Related papers: DNA Bubble Life Time in Denaturation
The existence of heterogeneity in the dynamics of supercooled liquids is believed to be one of the hallmarks of the glass transition. Intense research has been carried out in the past to understand the origin of this heterogeneity in…
We numerically examine dynamical heterogeneity in a highly supercooled three-dimensional liquid via molecular-dynamics simulations. To define the local dynamics, we consider two time intervals, $\tau_\alpha$ and $\tau_{\text{ngp}}$.…
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…
Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
We consider the hydrodynamic behavior of some conservative particle systems with degenerate jump rates without exclusive constraints. More precisely, we study the particle systems without restrictions on the total number of particles per…
We briefly review some of the models used to describe DNA denaturation dynamics, focusing on the value of the dynamical exponent $z$, which governs the scaling of the characteristic time $\tau\sim L^z$ as a function of the sequence length…
Hydrogen bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc...), hence the lifetime of such structures is an important microscopic parameter, which can be calculated in computer…
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…
Experiments have not only revealed the remarkably long lifetime of nanobubbles, but also demonstrated the diffusive instability of bubbles above micrometers, thus a full-scale physical understanding on the stability of bubbles is in urgent…
The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
Two significant consequences of quantum fluctuations are entanglement and criticality. Entangled states may not be critical but a critical state shows signatures of universality in entanglement. A surprising result found here is that the…
We search for a dependence of the lifetime of $^{20}\text{Na}$ nuclei on the nuclear spin direction. Such a directional dependence would be evidence for Lorentz-invariance violation in weak interactions. A difference in lifetime between…
We have investigated dynamical heterogeneity in a highly supercooled liquid using molecular-dynamics simulations in three dimensions. Dynamical heterogeneity can be characterized by three quantities: correlation length $\xi_4$, intensity…
We calculate the survival probability of a diffusing test particle in an environment of diffusing particles that undergo coagulation at rate lambda_c and annihilation at rate lambda_a. The test particle dies at rate lambda' on coming into…
Current precision big bang nucleosynthesis (BBN) studies motivate us to revisit the neutron lifespan in the plasma medium of the early universe. The mechanism we explore is the Fermi-blocking of decay electrons and neutrinos by plasma. As…
Membrane configurations in the Banks-Fischler-Shenker-Susskind matrix model are unstable due to the existence of flat directions in the potential and the decay process can be seen as a realization of chaotic scattering. In this note, we…
The long baseline between the Earth and the Sun makes solar neutrinos an excellent test beam for exploring possible neutrino decay. The signature of such decay would be an energy-dependent distortion of the traditional survival probability…