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In this paper, we discuss advanced
thermostatting techniques for sampling molecular systems in the canonical ensemble.
We first survey work on dynamical thermostatting methods, including the Nosé-Poincaré method, and generalized bath methods which introduce a more complicated extended model to obtain better ergodicity. We describe a general controlled temperature model, projective thermostatting molecular dynamics
(PTMD) and demonstrate that it flexibly accommodates existing alternative
thermostatting...
We study molecular motor-induced microtubule self-organization in dilute and semi-dilute
filament solutions. In the dilute case, we use a probabilistic model of microtubule
interaction via molecular motors to investigate microtubule bundle dynamics. Microtubules
are modeled as polar rods interacting through fully inelastic, binary collisions. Our
model indicates that initially disordered systems of interacting rods exhibit an
orientational instability...
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