Related papers: An intermediate phase in DNA melting
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
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…
The holographic dual of a finite-temperature gauge theory with a small number of flavours typically contains D-brane probes in a black hole background. At low temperature the branes sit outside the black hole and the meson spectrum is…
All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…
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…
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…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…
We present direct evidence for a reversible phase transition of DNA-linked colloidal gold assemblies. Transmission electron microscopy and optical absorption spectroscopy are used to monitor the colloidal gold phase transition, whose…
We study secondary structures of random RNA molecules by means of a renormalized field theory based on an expansion in the sequence disorder. We show that there is a continuous phase transition from a molten phase at higher temperatures to…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing-wave spectroscopy (DWS) to investigate the…
We study the phase transitions in a one dimensional Bose-Einstein condensate on a ring whose atomic scattering length is modulated periodically along the ring. By using a modified Bogoliubov method to treat such a nonlinear lattice in the…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
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…