GEMPIC: Geometric ElectroMagnetic Particle-In-Cell Methods

We present a novel framework for Finite Element Particle-in-Cell methods based on the discretization of the underlying Hamiltonian structure of the Vlasov-Maxwell system. We derive a semi-discrete Poisson bracket, which retains the defining properties of a bracket, anti-symmetry and the Jacobi identity, as well as conservation of its Casimir invariants, implying that the semi-discrete system is still a Hamiltonian system. In order to obtain a fully discrete Poisson integrator, the semi-discrete bracket is used in conjunction with Hamiltonian splitting methods for integration in time. Techniques from Finite Element Exterior Calculus ensure conservation of the divergence of the magnetic field and Gauss' law as well as stability of the field solver. The resulting methods are gauge invariant, feature exact charge conservation and show excellent long-time energy and momentum behaviour. Due to the generality of our framework, these conservation properties are guaranteed independently of a particular choice of the Finite Element basis, as long as the corresponding Finite Element spaces satisfy certain compatibility conditions.Comment: 57 Page

The Energy Conserving Particle-in-Cell Method

A new Particle-in-Cell (PIC) method, that conserves energy exactly, is presented. The particle equations of motion and the Maxwell's equations are differenced implicitly in time by the midpoint rule and solved concurrently by a Jacobian-free Newton Krylov (JFNK) solver. Several tests show that the finite grid instability is eliminated in energy conserving PIC simulations, and the method correctly describes the two-stream and Weibel instabilities, conserving exactly the total energy. The computational time of the energy conserving PIC method increases linearly with the number of particles, and it is rather insensitive to the number of grid points and time step. The kinetic enslavement technique can be effectively used to reduce the problem matrix size and the number of JFNK solver iterations

Particle-in-cell simulations of rf breakdown

Breakdown voltages of a capacitively coupled radio frequency argon discharge at 27 MHz are studied. We use a one-dimensional electrostatic PIC code to investigate the effect of changing the secondary emission properties of the electrodes on the breakdown voltage, particularly at low pd values. Simulation results are compared with the available experimental results and a satisfactory agreement is found.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Load management strategy for Particle-In-Cell simulations in high energy particle acceleration

In the wake of the intense effort made for the experimental CILEX project, numerical simulation cam- paigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. In this paper, we compare the results given by different codes and point out algorithmic lim- itations both in terms of physical accuracy and computational performances. These limitations are illu- strated in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-per- formance PIC code for high energy particle acceleration

Classical Radiation Reaction in Particle-In-Cell Simulations

Under the presence of ultra high intensity lasers or other intense electromagnetic fields the motion of particles in the ultrarelativistic regime can be severely affected by radiation reaction. The standard particle-in-cell (PIC) algorithms do not include radiation reaction effects. Even though this is a well known mechanism, there is not yet a definite algorithm nor a standard technique to include radiation reaction in PIC codes. We have compared several models for the calculation of the radiation reaction force, with the goal of implementing an algorithm for classical radiation reaction in the Osiris framework, a state-of-the-art PIC code. The results of the different models are compared with standard analytical results, and the relevance/advantages of each model are discussed. Numerical issues relevant to PIC codes such as resolution requirements, application of radiation reaction to macro particles and computational cost are also addressed. The Landau and Lifshitz reduced model is chosen for implementation.Comment: 12 pages, 8 figure

Dynamic acoustic field activated cell separation (DAFACS)

Advances in diagnostics, cell and stem cell technologies drive the development of application-specific tools for cell and particle separation. Acoustic micro-particle separation offers a promising avenue for highthroughput, label-free, high recovery, cell and particle separation and isolation in regenerative medicine. Here, we demonstrate a novel approach utilizing a dynamic acoustic field that is capable of separating an arbitrary size range of cells. We first demonstrate the method for the separation of particles with different diameters between 6 and 45 μm and secondly particles of different densities in a heterogeneous medium. The dynamic acoustic field is then used to separate dorsal root ganglion cells. The shearless, label-free and low damage characteristics make this method of manipulation particularly suited for biological applications. Advantages of using a dynamic acoustic field for the separation of cells include its inherent safety and biocompatibility, the possibility to operate over large distances (centimetres), high purity (ratio of particle population, up to 100%), and high efficiency (ratio of separated particles over total number of particles to separate, up to 100%)

Particle-based simulation of ellipse-shaped particle aggregation as a model for vascular network formation

Computational modelling is helpful for elucidating the cellular mechanisms driving biological morphogenesis. Previous simulation studies of blood vessel growth based on the Cellular Potts model (CPM) proposed that elongated, adhesive or mutually attractive endothelial cells suffice for the formation of blood vessel sprouts and vascular networks. Because each mathematical representation of a model introduces potential artifacts, it is important that model results are reproduced using alternative modelling paradigms. Here, we present a lattice-free, particle-based simulation of the cell elongation model of vasculogenesis. The new, particle-based simulations confirm the results obtained from the previous Cellular Potts simulations. Furthermore, our current findings suggest that the emergence of order is possible with the application of a high enough attractive force or, alternatively, a longer attraction radius. The methodology will be applicable to a range of problems in morphogenesis and noisy particle aggregation in which cell shape is a key determining factor.Comment: 9 pages, 11 figures, 2 supplementary videos (on Youtube), submitted to Computational Particle Mechanics, special issue: Jos\'e-Manuel Garcia Aznar (Ed.) Particle-based simulations on cell and biomolecular mechanic