Search results for "molecular dynamics"
showing 10 items of 1075 documents
Scaling behavior of topologically constrained polymer rings in a melt
2014
Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots and catenanes made up of two unknotted rings scale like $N^{1/3}$ in the limit of large ring sizes $N$. This is consistent with the crumpled globule model and similar findings for unknotted rings. For small ring lengths knots occupy a significant fraction of the ring. The scaling of typical ring sizes for small $N$ thus depends on the particular knot type and the exponent is generally larger than 0.4.
Molecular dynamics of solid polymers as revealed by deuteron NMR
1983
Pulsed deuteron NMR spectroscopy is described, which has recently been developed to become a powerful tool for studying molecular dynamics in solid polymers. It is shown that by analyzing the line shapes of2H absorption spectra and spectra obtained via solid echo and spin alignment, respectively, both type and timescale of rotational motions can be determined over an extraordinary wide range of characteristic frequencies, approximately 10 MHz to 1 Hz. By applying these techniques to selectively deuterated polymers, motional mechanisms involving different segments of the monomer unit can be monitored. In addition, motional heterogeneities in glassy polymers can be detected. The information a…
Glass transition of polymer melts: Test of theoretical concepts by computer simulation.
2003
Abstract Polymers are good glass formers and allow for the study of melts near the glass transition in (meta-)stable equilibrium. Theories of the glass transition imply such an equilibrium and can, hence, be tested by the study of polymer melts. After a brief summary of the basic experimental facts about the glass transition in polymers, the main theoretical concepts are reviewed: mode coupling theory (MCT), entropy theory, free-volume theory, the idea of a growing length describing the size of cooperative regions, etc. Then, two basic coarse-grained models of polymers are described, which have been developed aiming at a test of these concepts. The first model is the bond-fluctuation model …
Molecular dynamics simulations of the glass transition in polymer melts
2004
Computer simulations of polymer models have contributed strongly to our understanding of the glass transition in polymer melts. The ability of the simulation to provide information on experimentally not directly accessible quantities like the detailed spatial arrangement of the particles allows for stringent tests of theoretical concepts about the glass transition and provides additional insight for the interpretation of experimental data. Comparing coarse-grained simulations of a bead-spring model and chemically realistic simulations of 1,4-polybutadiene the importance of dihedral barriers for the glass transition phenomenon can be elucidated.
Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase.
2011
O-Glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) hydrolyzes O-linked 2-acetamido-2-deoxy-β-d-glucopyranoside (O-GlcNAc) residues from post-translationally modified serine/threonine residues of nucleocytoplasmic protein. The chemical process involves substrate-assisted catalysis, where two aspartate residues have been identified as the two key catalytic residues of O-GlcNAcase. In this report, the first step of the catalytic mechanism used by O-GlcNAcase involving substrate-assisted catalysis has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) Molecular Dynamics (MD) calculations. The free energy profile shows that the formation of the oxazol…
Monte Carlo simulations of chain dynamics in polymer brushes
1994
The bond-fluctuation model of polymer chains has been used to study layers of end-grafted polymers anchoring at repulsive walls for a broad range of chain length, grafting densities and solvent quality. The dynamics of monomers and associated relaxation times are investigated and interpreted by phenomenological theories and scaling arguments. The case is also considered where a chain is cut off from its anchor point and the chain is subsequently expelled from the brush. Both the velocity with which the chain leaves the brush and the associated conformational changes (chain contraction etc.) are analysed and interpreted in terms of recent theoretical concepts.
A comparison of neutron scattering studies and computer simulations of polymer melts
2000
Abstract Neutron scattering and computer simulations are powerful tools for studying structural and dynamical properties of condensed matter systems in general and of polymer melts in particular. When neutron scattering studies and quantitative atomistic molecular dynamics simulations of the same material are combined, synergy between the methods can result in exciting new insights into polymer melts not obtainable from either method separately. We present here an overview of our recent efforts to combine neutron scattering and atomistic simulations in the study of melt dynamics of polyethylene and polybutadiene. Looking at polymer segmental motion on a picosecond time scale, we show how at…
Anomalous Structure and Scaling of Ring Polymer Brushes
2011
A comparative simulation study of polymer brushes formed by grafting at a planar surface either flexible linear polymers (chain length $N_L$) or (non-catenated) ring polymers (chain length $N_R=2 N_L$) is presented. Two distinct off-lattice models are studied, one by Monte Carlo methods, the other by Molecular Dynamics, using a fast implementation on graphics processing units (GPUs). It is shown that the monomer density profiles $\rho(z)$ in the $z$-direction perpendicular to the surface for rings and linear chains are practically identical, $\rho_R(2 N_L, z)=\rho_L(N_L, z)$. The same applies to the pressure, exerted on a piston at hight z, as well. While the gyration radii components of ri…
Mechanical Properties of Single Molecules and Polymer Aggregates
2013
This chapter deals with the mechanical properties of single polymer chains, aggregates, and supramolecular complexes. The topics discussed cover a broad range from fundamental statistical mechanics of the equilibrium elastic properties of single polymer chains to details of the behavior of binding pockets in biomolecular assemblies as observed by force spectroscopy. The first section treats the equilibrium mechanical properties of single polymer chains in various environments, investigated via extensive simulations employing coarse-grained models that have proven extremely successful in many branches of polymer physics, namely the bond-fluctuation model and the self-avoiding walk model. Apa…
Microscopic verification of dynamic scaling in dilute polymer solutions: A molecular-dynamics simulation
1991
The dynamics of a single polymer chain immersed in a large number of solvent particles is studied by molecular dynamics. This is the first simulation where chain length (30, 40, and 60 monomers) and statistical accuracy are sufficient to test the predictions of the Zimm model as a result of the particle-particle interactions: The short-time diffusion constant is in good agreement with the Kirkwood prediction, and the monomer motions exhibit the expected dynamic scaling. The long-range hydrodynamic interaction requires a data analysis that explicitly includes the periodic images via Ewald sums.