Poland-Scheraga models and the DNA denaturation transition

Abstract

Poland-Scheraga models were introduced to describe the DNA denaturation transition. We give a rigorous and refined discussion of a family of these models. We derive possible scaling functions in the neighborhood of the phase transition point and review common examples. We introduce a self-avoiding Poland-Scheraga model displaying a first order phase transition in two and three dimensions. We also discuss exactly solvable directed examples. This complements recent suggestions as to how the Poland-Scheraga class might be extended in order to display a first order transition, which is observed experimentally.

arXiv comment23 pages, 4 figures; v2: new section 2.4, changes in introduction and conclusion; v3: major changes, version as published

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Cited by in corpus (31)

• Theory of Bubble Nucleation and Cooperativity in DNA Melting
• A review of Monte Carlo simulations of polymers with PERM
• Sequence sensitivity of breathing dynamics in heteropolymer DNA
• Breathing dynamics in heteropolymer DNA
• Phase transitions in large deviations of reset processes
• Pinning and wetting transition for (1+1)-dimensional fields with Laplacian interaction
• The depinning transition in presence of disorder: a toy model
• Path Integral Method for DNA Denaturation
• Stochastic approach to DNA breathing dynamics
• Denaturation Patterns in Heterogeneous DNA
• Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
• Stacking Interactions in Denaturation of DNA Fragments
• Master equation approach to DNA-breathing in heteropolymer DNA
• Numerical study of the disordered Poland-Scheraga model of DNA denaturation
• Numerical study on a disordered model for DNA denaturation transition
• Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities
• Direct observation of large temperature fluctuations during DNA thermal denaturation
• A large deviation perspective on ratio observables in reset processes: robustness of rate functions
• Random copolymer adsorption: Morita approximation compared to exact numerical simulations
• How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
• Role of helicity in DNA hairping folding dynamics
• Renormalisation group determination of the order of the DNA denaturation transition
• Thermodynamic phases in first detected return times of quantum many-body systems
• Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
• Exact solution of two friendly walks above a sticky wall with single and double interactions
• Variety of Scaling Laws for DNA Thermal Denaturation
• Dynamics and Control of DNA Sequence Amplification
• Adsorption transition of a self-avoiding polymer chain onto a rigid rod
• Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
• Exact solutions of directed walk models of polymeric zipping with pulling in two and three dimensions
• DNA thermal denaturation by polymer field theory approach: effects of the environment