Search results for "COMPUTATION"

Energy-stable linear schemes for polymer-solvent phase field models

2017

We present new linear energy-stable numerical schemes for numerical simulation of complex polymer-solvent mixtures. The mathematical model proposed by Zhou, Zhang and E (Physical Review E 73, 2006) consists of the Cahn-Hilliard equation which describes dynamics of the interface that separates polymer and solvent and the Oldroyd-B equations for the hydrodynamics of polymeric mixtures. The model is thermodynamically consistent and dissipates free energy. Our main goal in this paper is to derive numerical schemes for the polymer-solvent mixture model that are energy dissipative and efficient in time. To this end we will propose several problem-suited time discretizations yielding linear scheme…

A coarse-graining procedure for polymer melts applied to 1,4-polybutadiene

2009

We present a coarse-graining procedure for homopolymer melts mapping intra- as well as inter-molecular interactions from a chemically realistic united atom description to a bead-spring type molecular model. On the coarse-grained level the repeat units interact through bond-length and bond angle potentials and a non-bonded Lennard-Jones type interaction. The latter one is of the 7,4 form and softer than the typically employed 12,6 interactions. The coarse-graining of the intramolecular interactions follows well developed procedures, however, we point out in which way the non-bonded intramolecular interactions in the chemically realistic model should be treated. The parameters of the non-bond…

1982

The molecular weight distribution (MWD) of a high polymer is calculated from a weakly perturbed Zimm-plot of the classical light scattering on dilute solutions of Gaussian polymer coils (theta state). A typical Zimm-plot is simulated corresponding to the measurements of high accuracy as would be obtained by using the laser photometer described by Hack and Meyerhoff. The accuracy as published by these authors for small dissymmetries is used. Two inversion procedures are described in detail and tested, both of them avoiding the use of an empirical formula for the Laplace image of the calculated MWD. A complete numerical analysis of the results is given. The results are compared with those of …

Interactions between polymer brush-coated spherical nanoparticles: the good solvent case.

2011

The interaction between two spherical polymer brushes is studied by molecular dynamics simulation varying both the radius of the spherical particles and their distance, as well as the grafting density and the chain length of the end-grafted flexible polymer chains. A coarse-grained bead-spring model is used to describe the macromolecules, and purely repulsive monomer-monomer interactions are taken throughout, restricting the study to the good solvent limit. Both the potential of mean force between the particles as a function of their distance is computed, for various choices of the parameters mentioned above, and the structural characteristics are discussed (density profiles, average end-to…

Biomolecular-solvent stereodynamic coupling probed by deuteration.

1983

Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic str…

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…

Electronic structure of polysilanes: influence of substitution and conformation

1993

Abstract The valence effective Hamiltonian (VEH) quantum-chemical approach is used to investigate the electronic properties of polysilane. The valence band structure calculated for this fully saturated polymer is analyzed in terms of orbital contributions and compared to that of the closely related carbon polymer, polyethylene. The effects of alkyl substitution and silicon backbone conformation are studied by elucidating the modifications that these structural changes induce on the electronic valence band structure of all-trans unsubstituted polysilane. The VEH results predict a decrease of the band gap upon alkyl substitution and on going from helical to all-trans conformations.

Mechanism of Trichloroethene Hydrodehalogenation: A First-Principles Kinetic Monte Carlo Study

2014

A hydrodehalogenation (HDC) reaction of trichloroethene (TCE) has gained a lot of interest due to its possible application in water purification, but the reaction mechanism has been subject to much controversy. In this work, HDC of TCE on Pd(111) was examined by carrying out kinetic Monte Carlo simulations based on DFT-calculated thermodynamic and kinetic parameters. Obtained kMC results show that the HDC follows a so-called direct pathway, which means that, after adsorption on a catalyst, TCE quickly dechlorinates, producing CH–C and then, more slowly, hydrogenates to form hydrocarbon products. This is reflected in the surface coverage snapshots, where intermediates corresponding to the di…

The skeletal isomerization of but-1-ene catalyzed by theta-1 zeolite

2001

The complete mechanism for the skeletal isomerization of but-1-ene catalyzed by theta-1 zeolite was investigated theoretically by means of DFT calculations, and the influence of the local geometry of the active site and of electrostatic effects on the geometries of the species involved and on activation and reaction energies were analyzed. It was found that whereas the geometry and stability of alkoxide intermediates are strongly influenced by the local geometry of the active site, the ionic transition states are mainly stabilized by electrostatic effects. Both aspects result in a lowering of the activation energies of the elementary steps that form the mechanism and therefore in enhanced r…

Validation strategies for antibodies targeting modified ribonucleotides

2020

Chemical modifications are found on almost all RNAs and affect their coding and noncoding functions. The identification of m6A on mRNA and its important role in gene regulation stimulated the field to investigate whether additional modifications are present on mRNAs. Indeed, modifications including m1A, m5C, m7G, 2′-OMe, and Ψ were detected. However, since their abundances are low and tools used for their corroboration are often not well characterized, their physiological relevance remains largely elusive. Antibodies targeting modified nucleotides are often used but have limitations such as low affinity or specificity. Moreover, they are not always well characterized and due to the low abun…