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Double-stranded DNA (dsDNA) undergoes a denaturing transition above which the strands unbind completely. At temperatures (including the physiological temperature) below the transition the base pairs tend to unbind locally, giving way to loops, i.e., locally denatured states. In the flexible-chain model, the imaginary time Schrödinger equation describes the(More)
A detailed study of the direct synthesis of polymer nanocapsules, which does not require any template, and core removal, is presented. Thiol-ene "click" reaction between a CB[6] derivative (1) with 12 allyloxy groups at the periphery and dithiols directly produced polymer nanocapsules with a highly stable structure and relatively narrow size distribution.(More)
DNA stably exists as a double-stranded structure due to hydrogen-bonding and stacking interactions between bases. The stacking interactions are strengthened when DNA is paired, which results in great enhancement of bending rigidity. We study the effects of this stacking-induced stiffness difference on DNA denaturation and bubble formations. To this end, we(More)
A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 10(2)-10(6) than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly(More)
Double-stranded DNA (dsDNA) is known to form a locally denatured structure ("bubble") below its denaturation temperature (T(c)). We have investigated the physical behavior of the bubbles using a model of dsDNA as two wormlike chains containing interacting complementary base pairs. The model incorporates two biologically relevant features, i.e.,(More)
The bubbles in double-stranded DNA, essential for gene transcription and replication, occur in mechanically constrained situations. Through an elastic model incorporating topological constraint, we show that, when a stretched double helix is underwound above a critical value of twist, a bubble can spontaneously form, yielding extension and torque behaviors(More)
  • S Lee, W Sung
  • 2001
We study the thermally activated barrier crossing of a linear, flexible chain (polymer) under the Kramers bistable potential using the multidimensional barrier crossing theory and the functional integral method. We find that above a critical chain length or below a critical chain spring constant the chain at the barrier top undergoes coil-to-stretch(More)
We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the cis side subchain. We present theoretical and numerical evidence that the non-universal behavior observed in experiments and simulations are due to finite chain length effects(More)
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local(More)