The Lowe-Andersen thermostat is a momentum conserving and Galilean invariant analog of the Andersen thermostat. Like the Andersen thermostat it has the advantage of being local. We show that by using a minimal thermostat interaction radius in a molecular dynamics simulation, it perturbs the system dynamics to a far lesser extent than the Andersen method. This alleviates a well known drawback of the Andersen thermostat by allowing high thermostatting rates without the penalty of significantly suppressed diffusion in the system.
Three-dimensional morphologies of Madracis mirabilis were obtained using X-ray computed tomography scanning techniques. The morphologies were used to simulate the flow patterns around the colony. In the simulations, the thin-branching low-flow morph with a relatively larger branch-spacing was compared with the more compact high-flow morph of M. mirabilis. For both morphologies, the inside-colony flow velocities were computed for Reynolds numbers ranging from 154 to 3840. In the high-flow morph, it was found that in the range of investigated Reynolds numbers a stagnant region develops within the colony, whereas in the low-flow morph the stagnant region disappeared. Experiments done under natural conditions suggest that a morph is adapted to a certain external flow velocity and develops a stagnant region below a particular threshold for the external flow velocity. When the external flow velocity exceeds a certain threshold, which is characteristic for the growth form, the core velocity becomes equal to the external velocity. A potential application of a profile of core velocities for a range of Reynolds numbers for a certain morph is the prediction of the optimal external flow velocity for a certain morph, and this can be used to assess the state of the physical (palaeo-) environment.
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