg \ell_p$. Our theory captures the early time monomer dynamics of a stiff chain characterized by $t^{3/4}$ dependence for the mean square displacement(MSD) of the monomers, but predicts a first crossover to the Rouse regime of $t^{2\nu/{1+2\nu}}$ for $\tau_1 \sim \ell_p^3$, and a second crossover to the purely diffusive dynamics for the entire chain at $\tau_2 \sim L^{5/2}$. We confirm the predictions of this scaling descr…
A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.
2016
We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on …