Dissipative particle dynamics models of encapsulated microbubbles and nanoscale gas vesicles for biomedical ultrasound simulations

Ntarakas, Nikolaos (author), Lah, Maša (author), Svenšek, Daniel (author), Potisk, Tilen (author), Praprotnik, Matej (author)

Ultrasound-guided drug and gene delivery (USDG) enables controlled and spatially precise delivery of drugs and macromolecules, encapsulated in microbubbles (EMBs) and nanoscale gas vesicles (GVs), to target areas such as cancer tumors. It is a noninvasive, high precision, low toxicity process with drastically reduced drug dosage. Rheological and acoustic properties of GVs and EMBs critically affect the outcome of USDG and imaging. Detailed understanding and modeling of their physical properties is thus essential for ultrasound-mediated therapeutic applications. State-of-the-art continuum models of shelled bodies cannot incorporate critical details such as varying thickness of the encapsulating shell or specific interactions between its constituents and interior or exterior solvents. Such modeling approaches also do not allow for detailed modeling of chemical surface functionalizations, which are crucial for tuning the GV−blood interactions. We develop a general particle-based modeling framework for encapsulated bodies that accurately captures elastic and rheological properties of GVs and EMBs at the mesoscopic and nanoscale levels. We use dissipative particle dynamics to model the solvent, the gaseous phase in the capsid, and the triangulated surfaces of immersed objects. Their elastic behavior is studied and validated through stretching and buckling simulations, eigenmode analysis, shear flow simulations, and comparison of predicted GV buckling pressure with published experimental data. The presented modeling approach paves the way for large-scale simulations of nanoscale and microscale encapsulated bodies of different shapes and local anisotropy, capturing their dynamics, interactions, and collective behavior.

• Language: English
• Keywords: molecular simulations, molecular dynamics, liquid crystals, electrocaloric effect, ultrasound, gas vesicles, proteinaceous nanostructures, microbubbles, particle simulations, mesoscopic modeling, deformation, encapsulation, energy, fluid dynamics, membranes
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FMF - Faculty of Mathematics and Physics
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: Str. 16053−16070
• Numbering: Vol. 8, iss. 32
• PID: 20.500.12556/RUL-171386
• UDC: 536.91
• ISSN on article: 2574-0970
• DOI: 10.1021/acsanm.5c02783
• COBISS.SI-ID: 246402563
• Publication date in RUL: 25.08.2025

Record is a part of a journal

• Title: ACS applied nano materials
• Shortened title: ACS appl. nano mater.
• Publisher: American Chemical Society
• ISSN: 2574-0970
• COBISS.SI-ID: 32649255

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: molekulske simulacije, molekulska dinamika, tekoči kristali, elektrokalorični pojav

Projects

• Funder: EC - European Commission
• Funding programme: H2020
• Project number: 885155
• Name: Multiscale modeling and simulation approaches for biomedical ultrasonic applications
• Acronym: MULTraSonicA

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P1-0002
• Name: Večskalno modeliranje in simulacija mehke in biološke snovi v in izven ravnovesja