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The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices, and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30nm- 1mu m range and the confined DNA chains are 1 to 4mu m long. It is found that the knotting probability is maximum for slit widths in the 70-100nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region which drops significantly below D ~100nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications.
The non-equilibrium dynamics of condensation phenomena in nano-pores is studied via Monte Carlo simulation of a lattice gas model. Hysteretic behavior of the particle density as a function of the density of a reservoir is obtained for various pore ge
The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length ranging f
We propose a unifying, analytical theory accounting for the self-organization of colloidal systems in nano- or micro-cluster phases. We predict the distribution of cluter sizes with respect to interaction parameters and colloid concentration. In part
We discuss the distribution of ions around highly charged PEs when there is competition between monovalent and multivalent ions, pointing out that in this case the number of condensed ions is sensitive to short-range interactions, salt, and model-dep
It is generally believed that the intrinsic properties of glasses are intimately related to potential energy landscapes (PELs). However, little is known about the PELs of glasses below the glass transition temperature (T_g). Taking advantage of lower