Dynamics of a Closed Rod with Twist and Bend in Fluid

Lim, Sookkyung; Ferent, Anca; Wang, X. Sheldon; Peskin, Charles S.

doi:10.1137/070699780

Cited by 109 publications

(162 citation statements)

References 30 publications

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“…This type of approach has already been employed in the deterministic context to model suspensions of neutrally-buoyant semi-rigid rods [96,97]. To our knowledge, such an approach has not yet been applied to fluctuating hydrodynamics and the resulting rotational diffusion has not been investigated.…”

Section: Discussionmentioning

confidence: 99%

Inertial coupling method for particles in an incompressible fluctuating fluid

Usabiaga

Delgado‐Buscalioni

Griffith

et al. 2014

Computer Methods in Applied Mechanics and Engineering

155

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We develop an inertial coupling method for modeling the dynamics of point-like "blob" The coupling between the fluid and the blob is based on a no-slip constraint equating the particle velocity with the local average of the fluid velocity, and conserves momentum and energy. We demonstrate that the formulation obeys a fluctuation-dissipation balance, owing to the non-dissipative nature of the no-slip coupling. We develop a spatiotemporal discretization that preserves, as best as possible, these properties of the continuum formulation. In the spatial discretization, the local averaging and spreading operations are accomplished using compact kernels commonly used in immersed boundary methods. We find that the special properties of these kernels allow the blob to provide an effective model of a particle; specifically, the volume, mass, and hydrodynamic properties of the blob are remarkably grid-independent. We develop a second-order semi-implicit temporal integrator that maintains discrete fluctuation-dissipation balance, and is not limited in stability by viscosity. Furthermore, the temporal scheme requires only constant-coefficient Poisson and Helmholtz linear solvers, enabling a very efficient and simple FFT-based implementation on GPUs. We numerically investigate the performance of the method on several standard test problems. In the deterministic setting, we find the blob to be a remarkably robust approximation to a rigid sphere, at both low and high Reynolds numbers. In the stochastic setting, we study in detail the short and long-time behavior of the velocity autocorrelation function and observe agreement with all of the known behavior for rigid sphere immersed in a fluctuating fluid. The proposed inertial coupling method provides a low-cost coarse-grained (minimal resolution) model of particulate flows over a wide range of time-scales ranging from 2 Brownian to convection-driven motion.

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Section: Discussionmentioning

confidence: 99%

Inertial coupling method for particles in an incompressible fluctuating fluid

Usabiaga

Delgado‐Buscalioni

Griffith

et al. 2014

Computer Methods in Applied Mechanics and Engineering

155

View full text Add to dashboard Cite

show abstract

“…The above identities ensure that force and torque generated by the rod are correctly applied to the fluid by our numerical scheme. In equation (2.9), the first term describes how the force of the rod acts on the fluid and the second term describes how the torque of the rod acts on the fluid (see Lim et al 2008 for details).…”

Section: Equations Of Motionmentioning

confidence: 99%

“…The mathematical model discussed here is based on the model introduced by Lim et al (2008) with electrostatic and steric repulsion forces included in addition to the elastic force. The immersed rod is represented by a three-dimensional closed space curve with an associated orthonormal triad at each point of the curve.…”

Section: Equations Of Motionmentioning

confidence: 99%

“…The generalized IB method (Lim et al 2008) resolves this issue by using a smoothed delta function with a compact support, which has the effect of assigning a cross-sectional radius to the space curve. In addition, the generalized IB method incorporates the special Cosserat rod theory and is distinguished by two new features: (i) the local angular velocity of the fluid at the IB is evaluated, along with the local linear velocity of the fluid, and (ii) the IB applies torque as well as force to the surrounding fluid.…”

Section: Introductionmentioning

confidence: 99%

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Dynamics of an electrostatically charged elastic rod in fluid

2010

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We investigate the effects of electrostatic and steric repulsion on the dynamics of a pretwisted charged elastic rod immersed in a viscous incompressible fluid. Equations of motion of the rod include the fluid-structure interaction, rod elasticity and a combination of two interactions that prevent self-contact, namely the electrostatic interaction and hard-core repulsion. The governing equations are solved using the generalized immersedboundary method. We find that after perturbation, a pre-twisted minicircle collapses into a compact supercoiled configuration. The collapse proceeds along a complex trajectory that may pass near several unstable equilibrium configurations, before it settles in a locally stable equilibrium. The dwell time near an unstable equilibrium can be up to several microseconds. Both the final configuration and the transition path are sensitive to the initial excess link, ionic strength of the solvent and the initial perturbation.

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“…Within the IB method, there too exists different versions. Examples include the original versions [4], the vortex-method version [29], the volume-conserved version [30], the adaptive mesh refinement version [31], the (formally) second-order versions [33,34], the multigrid version [35], the penalty version [36], the implicit versions [37-39, 42, 43], the generalized version for a thick rod [44], the stochastic version [45], the porous media version, the lattice-Boltzmann version [3,48,49,60,61,[53][54][55][56]59,63], the fluid-solute-structure interaction version [50], and the variable viscosity version [52].…”

Section: Introductionmentioning

confidence: 99%

Interactive 3D simulation for fluid–structure interactions using dual coupled GPUs

2017

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The scope of this work involves the integration of high speed parallel computation with interactive, 3D visualization of the lattice-Boltzmannbased immersed boundary method for fluid-structure-interaction. An NVIDIA Tesla K40c is used for the computations while an NVIDIA Quadro K5000 is used for 3D vector field visualization. The simulation can be paused at any time step so that the vector field can be explored. The density and placement of streamlines and glyphs are adjustable by the user, while panning and zooming is controlled by the mouse. The simulation can then be resumed. Unlike most scientific applications in computational fluid dynamics where visualization is performed after the computations, our software allows for real-time visualizations of the flow fields while the computations take place. To the best of our knowledge, such a tool on GPUs for FSI does not exist. Our software can facilitate debugging, enable observation of detailed local fields of flow and deformation while computing, and expedite identification of 'correct' parameter combinations in parametric studies for new phenomenon. Therefore, our software is expected to shorten the 'time to solution' process and expedite the scientific discoveries via scientific computing.Keywords lattice Boltzmann method · the immersed boundary method · GPU computing · fluid structure interaction(FSI) · interactive simulation · real time visualization

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Dynamics of a Closed Rod with Twist and Bend in Fluid

Cited by 109 publications

References 30 publications

Inertial coupling method for particles in an incompressible fluctuating fluid

Inertial coupling method for particles in an incompressible fluctuating fluid

Dynamics of an electrostatically charged elastic rod in fluid

Interactive 3D simulation for fluid–structure interactions using dual coupled GPUs

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