Structure and aggregation of a helix-forming polymer (original) (raw)
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Kinetically driven helix formation during the homopolymer collapse process
Physical Review E Statistical Nonlinear and Soft Matter Physics, 2008
Using Langevin simulations, we find that simple “generic” bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The helix formation is initiated by the unstable modes of the straight chain, which drive the system towards a long-lived metastable transient state. The effect is most pronounced if hydrodynamic interactions are screened.
“Raindrop” Coalescence of Polymer Chains during Coil–Globule Transition
Macromolecules, 2013
We approach the problem of coil−globule transition dynamics numerically by Brownian dynamics simulations. This method allows us to study the behavior of polymer chains of varying stiffness and the effects of bending stiffness on chain morphology during the process of coil− globule collapse, imitating globule formation in poor solvent conditions. We record and analyze a three-stage process of globule formation for flexible chains: (1) nucleation, (2) coalescence of nuclei, and (3) collapsed globule formation. Stiffer chains undergo similar formation stages; however, the "raindrops" formed by these chains are elongated (unlike spherical structures formed by flexible chains) and exhibit regular packing of chains into antiparallel hairpin structures. In order to assess the transition dynamics quantitatively, polymer chain configurations were analyzed by generating contact maps and contact frequency histograms for all given configurations. These clusters are initial-configuration-dependent, and their growth and intercluster contacts have direct analogy with the process of raindrop coalescence.
Physical Review E, 1998
A discrete-to-continuum approach is introduced to study the static and dynamic properties of polymer chain systems with a bead-spring chain model in two dimensions. A finitely extensible nonlinear elastic potential is used for the bond between the consecutive beads with the Lennard-Jones ͑LJ͒ potential with smaller (R c ϭ2 1/6 ϭ0.95) and larger (R c ϭ2.5ϭ2.1) values of the upper cutoff for the nonbonding interaction among the neighboring beads. We find that chains segregate at temperature Tϭ1.0 with R c ϭ2.1 and remain desegregated with R c ϭ0.95. At low temperature (Tϭ0.2), chains become folded, in a ribbonlike conformation, unlike random and self-avoiding walk conformations at Tϭ1.0. The power-law dependence of the rms displacements of the center of mass (R c.m.) of the chains and their center node (R cn) with time are nonuniversal, with the range of exponents 1 Ӎ0.45Ϫ0.25 and 2 Ӎ0.30Ϫ0.10, respectively. Both radius of gyration (R g) and average bond length (͗l͘) decrease on increasing the range of interaction (R c), consistent with the extended state in good solvent to collapsed state in poor solvent description of the polymer chains. Analysis of the radial distribution function supports these observations. ͓S1063-651X͑98͒11205-9͔
Unfolding of globular polymers by external force
The Journal of Chemical Physics, 2015
We examine the problem of a polymer chain, folded into a globule in poor solvent, subjected to a constant tensile force. Such a situation represents a Gibbs thermodynamic ensemble and is useful for analysing forceclamp atomic force microscopy measurements, now very common in molecular biophysics. Using a basic Flory mean-field theory, we account for surface interactions of monomers with solvent. Under an increasing tensile force a first-order phase transition occurs from a compact globule to a fully extended chain, in an 'all-ornothing' unfolding event. This contrasts with the regime of imposed extension, first studied by Halperin and Zhulina, where there is a regime of coexistence of a partial globule with an extended chain segment. We relate the transition forces in this problem to the solvent quality and degree of polymerisation, and also find analytical expressions for the energy barriers present in the problem. Using these expressions, we analyse the kinetic problem of a force-ramp experiment, and show that the force at which a globule ruptures depends on the rate of loading.
Macromolecular Theory and Simulations, 2011
In the present work, we revisit the effect of macromolecular crowding on the sizes of flexible neutral polymer chains. Motivated by recent experimental measurements on crowding effects on neutral flexible polymers chains, we perform Monte Carlo simulations on a model system consisting of hard spheres (HS) and a neutral flexible polymer chain. We find that, depending on the ratio of the sizes of the colloidal particles to the sizes of the polymer chain, and thus, on the extent of the colloid partitioning among the chain segments and the solution, the flexible polymeric coil may be either continuously compressed, or initially compressed followed by a reswelling at high enough colloid concentration. The chain behavior is thus nonmonotonic, a point which, apart from the work of Khalatur et al., has not so far been stressed in simulations of flexible polymer chains under crowding conditions. A thermodynamic model for the polymer–colloid interactions based on the Gibbs–Duhem equation and ...
2000
The processes of the irreversible aggregation of chain molecules with various numbers of associating groups are studied by the Monte Carlo method using the Eden model. Three-dimensional lattice systems are considered. The model developed qualitatively reproduces the main structural (morphological) characteristics that are observed experimentally for the aggregates composed of macromolecules of ionic polymers under the conditions of strong segregation. It is established that the chains with one associating terminal group form tree-like coral-shaped aggregates; associating groups form the skeleton with a large number of branches at the periphery. It is shown that the chains with the number n s ≥ 2 of associating groups form aggregates whose structures correspond to a three-dimensional network. Integral characteristics of a system are scale-invariant; molecular parameters, such as the chain length N and the number of associating groups n s , enter into corresponding
Unwinding globules under tension and polymer collapse
Physical Review E, 2002
Polymer collapse is known to be mediated by the formation of pearls. These intermediate structures behave as small globules under tension. The globule size is studied by molecular dynamic simulations as a function of the strength of an external stretching force applied to its ends, for different values of the chain length. A very strong first-order-like transition from a compact globule state to a stretched one is observed. A model of this transition in terms of a globule-chain system is presented. The critical force, above which the globule unwinds, is shown to satisfy a power law scaling like N 1/3 in the number of monomers.