Related papers: Healing Length and Bubble Formation in DNA
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
A method is presented to derive electron temperatures and densities of planetary nebulae (PNe) simultaneously, using the observed hydrogen recombination spectrum, which includes continuum and line emission. By matching theoretical spectra…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
The impact of various types of external potentials to the Peyrard-Bishop DNA denaturation is investigated through statistical mechanics approach. The partition function is obtained using transfer integral method, and further the stretching…
We study how bubbles grow after the initial nucleation event in generic first-order cosmological phase transitions characterised by the values of latent heat, interface tension and correlation length, and driven by a scalar order parameter…
We present an analysis of late-O/early-B-powered, parsec-sized bubbles and associated star-formation using 2MASS, GLIMPSE, MIPSGAL and MAGPIS surveys. Three bubbles were selected from the Churchwell et al. (2007) catalog. We confirm that…
A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of…
The deep crustal heating, associated with exothermal nuclear reactions, is believed to be a key parameter for describing the thermal evolution of accreting neutron stars. In this paper, we present the first thermodynamically consistent…
We propose a phonon-assisted tunnelling model for explanation of conductivity dependence on temperature and temperature-dependent I-V characteristics in deoxyribonucleic acid (DNA) molecules. The capability of this model for explanation of…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
Big bang nucleosynthesis (BBN) is the standard model theory for the production of the light nuclides during the early stages of the universe, taking place for a period of about 20 minutes after the big bang. Deuterium production, in…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
The nucleation of vapor bubbles within a superheated fluid is studied using density functional theory. The nudged elastic band technique is used to find the minimum energy pathway from the metastable uniform liquid to the stable uniform gas…
3D-Particle Tracking (3D-PTV) and Phase Sensitive Constant Temperature Anemometry in pseudo-turbulence--i.e., flow solely driven by rising bubbles-- were performed to investigate bubble clustering and to obtain the mean bubble rise…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
We present results from direct, large-scale molecular dynamics (MD) simulations of homogeneous bubble (liquid-to-vapor) nucleation. The simulations contain half a billion Lennard-Jones (LJ) atoms and cover up to 56 million time-steps. The…
We study the viscosity corrections to the growth rate of nucleating bubbles in a first order phase transition in scalar field theory. We obtain the non-equilibrium equation of motion of the coordinate that describes small departures from…
The use of excessively long timesteps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational…
DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to…