Separation of long DNA chains using non-uniform electric field: a numerical study

We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation demonstrates that the chain captured by an electrode escapes from the binding electric field due to thermal fluctuation. We find that the mobility of chain would depend on the chain length; the mobility sharply increases when the length of a chain exceeds a critical value, which is strongly affected by the amplitude of the applied ac field. Thus we can adjust the length regime, in which this microchannel well separates DNA molecules, without changing the structure of the channel. We also present a theoretical insight into the relation between the critical chain length and the field amplitude.Comment: 12 pages, 9 figure

Local Reorientation Dynamics of Semiflexible Polymers in the Melt

The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local chain stiffness and by the overall chain length. It takes place by two different subsequent processes: A short-time non-exponential decay and a long-time exponential reorientation arising from the relaxation of medium-size chain segments. Both processes depend on stiffness and chain length. The strong influence of the chain length on the chain dynamics is in marked contrast to its negligible effect on the static structure of the melt. The local structure shows only a small dependence on the stiffness, and is independent of chain length. Calculated correlation functions related to double-quantum NMR experiments are in qualitative agreement with experiments on entangled melts. A plateau is observed in the dependence of segment reorientation on the mean-squared displacement of the corresponding chain segments. This plateau confirms, on one hand, the existence of reptation dynamics. On the other hand, it shows how the reptation picture has to be adapted if, instead of fully flexible chains, semirigid chains are considered.Comment: 29 pages, several figures, accepted by Macromolecule

Modelling diffusional transport in the interphase cell nucleus

In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles, a random walk chain model, and a self avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the 3D geometry of the fiber network on the particle diffusion is investigated in detail, while varying occupation volume, chain length, persistence length and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self avoiding random walk model, and, to a lesser extent, the persistence length, affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve.Comment: 9 pages, 8 figure

Determination of Boundary Scattering, Intermagnon Scattering, and the Haldane Gap in Heisenberg Chains

Low-lying magnon dispersion in a S=1 Heisenberg antiferromagnetic (AF) chain is analyzed using the non-Abelian DMRG method. The scattering length $a_{\rm b}$ of the boundary coupling and the inter-magnon scattering length $a$ are determined. The scattering length $a_{\rm b}$ is found to exhibit a characteristic diverging behavior at the crossover point. In contrast, the Haldane gap $\Delta$, the magnon velocity $v$, and $a$ remain constant at the crossover. Our method allowed estimation of the gap of the S=2 AF chain to be $\Delta = 0.0891623(9)$ using a chain length longer than the correlation length $\xi$.Comment: 6 pages, 3 figures, 1 table, accepted in Phys. Rev.

Monte Carlo simulations reveal the straightening up of an end-grafted flexible chain with a rigid side chain

We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we observe a considerable straightening of the flexible backbone as quantified via the gyration tensor. For $b=N$, i.e. when attaching the side chain to the free end of the flexible backbone, the effect was strongest