Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime

被引:6
作者
Zembrzycki, Krzysztof [1 ]
Pawlowska, Sylwia [2 ]
Pierini, Filippo [1 ]
Kowalewski, Tomasz Aleksander [1 ]
机构
[1] Polish Acad Sci, Inst Fundamental Technol Res, Dept Biosyst & Soft Matter, ul Pawinskiego 5B, PL-02106 Warsaw, Poland
[2] Gdansk Univ Technol, Fac Elect Telecommun & Informat, ul G Narutowicza 11-12, PL-80233 Gdansk, Poland
关键词
Brownian motion; molecular dynamics; optical tweezers; ballistic regime; water model comparison; INSTANTANEOUS VELOCITY; WATER; RATES; DIFFUSION; PARTICLES; DYNAMICS; TIP3P; MODEL;
D O I
10.3390/polym15030787
中图分类号
O63 [高分子化学(高聚物)];
学科分类号
070305 ; 080501 ; 081704 ;
摘要
The four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most popular water models, all of which take into account electrostatic interactions, are tested and compared based on yielded results and resources required. Three different conditions were simulated: a freely moving particle and one in a potential force field with two different strengths based on 1 pN/nm and 10 pN/nm. In all cases, the diameter of the colloidal particle was 50 nm. The acquired data were compared with experimental measurements performed using optical tweezers with position capture rates as high as 125 MHz. The experiments were performed in pure water on polystyrene particles with a 1 mu m diameter in special microchannel cells.
引用
收藏
页数:12
相关论文
共 46 条
[1]   Effects of surfaces and macromolecular crowding on bimolecular reaction rates [J].
Andrews, Steven S. .
PHYSICAL BIOLOGY, 2020, 17 (04)
[2]   Detailed Simulations of Cell Biology with Smoldyn 2.1 [J].
Andrews, Steven S. ;
Addy, Nathan J. ;
Brent, Roger ;
Arkin, Adam P. .
PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (03)
[3]  
[Anonymous], LAMMPS Molecular Dynamics Simulator
[4]   OBSERVATION OF A SINGLE-BEAM GRADIENT FORCE OPTICAL TRAP FOR DIELECTRIC PARTICLES [J].
ASHKIN, A ;
DZIEDZIC, JM ;
BJORKHOLM, JE ;
CHU, S .
OPTICS LETTERS, 1986, 11 (05) :288-290
[5]   ACCELERATION AND TRAPPING OF PARTICLES BY RADIATION PRESSURE [J].
ASHKIN, A .
PHYSICAL REVIEW LETTERS, 1970, 24 (04) :156-&
[6]   THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS [J].
BERENDSEN, HJC ;
GRIGERA, JR ;
STRAATSMA, TP .
JOURNAL OF PHYSICAL CHEMISTRY, 1987, 91 (24) :6269-6271
[7]  
Berendsen HJC., 1981, Interaction Model for Water in Relation to Protein Hydration, DOI [DOI 10.1007/978-94-015-7658-121, 10.1007/978-94-015-7658-121, 10.1007/978-94-015-7658-1_21]
[8]   Theory of Crowding Effects on Bimolecular Reaction Rates [J].
Berezhkovskii, Alexander M. ;
Szabo, Attila .
JOURNAL OF PHYSICAL CHEMISTRY B, 2016, 120 (26) :5998-6002
[9]   Sculpting and fusing biomimetic vesicle networks using optical tweezers [J].
Bolognesi, Guido ;
Friddin, Mark S. ;
Salehi-Reyhani, Ali ;
Barlow, Nathan E. ;
Brooks, Nicholas J. ;
Ces, Oscar ;
Elani, Yuval .
NATURE COMMUNICATIONS, 2018, 9
[10]   Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase [J].
Carney, Sean P. ;
Ma, Wen ;
Whitley, Kevin D. ;
Jia, Haifeng ;
Lohman, Timothy M. ;
Luthey-Schulten, Zaida ;
Chemla, Yann R. .
NATURE COMMUNICATIONS, 2021, 12 (01)