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The biological effects of energetic heavy ions are attracting increasing interest for their applications in cancer therapy and protection against space radiation. The cascade of events leading to cell death or late effects starts from stochastic energy deposition on the nanometer scale and the corresponding lesions in biological molecules, primarily DNA. We have developed experimental techniques to visualize DNA nanolesions induced by heavy ions. Nanolesions appear in cells as “streaks” which can be visualized by using different DNA repair markers. We have studied the kinetics of repair of these “streaks” also with respect to the chromatin conformation. Initial steps in the modeling of the energy deposition patterns at the micrometer and nanometer scale were made with MCHIT and TRAX models, respectively.
Far outside the surface of slabs, the exact exchange (EXX) potential vx falls off as −1/z , if z denotes the direction perpendicular to the surface and the slab is localized around z=0 . Similarly, the EXX energy density ex behaves as −n/(2z) , where n is the electron density. Here, an alternative proof of these relations is given, in which the Coulomb singularity in the EXX energy is treated in a particularly careful fashion. This new approach allows the derivation of the next-to-leading order contributions to the asymptotic vx and ex . It turns out that in both cases, the corrections are proportional to 1/z2 in general.
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.
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.
We present a calculation of the global polarization of Λ hyperons in relativistic Au–Au collisions at RHIC Beam Energy Scan range sNN−−−√=7.7−200 GeV with a 3+1-dimensional cascade+viscous hydro model, UrQMD+vHLLE. Within this model, the mean polarization of Λ in the out-of-plane direction is predicted to decrease rapidly with collision energy from a top value of about 2% at the lowest energy examined. We explore the connection between the polarization signal and thermal vorticity and estimate the feed-down contribution to Λ polarization due to the decay of higher mass hyperons.
We investigate the applicability of the well-known multilevel Monte Carlo (MLMC) method to the class of density-driven flow problems, in particular the problem of salinisation of coastal aquifers. As a test case, we solve the uncertain Henry saltwater intrusion problem. Unknown porosity, permeability and recharge parameters are modelled by using random fields. The classical deterministic Henry problem is non-linear and time-dependent, and can easily take several hours of computing time. Uncertain settings require the solution of multiple realisations of the deterministic problem, and the total computational cost increases drastically. Instead of computing of hundreds random realisations, typically the mean value and the variance are computed. The standard methods such as the Monte Carlo or surrogate-based methods are a good choice, but they compute all stochastic realisations on the same, often, very fine mesh. They also do not balance the stochastic and discretisation errors. These facts motivated us to apply the MLMC method. We demonstrate that by solving the Henry problem on multi-level spatial and temporal meshes, the MLMC method reduces the overall computational and storage costs. To reduce the computing cost further, parallelization is performed in both physical and stochastic spaces. To solve each deterministic scenario, we run the parallel multigrid solver ug4 in a black-box fashion.