Related papers: Dynamics of a bubble formed in double stranded DNA
Using results from Schramm Loewner evolution (SLE), we give the expression of the fluctuation-induced force exerted by a polymer on a small impenetrable disk, in various 2-dimensional domain geometries. We generalize to two polymers and…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
Dynamics of complex systems is often hierarchically organized on different time scales. To understand the physics of such hierarchy, here Brownian motion of a particle moving through a fluctuating medium with slowly varying temperature is…
We present a method to compute pairing fluctuations on top of the Gutzwiller approximation (GA). Our investigations are based on a charge-rotational invariant GA energy functional which is expanded up to second order in the pair…
We have studied the separation of a double stranded DNA (dsDNA), which is driven either by the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends…
Based on the trajectories of the separation between water molecule pairs from MD simulations, we investigate the bond breakage dynamics in bulk water. From the spectrum of mean first-passage times, the Fokker-Planck equation allows us to…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
Many active materials and biological systems are driven far from equilibrium by embedded agents that spontaneously generate forces and distort the surrounding material. Probing and characterizing these athermal fluctuations is essential for…
We calculate the entropic part of partition function of a bubble embedded in a double stranded DNA (dsDNA) by considering the total weights of possible configurations of a system of two single stranded DNA (ssDNA) of given length which…
We derive a new fluctuation-dissipation relation for non-equilibrium systems with long-term memory. We show how this relation allows one to access new experimental information regarding active forces in living cells that cannot otherwise be…
The dynamics and the steady states of a point-like tracer particle immersed in a confined critical fluid are studied. The fluid is modeled field-theoretically in terms of an order parameter (concentration or density field) obeying…
We discuss the dynamics of particles in one dimension in potentials that are random both in space and in time. The results are applied to recent optics experiments on Anderson localization, in which the transverse spreading of a beam is…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
We study motion of tagged particles in a harmonic chain of active particles. We consider three models of active particle dynamics - run and tumble particle, active Ornstein-Uhlenbeck particle and active Brownian particle. We investigate the…