Search results for "dynamics"

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…

Conformational studies of bottle-brush polymers absorbed on a flat solid surface.

2010

The adsorption of a bottle-brush polymer end-grafted with one chain end of its backbone to a flat substrate surface is studied by Monte Carlo simulation of a coarse-grained model, that previously has been characterized in the bulk, assuming a dilute solution under good solvent conditions. Applying the bond fluctuation model on the simple cubic lattice, we vary the backbone chain length $N_b$ from $N_b=67$ to $N_b = 259$ effective monomeric units, the side chain length $N$ from N=6 to N=48, and the grafting density $\sigma=1$, i.e., parameters that correspond well to the experimentally accessible range. When the adsorption energy strength $\epsilon$ is varied, we find that the adsorption tra…

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...

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…

1985

Viscosity measurements were carried out as a function of pressure and temperature with solutions of 8 wt.-% PVC (Mw ≈ 75 000) in ten thermodynamically good solvents by means of a Searle-type viscometer. A rollingxyhball viscometer was used for the investigation of the pure solvents. In all cases the viscosity increases in a more or less exponential manner when the pressure is raised. The viscosity ratio f1000 = η1000 bar/η1bar can be varied by the choice of the solvent from ca. 2 (tetrahydrofuran) to 3,0 (cyclohexanone) at 40°C. For a constant temperature of 40°C, the volumes of activation for the viscous flow of the solutions, V≠, or f1000 exceed that of the pure solvent, by typically 25%.…

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis.

2007

To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 ′. Similar energetic profiles featuring two minima corresponding to the anti and syn Gχ regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of ∼4 kcal/mol were obtained for the anti → syn transition. Str…

Scattering function and the dynamics of phase separation in polymer mixtures under shear flow

1988

The phenomenological mean-field theory describing concentration fluctuations and spinodal decomposition of binary mixtures of long flexible macromolecules is generalized to mixtures under steady shear flow. This shear flow leads to a partial orientation and stretching of the coils, as well as to an anisotropic deformation of concentration fluctuations. Generalizing the approach of Onuki and Kawasaki, we obtain the collective scattering function describing these concentration fluctuations in the mixture under shear flow. Both the steady-state situation in the one-phase region and the initial stages of spinodal decomposition for concentrations inside of the spinodal curve are considered.

Self-diffusion in polymer solutions using the bond-fluctuation MC-algorithm

1991

Abstract A lattice Monte Carlo study of the self-diffusion of polymer chains in an athermal solution of equal chains is presented. The examined chain lengths, N (= 20–200), and volume fractions, φ (= 0.025-0.5), cover the range from dilute solution to concentrated solution, respectively. The dynamics show a gradual crossover from Rouse to reptation-like behaviour. Analysing the data according to a scaling theory and taking into account the density dependence of the microscopic length and time-scales, an almost perfect scaling of the self-diffusion coefficient is achieved. The high statistical accuracy of the data (103–104 chains per parameter combination) was obtainable by using a transpute…

A friction factor analysis of the coupling between polymer/solvent self- and mutual-diffusion: polystyrene/toluene

1996

The Bearman statistical mechanical theory, which couples the mutual-diffusion and self-diffusion coefficients via friction factors, has been applied to polystyrene/toluene solutions with polystyrene molecular weights of 18 kDa and 900 kDa. Toluene and polystyrene self-diffusion coefficients, obtained from the literature and measured here, along with polystyrene/toluene binary mutual-diffusion coefficients and thermodynamic data, were employed to independently calculate the three friction coefficients (ξ 12 , ξ 11 , and ξ 22 ) required to describe transport within binary solutions. Results reveal that the frequently used geometric mean approximation (GMA) for relating the friction coefficien…

Self-Diffusion of Small Molecules into Rubbery Polymers: A Lattice Free-Volume Theory

2010

In the framework of the Free Volume Theory, a new equation was derived for the evaluation of self-diffusion coefficients of small molecules in polymers above the mixture glass transition temperature. The derivation of the equation turned out to be straightforward once the equivalence between the free-volume and the unoccupied volume given by Thermodynamic Lattice Theories is assumed. A parameter evaluation scheme is proposed, which is substantially simpler compared to the conventional Vrentas-Duda approach, even without losing generality. The key assumption is discussed and its consistency is verified from a numerical viewpoint. A comparison with experimental solvent self-diffusion coeffici…