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Register a new userThermal decomposition of a honeycomb-network sheet - A Molecular Dynamics simulation study
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The thermal degradation of a graphene-like two-dimensional triangular membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet at lower temperature whereas at higher temperature bonds break at random anywhere in the hexagonal flake. The mean breakage time $tau$ is found to decrease with the total number of network nodes $N$ by a power law $tau propto N^{-0.5}$ and reveals an Arrhenian dependence on temperature $T$. Scission times are themselves exponentially distributed. The fragmentation kinetics of the average number of clusters can be described by first-order chemical reactions between network nodes $n_i$ of different coordination. The distribution of fragments sizes evolves with time elapsed from a $delta$-function through a bimodal one into a single-peaked again at late times. Our simulation results are complemented by a set of $1^{st}$-order kinetic differential equations for $n_i$ which can be solved exactly and compared to data derived from the computer experiment, providing deeper insight into the thermolysis mechanism.
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Endothelial cells are responsible for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two-dimensional molecular dynamics simulations of point-like particles. Cells motion is governed by the gradient of the concentration of a chemical substance that they produce (chemotaxis). The typical time of degradation of the chemical substance introduces a characteristic length in the system. We show that point-like model cells form network resembling structures tuned by this characteristic length, before collapsing altogether. Successively, we improve the non-realistic point-like model cells by introducing an isotropic strong repulsive force between them and a velocity dependent force mimicking the observed peculiarity of endothelial cells to preserve the direction of their motion (persistence). This more realistic model does not show a clear network formation. We ascribe this partial fault in reproducing the experiments to the static geometry of our model cells that, in reality, change their shapes by elongating toward neighboring cells.
Three different polarizable ion models for molten AgBr have been studied by molecular dynamics simulations. The three models are based on a rigid ion model (RIM) with a pair potential of the type proposed by Vashishta and Rahman for alpha-AgI, to which the induced dipole polarization of the ions is added. In the first (PIM1), the dipole moments are only induced by the local electric field; while in the other two (PIM1s and PIM2s), a short-range overlap induced polarization opposes the electrically induced dipole moments. In the PIM1 and the PIM1s only the anions are assumed polarizable, while in the PIM2s both species are polarizable. Long molecular dynamics simulations show that the PIM2s is an unphysical model since, for some improbable but possible critical configurations, the ions become infinitely polarized. The results of using the PIM1, the PIM1s, as well as those of the simple RIM, have been compared for the static structure and ionic transport properties. The PIM1 reproduces the broad main peak of the total structure factor present in the neutron diffraction data, although the smoothed three-peak feature of this broad peak is slightly overestimated. The structural results for the PIM1s are intermediate between those for the RIM and the PIM1, but fail to reproduce the experimental features within the broad principal peak. Concerning the ionic transport properties, the value of the conductivity obtained using PIM1 is in good agreement with experimental values, while the self-diffusion coefficients and the conductivity for the PIM1s are lower than the corresponding values using the PIM1 and the RIM.
The scission kinetics of bottle-brush molecules in solution and on an adhesive substrate is modeled by means of Molecular Dynamics simulation with Langevin thermostat. Our macromolecules comprise a long flexible polymer backbone with $L$ segments, consisting of breakable bonds, along with two side chains of length $N$, tethered to each segment of the backbone. In agreement with recent experiments and theoretical predictions, we find that bond cleavage is significantly enhanced on a strongly attractive substrate even though the chemical nature of the bonds remains thereby unchanged. We find that the mean bond life time $<tau>$ decreases upon adsorption by more than an order of magnitude even for brush molecules with comparatively short side chains $N=1 div 4$. The distribution of scission probability along the bonds of the backbone is found to be rather sensitive regarding the interplay between length and grafting density of side chains. The life time $<tau>$ declines with growing contour length $L$ as $<tau>propto L^{-0.17}$, and with side chain length as $<tau>propto N^{-0.53}$. The probability distribution of fragment lengths at different times agrees well with experimental observations. The variation of the mean length $L(t)$ of the fragments with elapsed time confirms the notion of the thermal degradation process as a first order reaction.
The properties of model solutions consisting of a solute --- single curcumin molecule in water, methanol and dimethyl sulfoxide solvents have been studied using molecular dynamics (MD) computer simulations in the isobaric-isothermal ensemble. The united atom OPLS force field (OPLS-UA) model for curcumin molecule proposed by us recently [J. Mol. Liq., 2016, 223, 707] in combination with the SPC/E water, and the OPLS-UA type models for methanol and dimethyl sulfoxide have been applied. We have described changes of the internal structure of the solute molecule induced by different solvent media in very detail. The pair distribution functions between particular fragments of a solute molecule with solvent particles have been analyzed. Statistical features of the hydrogen bonding between different species were explored. Finally, we have obtained a self-diffusion coefficient of curcumin molecules in three model solvents.
Molecular dynamics (MD) simulations were performed to study the formation process of nanopores in a suspended graphene sheet irradiated by using energetic ions though a mask. By controlling the ion parameters including mass, energy and incident angle, different kinds of topography were observed in the graphene sheet. Net-like defective strucutures with carbon atom chains can be formed at low ion fluence, which provides the possibility to functionalize the irradiated sample with subsequent chemical methods; finally a perfect nanopore with smooth edge appears as the ion fluence is high enough. We found that the dependence of ion damage efficiency on ion fluence, energy and incident angle are different from that predicted by the semi-empirical model based on the binary-collision approximation, which results from the special structure of graphene. Our results demonstrate that it is feasible to fabricate controlled nanopores/nanostructures in graphene via heavy ion irradiation.
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