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Semiflexible polymers in concentrated lyotropic solution are studied within a bead-spring model by molecular dynamics simulations, focusing on the emergence of a smectic A phase and its properties. We systematically vary the density of the monomeric units for several contour lengths that are taken smaller than the chain persistence length. The difficulties concerning the equilibration of such systems and the choice of appropriate ensemble (constant volume versus constant pressure, where all three linear dimensions of the simulation box can fluctuate independently) are carefully discussed. Using HOOMD-blue on graphics processing units, systems containing more than a million monomeric units are accessible, making it possible to distinguish the order of the phase transitions that occur. While in this model the nematic-smectic transition is continuous, the transition from the smectic phase to a related crystalline structure with true three-dimensional long-range order is clearly of first order. Further, both orientational and positional correlations of monomeric units are studied as well as the order parameters characterizing the nematic, smectic A, and crystalline phases. The analogy between smectic order and one-dimensional harmonic crystals with respect to the behavior of the structure factor is also explored. Finally, the results are put in perspective with pertinent theoretical predictions and possible experiments.
Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting s
We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^*$ and $ u$, are chosen to match its experimental force-extension curve. The
The cytoskeleton of eukaryotic cells provides mechanical support and governs intracellular transport. These functions rely on the complex mechanical properties of networks of semiflexible protein filaments. Recent theoretical interest has focused on
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their persistent directi
We develop a theory of Smectic A - Smectic C phase transition with anomalously weak smectic layer contraction. We construct a phenomenological description of this transition by generalizing the Chen-Lubensky model. Using a mean-field molecular model,