Simulating the complex cell design of Trypanosoma brucei and its motility

The flagellate Trypanosoma brucei, which causes the sleeping sickness when infecting a mammalian host, goes through an intricate life cycle. It has a rather complex propulsion mechanism and swims in diverse microenvironments. These continuously exert selective pressure, to which the trypanosome adjusts with its architecture and behavior. As a result, the trypanosome assumes a diversity of complex morphotypes during its life cycle. However, although cell biology has detailed form and function of most of them, experimental data on the dynamic behavior and development of most morphotypes is lacking. Here we show that simulation science can predict intermediate cell designs by conducting specific and controlled modifications of an accurate, nature-inspired cell model, which we developed using information from live cell analyses. The cell models account for several important characteristics of the real trypanosomal morphotypes, such as the geometry and elastic properties of the cell body, and their swimming mechanism using an eukaryotic flagellum. We introduce an elastic network model for the cell body, including bending rigidity and simulate swimming in a fluid environment, using the mesoscale simulation technique called multi-particle collision dynamics. The in silico trypanosome of the bloodstream form displays the characteristic in vivo rotational and translational motility pattern that is crucial for survival and virulence in the vertebrate host. Moreover, our model accurately simulates the trypanosome's tumbling and backward motion. We show that the distinctive course of the attached flagellum around the cell body is one important aspect to produce the observed swimming behavior in a viscous fluid, and also required to reach the maximal swimming velocity. Changing details of the flagellar attachment generates less efficient swimmers. We also simulate different morphotypes that occur during the parasite's development in the tsetse fly, and predict a flagellar course we have not been able to measure in experiments so far

Numerical simulations of complex fluid-fluid interface dynamics

Interfaces between two fluids are ubiquitous and of special importance for industrial applications, e.g., stabilisation of emulsions. The dynamics of fluid-fluid interfaces is difficult to study because these interfaces are usually deformable and their shapes are not known a priori. Since experiments do not provide access to all observables of interest, computer simulations pose attractive alternatives to gain insight into the physics of interfaces. In the present article, we restrict ourselves to systems with dimensions comparable to the lateral interface extensions. We provide a critical discussion of three numerical schemes coupled to the lattice Boltzmann method as a solver for the hydrodynamics of the problem: (a) the immersed boundary method for the simulation of vesicles and capsules, the Shan-Chen pseudopotential approach for multi-component fluids in combination with (b) an additional advection-diffusion component for surfactant modelling and (c) a molecular dynamics algorithm for the simulation of nanoparticles acting as emulsifiers.Comment: 24 pages, 12 figure

Dynamics of flexible fibers in viscous flows and fluids

International audienceThe dynamics and deformations of immersed flexible fibers are at the heart of important industrial and biological processes, induce peculiar mechanical and transport properties in the fluids that contain them, and are the basis for novel methods of flow control. Here we focus on the low Reynolds number regime where advances in studying these fiber-fluid systems have been especially rapid. On the experimental side this is due to new methods of fiber synthesis, microfluidic flow control, and of microscope based tracking measurement techniques. Likewise, there have been continuous improvements in the specialized mathematical modeling and numerical methods needed to capture the interactions of slender flexible fibers with flows, boundaries, and each other

A general formulation of Bead Models applied to flexible fibers and active filaments at low Reynolds number

This contribution provides a general framework to use Lagrange multipliers for the simulation of low Reynolds number fiber dynamics based on Bead Models (BM). This formalism provides an efficient method to account for kinematic constraints. We illustrate, with several examples, to which extent the proposed formulation offers a flexible and versatile framework for the quantitative modeling of flexible fibers deformation and rotation in shear flow, the dynamics of actuated filaments and the propulsion of active swimmers. Furthermore, a new contact model called Gears Model is proposed and successfully tested. It avoids the use of numerical artifices such as repulsive forces between adjacent beads, a source of numerical difficulties in the temporal integration of previous Bead Models.Comment: 41 pages, 15 figure

A Necklace Model for Vesicles Simulations in 2D

International audienceThe aim of this paper is to propose a new numerical model to simulate 2D vesicles interacting with a newtonian fluid. The inextensible membrane is modeled by a chain of circular rigid particles which are maintained in cohesion by using two different type of forces. First, a spring force is imposed between neighboring particles in the chain. Second, in order to model the bending of the membrane, each triplet of successive particles is submitted to an angular force. Numerical simulations of vesicles in shear flow have been run using Finite Element Method and the FreeFem++[1] software. Exploring different ratios of inner and outer viscosities, we recover the well known "Tank-Treading" and "Tumbling" motions predicted by theory and experiments. Moreover, for the first time, 2D simulations of the "Vacillating-Breathing" regime predicted by theory in [2] and observed experimentally in [3] are done without special ingredient like for example thermal fluctuations used in [4]

Three-Dimensional Lattice Boltzmann Simulation of Two-Phase Flow Containing a Deformable Body with a Viscoelastic Membrane

First published in Communications in Commun. Comput. Phys. in No. 5, 9 (2011), published by Global Science PressThe lattice Boltzmann method (LBM) with an elastic model is applied to the simulation of two-phase flows containing a deformable body with a viscoelastic membrane. The numerical method is based on the LBM for incompressible two-phase fluid flows with the same density. The body has an internal fluid covered by a viscoelastic membrane of a finite thickness. An elastic model is introduced to the LBM in order to determine the elastic forces acting on the viscoelastic membrane of the body. In the present method, we take account of changes in surface area of the membrane and in total volume of the body as well as shear deformation of the membrane. By using this method, we calculate two problems, the behavior of an initially spherical body under shear flow and the motion of a body with initially spherical or biconcave discoidal shape in square pipe flow. Calculated deformations of the body (the Taylor shape parameter) for various shear rates are in good agreement with other numerical results. Moreover, tank-treading motion, which is a characteristic motion of viscoelastic bodies in shear flows, is simulated by the present method.ArticleCommunications in Computational Physics. 9(5):1397-1413 (2011)journal articl

Kayaking and wagging of liquid crystals under shear: Comparing director and mesogen motions

Rod-like colloids in dense solutions perform collective orientational motions under shear flow. The periodic tumbling motions of the director, i.e. the average orientation of the rods, are commonly characterized as kayaking, wagging and flow-aligning, in order of increasing shear rate. Our event-driven Brownian dynamics simulations of rigid spherocylinders reproduce these three distinct director motions, but also clearly show, for the first time, that the individual mesogens are kayaking at all shear rates. The synchrony of the mesogens's motions gradually decreases with increasing shear rate, which at a critical shear rate causes a transition of the apparent collective motion from kayaking to wagging. The rods's persistent kayaking also explains the continuity of the tumbling period at this transition and the smooth change from wagging to flow-aligning observed at higher shear rates