622 research outputs found
Spatially Adaptive Stochastic Multigrid Methods for Fluid-Structure Systems with Thermal Fluctuations
In microscopic mechanical systems interactions between elastic structures are
often mediated by the hydrodynamics of a solvent fluid. At microscopic scales
the elastic structures are also subject to thermal fluctuations. Stochastic
numerical methods are developed based on multigrid which allow for the
efficient computation of both the hydrodynamic interactions in the presence of
walls and the thermal fluctuations. The presented stochastic multigrid approach
provides efficient real-space numerical methods for generating the required
stochastic driving fields with long-range correlations consistent with
statistical mechanics. The presented approach also allows for the use of
spatially adaptive meshes in resolving the hydrodynamic interactions. Numerical
results are presented which show the methods perform in practice with a
computational complexity of O(N log(N))
Systematic Stochastic Reduction of Inertial Fluid-Structure Interactions subject to Thermal Fluctuations
We present analysis for the reduction of an inertial description of
fluid-structure interactions subject to thermal fluctuations. We show how the
viscous coupling between the immersed structures and the fluid can be
simplified in the regime where this coupling becomes increasingly strong. Many
descriptions in fluid mechanics and in the formulation of computational methods
account for fluid-structure interactions through viscous drag terms to transfer
momentum from the fluid to immersed structures. In the inertial regime, this
coupling often introduces a prohibitively small time-scale into the temporal
dynamics of the fluid-structure system. This is further exacerbated in the
presence of thermal fluctuations. We discuss here a systematic reduction
technique for the full inertial equations to obtain a simplified description
where this coupling term is eliminated. This approach also accounts for the
effective stochastic equations for the fluid-structure dynamics. The analysis
is based on use of the Infinitesmal Generator of the SPDEs and a singular
perturbation analysis of the Backward Kolomogorov PDEs. We also discuss the
physical motivations and interpretation of the obtained reduced description of
the fluid-structure system. Working paper currently under revision. Please
report any comments or issues to [email protected]: 19 pages, 1 figure. arXiv admin note: substantial text overlap with
arXiv:1009.564
Hydrodynamic Coupling of Particle Inclusions Embedded in Curved Lipid Bilayer Membranes
We develop theory and computational methods to investigate particle
inclusions embedded within curved lipid bilayer membranes. We consider the case
of spherical lipid vesicles where inclusion particles are coupled through (i)
intramembrane hydrodynamics, (ii) traction stresses with the external and
trapped solvent fluid, and (iii) intermonolayer slip between the two leaflets
of the bilayer. We investigate relative to flat membranes how the membrane
curvature and topology augment hydrodynamic responses. We show how both the
translational and rotational mobility of protein inclusions are effected by the
membrane curvature, ratio of intramembrane viscosity to solvent viscosity, and
inter-monolayer slip. For general investigations of many-particle dynamics, we
also discuss how our approaches can be used to treat the collective diffusion
and hydrodynamic coupling within spherical bilayers.Comment: 32 pages, double-column format, 15 figure
Spectral Numerical Exterior Calculus Methods for Differential Equations on Radial Manifolds
We develop exterior calculus approaches for partial differential equations on
radial manifolds. We introduce numerical methods that approximate with spectral
accuracy the exterior derivative , Hodge star , and their
compositions. To achieve discretizations with high precision and symmetry, we
develop hyperinterpolation methods based on spherical harmonics and Lebedev
quadrature. We perform convergence studies of our numerical exterior derivative
operator and Hodge star operator
showing each converge spectrally to and . We show how the
numerical operators can be naturally composed to formulate general numerical
approximations for solving differential equations on manifolds. We present
results for the Laplace-Beltrami equations demonstrating our approach.Comment: 22 pages, 13 figure
Hydrodynamic Flows on Curved Surfaces: Spectral Numerical Methods for Radial Manifold Shapes
We formulate hydrodynamic equations and spectrally accurate numerical methods
for investigating the role of geometry in flows within two-dimensional fluid
interfaces. To achieve numerical approximations having high precision and level
of symmetry for radial manifold shapes, we develop spectral Galerkin methods
based on hyperinterpolation with Lebedev quadratures for -projection to
spherical harmonics. We demonstrate our methods by investigating hydrodynamic
responses as the surface geometry is varied. Relative to the case of a sphere,
we find significant changes can occur in the observed hydrodynamic flow
responses as exhibited by quantitative and topological transitions in the
structure of the flow. We present numerical results based on the
Rayleigh-Dissipation principle to gain further insights into these flow
responses. We investigate the roles played by the geometry especially
concerning the positive and negative Gaussian curvature of the interface. We
provide general approaches for taking geometric effects into account for
investigations of hydrodynamic phenomena within curved fluid interfaces.Comment: 14 figure
Theoretical Framework for Microscopic Osmotic Phenomena
The basic ingredients of osmotic pressure are a solvent fluid with a soluble
molecular species which is restricted to a chamber by a boundary which is
permeable to the solvent fluid but impermeable to the solute molecules. For
macroscopic systems at equilibrium, the osmotic pressure is given by the
classical van't Hoff Law, which states that the pressure is proportional to the
product of the temperature and the difference of the solute concentrations
inside and outside the chamber. For microscopic systems the diameter of the
chamber may be comparable to the length-scale associated with the solute-wall
interactions or solute molecular interactions. In each of these cases, the
assumptions underlying the classical van't Hoff Law may no longer hold. In this
paper we develop a general theoretical framework which captures corrections to
the classical theory for the osmotic pressure under more general relationships
between the size of the chamber and the interaction length scales. We also show
that notions of osmotic pressure based on the hydrostatic pressure of the fluid
and the mechanical pressure on the bounding walls of the chamber must be
distinguished for microscopic systems. To demonstrate how the theoretical
framework can be applied, numerical results are presented for the osmotic
pressure associated with a polymer of N monomers confined in a spherical
chamber as the bond strength is varied
Dynamic Implicit-Solvent Coarse-Grained Models of Lipid Bilayer Membranes : Fluctuating Hydrodynamics Thermostat
Many coarse-grained models have been developed for equilibrium studies of
lipid bilayer membranes. To achieve in simulations access to length-scales and
time-scales difficult to attain in fully atomistic molecular dynamics, these
coarse-grained models provide a reduced description of the molecular degrees of
freedom and often remove entirely representation of the solvent degrees of
freedom. In such implicit-solvent models the solvent contributions are treated
through effective interaction terms within an effective potential for the free
energy. For investigations of kinetics, Langevin dynamics is often used.
However, for many dynamical processes within bilayers this approach is
insufficient since it neglects important correlations and dynamical
contributions that are missing as a result of the momentum transfer that would
have occurred through the solvent. To address this issue, we introduce a new
thermostat based on fluctuating hydrodynamics for dynamic simulations of
implicit-solvent coarse-grained models. Our approach couples the coarse-grained
degrees of freedom to a stochastic continuum field that accounts for both the
solvent hydrodynamics and thermal fluctuations. We show our approach captures
important correlations in the dynamics of lipid bilayers that are missing in
simulations performed using conventional Langevin dynamics. For both planar
bilayer sheets and bilayer vesicles, we investigate the diffusivity of lipids,
spatial correlations, and lipid flow within the bilayer. The presented
fluctuating hydrodynamics approaches provide a promising way to extend
implicit-solvent coarse-grained lipid models for use in studies of dynamical
processes within bilayers
A Stochastic Immersed Boundary Method for Fluid-Structure Dynamics at Microscopic Length Scales
In this work it is shown how the immersed boundary method of (Peskin2002) for
modeling flexible structures immersed in a fluid can be extended to include
thermal fluctuations. A stochastic numerical method is proposed which deals
with stiffness in the system of equations by handling systematically the
statistical contributions of the fastest dynamics of the fluid and immersed
structures over long time steps. An important feature of the numerical method
is that time steps can be taken in which the degrees of freedom of the fluid
are completely underresolved, partially resolved, or fully resolved while
retaining a good level of accuracy. Error estimates in each of these regimes
are given for the method. A number of theoretical and numerical checks are
furthermore performed to assess its physical fidelity. For a conservative
force, the method is found to simulate particles with the correct Boltzmann
equilibrium statistics. It is shown in three dimensions that the diffusion of
immersed particles simulated with the method has the correct scaling in the
physical parameters. The method is also shown to reproduce a well-known
hydrodynamic effect of a Brownian particle in which the velocity
autocorrelation function exhibits an algebraic tau^(-3/2) decay for long times.
A few preliminary results are presented for more complex systems which
demonstrate some potential application areas of the method.Comment: 52 pages, 11 figures, published in journal of computational physic
Spatially Adaptive Stochastic Methods for Fluid-Structure Interactions Subject to Thermal Fluctuations in Domains with Complex Geometries
We develop stochastic mixed finite element methods for spatially adaptive
simulations of fluid-structure interactions when subject to thermal
fluctuations. To account for thermal fluctuations, we introduce a discrete
fluctuation-dissipation balance condition to develop compatible stochastic
driving fields for our discretization. We perform analysis that shows our
condition is sufficient to ensure results consistent with statistical
mechanics. We show the Gibbs-Boltzmann distribution is invariant under the
stochastic dynamics of the semi-discretization. To generate efficiently the
required stochastic driving fields, we develop a Gibbs sampler based on
iterative methods and multigrid to generate fields with computational
complexity. Our stochastic methods provide an alternative to uniform
discretizations on periodic domains that rely on Fast Fourier Transforms. To
demonstrate in practice our stochastic computational methods, we investigate
within channel geometries having internal obstacles and no-slip walls how the
mobility/diffusivity of particles depends on location. Our methods extend the
applicability of fluctuating hydrodynamic approaches by allowing for spatially
adaptive resolution of the mechanics and for domains that have complex
geometries relevant in many applications
- β¦