Orellana Alberto Giacomo, De Michele Cristiano
SISSA, Scuola Internazionale Superiore Studi Avanzati, Via Bonomea 265, I-34136, Trieste, Italy.
Dipartimento di Fisica, "Sapienza" Università di Roma, P.le A. Moro 2, 00185, Roma, Italy.
Eur Phys J E Soft Matter. 2019 Jun 7;42(6):71. doi: 10.1140/epje/i2019-11836-5.
Liquid-crystalline phases in all-DNA systems have been extensively studied in the past and although nematic, cholesteric and columnar mesophases have been observed, the smectic phase remained elusive. Recently, it has been found evidence of a smectic-A ordering in an all-DNA system, where the constituent particles, which are gapped DNA duplexes, resemble chain-sticks. It has been argued that in the smectic-A phase these DNA chain-sticks should be folded as a means to suppress aggregate polydispersity and excluded volume. Nevertheless, if initial crystalline configurations are prepared in silico with gapped DNA duplexes either fully unfolded or fully folded by carrying out computer simulations one can end up with two different phases having at the same concentration and temperature the majority of gapped DNA duplexes either folded or unfolded. This result suggests that these two phases have a small free energy difference, since no transition is observed from one to the other within the simulation time span. In the present manuscript, we assess which of these two phases is thermodynamically stable through a suitable protocol based on thermodynamic integration. Our method is rather general and it can be used to discriminate stable states from metastable ones of comparable free energy.
过去，全DNA系统中的液晶相已得到广泛研究。尽管已观察到向列相、胆甾相和柱状中间相，但近晶相仍然难以捉摸。最近，在一个全DNA系统中发现了近晶-A有序的证据，其中组成颗粒是有缺口的DNA双链体，类似于链棒。有人认为，在近晶-A相中，这些DNA链棒应该折叠起来，以抑制聚集体多分散性和排除体积。然而，如果通过计算机模拟在计算机上制备初始晶体构型，使有缺口的DNA双链体完全展开或完全折叠，那么在相同浓度和温度下，最终可能会得到两个不同的相，其中大多数有缺口的DNA双链体要么折叠要么展开。这一结果表明，这两个相的自由能差很小，因为在模拟时间范围内未观察到从一个相到另一个相的转变。在本手稿中，我们通过基于热力学积分的合适方案评估这两个相中的哪一个在热力学上是稳定的。我们的方法相当通用，可用于区分自由能相当的稳定态和亚稳态。
