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Register a new userThermal Degradation of Adsorbed Bottle-Brush Macromolecules: Molecular Dynamics Simulation
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Added by
Vakhtang Rostiashvili
Publication date
2011
fields
Physics
and research's language is
English
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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.
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The absorption of free linear chains in a polymer brush was studied with respect to chain size $L$ and compatibility $chi$ with the brush by means of Monte Carlo (MC) simulations and Density Functional Theory (DFT) / Self-Consistent Field Theory (SCFT) at both moderate, $sigma_g = 0.25$, and high, $sigma_g = 1.00$, grafting densities using a bead-spring model. Different concentrations of the free chains $0.0625 le phi_o le 0.375$ are examined. Contrary to the case of $chi = 0$ when all species are almost completely ejected by the polymer brush irrespective of their length $L$, for $chi < 0$ we find that the degree of absorption (absorbed amount) $Gamma(L)$ undergoes a sharp crossover from weak to strong ($approx 100%$) absorption, discriminating between oligomers, $1le Lle 8$, and longer chains. For a moderately dense brush, $sigma_g = 0.25$, the longer species, $L > 8$, populate predominantly the deep inner part of the brush whereas in a dense brush $sigma_g = 1.00$ they penetrate into the fluffy tail of the dense brush only. Gyration radius $R_g$ and end-to-end distance $R_e$ of absorbed chains thereby scale with length $L$ as free polymers in the bulk. Using both MC and DFT/SCFT methods for brushes of different chain length $32 le N le 256$, we demonstrate the existence of unique {em critical} value of compatibility $chi = chi^{c}<0$. For $chi^{c}(phi_o)$ the energy of free chains attains the {em same} value, irrespective of length $L$ whereas the entropy of free chain displays a pronounced minimum. At $chi^{c}$ all density profiles of absorbing chains with different $L$ intersect at the same distance from the grafting plane. The penetration/expulsion kinetics of free chains into the polymer brush after an instantaneous change in their compatibility $chi$ displays a rather rich behavior. We find three distinct regimes of penetration kinetics of free chains regarding the length $L$: I ($1le Lle 8$), II ($8 le L le N$), and III ($L > N$), in which the time of absorption $tau$ grows with $L$ at a different rate. During the initial stages of penetration into the brush one observes a power-law increase of $Gamma propto t^alpha$ with power $alpha propto -ln phi_o$ whereby penetration of the free chains into the brush gets {em slower} as their concentration rises.
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.
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.
Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight backbone, both radial density profiles of monomers and side chain ends are obtained, as well as structure factors describing the scattering from a single side chain and from the total bottle-brush polymer. To describe the structure in the interior of a very long bottle-brush, a periodic boundary condition in the direction along the backbone is used, and to describe effects due to the finiteness of the backbone length, a second set of simulations with free ends of the backbone is performed. In the latter case, the inhomogeneity of the structure in the direction along the backbone is carefully investigated. We use these results to test various phenomenological models that have been proposed to interpret experimental scattering data for bottle-brush macromolecules. These models aim to extract information on the radial density profile of a bottle-brush from the total scattering via suitable convolution approximations. Possibilities to improve such models, guided by our simulation results, are discussed.
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.
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