اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدDoes the dynamics of sine-Gordon solitons predict active regions of DNA?
65
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
In this work we analyze the possibility that soliton dynamics in a simple nonlinear model allows functionally relevant predictions of the behaviour of DNA. This suggestion was first put forward by Salerno [Phys. Rev. A, vol. 44, p. 5292 (1991)] by showing results indicating that sine-Gordon kinks were set in motion at certain regions of a DNA sequence that include promoters. We revisit that system and show that the observed behaviour has nothing to do with promoters; on the contrary, it originates from the bases at the boundary, which are not part of the studied genome. We explain this phenomenology in terms of an effective potential for the kink center. This is further extended to disprove recent claims that the dynamics of kinks [Lenholm and Hornquist, Physica D, vol. 177, p. 233 (2003)] or breathers [Bashford, J. Biol. Phys., vol. 32, p. 27 (2006)] has functional significance. We conclude that no such information can be extracted from this simple nonlinear model or its associated effective potential.
قيم البحث
اقرأ أيضاً
We analyze the diffusive motion of kink solitons governed by the thermal sine-Gordon equation. We analytically calculate the correlation function of the position of the kink center as well as the diffusion coefficient, both up to second-order in temp
erature. We find that the kink behavior is very similar to that obtained in the overdamped limit: There is a quadratic dependence on temperature in the diffusion coefficient that comes from the interaction among the kink and phonons, and the average value of the wave function increases with $sqrt{t}$ due to the variance of the centers of individual realizations and not due to kink distortions. These analytical results are fully confirmed by numerical simulations.
Extending our previous construction in the sine-Gordon model, we show how to introduce two kinds of fermionic screening operators, in close analogy with conformal field theory with c<1.
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA methylation can howe
ver be subject to specific and fast changes over a short time scale even in non-dividing (i.e. not-replicating) cells. Such dynamic DNA methylation changes are caused by a combination of active demethylation and de novo methylation processes which have not been investigated in integrated models. Here we present a hybrid (hidden) Markov model to describe the cycle of methylation and demethylation over (short) time scales. Our hybrid model decribes several molecular events either happening at deterministic points (i.e. describing mechanisms that occur only during cell division) and other events occurring at random time points. We test our model on mouse embryonic stem cells using time-resolved data. We predict methylation changes and estimate the efficiencies of the different modification steps related to DNA methylation and demethylation.
We study the one-dimensional sine-Gordon model as a prototype of roughening phenomena. In spite of the fact that it has been recently proven that this model can not have any phase transition [J. A. Cuesta and A. Sanchez, J. Phys. A 35, 2373 (2002)],
Langevin as well as Monte Carlo simulations strongly suggest the existence of a finite temperature separating a flat from a rough phase. We explain this result by means of the transfer operator formalism and show as a consequence that sine-Gordon lattices of any practically achievable size will exhibit this apparent phase transition at unexpectedly large temperatures.
The bipartite ground state entanglement in a finite linear harmonic chain of particles is numerically investigated. The particles are subjected to an external on-site periodic potential belonging to a family parametrized by the unit interval encompas
sing the sine-Gordon potential at both ends of the interval. Strong correspondences between the soliton entanglement entropy and the kink energy distribution profile as functions of the sub-chain length are found.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
