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Journal Articles

Normal-mode analysis of circular DNA at the base-pair level, 2; Large-scale configurational transformation of a naturally curved molecule

Matsumoto, Atsushi; Tobias, I.*; Olson, W. K.*

Journal of Chemical Theory and Computation, 1(1), p.130 - 142, 2005/01

Times Cited Count：9 Percentile：30.01(Chemistry, Physical)

Fine structural and energetic details embedded in the DNA base sequence, such as intrinsic curvature, are important to the packaging and processing of the genetic material. Here we investigate the internal dynamics of a 200 bp closed circular molecule with natural curvature using a newly developed normal-mode treatment of DNA in terms of neighboring base-pair "step" parameters. As superhelical stress is accumulated in the DNA, the frequency, i.e., energy, of the dominant bending mode decreases in value, and if the imposed stress is sufficiently large, a global configurational rearrangement of the circle to the figure-8 form takes place. We combine energy minimization with normal-mode calculations of the two states to decipher the configurational pathway between the two states.

Journal Articles

Normal-mode analysis of circular DNA at the base-pair level, 1; Comparison of computed motions with the predicted behavior of an ideal elastic rod

Matsumoto, Atsushi; Tobias, I.*; Olson, W. K.*

Journal of Chemical Theory and Computation, 1(1), p.117 - 129, 2005/01

https://doi.org/10.1021/ct049950r

Times Cited Count：11 Percentile：35.65(Chemistry, Physical)

We have extended a newly developed approach to study the low frequency normal modes of mesoscopic fragments of linear DNA in order to investigate the dynamics of closed circular molecules of comparable size, i.e., a few hundred base pairs. We have added restraint energy terms and a global minimization step to treat the more complicated, spatially constrained duplex in terms of the intrinsic conformation and flexibility of the constituent base-pair "step" parameters.

Journal Articles

Theory of the Newcomb equation and applications to MHD stability analysis of a tokamak

Tokuda, Shinji; Aiba, Nobuyuki*

Journal of Plasma and Fusion Research SERIES, Vol.6, p.207 - 209, 2004/00

Recent progress in the theory of the Newcomb equation is reported. Emphasis is put on the analysis of external modes including peeling modes (high kink modes), where is the toroidal mode number. A theory for low external modes is developed so that it is also useful for the analysis of resistive wall modes.

Journal Articles

Possible nature of nonideal perturbations limiting plasma pressure in Tokamaks

Mikhailovskii, A. B.*; Churikov, A. P.*; Konovalov, S. V.; Shirokov, M. S.*; Tsypin, V. S.*

Doklady Physics, 48(4), p.159 - 162, 2003/04

https://doi.org/10.1134/1.1574369

Times Cited Count：1 Percentile：12.84(Mechanics)

It is shown that there is a new class of perturbations, limiting the pressure of ideally stable plasma in the conditions of fusion reactors of tokamak type. localization of such modes includes three characteristic regions: large-scale (MHD), Larmor and sub-Larmor ones. It is suggested that these modes can be responsible for spontaneous generation of neoclassical tearing modes observed experimentally.

Journal Articles

Inner layer problem for ideal MHD modes in a toroidal system

Tokuda, Shinji

Proceedings of 30th EPS Conference on Controlled Fusion and Plasma Physics (CD-ROM), 4 Pages, 2003/00

When we solve the eigenvalue problem associated with the two-dimensional Newcomb equation, we can identify the stability of a tokamak plasma against ideal MHD perturbations. The eigenvalue problem does not give the physical growth rate when the plasma is unstable. However, we can determine the growth rate by constructing a dispersion relation that gives the relation between the growth rate and the eigenvalue. It is expected that the dispersion relation provides an effective and fast method of stability analysis of MHD modes close to the marginal stability against ideal MHD perturbations, and the relation can be extended for non-ideal MHD modes close to the marginal stability.

Journal Articles