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非平衡驱动下补丁粒子的耗散自组装:一项计算研究

Dissipative Self-Assembly of Patchy Particles under Nonequilibrium Drive: A Computational Study.

作者信息

Nag Shubhadeep, Bisker Gili

机构信息

Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel.

The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel.

出版信息

J Chem Theory Comput. 2024 Oct 22;20(20):8844-8861. doi: 10.1021/acs.jctc.4c00856. Epub 2024 Oct 4.

DOI:10.1021/acs.jctc.4c00856
PMID:39365844
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11500309/
Abstract

Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore the dissipative self-assembly of patchy particles under nonequilibrium conditions, with the aim of overcoming the constraints imposed by equilibrium assembly. Utilizing extensive Monte Carlo (MC) and Molecular Dynamics (MD) simulations, we provide insight into the effects of external forces that mirror natural and chemical processes on the assembly rates and the stability of the resulting assemblies comprising 8, 10, and 13 patchy particles. Implemented by a favorable bond-promoting drive in MC or a pulsed square wave potential in MD, our simulations reveal the role these external drives play in accelerating assembly kinetics and enhancing structural stability, evidenced by a decrease in the time to first assembly and an increase in the duration the system remains in an assembled state. Through the analysis of an order parameter, entropy production, bond dynamics, and interparticle forces, we unravel the underlying mechanisms driving these advancements. We also validated our key findings by simulating a larger system of 100 patchy particles. Our comprehensive results not only shed light on the impact of external stimuli on self-assembly processes but also open a promising pathway for expanding the application by leveraging patchy particles for novel nanostructures.

摘要

受生物学启发并利用纳米技术实现,补丁粒子的自组装已成为构建复杂结构的关键机制,这些结构可模仿具有多种功能的自然系统。在此,我们探索非平衡条件下补丁粒子的耗散自组装,旨在克服平衡组装所带来的限制。通过广泛的蒙特卡罗(MC)和分子动力学(MD)模拟,我们深入了解了模拟自然和化学过程的外力对由8个、10个和13个补丁粒子组成的组装体的组装速率和稳定性的影响。通过MC中有利的键促进驱动力或MD中的脉冲方波势来实现,我们的模拟揭示了这些外部驱动力在加速组装动力学和增强结构稳定性方面所起的作用,这表现为首次组装时间的减少以及系统保持组装状态的持续时间的增加。通过分析序参量、熵产生、键动力学和粒子间作用力,我们揭示了推动这些进展的潜在机制。我们还通过模拟100个补丁粒子的更大系统验证了我们的关键发现。我们的综合结果不仅阐明了外部刺激对自组装过程的影响,还为利用补丁粒子构建新型纳米结构来扩展应用开辟了一条有前景的途径。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/7b1aa7245b45/ct4c00856_0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/0e6acb400252/ct4c00856_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/3d97c3b06657/ct4c00856_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/31029df56b87/ct4c00856_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/1f3a8ad5892d/ct4c00856_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/6f88ea7f75c7/ct4c00856_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/1a6f7ff3dd00/ct4c00856_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/22ce1f594a6f/ct4c00856_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/7a9d69bb477a/ct4c00856_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/1bd92296d7b6/ct4c00856_0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/bc7c54754532/ct4c00856_0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/7b1aa7245b45/ct4c00856_0011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/0e6acb400252/ct4c00856_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/3d97c3b06657/ct4c00856_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/31029df56b87/ct4c00856_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/1f3a8ad5892d/ct4c00856_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/6f88ea7f75c7/ct4c00856_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/1a6f7ff3dd00/ct4c00856_0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/22ce1f594a6f/ct4c00856_0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/7a9d69bb477a/ct4c00856_0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/1bd92296d7b6/ct4c00856_0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/bc7c54754532/ct4c00856_0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0da3/11500309/7b1aa7245b45/ct4c00856_0011.jpg

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