Predicting the Interfacial Energy and Morphology of DNA Condensates
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866914206827151360 |
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| author | Liu, Sihan Košmrlj, Andrej |
| author_facet | Liu, Sihan Košmrlj, Andrej |
| contents | The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we develop a theoretical and computational framework to understand and predict multiphase morphologies in DNA-nanostar solutions. Because morphology is governed by interfacial energies between coexisting phases, we combine Flory-Huggins theory with coarse-grained molecular dynamics simulations to examine how these energies depend on key microscopic features of DNA nanostars, including size, valence, bending rigidity, Debye screening length, binding strength, and sticky-end distribution. The phase behavior of DNA nanostars is quantitatively captured by a generalized lattice model, in which the interplay between sticky-end binding energy and conformational entropy determines the effective interactions. Focusing on condensates comprising two dense phases, we find that Janus-like morphologies are ubiquitous because the interfacial energies between the dense and dilute phases, $γ_{i\in\{1,2\}}$, are typically comparable. In contrast, nested morphologies are rare as they require a large asymmetry in $γ_i$, which arises only for highly dissimilar nanostars such as those differing markedly in valence or size. Moreover, the interfacial energy between the two dense phases, $γ_{12}$, can be modulated either discretely, by varying sticky-end distribution, or continuously, by tuning the crosslinker ratio; the former may even eliminate nested configurations. These findings establish physical design principles for constructing complex condensate architectures directly from microscopic molecular parameters. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2512_16150 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Predicting the Interfacial Energy and Morphology of DNA Condensates Liu, Sihan Košmrlj, Andrej Biological Physics Soft Condensed Matter The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we develop a theoretical and computational framework to understand and predict multiphase morphologies in DNA-nanostar solutions. Because morphology is governed by interfacial energies between coexisting phases, we combine Flory-Huggins theory with coarse-grained molecular dynamics simulations to examine how these energies depend on key microscopic features of DNA nanostars, including size, valence, bending rigidity, Debye screening length, binding strength, and sticky-end distribution. The phase behavior of DNA nanostars is quantitatively captured by a generalized lattice model, in which the interplay between sticky-end binding energy and conformational entropy determines the effective interactions. Focusing on condensates comprising two dense phases, we find that Janus-like morphologies are ubiquitous because the interfacial energies between the dense and dilute phases, $γ_{i\in\{1,2\}}$, are typically comparable. In contrast, nested morphologies are rare as they require a large asymmetry in $γ_i$, which arises only for highly dissimilar nanostars such as those differing markedly in valence or size. Moreover, the interfacial energy between the two dense phases, $γ_{12}$, can be modulated either discretely, by varying sticky-end distribution, or continuously, by tuning the crosslinker ratio; the former may even eliminate nested configurations. These findings establish physical design principles for constructing complex condensate architectures directly from microscopic molecular parameters. |
| title | Predicting the Interfacial Energy and Morphology of DNA Condensates |
| topic | Biological Physics Soft Condensed Matter |
| url | https://arxiv.org/abs/2512.16150 |