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Gradient-consistent enrichment of finite element spaces for the DNS of fluid-particle interaction
(2019)
Highlights
• Monolithic scheme for particulate flows preventing an oscillating pressure along the interface.
• The choice of enriching shape functions is driven by the properties of its gradient instead of its value.
• The choice of enriching shape functions inherits a natural stabilization on small cut elements.
Abstract
We present gradient-consistent enriched finite element spaces for the simulation of free particles in a fluid. This involves forces being exchanged between the particles and the fluid at the interface. In an earlier work [23] we derived a monolithic scheme which includes the interaction forces into the Navier-Stokes equations by means of a fictitious domain like strategy. Due to an inexact approximation of the interface oscillations of the pressure along the interface were observed. In multiphase flows oscillations and spurious velocities are a common issue. The surface force term yields a jump in the pressure and therefore the oscillations are usually resolved by extending the spaces on cut elements in order to resolve the discontinuity. For the construction of the enriched spaces proposed in this paper we exploit the Petrov-Galerkin formulation of the vertex-centered finite volume method (PG-FVM), as already investigated in [23]. From the perspective of the finite volume scheme we argue that wrong discrete normal directions at the interface are the origin of the oscillations. The new perspective of normal vectors suggests to look at gradients rather than values of the enriching shape functions. The crucial parameter of the enrichment functions therefore is the gradient of the shape functions and especially the one of the test space. The distinguishing feature of our construction therefore is an enrichment that is based on the choice of shape functions with consistent gradients. These derivations finally yield a fitted scheme for the immersed interface. We further propose a strategy ensuring a well-conditioned system independent of the location of the interface. The enriched spaces can be used within any existing finite element discretization for the Navier-Stokes equation. Our numerical tests were conducted using the PG-FVM. We demonstrate that the enriched spaces are able to eliminate the oscillations.
Rotational test spaces for a fully-implicit FVM and FEM for the DNS of fluid-particle interaction
(2019)
The paper presents a fully-implicit and stable finite element and finite volume scheme for the simulation of freely moving particles in a fluid. The developed method is based on the Petrov-Galerkin formulation of a vertex-centered finite volume method (PG-FVM) on unstructured grids. Appropriate extension of the ansatz and test spaces lead to a formulation comparable to a fictitious domain formulation. The purpose of this work is to introduce a new concept of numerical modeling reducing the mathematical overhead which many other methods require. It exploits the identification of the PG-FVM with a corresponding finite element bilinear form. The surface integrals of the finite volume scheme enable a natural incorporation of the interface forces purely based on the original bilinear operator for the fluid. As a result, there is no need to expand the system of equations to a saddle-point problem. Like for fictitious domain methods the extended scheme treats the particles as rigid parts of the fluid. The distinguishing feature compared to most existing fictitious domain methods is that there is no need for an additional Lagrange multiplier or other artificial external forces for the fluid-solid coupling. Consequently, only one single solve for the derived linear system for the fluid together with the particles is necessary and the proposed method does not require any fractional time stepping scheme to balance the interaction forces between fluid and particles. For the linear Stokes problem we will prove the stability of both schemes. Moreover, for the stationary case the conservation of mass and momentum is not violated by the extended scheme, i.e. conservativity is accomplished within the range of the underlying, unconstrained discretization scheme. The scheme is applicable for problems in two and three dimensions.
The hepatitis C virus (HCV) RNA replication cycle is a dynamic intracellular process occurring in three-dimensional space (3D), which is difficult both to capture experimentally and to visualize conceptually. HCV-generated replication factories are housed within virus-induced intracellular structures termed membranous webs (MW), which are derived from the Endoplasmatic Reticulum (ER). Recently, we published 3D spatiotemporal resolved diffusion–reaction models of the HCV RNA replication cycle by means of surface partial differential equation (sPDE) descriptions. We distinguished between the basic components of the HCV RNA replication cycle, namely HCV RNA, non-structural viral proteins (NSPs), and a host factor. In particular, we evaluated the sPDE models upon realistic reconstructed intracellular compartments (ER/MW). In this paper, we propose a significant extension of the model based upon two additional parameters: different aggregate states of HCV RNA and NSPs, and population dynamics inspired diffusion and reaction coefficients instead of multilinear ones. The combination of both aspects enables realistic modeling of viral replication at all scales. Specifically, we describe a replication complex state consisting of HCV RNA together with a defined amount of NSPs. As a result of the combination of spatial resolution and different aggregate states, the new model mimics a cis requirement for HCV RNA replication. We used heuristic parameters for our simulations, which were run only on a subsection of the ER. Nevertheless, this was sufficient to allow the fitting of core aspects of virus reproduction, at least qualitatively. Our findings should help stimulate new model approaches and experimental directions for virology.