70,255 research outputs found
A general formulation of Bead Models applied to flexible fibers and active filaments at low Reynolds number
This contribution provides a general framework to use Lagrange multipliers
for the simulation of low Reynolds number fiber dynamics based on Bead Models
(BM). This formalism provides an efficient method to account for kinematic
constraints. We illustrate, with several examples, to which extent the proposed
formulation offers a flexible and versatile framework for the quantitative
modeling of flexible fibers deformation and rotation in shear flow, the
dynamics of actuated filaments and the propulsion of active swimmers.
Furthermore, a new contact model called Gears Model is proposed and
successfully tested. It avoids the use of numerical artifices such as repulsive
forces between adjacent beads, a source of numerical difficulties in the
temporal integration of previous Bead Models.Comment: 41 pages, 15 figure
Molecular dynamics simulation of polymer helix formation using rigid-link methods
Molecular dynamics simulations are used to study structure formation in
simple model polymer chains that are subject to excluded volume and torsional
interactions. The changing conformations exhibited by chains of different
lengths under gradual cooling are followed until each reaches a state from
which no further change is possible. The interactions are chosen so that the
true ground state is a helix, and a high proportion of simulation runs succeed
in reaching this state; the fraction that manage to form defect-free helices is
a function of both chain length and cooling rate. In order to demonstrate
behavior analogous to the formation of protein tertiary structure, additional
attractive interactions are introduced into the model, leading to the
appearance of aligned, antiparallel helix pairs. The simulations employ a
computational approach that deals directly with the internal coordinates in a
recursive manner; this representation is able to maintain constant bond lengths
and angles without the necessity of treating them as an algebraic constraint
problem supplementary to the equations of motion.Comment: 15 pages, 14 figure
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