Monte Carlo simulation of AB-copolymers with saturating bonds.

A.C. Chertovich, V.A. Ivanov, A.R. Khokhlov, Jakob Bohr

Research output: Contribution to journalJournal articleResearch

Abstract

Structural transitions in a single AB-copolymer chain where saturating bonds can be formed between A- and B-units are studied by means of Monte Carlo computer simulations using the bond fluctuation model. Three transitions are found, coil-globule, coil-hairpin and globule-hairpin, depending on the nature of a particular AB-sequence: statistical random sequence, diblock sequence and 'random-complementary' sequence (one-half of such an AB-sequence is random with Bernoulli statistics while the other half is complementary to the first one). The properties of random-complementary sequences are closer to those of diblock sequences than to the properties of random sequences. The model (although quite rough) is expected to represent some basic features of real RNA molecules, i.e. the formation of secondary structure of RNA due to hydrogen bonding of corresponding bases and stacking interactions of the base pairs in helixes. We introduce the notation of RNA-like copolymers and discuss in what sense the sequences studied here can be considered as RNA-like copolymers.
Original languageEnglish
JournalJournal of Physics: Condensed Matter
Volume15
Issue number19
Pages (from-to)3013-3027
ISSN0953-8984
Publication statusPublished - 2003

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