On the dimensionless model of the transcription bubble dynamics

IF 1.1 Q4 BIOPHYSICS
L. Krasnobaeva, L. Yakushevich
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引用次数: 0

Abstract

The dynamics of transcription bubbles is modeled using a system of nonlinear differential equations, the one-soliton solutions of which (kinks), are interpreted as a mathematical images of transcription bubbles. These equations contain a lot of DNA dynamic parameters, including the moments of inertia of nitrous bases, distances between base pairs, distances from the centers of mass of bases to sugar-phosphate chains, rigidity of the sugar-phosphate backbone, and interactions between bases within pairs. However, estimates of the parameter values are often difficult, and it is not convenient or simple to operate with such multi-parameter systems. One of the ways to reduce the number of the DNA dynamic parameters is to transform the model equations to a dimensionless form. In this work, we construct a dimensionless DNA model and apply it to study transcription bubbles dynamics. We show that transformation to a dimensionless form really leads to a decrease in the number of the model parameters and really simplifies the analysis of model equations and their solutions.
转录泡动力学的无量纲模型
转录泡的动力学是用非线性微分方程系统建模的,其单孤子解(扭结)被解释为转录泡的数学图像。这些方程包含了大量的DNA动力学参数,包括亚氮碱基的转动惯量、碱基对之间的距离、碱基质心到糖-磷酸链的距离、糖-磷酸主链的刚性以及碱基对之间的相互作用。然而,参数值的估计往往是困难的,并且在这种多参数系统中操作并不方便或简单。将模型方程转化为无量纲形式是减少DNA动态参数数目的方法之一。在这项工作中,我们构建了一个无量纲DNA模型,并将其应用于转录泡动力学研究。我们证明,转换为无量纲形式确实导致模型参数数量的减少,并且确实简化了模型方程及其解的分析。
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来源期刊
AIMS Biophysics
AIMS Biophysics BIOPHYSICS-
CiteScore
2.40
自引率
20.00%
发文量
16
审稿时长
8 weeks
期刊介绍: AIMS Biophysics is an international Open Access journal devoted to publishing peer-reviewed, high quality, original papers in the field of biophysics. We publish the following article types: original research articles, reviews, editorials, letters, and conference reports. AIMS Biophysics welcomes, but not limited to, the papers from the following topics: · Structural biology · Biophysical technology · Bioenergetics · Membrane biophysics · Cellular Biophysics · Electrophysiology · Neuro-Biophysics · Biomechanics · Systems biology
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