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Conformations of Semiflexible Polymers Confined between Two Coaxial Cylindrical Layers

Author: XiangZhangHeng
Tutor: ZhangLinXi
School: Zhejiang University
Course: Physics
Keywords: Monte Carlo simulation Polymer polymer chain Coaxial concentric cylindrical Free energy Entropy Helical conformation
CLC: O631.1
Type: Master's thesis
Year: 2011
Downloads: 30
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Abstract

In 2005, Yehuda Snir know Randall D.Kamien an entropy change drive helical conformation of the articles published in the journal Science on the Natural Science of chain spontaneous formation of spiral structure point of view to avoid excluded volume overlap and do some theory to explain . We are trying calculated by theoretical simulations to further verify this conclusion. We know that when a semi-rigid tube in a crowded environment, the tube will often change their shape to achieve a more stable state. When the thickness of the tubes to achieve the appropriate ratio with its length, the tube will be formed naturally most compact helical structure. This phenomenon is easy to see, the the densely crowded cell environment, for example, the long molecular chains (e.g., DNA) in a cell is frequently used in the rules of the spiral structure to form a preferred mode of existence. Recently, biopolymers polymer chain is limited by the emergence of the helical structure in the process of its restricted, has aroused widespread concern. Using the Monte Carlo method in a semi-flexible polymer chain in the helical conformation of the cylindrical surface with weak adsorption potential behavior. The one hand, due to the presence of the molecular and intermolecular interaction between the tube and chain competing in the van der Waals force, on the other hand due to the presence of bending and entropy of absorption change around the tube around the polymer chain generated rules, which eventually led to the a spiral structure, and almost in the form of a single molecular layer adsorbed on the outside of the cylinder radius. Not consider the force between the chain and the tube, only to consider the limited space of the chain, whether there will be a similar situation to do?-Lattice Monte Carlo simulation method of polymer polymer chain in the coaxial concentric constrained between the cylindrical helical conformation conduct research at the same time without any force assumes that chain and pipe. First, by changing the rigidity of the constrained environment, and the polymer chain, to constitute a helical structure of the polymer chain a series of parameters in this model. Secondly, a helical structure of the polymer chain conformation parameters are analyzed and discussed, for example: the mean square of the polymer chain end distance, the persistence length of the polymer chain, the polymer chain of the helical orientation parameter G (m). Finally, contrast the same environment, the stability of the different rigid flexible chain conformation difference. 1. Limited the coaxial concentric cylindrical polymer between polymer chain, the conformation of the polymer chain will vary with the chain itself Goju change. Thermodynamic equilibrium is reached, limited flexible polymer chain chaotic intertwined structure was clew could not find any law; the constrained rigid polymer chain will become an almost straightened chain, and along the cylinder extend the central axis direction; conformation of the semi-flexible polymer chain, become very regular helical structure capable of forming the most common in nature. 2 the formation of the helical structure of the polymer chain is also affected by the impact of the restricted environment. Limited semi-flexible polymer chains between the two cylinders, only in certain internal and external cylindrical radius, in order to form a spiral structure legible. The smaller the radius of the inner cylinder, or the radius of the outer cylinder, will spiral structure to slow down or even disappear. 3 the formation of the helical structure of the polymer chains and the chain of its own length. The shorter the chain length, to achieve stable conformations required shorter simulation time, small number of spiral, helix formation is higher restricted environment requirements; longer chain length, the simulated time is longer, a large number of helical, helix formation would be appropriate to reduce the environmental requirements. 4 external cylindrical radius R1 = 2.0 and R2 = 5.0. When b = 0, the polymer chains of the monomer percentage content of the radial direction along the cylinder is almost stats participation spiral number of monomers is very low percentage, is almost 0. In this case, a chain messy wound together, will not form a helical conformation and therefore the direction of the cylinder radius to approximate a uniform distribution and no monomer in a spiral. 5 external cylindrical radius R1 = 2.0 and R2 = 5.0. When the percentage of number of monomer b in the vicinity of 20, the monomer in the polymer chain, including the vicinity of the cylindrical outer wall of enrichment, a high percentage content, STATS participation spiral, few can be more than 70%. This is because the cylindrical outer surface, including the semi-flexible chain wound and maintain the helical structure. 6 external cylindrical radius R1 = 2.0 and R2 = 5.O. When b close to 100, the polymer chains become almost a straight chain, the small number of spiral STATS monomers involved in helix hundreds stars also relatively low, and with the increase of the b, gradually tends to 0. True biological macromolecules are often completed its functional role in the crowded cellular environment, these may be able to further research on the future of biological macromolecules to help work in constrained environments.

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CLC: > Mathematical sciences and chemical > Chemistry > Polymer chemistry ( polymer ) > Polymer physics and physical chemistry of polymers > Theory of polymer structure
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