Coarse-grain models are essential to understand the biological function of DNA molecules because the length and time scales of the sequence-dependent physical properties of DNA are often beyond the reach of experimental and all-atom computational methods. Simulating coarse-grain models of DNA, e.g. using Langevin dynamics, requires the parametrization of both potential and kinetic energy functions. Many studies have shown that the flexibility (i.e., potential energy) of a DNA molecule depends on its sequence. In contrast, little is known about the sequence-dependence of DNA mass parameters required to model its kinetic energy. In this paper, an algebraic expression is derived for the kinetic energy as a function of linear and angular velocities of each DNA base parameterized by its mass, center of mass, and rotational inertia tensor. The parameters of this function are then approximated from a set of fine-grain molecular dynamics simulations representing all combinations of the four DNA base pairs AT, TA, GC, and CG, in different sequence contexts. Compatibility conditions associated with the assumption of each base being modeled as a rigid body were verified to be good approximations. The kinetic parameters were found to be significantly different between the four G, C, A, and T bases, and to not be dependent on the sequence context. This suggests that the effective kinetic parameters of a DNA base may depend only on the base itself, not on its neighbors.

Jeremy Curuksu

Acta Biotheoretica

ACTA BIOTHEORETICA 致力于推动理论生物学，涵盖数学生物学和生物学哲学，特别关注生物学理论形成的方法学。欢迎各种生物学理论的论文。有趣的科目包括生物学哲学、生物数学、计算生物学、遗传学、生态学和形态学。理论形成的过程可以用语言或数学的形式呈现。此外，纯方法论论文可以致力于生物学理论和概念背后的哲学的历史渊源。论文应包含对生物学假设的清晰陈述，并在适用的情况下，将其翻译成数学形式的理由以及对数学处理的详细讨论.应澄清与经验数据的联系。ACTA BIOTHEORETICA 还欢迎批评性书评、对先前论文的简短评论以及将注意力集中在有趣的新理论思想上的简短笔记。

Acta Biotheoretica is dedicated to advancing the field of theoretical biology, encompassing mathematical biology and the philosophy of biology, with a particular focus on the methodologies of theory formation in biology. We welcome papers on a variety of biological theories, with interesting topics including the philosophy of biology, biomathematics, computational biology, genetics, ecology, and morphology. The process of theory formation can be presented in either linguistic or mathematical forms. Additionally, purely methodological papers may delve into the historical origins of the philosophy behind biological theories and concepts. Papers should include a clear statement of biological hypotheses and, where applicable, provide justifications for translating these into mathematical forms, along with detailed discussions of the mathematical treatment. The connection to empirical data should also be clarified. Acta Biotheoretica also welcomes critical book reviews, brief comments on previous papers, and short notes focusing on intriguing new theoretical ideas.

《Acta Biotheoretica》致力于推动理论生物学的研究，涵盖数学生物学和生物学哲学，特别关注生物学理论形成的方法论。我们欢迎各种生物学理论的论文，感兴趣的主题包括生物学哲学、生物数学、计算生物学、遗传学、生态学和形态学。理论形成的过程可以通过语言或数学的形式呈现。此外，纯方法论的论文也可以探讨生物学理论和概念背后的哲学历史渊源。论文应包含对生物学假设的清晰陈述，并在适用的情况下，提供将其翻译成数学形式的理由以及对数学处理的详细讨论。同时，应明确与经验数据的联系。《Acta Biotheoretica》还欢迎批评性书评、对先前论文的简短评论，以及关注有趣的新理论思想的简短笔记。

Category	Quartile
生物学	4
生物学, 数学与计算生物学	4

From Fine-Grain to Coarse-Grain Modeling: Estimating Kinetic Parameters of DNA Molecules

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Category	Quartile
MATHEMATICAL & COMPUTATIONAL BIOLOGY	4