Direct numerical simulations of vortex rings at ReΓ = 7500

We present direct numerical simulations of the turbulent decay of vortex rings with ReΓ = 7500. We analyse the vortex dynamics during the nonlinear stage of the instability along with the structure of the vortex wake during the turbulent stage. These simulations enable the quantification of vorticity dynamics and their correlation with structures from dye visualization and the observations of circulation decay that have been reported in related experimental works. Movies are available with the online version of the paper

Direct numerical simulations of vortex rings at ReΓ: 7500

We present direct numerical simulations of the turbulent decay of vortex rings with ReΓ = 7500. We analyse the vortex dynamics during the nonlinear stage of the instability along with the structure of the vortex wake during the turbulent stage. These simulations enable the quantification of vorticity dynamics and their correlation with structures from dye visualization and the observations of circulation decay that have been reported in related experimental works. Movies are available with the online version of the pape

A Lagrangian particle method for reaction-diffusion systems on deforming surfaces

Reaction-diffusion processes on complex deforming surfaces are fundamental to a number of biological processes ranging from embryonic development to cancer tumor growth and angiogenesis. The simulation of these processes using continuum reaction-diffusion models requires computational methods capable of accurately tracking the geometric deformations and discretizing on them the governing equations. We employ a Lagrangian level-set formulation to capture the deformation of the geometry and use an embedding formulation and an adaptive particle method to discretize both the level-set equations and the corresponding reaction-diffusion. We validate the proposed method and discuss its advantages and drawbacks through simulations of reaction-diffusion equations on complex and deforming geometrie

Benchmark Chemical Systems and Simulation Parameters

Performance results were measured for two chemical systems that are commonly used for MD code benchmarking, and one additional system that is characteristic for free energy perturbation (FEP) simulations

A Hybrid Model for Three-Dimensional Simulations of Sprouting Angiogenesis

Recent advances in cancer research have identified critical angiogenic signaling pathways and the influence of the extracellular matrix on endothelial cell migration. These findings provide us with insight into the process of angiogenesis that can facilitate the development of effective computational models of sprouting angiogenesis. In this work, we present the first three-dimensional model of sprouting angiogenesis that considers explicitly the effect of the extracellular matrix and of the soluble as well as matrix-bound growth factors on capillary growth. The computational model relies on a hybrid particle-mesh representation of the blood vessels and it introduces an implicit representation of the vasculature that can accommodate detailed descriptions of nutrient transport. Extensive parametric studies reveal the role of the extracellular matrix structure and the distribution of the different vascular endothelial growth factors isoforms on the dynamics and the morphology of the generated vascular networks

Large Scale, Multiresolution Flow Simulations Using Remeshed Particle Methods

Particle methods are a robust and versatile computational tool for the simulation of continuous and discrete physical systems ranging from Fluid Mechanics to Biology and Social Sciences. In advection dominated problems particle methods can be considered as the method of choice due to their inherent robustness, stability and Lagrangian adaptivity. At the same time however, smooth particle methods encounter major difficulties in simulating the equations they set out to discretize when their computational elements fail to overlap, a condition necessary for their convergence [2]. A number of ad-hoc parameters and artificial dissipation techniques are often introduced in techniques such as Smoothed Particle Hydrodynamics (SPH) [15, 19] in order to remedy these difficulties. In the present paper we demonstrate that the convergence of smooth particle methods can be ensured by a periodic remeshing of the particles using high-order interpolation kernels. This procedure retains the Lagrangian character and stability of particle methods and enables the control of their accuracy [5, 9, 16, 17] while introducing numerical dissipation at levels well below those introduced by temporal discretizations. In addition, remeshing enables two major improvements over grid-free particle methods: First by exploiting the regularity of the remeshed particles, it reduces by at least an order of magnitude their computational cost [6, 10] and facilitates their massively parallel implementation. Second, remeshing enables the development of consistent multiresolution techniques such as wavelet-particle methods [4]. This approach has been implemented efficiently in massively parallel computer architectures allowing for unprecedented vortex dynamics simulations using billions of particles

A Lagrangian particle method for reaction-diffusion systems on deforming surfaces

ISSN:1432-1416ISSN:0303-681

Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions : A continuum electrostatics study

A new algorithm relying on finite integration is presented that solves the equations of continuum electrostatics for truncated (and possibly reaction-field corrected) solute–solvent and solvent–solvent interactions under either nonperiodic or periodic boundary conditions. After testing and validation by comparison with existing methods, the algorithm is applied to investigate the effect of cut-off truncation and artificial periodicity in explicit-solvent simulations of ionic solvation and ion–ion interactions. Both cut-off truncation and artificial periodicity significantly alter the polarization around a spherical ion and thus, its solvation free energy. The nature and magnitude of the two perturbations are analyzed in details, and correction terms are proposed for both effects. Cut-off truncation is also shown to induce strong alterations in the potential of mean force for ion–ion interaction. These observations help to rationalize artifacts previously observed in explicit–solvent simulations, namely spurious features in the radial distribution functions close to the cut-off distance and alterations in the relative stabilities of contact, solvent-separated and free ion pairs.publishe