Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils

Man, Viet Hoang; Derreumaux, Philippe; Nguyen, Phuong H.

doi:10.1063/1.4966263

Cited by 33 publications

(22 citation statements)

References 51 publications

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“…The conformational change during the aggregation and disaggregation process can be clarified by molecular dynamics (MD) simulation. To reveal the aggregation and disaggregation mechanisms of proteins and peptides, several computational studies [ 13 , 14 ] have been performed on the monomeric state [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 ], dimerization [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ], oligomerization [ 39 , 40 , 41 , 42 , 43 , 44 , 45 ], amyloid fibril elongation [ 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 ], amyloid fibril stability [ 59 , 60 , 61 , 62 , 63 , 64 , 65 ], and disruption of amyloid fibrils [ 66 , 67 ...…”

Section: Introductionmentioning

confidence: 99%

Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

Itoh

Okumura

2021

IJMS

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Aggregates of amyloid-β (Aβ) peptides are known to be related to Alzheimer’s disease. Their aggregation is enhanced at hydrophilic–hydrophobic interfaces, such as a cell membrane surface and air-water interface, and is inhibited by polyphenols, such as myricetin and rosmarinic acid. We review molecular dynamics (MD) simulation approaches of a full-length Aβ peptide, Aβ40, and Aβ(16–22) fragments in these environments. Since these peptides have both hydrophilic and hydrophobic amino acid residues, they tend to exist at the interfaces. The high concentration of the peptides accelerates the aggregation there. In addition, Aβ40 forms a β-hairpin structure, and this structure accelerates the aggregation. We also describe the inhibition mechanism of the Aβ(16–22) aggregation by polyphenols. The aggregation of Aβ(16–22) fragments is caused mainly by the electrostatic attraction between charged amino acid residues known as Lys16 and Glu22. Since polyphenols form hydrogen bonds between their hydroxy and carboxyl groups and these charged amino acid residues, they inhibit the aggregation.

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Section: Introductionmentioning

confidence: 99%

Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

Itoh

Okumura

2021

IJMS

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“…The repulsive potential creates an empty cavity, mimicking a bubble in the liquid. This The Journal of Chemical Physics ARTICLE scitation.org/journal/jcp bubble model has been developed and applied to study effects of the stable bubble cavitation on the amyloid fibril and lipid membrane models, 25,26 and to verify the Rayleigh-Plesset (RP) equation for the description of the dynamics of nanosized bubbles. 27 The bubble growth/shrinkage is generally described by the Rayleigh-Plesset (RP) equation.…”

Section: The Model and Simulation Detailsmentioning

confidence: 99%

Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion

Man

Wang

et al. 2019

The Journal of Chemical Physics

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We develop a molecular nanoscaled model for tubular motors propelled by bubble propulsion. The motor is modeled by a carbon nanotube, and the bubble is represented by a particle interacting with water by a time-dependent potential. Effects of liquid viscosity, fuel concentration, geometry, and size of the tube on the performance of the motor are effectively encoded into two parameters: time scales of the bubble expansion and bubble formation. Our results are qualitatively consistent with experimental data of much larger motors. Simulations suggest that (i) the displacement of the tube is optimized if two time scales are as short as possible, (ii) the compromise between the performance and fuel consumption is achieved if the bubble formation time is shorter than the velocity correlation time of the tube, (iii) the motor efficiency is higher with slow expansion, short formation of the bubble than fast growth but long formation time, and (iv) the tube is propelled by strong forces on the order of mN, reaching high speeds up to ∼60 m/s. Our simulation may be useful for refining and encouraging future experimental work on nanomotors having the size of a few nanometers. The tiny size and high speed motors could have great potential applications in real life.

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“…Recently, we have developed a method to simulate the bubble stable cavitation in water. 26 It is useful to briefly summarize the main aspects of the bubble model here. A bubble is represented by a particle with low mass and no charge, and interacts with surrounding waters by a time-dependent Lennard-Jones potential,…”

Section: A the Bubble Model And Inner Pressurementioning

confidence: 99%

Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

Man

Derreumaux

et al. 2018

The Journal of Chemical Physics

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The Rayleigh-Plesset (RP) equation was derived from the first principles to describe the bubble cavitation in liquids in terms of macroscopic hydrodynamics. A number of nonequilibrium molecular dynamics studies have been carried out to validate this equation in describing the bubble inertial cavitation, but their results are contradictory and the applicability of the RP equation still remains to be examined, especially for the stable cavitation. In this work, we carry out nonequilibrium all-atom simulation to validate the applicability of the RP equation in the description of the stable cavitation of nano-sized bubbles in water. We show that although microscopic effects are not explicitly included, this equation still describes the dynamics of subnano-bubbles quite well as long as the contributions of various terms including inertial, surface tension, and viscosity are correctly taken into account. These terms are directly and inversely proportional to the amplitude and period of the cavitation, respectively. Thus, their contributions to the RP equation depend on these two parameters. This may explain the discrepancy between the current results obtained using different parameters. Finally, the accuracy of the RP equation in the current mathematical modeling studies of the ultrasoundinduced blood-brain-barrier experiments is discussed in some detail.

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Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils

Cited by 33 publications

References 51 publications

Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion

Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

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