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Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of(More)
We present a statistical physics model to describe the stochastic behaviorof ion transport and channel transitions under an applied membrane voltage.To get pertinent ideas we apply our general theoretical scheme to ananalytically tractable model of the channel with a deep binding site whichinteracts with the permeant ions electrostatically. It is found that(More)
The biological systems described as soft matter on mesoscopic scales manifest, in contrast to hard (condensed) matter, a number of characteristics: complexity, exibility, and uctuations. Due to these, there arise a variety of conformational and nonequilibrium phase transitions at physiological temperatures, which seems to be relevant to biological(More)
The bending of double-stranded(ds) DNA on the nano-meter scale plays a key role in many cellular processes such as nucleosome packing, transcription-control, and viral-genome packing. In our recent study, a nanometer-sized dsDNA bent into a D shape was formed by hybridizing a circular single-stranded(ss) DNA and a complementary linear ssDNA. Our(More)
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static or temporally fluctuating far away from equilibrium. We study the dynamics of semiflexible polymer looping in the presence of such tensions by using(More)
DNA exists stably in the double-stranded structure at physiological temperatures, but base pairs are observed to unbind locally, giving way to bubbles (i.e., locally denatured states) due to thermal fluctuation. In this study, we consider the effect of sequence on the bubble statistics. On the basis of the Edwards equation description [W. Sung and J.-H.(More)
TRUSTEES AUDITORS EDITORS Theoretical physics, the description of fundamental natural phenomena using mathematics, is something I love deeply and have invested a significant fraction of my life mastering and promoting. Nonetheless it is clear to me that the profession of theoretical physics is in trouble, and that some major rethinking of the business model(More)
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of α-helix integration into the membrane that results depending upon membrane permeability and polymer adsorptiv-ity. For a membrane with a permeability larger than a critical value,(More)
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