Related papers: DNA Bubble Life Time in Denaturation
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We…
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 investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The…
The precise value of the neutron lifetime is of fundamental importance to particle physics and cosmology. The neutron lifetime recently obtained, 878.5 +/- 0.7stat +/- 0.3sys s, is the most accurate one to date. The new result for the…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…
In this paper it is shown that if one accept assumption of de Broglie that "unitary wave-particle" exists simultaneously and this coexistence is real, then one can find the mean life time of the hydrogen atom of Bohr (intensities).…
It is possible that the proton is stable while atomic hydrogen is not. This is the case in models with new particles carrying baryon number which are light enough to be stable themselves but heavy enough so that proton decay is…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
The Poland-Scheraga model is a celebrated model for the denaturation transition of DNA, which has been widely used in the bio-physical literature to study, and investigated by mathematicians. In the original model, only opposite bases of…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
Bubbles at the air-liquid interface are important for many natural and industrial processes. Factors influencing the lifetime of such surface bubbles have been investigated extensively, yet the impact of dissolved gas concentration remains…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally…