Search results for "molecular dynamics"
showing 10 items of 1075 documents
Polymer brushes in solvents of variable quality: Molecular dynamics simulations using explicit solvent
2007
The structure and thermodynamic properties of a system of end-grafted flexible polymer chains grafted to a flat substrate and exposed to a solvent of variable quality are studied by molecular dynamics methods. The macromolecules are described by a coarse-grained bead-spring model, and the solvent molecules by pointlike particles, assuming Lennard-Jones-type interactions between pairs of monomers (epsilon(pp)), solvent molecules (epsilon(ss)), and solvent monomer (epsilon(ps)), respectively. Varying the grafting density sigma(g) and some of these energy parameters, we obtain density profiles of solvent particles and monomers, study structural properties of the chain (gyration radius componen…
Atomistic Molecular Dynamics Simulations of the Static and Dynamic Properties of a Polyethylene Melt
1999
I will discuss in this work the atomistic modelling of polymer melts using Molecular Dynamics (MD) simulations. After a general introduction into the problems one faces in the computer simulation of polymers in general and the atomistic simulations in particular, I will present some recent work on the atomistic modelling of an — C 100 H 202 melt,i.e. short chain polyethylene (PE). The aim of this work is to establish a quantitatively validated atomistic model which then can be used in two directions. One direction is the generation of input for the calibration of parameters in coarse-grained models, which in turn can be used to simulate the polymer under investigation over a much broader te…
Hydrodynamic mechanisms of spinodal decomposition in confined colloid-polymer mixtures: A multiparticle collision dynamics study
2013
A multiscale model for a colloid-polymer mixture is developed. The colloids are described as point particles interacting with each other and with the polymers with strongly repulsive potentials, while polymers interact with each other with a softer potential. The fluid in the suspension is taken into account by the multiparticle collision dynamics method (MPC). Considering a slit geometry where the suspension is confined between parallel repulsive walls, different possibilities for the hydrodynamic boundary conditions (b.c.) at the walls (slip versus stick) are treated. Quenching experiments are considered, where the system volume is suddenly reduced (keeping the density of the solvent flui…
On the tribology and rheology of polymer brushes in good solvent conditions: a molecular dynamics study
2003
Tribological and rheological properties of two polymer brushes in relative sliding motion and good solvent conditions are investigated by means of molecular dynamics (MD) simulations. The lateral forces between the brushes are found to decrease logarithmically with increasing relative sliding velocity v0 over a range of more than one decade in v0. We also observe an almost logarithmic relaxation of the end-to-end distance vector that occurs after sliding is stopped. The coincidence of these logarithmic dependencies support the picture that friction between polymer brushes is small due to the retraction of the polymers from the interpenetration zone. The shear stress relaxes almost instantly…
Demixing and polymerization in systems of anisotropic globular particles: A molecular dynamics simulation study
1991
We report a first set of results of Molecular Dynamics simulations of phase separation in a two-dimensional system of identical particles bearing attachment sites at their surface. Morphology of regions of aggregation so obtained appear similar to images of biologically self-assembled structures. Also, they evidence the relevance of the region of thermodynamic instability and of the presence and range of interaction of specific attachment sites. Particles of our system are apt to represent indifferently, though grossly, globular proteins or rigid cells, bearing specific and fixed adhesion sites at their surface. Results illustrate some basic aspects of the origin of the morphology of extend…
On the Nature of the Enzyme–Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study
2020
We present here a detailed theoretical analysis of L-arginine hydrolysis catalyzed by Human Arginase I (HARGI). Our study combines classical molecular dynamic simulations of different model for the...
From orientational glasses to structural glasses: What computer simulations have contributed to understand experiments
2002
Abstract Orientational glasses, produced by random dilution of molecular crystals, exhibit a freezing transition of the quadrupole moments. Monte Carlo simulations of lattice models (generalization of the Edwards–Anderson spin glass model) have been used to elucidate this behavior. While short range models exhibit a static glass transition at zero temperature only, the infinite range Potts glass exhibits a transition where a glass order parameter appears discontinuously. At higher temperature, a dynamical transition occurs, described by mode-coupling theory (MCT). MCT has also been tested by Monte Carlo and molecular dynamics simulations of coarse-grained models of glass-forming polymers. W…
Structure and Dynamics of NaCl in Methanol. A Molecular Dynamics Study
1991
Abstract A recently developed flexible three-site model for methanol was employed to perform a Molecular Dynamics simulation of a 0.6 molal NaCl solution. The ion-methanol and ion-ion potential functions were derived from ab initio calculations. The structural properties of the solution are discussed on the basis of radial and angular distribution functions, the orientation of the methanol molecules, and their geometrical arrangement in the solvation shells of the ions. The dynamical properties of the solution - like self-diffusion coefficients, hindered translations, librations, and internal vibrations of the methanol molecules - are calculated from various autocorrelation functions.
On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure a…
2005
The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar…
Tritopic phenanthroline and pyridine tail-tied aza-scorpiands
2010
The synthesis of two new tritopic double-scorpiand receptors in which two equivalent 5-(2-aminoethyl)-2,5,8-triaza[9]-(2,6)-pyridinophane moieties have been linked with 2,6-dimethylpyridine (L1) or 2,9-dimethylphenanthroline (L2) units is reported for the first time. Their acid-base behaviour and Zn(2+) coordination chemistry have been studied by pH-metric titrations, molecular dynamic calculations, NMR, UV-Vis and steady-state fluorescence techniques. L1 and L2 behave, respectively, as hexaprotic and heptaprotic bases in the experimental conditions used (298.1 +/- 0.1 K, 0.15 mol dm(-3) NaCl, pH range under study 2.0-11.0). These ligands are able to form mono-, bi- and trinuclear Zn(2+) co…