{"title":"基于 DNA 的流体中的粗粒度相分离模型","authors":"Soumen De Karmakar, Thomas Speck","doi":"arxiv-2408.04435","DOIUrl":null,"url":null,"abstract":"DNA is now firmly established as a versatile and robust platform for\nachieving synthetic nanostructures. While the folding of single molecules into\ncomplex structures is routinely achieved through engineering basepair\nsequences, much less is known about the emergence of structure on larger scales\nin DNA fluids. The fact that polymeric DNA fluids can undergo phase separation\ninto dense fluid and dilute gas opens avenues to design hierachical and\nmultifarious assemblies. Here we investigate to which extent the phase behavior\nof single-stranded DNA fluids is captured by a minimal model of semiflexible\ncharged homopolymers while neglecting specific hybridization interactions. We\nfirst characterize the single-polymer behavior and then perform direct\ncoexistence simulations to test the model against experimental data. We\nconclude that counterions not only determine the effective range of direct\nelectrostatic interactions but also the effective attractions.","PeriodicalId":501146,"journal":{"name":"arXiv - PHYS - Soft Condensed Matter","volume":"11 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Coarse-grained models for phase separation in DNA-based fluids\",\"authors\":\"Soumen De Karmakar, Thomas Speck\",\"doi\":\"arxiv-2408.04435\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"DNA is now firmly established as a versatile and robust platform for\\nachieving synthetic nanostructures. While the folding of single molecules into\\ncomplex structures is routinely achieved through engineering basepair\\nsequences, much less is known about the emergence of structure on larger scales\\nin DNA fluids. The fact that polymeric DNA fluids can undergo phase separation\\ninto dense fluid and dilute gas opens avenues to design hierachical and\\nmultifarious assemblies. Here we investigate to which extent the phase behavior\\nof single-stranded DNA fluids is captured by a minimal model of semiflexible\\ncharged homopolymers while neglecting specific hybridization interactions. We\\nfirst characterize the single-polymer behavior and then perform direct\\ncoexistence simulations to test the model against experimental data. We\\nconclude that counterions not only determine the effective range of direct\\nelectrostatic interactions but also the effective attractions.\",\"PeriodicalId\":501146,\"journal\":{\"name\":\"arXiv - PHYS - Soft Condensed Matter\",\"volume\":\"11 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-08-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"arXiv - PHYS - Soft Condensed Matter\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/arxiv-2408.04435\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - PHYS - Soft Condensed Matter","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2408.04435","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
DNA 现已成为实现合成纳米结构的通用而强大的平台。单分子折叠成复杂结构通常是通过碱基配对序列工程实现的,但人们对 DNA 流体中更大规模结构的出现却知之甚少。事实上,聚合 DNA 流体可以在稠密流体和稀薄气体之间发生相分离,这为设计层次丰富的组装体开辟了道路。在这里,我们研究了单链 DNA 流体的相行为在多大程度上可以被忽略特定杂交相互作用的半柔性带电均聚物的最小模型所捕获。我们首先描述了单聚合物的行为特征,然后进行了直接共存模拟,根据实验数据对模型进行了检验。我们得出结论:反离子不仅决定了直接静电相互作用的有效范围,还决定了有效吸引力。
Coarse-grained models for phase separation in DNA-based fluids
DNA is now firmly established as a versatile and robust platform for
achieving synthetic nanostructures. While the folding of single molecules into
complex structures is routinely achieved through engineering basepair
sequences, much less is known about the emergence of structure on larger scales
in DNA fluids. The fact that polymeric DNA fluids can undergo phase separation
into dense fluid and dilute gas opens avenues to design hierachical and
multifarious assemblies. Here we investigate to which extent the phase behavior
of single-stranded DNA fluids is captured by a minimal model of semiflexible
charged homopolymers while neglecting specific hybridization interactions. We
first characterize the single-polymer behavior and then perform direct
coexistence simulations to test the model against experimental data. We
conclude that counterions not only determine the effective range of direct
electrostatic interactions but also the effective attractions.