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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.
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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.
The mobility of polymer chains in perfect polyethylene (PE) crystal was calculated as a function of temperature and chain length through Molecular dynamics (MD) in united atom approximation. The results demonstrate that the chain mobility drastically increases in the vicinity of the phase transition from the orthorhombic to quasi-hexagonal phase. In the quasi-hexagonal phase, the chain mobility is almost independent on temperature and inversely proportional to the chain length.
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimers disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40) dimers. We find that (a) all dimer conformations have higher free energies compared to their corresponding monomeric states, and (b) the free energy difference between the Abeta(1-42) and the analogous Abeta(1-40) dimer conformation is not significant. Our results suggest that Abeta oligomerization is not accompanied by the formation of stable planar beta-strand Abeta dimers.
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.
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics (MD) simulations with Langevin thermostat. The suggested approach makes it possible to go beyond the limitations of the conventional Bell-Evans model. We observe a series of characteristic force spikes when the pulling force is measured against the cantilever displacement during detachment at constant velocity $v_c$ (displacement control mode) and find that the average magnitude of this force increases as $v_c$ grows. The probability distributions of the pulling force and the end-monomer distance from the surface at the moment of final detachment are investigated for different adsorption energy $epsilon$ and pulling velocity $v_c$. Our extensive MD-simulations validate and support the main theoretical findings. Moreover, the simulation reveals a novel behavior: for a strong-friction and massive cantilever the force spikes pattern is smeared out at large $v_c$. As a challenging task for experimental bio-polymers sequencing in future we suggest the fabrication of stiff, super-light, nanometer-sized AFM probe.
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