Related papers: DNA melting in poor solvent
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.…
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…
Melting and hybridization of DNA-capped gold nanoparticle networks are investigated with optical absorption spectroscopy. Single-stranded, 12-base DNA-capped gold nanoparticles are linked with complementary, single-stranded, 24-base linker…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The aggregate is modeled as a cluster of gold nanoparticles on a periodic lattice connected by DNA bonds, and the extinction coefficient…
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…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic…
We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
We perform extensive simulations of $10^4$ Lennard-Jones particles to study the effect of particle size dispersity on the thermodynamic stability of two-dimensional solids. We find a novel phase diagram in the dispersity-density parameter…
A general theory for the melting of two dimensional solids explaining the universal and non-universal properties is an open problem up to date. Although the celebrated KTHNY theory have been able to predict the critical properties of the…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We study by extensive Monte Carlo simulations the effect of random bond dilution on the phase transition of the three-dimensional 4-state Potts model which is known to exhibit a strong first-order transition in the pure case. The phase…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
Melting in two spatial dimensions, as realized in thin films or at interfaces, represents one of the most fascinating phase transitions in nature, but it remains poorly understood. Even for the fundamental hard-disk model, the melting…
Melting and freezing transitions in two dimensional systems are known to show highly unusual characteristics. Most of the earlier studies considered atomic systems; the melting behavior in two dimensional molecular solids is still largely…
For doped two-dimensional Mott insulators in their normal state, the challenge is to understand the evolution from a conventional metal at high doping to a strongly correlated metal near the Mott insulator at zero doping. To this end, we…
We use quantum Monte Carlo simulations to determine the finite temperature phase diagram and to investigate the thermal and quantum melting of stripe phases in a two-dimensional hard-core boson model. At half filling and low temperatures…