Free energy of conformational isomers: The case of gapped DNA duplexes.

摘要: Liquid-crystalline phases in all-DNA systems have been extensively studied the past and although nematic, cholesteric columnar mesophases observed, smectic phase remained elusive. Recently, it has found evidence of a smectic-A ordering an system, where constituent particles, which are gapped DNA duplexes, resemble chain-sticks. It argued that these chain-sticks should be folded as means to suppress aggregate polydispersity excluded volume. Nevertheless, if initial crystalline configurations prepared silico with duplexes either fully unfolded or by carrying out computer simulations one can end up two different having at same concentration temperature majority unfolded. This result suggests small free energy difference, since no transition is observed from other within simulation time span. In present manuscript, we assess thermodynamically stable through suitable protocol based on thermodynamic integration. Our method rather general used discriminate states metastable ones comparable energy.