Related papers: Healing Length and Bubble Formation in DNA
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
We investigate nuclear pasta structures at high temperatures in the framework of relativistic mean field model with Thomas-Fermi approximation. Typical pasta structures (droplet, rod, slab, tube, and bubble) are obtained, which form various…
The formation and growth of helium bubbles due to self-irradiation in plutonium has been modelled by a discrete kinetic equations for the number densities of bubbles having $k$ atoms. Analysis of these equations shows that the bubble size…
The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical Molecular Dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
The rise in temperature from the adiabatic compression of a bubble is computed in thermodynamic mean field (van der Waals) theory. It is shown that the temperature rise is higher for the noble gas atoms than for more complex gas molecules.…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
The spontaneous formation of tiny bubbles in a liquid is at the root of the nucleation mechanism during the liquid-to-vapor transition of a metastable liquid. The smaller the bubbles the larger their probability to appear, and even for…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
We present results of numerical studies of the Landau-Ginzburg dynamics of the order parameter in one-dimensional models inspired by the condensed matter analogues of cosmological phase transitions. The main goal of our work is to show…
We carry out high resolution two-dimensional radiation-hydrodynamic numerical simulations to study the formation and evolution of hot bubbles inside planetary nebulae (PNe). We take into account the evolution of the stellar parameters, wind…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
We calculate the bulk-viscous dissipation time for adiabatic density oscillations in nuclear matter at densities of 1-7 times nuclear saturation density and at temperatures ranging from 1 MeV, where corrections to previous low-temperature…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The bubble size distribution is a summary statistics that can be computed from the observed 21-cm signal from the Epoch of Reionization. As it depends only on the ionization field and is not limited to gaussian information, it is an…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
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.…