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Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of conformational change in the model have been investigated and several reduced order models developed, the conformational dynamics as a function of the length of the oscillator chain is relatively less clear. To address this, we used a modified Lindstedt-Poincare method and numerical computations. We calculate a perturbation expansion of the frequency of the models nonzero modes, finding that approximating these modes with their unperturbed dynamics, as in a previous reduced order model, may not hold when the length of the DNA model increases. We investigate the conformational change to local perturbation in models of varying lengths, finding that for chosen input and parameters, there are two regions of DNA length in the model, first where the minimum energy required to undergo the conformational change increases with DNA length; and second, where it is almost independent of the length of the DNA model. We analyze the conformational change in these models by adding randomness to the local perturbation, finding that the tendency of the system to remain in a stable conformation against random perturbation decreases with an increase in the DNA length. These results should help to understand the role of the length of a DNA molecule in influencing its conformational dynamics.
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this melting transition have been intensively investigated. Recently t
The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of para
The determination of a patients DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design personalized medicine [3]. Moreover, statistical studies and comparison of genomes [4] of a large n
Semiflexible polymers characterized by the contour length $L$ and persistent length $ell_p$ confined in a spatial region $D$ have been described as a series of ``{em spherical blobs} and ``{em deflecting lines} by de Gennes and Odjik for $ell_p < D$
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-str