Extension of Rod-Coil Multiblock Copolymers and the Effect of the Helix-Coil Transition (original) (raw)
Related papers
The Journal of Chemical Physics
We study force-extension curves of a single semiflexible chain consisting of several rigid rods connected by flexible spacers. The atomic force microscopy and laser optical or magnetic tweezers apparatus stretching these rod-coil macromolecules are discussed. In addition, the stretching by external isotropic force is analyzed. The main attention is focused on computer simulation and analytical results. We demonstrate that the force-extension curves for rod-coil chains composed of two or three rods of equal length differ not only quantitatively but also qualitatively in different probe methods. These curves have an anomalous shape for a chain of two rods. End-to-end distributions of rod-coil chains are calculated by Monte Carlo method and compared with analytical equations. The influence of the spacer's length on the force-extension curves in different probe methods is analyzed. The results can be useful for interpreting experiments on the stretching of rod-coil block-copolymers.
Globular structures of a helix-coil copolymer: Self-consistent treatment
The Journal of Chemical Physics, 2007
A self-consistent field theory was developed in the grand-canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths correspondingly. The resulting field-theory takes, in addition to the conventional Zimm-Bragg parameters, also three-dimensional interaction terms into account. The appropriate differential equations which determine the self-consistent fields were solved numerically with finite element method. Three different phase states are found: open chain, amorphous globule and nematic liquid-crystalline (LC) globule. The LC-globule formation is driven by the interplay between the hydrophobic helical segments attraction and the anisotropic globule surface energy of an entropic nature. The full phase diagram of the helix-coil copolymer was calculated and thoroughly discussed. The suggested theory shows a clear interplay between secondary and tertiary structures in globular homopolypeptides.
Statistical mechanics of stretching of biopolymers
We developed a simple model of polymers on a triangular lattice to study the force-induced transitions related to biopolymers. Using an exact enumeration technique, we calculate various thermodynamic quantities associated with it. We show here, by including different parameters, e.g. bending and paring interactions in the model system, that one can understand the qualitative differences in the force-extension curves exhibited by different biopolymers. Our study also shows that the solvent plays an important role in the unfolding of proteins.
Macromolecular Theory and Simulations, 2014
Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between different length scales, namely, the persistence length p, and the disorder correlation length p, in addition to the fraction of hydrophobic patches f play a major role in altering the equilibrium morphologies and mechanical response. In particular, we show a plethora of equilibrium morphologies for this system, e.g. core-shell, looped (with hybridised hydrophilic-hydrophobic sections), and extended coils as a function of these parameters. A competition of bending energy and hybridisation energies between two types of beads determines the equilibrium morphology. Further, mechanical properties of such polymer architectures are crucially dependent on their native conformations, and in turn on the disorder realisation along the chain backbone. Thus, for flexible chains, a globule to extended coil transition is effected via a tensile force for all disorder realisations. However, the exact nature of the force-extension curves are different for the different disorder realisations. In contrast, we find that force-extension behavior of semi-flexible chains with different equilibrium configurations e.g. core-shell, looped, etc. reveal a cascade of force-induced conformational transitions.
Effects of Stiffness on Short, Semiflexible Homopolymer Chains
International Journal of Modern Physics C, 2012
Conformational and transition behavior of finite, semiflexible homopolymers is studied using an extension of the Wang–Landau algorithm. Generation of a flat distribution in the sampling parameters energy and stiffness allows for efficient investigation of transitions between various conformational phases. Of particular importance is the ability to predict behavior for a given stiffness value, where three classes of minimum energy conformations are expected: Solid-globular, rod-like and toroidal. We present first results highlighting the behavior of a single N = 20 length chain.
A ug 2 00 5 A generalized theory of semiflexible polymers
2017
NA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the polymer mechanics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. Recent experimental results from DNA cyclization studies have cast doubt on the applicability of the canonical semiflexible polymer theory, the wormlike chain (WLC) model, to DNA bending on biologically relevant length scales. This paper develops a theory of the chain statistics of a class of generalized semiflexible polymer models. Our focus is on the theoretical development of these models and the calculation of experimental observables. To illustrate our methods, we focus on a specific, illustrative model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics...
Chain stiffness bridges conventional polymer and bio-molecular phases
2019
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses – one yielding an energy penalty for local bends (energetic stiffness) and the other two forbidding certain classes of chain conformations (entropic stiffness). Using detailed Wang-Landau microcanonical Monte Carlo simulations, we study the interplay between the nature of the stiffness and the ground state conformation of a self-attracting chain. We find a wide range of ground state conformations including a coil, a globule, a toroid, rods, helices, zig-zag strands resembling β-sheets, as well as knotted conformations allowing us to bridge conventional polymer phases and biomolecular phases. An analytical mapping is derived between the persistence lengths stemming from energetic and entropic stiffness. Our study shows unambiguously that different stiffness play different physical roles ...