Related papers: Theoretical investigation of finite size effects a…
We study a process of heat transfer between a body of heat capacity C(T) and a sequence of N heat reservoirs, with temperatures equally spaced between an initial temperature T_0 and a final temperature T_N. The body and the heat reservoirs…
In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
The theory of finite-size scaling explains how the singular behavior of thermodynamic quantities in the critical point of a phase transition emerges when the size of the system becomes infinite. Usually, this theory is presented in a…
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…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we…
We explore the occurrence of a magnetic field induced finite size effect on the specific heat and correlation lengths of anisotropic type-II superconductors near the zero field transition temperature Tc. Since near the zero field transition…
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…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies.…
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
We consider discrete and continuous representations of a thermodynamic process in which a random walker (e.g. a molecular motor on a molecular track) uses a periodically pumped energy (work) to pass $N$ sites and move energetically downhill…
In recent years many groups have used Fisher, Fisher, and Huse (FFH) dynamical scaling to investigate and demonstrate details of the superconducting phase transition. Some attention has been focused on two dimensions where the phase…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown…
Within generalized random energy models, we study the effects of energy discreteness and of entropy extensivity in the low temperature phase. At zero temperature, discreteness of the energy induces replica symmetry breaking, in contrast to…
We reaccess the droplet condensation-evaporation transition of a three-dimensional Lennard-Jones system upon a temperature change. With the help of parallel multicanonical simulations we obtain precise estimates of the transition…