Thermal denaturation of an helicoidal DNA model
arXiv:cond-mat/0309454 · doi:10.1103/PhysRevE.68.061909
Abstract
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's ``universality class'' strongly suggests the presence of an ``underlying'' continuous transition.
arXiv commentSubmitted to Phys. Rev. E
References in corpus (12)
- Why is the DNA Denaturation Transition First Order?
- Denaturation of Heterogeneous DNA
- Helicoidal model for DNA opening
- Statistical Mechanics of Torque Induced Denaturation of DNA
- Order of the phase transition in models of DNA thermal denaturation
- Roles of stiffness and excluded volume in DNA denaturation
- A Simple Model for the DNA Denaturation Transition
- Theoretical study of collective modes in DNA at ambient temperature
- Bubble propagation in a helicoidal molecular chain
- Thermodynamic instabilities in one dimension: correlations, scaling and solitons
- Vector Nonlinear Klein-Gordon Lattices: General Derivation of Small Amplitude Envelope Soliton Solutions
- Thermodynamic instabilities in one dimensional particle lattices: a finite-size scaling approach
Cited by in corpus (32)
- Physics of base-pairing dynamics in DNA
- Modelling DNA at the mesoscale: a challenge for nonlinear science?
- Thermodynamics of Twisted DNA with Solvent Interaction
- Statistical Theory of Force Induced Unzipping of DNA
- A composite model for DNA torsion dynamics
- Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics
- Modelling DNA Response to THz Radiation
- The probability analysis of opening of DNA
- Solitons in the Yakushevich model of DNA beyond the contact approximation
- Functionals linear in curvature and statistics of helical proteins
- Soliton-like base pair opening in a helicoidal DNA: An analogy with helimagnet and cholesterics
- Nonlinear molecular excitations in a completely inhomogeneous DNA chain
- Dynamical versus statistical mesoscopic models for DNA denaturation
- Theoretical investigation of finite size effects at DNA melting
- Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
- Theoretical and Experimental Investigations of DNA Open States
- Simple Combined Model for Nonlinear Excitations in DNA
- Solitons in a double pendulums chain model, and DNA roto-torsional dynamics
- Direct observation of large temperature fluctuations during DNA thermal denaturation
- A helicoidal transfer matrix model for inhomogeneous DNA melting
- Unwinding dynamics of double-stranded polymers
- Equilibrium winding angle of a polymer around a bar
- Multiple timescales in a model for DNA denaturation dynamics
- Anharmonic stacking in supercoiled DNA
- Sharp DNA denaturation in a helicoidal mesoscopic model
- Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
- Effect of genome sequence on the force-induced unzipping of a DNA molecule
- Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models
- Stability domains of actin genes and genomic evolution
- Unbinding of mutually avoiding random walks and two dimensional quantum gravity
- On the thermodynamics of DNA in the Peyrard-Bishop-Dauxois model
- Nonlinear waves in double-stranded DNA