2008
DOI: 10.1103/physreve.78.011903
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Unzipping of two random heteropolymers: Ground-state energy and finite-size effects

Abstract: We have analyzed the dependence of average ground state energy per monomer, e, of the complex of two random heteropolymers with quenched sequences, on chain length, n, in the ensemble of chains with uniform distribution of primary sequences. Every chain monomer is randomly and independently chosen with the uniform probability distribution p = 1/c from a set of c different types at sufficiently low temperatures when the entropic contribution of the loop formation is negligible compared to direct energetic inter… Show more

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Cited by 6 publications
(5 citation statements)
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References 44 publications
(88 reference statements)
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“…It is not obvious how to do that directly in the frameworks of the dynamic programming approach formalized in the recursion relation ( 7)- (8). To proceed, we exploit some trick (formulated for the first time in [33]), which consists of two consecutive steps.…”
Section: Matching Versus Pairing Of Two Random Linear Heteropolymersmentioning
confidence: 99%
See 1 more Smart Citation
“…It is not obvious how to do that directly in the frameworks of the dynamic programming approach formalized in the recursion relation ( 7)- (8). To proceed, we exploit some trick (formulated for the first time in [33]), which consists of two consecutive steps.…”
Section: Matching Versus Pairing Of Two Random Linear Heteropolymersmentioning
confidence: 99%
“…In this section, we show how the algorithm used for the computation of the ground state energy of the RNA-like complexes can help to recover the details of the ground state secondary structure. We start with recalling the corresponding procedure for linear matching [28,29,33], and then we pass on to the more complicated RNA-like case.…”
Section: Secondary Structure Recoverymentioning
confidence: 99%
“…For example, we could choose ω j taking only two values e AT and e GC and then make a choice for f that reflects the fact that AT bounds are weaker than GC bounds, and that all other possible bounds are even weaker. Even restricting to {ω j } j=1,2,... that is IID, this model is highly non trivial (gPS model with this type of disorder has been considered at a numerical level in [30,31], see also [28,54] for related work). But one could also choose to consider the binding of two sequences that are not complementary (the case considered in [49] goes in this direction, even if only heuristics and numerics are presented): choose for example two independent sequences {ω (1) j } j=1,2,... and {ω…”
Section: Theorem 12 ([35]mentioning
confidence: 99%
“…It is not obvious how to do that directly in the frameworks of the dynamic programming approach formalized in the recursion relation (7). To proceed, we exploit the idea (formulated for the first time in [32]), which consists of two consecutive steps:…”
Section: Matching Vs Pairing Of Two Random Rna-type Heteropolymersmentioning
confidence: 99%