A formally second-order accurate immersed boundary method is presented and tested in this paper. We apply this new scheme to simulate the flow past a circular cylinder and study the effect of numerical viscosity on the accuracy of the computation by comparing the numerical results with those of a first-order method. The numerical evidence shows that the new scheme has less numerical viscosity and is therefore a better choice for the simulation of high Reynolds number flows with immersed boundaries.

Peskin's Immersed Boundary Method has been widely used for simulating many fluid mechanics and biology problems. One of the essential components of the method is the usage of certain discrete delta functions to deal with singular forces along one or several interfaces in the fluid domain. However, the Immersed Boundary Method is known to be first-order accurate and usually smears out the solutions. In this paper, we propose an immersed interface method for the incompressible Navier-Stokes equations with singular forces along one or several interfaces in the solution domain. The new method is based on a second-order projection method with modifications only at grid points near or on the interface. From the derivation of the new method, we expect fully second-order accuracy for the velocity and nearly second-order accuracy for the pressure in the maximum norm including those grid points near or on the interface. This has been confirmed in our numerical experiments. Furthermore, the computed solutions are sharp across the interface. Nontrivial numerical results are provided and compared with the Immersed Boundary Method. Meanwhile, a new version of the Immersed Boundary Method using the level set representation of the interface is also proposed in this paper.

We develop a method for computing a nearly singular integral, such as a double layer potential due to sources on a curve in the plane, evaluated at a point near the curve. The approach is to regularize the singularity and obtain a preliminary value from a standard quadrature rule. Then we add corrections for the errors due to smoothing and discretization, which are found by asymptotic analysis. We prove an error estimate for the corrected value, uniform with respect to the point of evaluation. One application is a simple method for solving the Dirichlet problem for Laplace's equation on a grid covering an irregular region in the plane, similar to an earlier method of A. Mayo [SIAM J. Sci. Statist. Comput., 6 (1985), pp. 144-157]. This approach could also be used to compute the pressure gradient due to a force on a moving boundary in an incompressible fluid. Computational examples are given for the double layer potential and for the Dirichlet problem.

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Many eukaryotic cells undergo frequent shape changes (described as amoeboid motion) that enable them to move forward. We investigate the effect of confinement on a minimal model of amoeboid swimmer. A complex picture emerges: (i) The swimmer's nature (i.e., either pusher or puller) can be modified by confinement, thus suggesting that this is not an intrinsic property of the swimmer. This swimming nature transition stems from intricate internal degrees of freedom of membrane deformation. (ii) The swimming speed might increase with increasing confinement before decreasing again for stronger confinements. (iii) A straight amoeoboid swimmer's trajectory in the channel can become unstable, and ample lateral excursions of the swimmer prevail. This happens for both pusher- and puller-type swimmers. For weak confinement, these excursions are symmetric, while they become asymmetric at stronger confinement, whereby the swimmer is located closer to one of the two walls. In this study, we combine numerical and theoretical analyses.