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Polymers 2018, 10(4), 447; https://doi.org/10.3390/polym10040447

An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids

1
Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
2
CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
3
Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
*
Author to whom correspondence should be addressed.
Received: 23 March 2018 / Revised: 13 April 2018 / Accepted: 13 April 2018 / Published: 16 April 2018
(This article belongs to the Special Issue Selected Papers from "ECIS 2017")
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Abstract

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. View Full-Text
Keywords: DNA; DNA nanotechnology; patchy particles; Wertheim theory; thermodynamic integration; phase coexistence DNA; DNA nanotechnology; patchy particles; Wertheim theory; thermodynamic integration; phase coexistence
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Locatelli, E.; Rovigatti, L. An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids. Polymers 2018, 10, 447.

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