Related papers: First-passage probability: a test for DNA Hamilton…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
The first passage time (FPT) problem is studied for superstatistical models assuming that the mesoscopic system dynamics is described by a Fokker-Planck equation. We show that all moments of the random intensive parameter associated to the…
We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
We solve the first-passage problem for the Heston random diffusion model. We obtain exact analytical expressions for the survival and hitting probabilities to a given level of return. We study several asymptotic behaviors and obtain…
Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the…
To describe the nonequilibrium states of a system we introduce a new thermodynamic parameter - the lifetime (the first passage time) of a system. The statistical distributions that can be obtained out of the mesoscopic description…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
The first-passage time is proposed as an independent thermodynamic parameter of the statistical distribution that generalizes the Gibbs distribution. The theory does not include the determination of the first passage statistics itself. A…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
A criterion is derived for the determination of parameter domains of first order phase transitions in quantum mechanical tunneling models. The criterion is tested by application to various models, in particular to some which have been used…