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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 spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiatio
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 up to a few kBT. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We inve
Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quant
We study the search process of a target on a rapidly folding polymer (“DNA”) by an ensemble of particles (“proteins”), whose search combines 1D diffusion along the chain, Lévy type diffusion mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search.
We use a master equation approach based on the Poland–Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore–quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins that se
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We investigate the translocation of a stiff polymer consisting of M monomersthrough a nanopore in a membrane, in the presence of binding particles(chaperones) that bind onto the polymer, and partially prevent backsliding ofthe polymer through the pore. The process is characterized by the rates: kfor the polymer to make a diffusive jump through the pore, q for unbinding ofa chaperone, and the rate
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 also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in de
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out
We investigate the dynamics of a single local denaturation zone in a DNA molecule, a so-called DNA bubble, in the presence of single-stranded DNA binding proteins (SSBs). In particular, we develop a dynamical description of the process in terms of a two-dimensional master equation for the time evolution of the probability distribution of having a bubble of size m with n bound SSBs, for the case wh
We derive an expression for the polarizability of an ellipsoidally shaped cell-like structure at field frequencies where membrane molecular resonances (vibrational and electronic) are important. We first present analytical results for the dielectric function of a flat, dipole coupled, bilayer consisting of molecules with one prominent resonance frequency. Due to the nature of the dipole coupling t
In this paper we study the response of an ellipsoidal particle with a dielectrically anisotropic coating (the coating dielectric function being different parallel and perpendicular to the coating normal) placed in a constant external electric field. For the coating region we find that potential can be written in terms of solutions to a one-dimensional Heun's equation which is derived from the thre
We investigate the vdrift velocity vdrift of ellipsoidal polarizable particles (ellipsoids and coated ellipsoids), driven through a viscous fluid by an electric or electromagnetic field intensity gradient. At low Reynolds number and in the dipole approximation vdrift is proportional to the square of the principal axis along the direction of motion multiplied by a form factor, which is weakly depen
