Search results for "Biomolecule"
showing 10 items of 666 documents
Semiflexible polymers confined in a slit pore with attractive walls: two-dimensional liquid crystalline order versus capillary nematization
2017
Semiflexible polymers under good solvent conditions interacting with attractive planar surfaces are investigated by Molecular Dynamics (MD) simulations and classical Density Functional Theory (DFT). A bead-spring type potential complemented by a bending potential is used, allowing variation of chain stiffness from completely flexible coils to rod-like polymers whose persistence length by far exceeds their contour length. Solvent is only implicitly included, monomer-monomer interactions being purely repulsive, while two types of attractive wall-monomer interactions are considered: (i) a strongly attractive Mie-type potential, appropriate for a strictly structureless wall, and (ii) a corrugat…
Characteristic Length Scales and Radial Monomer Density Profiles of Molecular Bottle-Brushes: Simulation and Experiment
2010
Extensive Monte Carlo simulations are presented for bottle-brush polymers under good solvent conditions, using the bond fluctuation model on the simple cubic lattice. Varying the backbone length (from Nb = 67 to Nb = 259 effective monomers) as well as the side chain length (from N = 6 to N = 48), for a physically reasonable grafting density of one chain per backbone monomer, we find that the structure factor describing the total scattering from the bottle-brush provides an almost perfect match for some combinations of (Nb, N) to experimental data of Rathgeber et al. [J. Chem. Phys. 2005, 122, 124904], when we adjust the length scale of the simulation to reproduce the experimental gyration r…
Stretching semiflexible polymer chains: Evidence for the importance of excluded volume effects from Monte Carlo simulation
2011
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy penalty $\epsilon_b$ for chain bending. In the absence of excluded volume interactions, the persistence length $\ell_p$ of the polymers would then simply be $\ell_p=\ell_b(2d-2)^{-1}q_b^{-1}$ with $q_b= \exp(-\epsilon_b/k_BT)$, the bond length $\ell_b$ being the lattice spacing, and $k_BT$ is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both $q_b$ and the chain length $N$ are varied over a wide r…
Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles
2015
The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymer…
Nematic order in solutions of semiflexible polymers: Hairpins, elastic constants, and the nematic-smectic transition
2018
Coarse-grained models of lyotropic solutions of semiflexible polymers are studied by both molecular dynamics simulations and density functional theory calculations, using an implicit solvent bead-spring model with a bond-angle potential. We systematically vary the monomer density, persistence length, and contour length over a wide range and explore the full range from the isotropic-nematic transition to the nematic-smectic transition. In the nematic regime, we span the entire regime from rigid-rod like polymers to thin wormlike chains, confined in effective straight tubes caused by the collective nematic effective ordering field. We show that the distribution of bond angles relative to the …
Semiflexible Macromolecules with Discrete Bond Angles Confined in Nanoslits: A Monte Carlo Test of Scaling Concepts
2013
Single semiflexible polymer chains confined in a planar slit geometry between parallel nonadsorbing repulsive walls a distance D apart are studied by Monte Carlo simulations of a lattice model, for the case of good solvent conditions. The polymers are modeled as self-avoiding walks on the simple cubic lattice, where every 90° kink requires a bending energy eb. For small qb = exp(−eb/kBT) the model has a large persistence length lp (given by lp ≈ 1/(4qb) in the bulk three-dimensional dilute solution, in units of the lattice spacing). Unlike the popular Kratky–Porod model of worm-like chains, this model takes both excluded volume into account and approximates the fact that bond angles between…
Breakdown of the Kratky-Porod Wormlike Chain Model for Semiflexible Polymers in Two Dimensions
2011
By large-scale Monte Carlo simulations of semiflexible polymers in $d=2$ dimensions the applicability of the Kratky-Porod model is tested. This model is widely used as "standard model" for describing conformations and force versus extension curves of stiff polymers. It is shown that semiflexible polymers in $d=2$ show a crossover from hard rods to self-avoiding walks, the intermediate Gaussian regime (implied by the Kratky-Porod model) is completely absent. Hence the latter can also describe force versus extension curves only if the contour length is only a few times larger than the persistence length. Consequences for experiments on biopolymers at interfaces are briefly discussed.
Universal monomer dynamics of a two dimensional semi-flexible chain
2013
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square displacements (MSDs) of stiff chains growing like t^{3/4} with time due to bending motions, and the Rouse-like regime t^{2 \nu / (1+ 2\nu)} where \nu is the Flory exponent describing the radius R of a swollen flexible coil. We identify how the prefactors of these laws scale with the persistence length l_p, and show that a crossover from stiff to flexible behavior occurs at a MSD of order l^2_p (at a time proportional to l^3_p). A second crossover (to diffusive moti…
Semiflexible polymers under good solvent conditions interacting with repulsive walls.
2016
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion caused by the monomer-wall repulsion. A coarse-grained bead-spring model with bond bending potential is studied, varying both the contour length and the persistence length of the polymers, as well as the monomer concentration in the solution (good solvent conditions are assumed throughout, and solvent molecules are not included explicitly). The profiles of monomer density and pressure tensor components near the wall are studied, and the surface tension of…
Understanding the Multiple Length Scales Describing the Structure of Bottle-brush Polymers by Monte Carlo Simulation Methods
2011
Bottle-brush polymers contain a long flexible macromolecule as a backbone to which flexible side chains are grafted. Through the choice of the grafting density and the length of the side chains the local stiffness of this cylindrical molecular brush can be controlled, but a quantitative understanding of these phenomena is lacking. Monte Carlo simulation results are presented and discussed which address this issue, extractingmesoscopic length scales (such as the cross-sectional radius, persistence length, and contour length of these objects). Large-scale simulations of the bond fluctuation model are combined with simulations of the simple selfavoiding walk (SAW) model with flexibility contro…