Dissipative Particle Dynamics Simulation of Ultrasound Propagation Through Liquid Water

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2022 Jan 10

PMID 35001631

Authors

Petra Papez

Matej Praprotnik

Affiliations

Soon will be listed here.

Abstract

Ultrasound is widely used as a noninvasive method in therapeutic and diagnostic applications. These can be further optimized by computational approaches, as they allow for controlled testing and rational optimization of the ultrasound parameters, such as frequency and amplitude. Usually, continuum numerical methods are used to simulate ultrasound propagating through different tissue types. In contrast, ultrasound simulations using particle description are less common, as the implementation is challenging. In this work, a dissipative particle dynamics model is used to perform ultrasound simulations in liquid water. The effects of frequency and thermostat parameters are studied and discussed. We show that frequency and thermostat parameters affect not only the attenuation but also the computed speed of sound. The present study paves the way for development and optimization of a virtual ultrasound machine for large-scale biomolecular simulations.

References

Delgado-Buscalioni R, Kremer K, Praprotnik M . Coupling atomistic and continuum hydrodynamics through a mesoscopic model: application to liquid water. J Chem Phys. 2010; 131(24):244107. DOI: 10.1063/1.3272265. View

Zavadlav J, Melo M, Marrink S, Praprotnik M . Adaptive resolution simulation of an atomistic protein in MARTINI water. J Chem Phys. 2014; 140(5):054114. DOI: 10.1063/1.4863329. View

Korotkin I, Karabasov S . A generalised Landau-Lifshitz fluctuating hydrodynamics model for concurrent simulations of liquids at atomistic and continuum resolution. J Chem Phys. 2019; 149(24):244101. DOI: 10.1063/1.5058804. View

Reith D, Putz M, Muller-Plathe F . Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem. 2003; 24(13):1624-36. DOI: 10.1002/jcc.10307. View

Zavadlav J, Sablic J, Podgornik R, Praprotnik M . Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution. Biophys J. 2018; 114(10):2352-2362. PMC: 6129463. DOI: 10.1016/j.bpj.2018.02.042. View

Espanol . Hydrodynamics from dissipative particle dynamics. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995; 52(2):1734-1742. DOI: 10.1103/physreve.52.1734. View

Korotkin I, Karabasov S, Nerukh D, Markesteijn A, Scukins A, Farafonov V . A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time. J Chem Phys. 2015; 143(1):014110. DOI: 10.1063/1.4923011. View

Maresca D, Sawyer D, Renaud G, Lee-Gosselin A, Shapiro M . Nonlinear X-wave ultrasound imaging of acoustic biomolecules. Phys Rev X. 2021; 8(4). PMC: 8147876. DOI: 10.1103/physrevx.8.041002. View

Groot R, Rabone K . Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. Biophys J. 2001; 81(2):725-36. PMC: 1301549. DOI: 10.1016/S0006-3495(01)75737-2. View

10.

Praprotnik M, Delle Site L . Multiscale molecular modeling. Methods Mol Biol. 2012; 924:567-83. DOI: 10.1007/978-1-62703-017-5_21. View

11.

Zavadlav J, Melo M, Cunha A, De Vries A, Marrink S, Praprotnik M . Adaptive Resolution Simulation of MARTINI Solvents. J Chem Theory Comput. 2015; 10(6):2591-8. DOI: 10.1021/ct5001523. View

12.

Chou K . Identification of low-frequency modes in protein molecules. Biochem J. 1983; 215(3):465-9. PMC: 1152424. DOI: 10.1042/bj2150465. View

13.

Lee H, Kim H, Han H, Lee M, Lee S, Yoo H . Microbubbles used for contrast enhanced ultrasound and theragnosis: a review of principles to applications. Biomed Eng Lett. 2019; 7(2):59-69. PMC: 6208473. DOI: 10.1007/s13534-017-0016-5. View

14.

Tavakkoli J, Cathignol D, Souchon R, Sapozhnikov O . Modeling of pulsed finite-amplitude focused sound beams in time domain. J Acoust Soc Am. 1999; 104(4):2061-72. DOI: 10.1121/1.423720. View

15.

Junghans C, Praprotnik M, Kremer K . Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat. Soft Matter. 2020; 4(1):156-161. DOI: 10.1039/b713568h. View

16.

Zeng X, McGough R . Optimal simulations of ultrasonic fields produced by large thermal therapy arrays using the angular spectrum approach. J Acoust Soc Am. 2009; 125(5):2967-77. PMC: 2806438. DOI: 10.1121/1.3097499. View

17.

Vyas U, Christensen D . Ultrasound beam propagation using the hybrid angular spectrum method. Annu Int Conf IEEE Eng Med Biol Soc. 2009; 2008:2526-9. DOI: 10.1109/IEMBS.2008.4649714. View

18.

Udroiu I . Ultrasonic drug delivery in Oncology. J BUON. 2015; 20(2):381-90. View

19.

Praprotnik M, Janezic D . Molecular dynamics integration meets standard theory of molecular vibrations. J Chem Inf Model. 2005; 45(6):1571-9. DOI: 10.1021/ci050168+. View

20.

Deshpande N, Needles A, Willmann J . Molecular ultrasound imaging: current status and future directions. Clin Radiol. 2010; 65(7):567-81. PMC: 3144865. DOI: 10.1016/j.crad.2010.02.013. View