Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userSimulation of polymers in a curved box: Variable range bonding models
61
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We propose new polymer models for Monte Carlo simulation and apply them to a polymer chain confined in a relatively thin box which has both curved and flat sides, and show that either an ideal or an excluded-volume chain spends more time in the curved region than in the flat region. The ratio of the probability of finding a chain in the curved region and in flat region increases exponentially with increasing chain length. The results for ideal chains are quantitatively consistent with a previously published theory. We find that the same effect appears with excluded-volume chains and a similar scaling relation can be applied to them up to a certain length of the polymer.
rate research
Read More
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the absence of hydrodynamic interactions. The dsDNA is modelled with one bead-spring element per basepair, and the polymer dynamics is described by the Langevin equation. The key to efficiency is that we describe the equations of motion for the polymer in terms of the amplitudes of the polymers fluctuation modes, as opposed to the use of the physical positions of the beads. We show that, within an accuracy tolerance level of $5%$ of several key observables, the model allows for single Langevin time steps of $approx1.6$, 8, 16 and 16 ps for a dsDNA model-chain consisting of 64, 128, 256 and 512 basepairs (i.e., chains of 0.55, 1.11, 2.24 and 4.48 persistence lengths) respectively. Correspondingly, in one hour, a standard desktop computer can simulate 0.23, 0.56, 0.56 and 0.26 ms of these dsDNA chains respectively. We compare our results to those obtained from other methods, in particular, the (inextensible discretised) WLC model. Importantly, we demonstrate that at the same level of discretisation, i.e., when each discretisation element is one basepair long, our algorithm gains about 5-6 orders of magnitude in the size of time steps over the inextensible WLC model. Further, we show that our model can be mapped one-on-one to a discretised version of the extensible WLC model; implying that the speed-up we achieve in our model must hold equally well for the latter. We also demonstrate the use of the method by simulating efficiently the tumbling behaviour of a dsDNA segment in a shear flow.
We present results for a lattice model of bio-polymers where the type of $beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these different interaction strengths leads to low-temperature structures with different types of orientational order. We perform simulations of this model and so present the phase diagram, ascertaining the nature of the phases and the order of the transitions between these phases.
Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight backbone, both radial density profiles of monomers and side chain ends are obtained, as well as structure factors describing the scattering from a single side chain and from the total bottle-brush polymer. To describe the structure in the interior of a very long bottle-brush, a periodic boundary condition in the direction along the backbone is used, and to describe effects due to the finiteness of the backbone length, a second set of simulations with free ends of the backbone is performed. In the latter case, the inhomogeneity of the structure in the direction along the backbone is carefully investigated. We use these results to test various phenomenological models that have been proposed to interpret experimental scattering data for bottle-brush macromolecules. These models aim to extract information on the radial density profile of a bottle-brush from the total scattering via suitable convolution approximations. Possibilities to improve such models, guided by our simulation results, are discussed.
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific polymer and reflect the underlying atomistic details to some extent, and those which retain only the most basic features of a polymer chain (chain connectivity, short-range excluded-volume interactions, etc.). In this review we mainly focus on the second class of generic polymer models, while the first class of specific coarse-grained models is only touched upon briefly.
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by a special three body interaction and impacts on the behaviour both locally and non-locally. When thick polymers undergo compaction due to an attractive self-interaction, we find a new type of phase transition between a compact phase and a swollen phase at zero temperature on increasing the thickness. In the vicinity of this transition, short tubes form space filling helices and sheets as observed in protein native state structures. Upon increasing the chain length, or the number of chains, we numerically find a crossover from secondary structure motifs to a quite distinct class of structures akin to the semi-crystalline phase of polymers or amyloid fibers in polypeptides.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
