Search results for "Condensed Matter - Soft Condensed Matter"
showing 10 items of 364 documents
Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation
2006
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide range and the crossover from ``mushroom'' to ``brush'' behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of $N$ and $\sigma$ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enoug…
Conformations, Transverse Fluctuations and Crossover Dynamics of a Semi-Flexible Chain in Two Dimensions
2014
We present a unified scaling description for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence length $\ell_p$ and the case $L\gg \ell_p$. Our theory captures the early time monomer dynamics of a stiff chain characterized by $t^{3/4}$ dependence for the mean square displacement(MSD) of the monomers, but predicts a first crossover to the Rouse regime of $t^{2\nu/{1+2\nu}}$ for $\tau_1 \sim \ell_p^3$, and a second crossover to the purely diffusive dynamics for the entire chain at $\tau_2 \sim L^{5/2}$. We confirm the predictions of this scaling descr…
Sequence Determines Degree of Knottedness in a Coarse-Grained Protein Model
2015
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar (HP) lattice protein model. By employing large scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that, even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just o…
On the applicability of density dependent effective interactions in cluster-forming systems
2016
We systematically studied the validity and transferability of effective, coarse-grained, pair potentials in ultrasoft colloidal systems. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding (implicit) solvent. Simulations were performed for both the monomeric and coarse-grained model in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. For every state point, each macromolecule was mapped onto a single interaction site and the effective pair potential was computed using a coarse-graining technique based on force-matching. We found e…
Dynamic force spectroscopy: analysis of reversible bond-breaking dynamics
2008
The problem of diffusive bond-dissociation in a double well potential under application of an external force is scrutinized. We compute the probability distribution of rupture forces and present a detailed discussion of the influence of finite rebinding probabilities on the dynamic force spectrum. In particular, we focus on barrier crossing upon extension, i.e. under linearly increased load, and upon relaxation starting from completely separated bonds. For large loading rates the rupture force and the rejoining force depend on the loading rate in the expected manner determined by the shape of the potential. For small loading rates the mean forces obtained from pull and relax modes approach …
Structural and conformational dynamics of supercooled polymer melts: Insights from first-principles theory and simulations
2007
We report on quantitative comparisons between simulation results of a bead-spring model and mode-coupling theory calculations for the structural and conformational dynamics of a supercooled, unentangled polymer melt. We find semiquantitative agreement between simulation and theory, except for processes that occur on intermediate length scales between the compressibility plateau and the amorphous halo of the static structure factor. Our results suggest that the onset of slow relaxation in a glass-forming melt can be described in terms of monomer-caging supplemented by chain connectivity. Furthermore, a unified atomistic description of glassy arrest and of conformational fluctuations that (as…
Intermolecular structure factors of macromolecules in solution: Integral equation results
1999
The inter-molecular structure of semidilute polymer solutions is studied theoretically. The low density limit of a generalized Ornstein-Zernicke integral equation approach to polymeric liquids is considered. Scaling laws for the dilute-to-semidilute crossover of random phase (RPA) like structure are derived for the inter-molecular structure factor on large distances when inter-molecular excluded volume is incorporated at the microscopic level. This leads to a non-linear equation for the excluded volume interaction parameter. For macromolecular size-mass scaling exponents, $\nu$, above a spatial-dimension dependent value, $\nu_c=2/d$, mean field like density scaling is recovered, but for $\n…
Molecular-dynamics simulation of a glassy polymer melt: Rouse model and cage effect
1999
We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the mode coupling theory. The physical process of `caging' of a monomer by its spatial neighbors leads to a distinct two step behavior in the particle mean square displacements. In this work we analyze the effects of this caging process on the Rouse description of the melt's dynamics. We show that the Rouse theory is applicable for length and time scales above the typical scales for the caging process. Futhermore, the monomer displacement is compared with si…
Motion of magnetotactic bacteria swarms in an external field
2017
Magnetotactic bacteria moving on circular orbits form hydrodynamically bound states. When close to a surface and with the tilting of the field in a direction close to the perpendicular to this surface these swarms move perpendicularly to the tilting angle. We describe quantitatively this motion by a continuum model with couple stress arising from the torques produced by the rotary motors of the amphitrichous magnetotactic bacteria. The model not only correctly describes the change of direction of swarm motion while inverting the tangential field but also predicts reasonable value of the torque produced by the rotary motors.
Phase behaviour of deionized binary mixtures of charged colloidal spheres.
2009
We review recent work on the phase behaviour of binary charged sphere mixtures as a function of particle concentration and composition. Both size ratios and charge ratios are varied over a wide range. By contrast to hard spheres the long ranged Coulomb interaction stabilizes the crystal phase at low particle concentrations and shifts the occurrence of amorphous solids to particle concentrations considerably larger than the freezing concentration. Depending on size- and charge ratios we observe upper azeotrope, spindle, lower azeotrope and eutectic types of phase diagrams, all known well from metal systems. Most solids are of body centred cubic structure. Occasionally stoichiometric compound…