Nano-swimmers in biological membranes and propulsion hydrodynamics in two dimensions

Mei-Chun, Huang; Chen, Hsuan‐Yi; Mikhailov, Alexander S.

doi:10.1140/epje/i2012-12119-5

Cited by 25 publications

(35 citation statements)

References 30 publications

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“…By now, it has been developed into one of the major simulation techniques for complex fluids and has been applied to a broad range of soft matter systems. Examples cover equilibrium colloid [1,[3][4][5][6][7][8][9][10][11][12] and polymer [3,4,[13][14][15][16][17] solutions and, more importantly, nonequilibrium systems such as colloids [18][19][20][21][22][23][24][25], polymers [16,[26][27][28][29][30][31][32][33][34][35], vesicles [36], and cells [37,38] in flow fields, colloids in viscoelastic fluids [39][40][41], as well as of self-propelled spheres [42][43][44], rods [3,45], and other microswimmers …”

Section: Introductionmentioning

confidence: 99%

Thermostat for nonequilibrium multiparticle-collision-dynamics simulations

et al. 2015

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Multiparticle collision dynamics (MPC), a particle-based mesoscale simulation technique for complex fluid, is widely employed in nonequilibrium simulations of soft matter systems. To maintain a defined thermodynamic state, thermalization of the fluid is often required for certain MPC variants. We investigate the influence of three thermostats on the nonequilibrium properties of a MPC fluid under shear or in Poiseuille flow. In all cases, the local velocities are scaled by a factor, which is either determined via a local simple scaling approach (LSS), a Monte Carlo-like procedure (MCS), or by the Maxwell-Boltzmann distribution of kinetic energy (MBS). We find that the various scaling schemes leave the flow profile unchanged and maintain the local temperature well. The fluid viscosities extracted from the various simulations are in close agreement. Moreover, the numerically determined viscosities are in remarkably good agreement with the respective theoretically predicted values. At equilibrium, the calculation of the dynamic structure factor reveals that the MBS method closely resembles an isothermal ensemble, whereas the MCS procedure exhibits signatures of an adiabatic system at larger collision-time steps. Since the velocity distribution of the LSS approach is non-Gaussian, we recommend to apply the MBS thermostat, which has been shown to produce the correct velocity distribution even under nonequilibrium conditions.

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Section: Introductionmentioning

confidence: 99%

Thermostat for nonequilibrium multiparticle-collision-dynamics simulations

et al. 2015

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“…However, angular-m om entumconserving extensions have been introduced for both the stochastic rotation version of M PC (M P C -S R D + a) and the ' m.theers@fz-juelich.de T.winkler@fz-juelich.de PACS number(s): 47.11 ,-j , 02.70.Ns, 6 6 .20.-d A ndersen variant (M PC -A T + a) [17,18]. The M PC m ethod has successfully been applied to a broad range o f soft m atter system s ranging from equilibrium colloid [6,8,9,[19][20][21][22][23][24][25][26][27] and polym er [8,9,[28][29][30] solutions and, m ore importantly, nonequilibrium system s such as colloids [16,[31][32][33][34][35], poly mers [29,[36][37][38][39][40][41][42][43][44][45], vesicles [46], and cells [47,48] in flow fields, colloids in viscoelastic fluids [49][50][51], to selfpropelled spheres [52][53][54], rods …”

Section: Introductionmentioning

confidence: 99%

Bulk viscosity of multiparticle collision dynamics fluids

Theers

Winkler

2015

Phys. Rev. E

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We determine the viscosity parameters of the multiparticle collision dynamics (MPC) approach, a particle-based mesoscale hydrodynamic simulation method for fluids. We perform analytical calculations and verify our results by simulations. The stochastic rotation dynamics and the Andersen thermostat variant of MPC are considered, both with and without angular momentum conservation. As an important result, we find a nonzero bulk viscosity for every MPC version. The explicit calculation shows that the bulk viscosity is determined solely by the collisional interactions of MPC.

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“…Also, the effects of hydrodynamic interactions on the internal dynamics have been analyzed (28). Active protein inclusions in lipid bilayers can act as hydrodynamic dipoles (29) and, under certain conditions, such inclusions can behave as active membrane swimmers (30).…”

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confidence: 99%

Hydrodynamic collective effects of active protein machines in solution and lipid bilayers

Mikhailov

Kapral

2015

Proc. Natl. Acad. Sci. U.S.A.

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100

113

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The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out various other tasks in the cell. Many enzymes also undergo conformational changes within their turnover cycles. We analyze the advection effects that nonthermal fluctuating hydrodynamic flows induced by active proteins have on other passive molecules in solution or membranes. We show that the diffusion constants of passive particles are enhanced substantially. Furthermore, when gradients of active proteins are present, a chemotaxis-like drift of passive particles takes place. In lipid bilayers, the effects are strongly nonlocal, so that active inclusions in the entire membrane contribute to local diffusion enhancement and the drift. All active proteins in a biological cell or in a membrane contribute to such effects and all passive particles, and the proteins themselves, will be subject to them

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Nano-swimmers in biological membranes and propulsion hydrodynamics in two dimensions

Cited by 25 publications

References 30 publications

Thermostat for nonequilibrium multiparticle-collision-dynamics simulations

Thermostat for nonequilibrium multiparticle-collision-dynamics simulations

Bulk viscosity of multiparticle collision dynamics fluids

Hydrodynamic collective effects of active protein machines in solution and lipid bilayers

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