A Language Model-Informed Minimalistic Design of Functional Coacervate Vesicles

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Abstract

We employ coarse-grained molecular dynamics (CGMD) simulations to investigate the emergence of hollow biomolecular condensates. Our system consists of four types of particles representing coarse-grained (CG) units of single-stranded DNA (ssDNA), RNA, arginine-rich peptides (R$_{10}$), and explicit solvent molecules. Each bead represents a single nucleotide or amino acid, with a characteristic diameter $\sigma$, which sets the unit length scale.

Authors 14

1. Wei Guo

   Shenzhen University

   Affiliation as printed

   Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China

2. Yuchao Wang

   University of Hong Kong

   Affiliation as printed

   Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China

3. Subhadip Biswas

   Iowa State University

   Affiliation as printed

   Department of Chemistry, Iowa State University, Ames IA 50011, USA

4. Zhong Junnan

   Shenzhen University

   Affiliation as printed

   Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China

5. Gurudas Chakraborty Aachen DWI - Leibniz Institute for Interactive Materials

   DWI – Leibniz Institute for Interactive Materials

   Affiliation as printed

   DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany

6. Melina Schadt Aachen DWI - Leibniz Institute for Interactive Materials

   DWI – Leibniz Institute for Interactive Materials

   Affiliation as printed

   DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany

7. Fabian Wiertz Aachen DWI - Leibniz Institute for Interactive Materials

   DWI – Leibniz Institute for Interactive Materials

   Affiliation as printed

   DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany

8. Guobo Chen

   Shanghai Jiao Tong University · State Key Laboratory of Metal Matrix Composites

   Affiliation as printed

   State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

9. Sihan Liu

   University of Hong Kong

   Affiliation as printed

   Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China

10. Yang Song

    Shanghai Jiao Tong University · State Key Laboratory of Metal Matrix Composites

    Affiliation as printed

    State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

11. Yuan Lin

    University of Hong Kong

    Affiliation as printed

    Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), Hong Kong, China

12. Andreas Peter Herrmann Aachen DWI - Leibniz Institute for Interactive Materials

    DWI – Leibniz Institute for Interactive Materials

    Affiliation as printed

    DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany

13. Davit A. Potoyan

    Iowa State University

    Affiliation as printed

    Department of Chemistry, Iowa State University, Ames IA 50011, USA

14. Ho Cheung Shum
    Affiliation as printed

    Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China