Locatelli Emanuele, Rovigatti Lorenzo
Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria.
CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy.
Polymers (Basel). 2018 Apr 16;10(4):447. doi: 10.3390/polym10040447.
We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.
我们进行了一项数值研究，其中使用一个逼真的粗粒度模型对自组装DNA构建体进行了大规模的整体模拟。该研究旨在获得此类系统自由能的精确估计，尽管这在数值计算上要求较高。然后，我们利用这些精确结果来验证一种最近提出的理论方法，该方法基于液态理论——韦特海姆理论，用于计算全DNA流体的相图。这种基于最低阶维里展开和最近邻DNA模型的理论/数值混合方法，能够以一种简便的方式提供与实验半定量相符的、无参数的DNA缔合流体热力学描述。我们表明，该方案的预测与使用更复杂方法得到的预测一样准确。我们还通过纳入超越最近邻模型的非平凡额外贡献来计算DNA杂交自由能，展示了该方法的灵活性。
