NDLI: Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement

Content Provider	Springer Nature Link
Author	Račko, Dušan Cifra, Peter
Copyright Year	2015
Abstract	We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and number of arms aligned together in the given region along the channel. We focused on the conformation transition, where all arms are initially stretched in one direction of the narrow channel and were interested in the process of how individual arms escape into a free volume region of channel. We found that the escape transition does not proceed from arm ends but progresses by extension of a loop starting from the branch point; the arms escape in individual steps and the extension of arms depends on how many arms align in parallel in the channel. Graphical abstract Indexes of the most distant beads in a star-shaped polymer during transition. The chain is indexed from the connecting point as I = 1 to the chain’s end with I = 100 as computed for semi-flexible molecules with b = 20, in a narrow channel with D = 10. Dashed line Process of arm retraction if it proceeded from arm end (opposite to what is observed)
Starting Page	1
Ending Page	10
Page Count	10
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	21
Issue Number	7
e-ISSN	09485023
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2015-07-04
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Semi-flexible DNA Molecular dynamics Confined Nano-channel Electrophoresis Computer Applications in Chemistry Molecular Medicine Computer Application in Life Sciences Characterization and Evaluation of Materials Theoretical and Computational Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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