A minimal coarse-grained model to study the gelation of multi-armed DNA nanostars

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dc.contributor.author Naskar, Supriyo
dc.contributor.author Bhatia, Dhiraj
dc.contributor.author Lin, Shiang-Tai
dc.contributor.author Maiti, Prabal K.
dc.date.accessioned 2021-11-10T09:32:18Z
dc.date.available 2021-11-10T09:32:18Z
dc.date.issued 2021-10
dc.identifier.citation Naskar, Supriyo; Bhatia, Dhiraj; Lin, Shiang-Tai and Maiti, Prabal K., "A minimal coarse-grained model to study the gelation of multi-armed DNA nanostars", arXiv, Cornell University Library, DOI: arXiv:2110.11251, Oct. 2021. en_US
dc.identifier.uri http://arxiv.org/abs/2110.11251
dc.identifier.uri https://repository.iitgn.ac.in/handle/123456789/7256
dc.description.abstract DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and five arms and study their self-assembly using molecular dynamics simulations. Our simulations show that the DNA nanostars form thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from the arrested gel phase to an unstructured liquid phase has been modelled using two-state theoretical model. We find that this transition is enthalpic driven and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends which is giving rise to gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using two-phase thermodynamic model, also substantiate the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature, demonstrating the phase transition to the gel phase. The detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, easily extensible to other polymeric systems, and has remarkable implications in the DNA nanotechnology field.
dc.description.statementofresponsibility by Supriyo Naskar, Dhiraj Bhatia, Shiang-Tai Lin and Prabal K. Maiti
dc.language.iso en_US en_US
dc.publisher Cornell University Library en_US
dc.subject Soft Condensed Matter en_US
dc.subject Materials Science en_US
dc.subject Statistical Mechanics en_US
dc.subject Biological Physics en_US
dc.subject Computational Physics en_US
dc.title A minimal coarse-grained model to study the gelation of multi-armed DNA nanostars en_US
dc.type Pre-Print en_US
dc.relation.journal arXiv

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