Simulated acoustic emissions from coupled strings

We consider traveling transverse waves on two identical uniform taut strings that are elastically coupled through springs that gradually decrease their stiffness over a region of finite length. The wave system can be decomposed into two modes: an in-phase mode ( + ) that is transparent to the coupling springs, and an out-of-phase mode ( − ) that engages the coupling springs and can resonate at a particular location depending on the excitation frequency. The system exhibits linear mode conversion whereby an incoming ( + ) wave is reflected back from the resonance location both as a propagating ( + ) wave and an evanescent ( − ) wave, while both types emerge as propagating forward through the resonance location. We match a local transition layer expansion to the WKB expansion to obtain estimates of the reflection and transmission coefficients. The reflected waves may be an analog for stimulated emissions from the ear

Reflecting on Crisis: Ethics of Dis/Engagement in Migration Research

This article offers a collective “gaze from within” the process of migration research, on the effects the pandemic has had on our interlocutors, our research fields, and our positionalities as researchers. Drawing from our experiences of researching a field in increasing crisis, and following the methodological reflections of the article written by our colleagues in this issue, we discuss a number of dilemmas and repositionings stemming from—and extending beyond—the effects of the COVID-19 pandemic. Focusing on issues of positionality, ethics of (dis)engaging from the research field, and the underlying extractivist nature of Global North academia, we propose our own vision of more egalitarian and engaged research ethics and qualitative methodologies in the post-pandemic world

A Comprehensive Three-Dimensional Model of the Cochlea

The human cochlea is a remarkable device, able to discern extremely small amplitude sound pressure waves, and discriminate between very close frequencies. Simulation of the cochlea is computationally challenging due to its complex geometry, intricate construction and small physical size. We have developed, and are continuing to refine, a detailed three-dimensional computational model based on an accurate cochlear geometry obtained from physical measurements. In the model, the immersed boundary method is used to calculate the fluid-structure interactions produced in response to incoming sound waves. The model includes a detailed and realistic description of the various elastic structures present. In this paper, we describe the computational model and its performance on the latest generation of shared memory servers from Hewlett Packard. Using compiler generated threads and OpenMP directives, we have achieved a high degree of parallelism in the executable, which has made possible several large scale numerical simulation experiments that study the interesting features of the cochlear system. We show several results from these simulations, reproducing some of the basic known characteristics of cochlear mechanics.Comment: 22 pages, 5 figure

Initial/boundary-value problems of tumor growth within a host tissue

This paper concerns multiphase models of tumor growth in interaction with a surrounding tissue, taking into account also the interplay with diffusible nutrients feeding the cells. Models specialize in nonlinear systems of possibly degenerate parabolic equations, which include phenomenological terms related to specific cell functions. The paper discusses general modeling guidelines for such terms, as well as for initial and boundary conditions, aiming at both biological consistency and mathematical robustness of the resulting problems. Particularly, it addresses some qualitative properties such as a priori nonnegativity, boundedness, and uniqueness of the solutions. Existence of the solutions is studied in the one-dimensional time-independent case.Comment: 30 pages, 5 figure

Resultant pressure distribution pattern along the basilar membrane in the spiral shaped cochlea

Cochlea is an important auditory organ in the inner ear. In most mammals, it is coiled as a spiral. Whether this specific shape influences hearing is still an open problem. By employing a three dimensional fluid model of the cochlea with an idealized geometry, the influence of the spiral geometry of the cochlea is examined. We obtain solutions of the model through a conformal transformation in a long-wave approximation. Our results show that the net pressure acting on the basilar membrane is not uniform along its spanwise direction. Also, it is shown that the location of the maximum of the spanwise pressure difference in the axial direction has a mode dependence. In the simplest pattern, the present result is consistent with the previous theory based on the WKB-like approximation [D. Manoussaki, Phys. Rev. Lett. 96, 088701(2006)]. In this mode, the pressure difference in the spanwise direction is a monotonic function of the distance from the apex and the normal velocity across the channel width is zero. Thus in the lowest order approximation, we can neglect the existance of the Reissner's membrane in the upper channel. However, higher responsive modes show different behavior and, thus, the real maximum is expected to be located not exactly at the apex, but at a position determined by the spiral geometry of the cochlea and the width of the cochlear duct. In these modes, the spanwise normal velocities are not zero. Thus, it indicates that one should take into account of the detailed geometry of the cochlear duct for a more quantitative result. The present result clearly demonstrates that not only the spiral geometry, but also the geometry of the cochlear duct play decisive roles in distributing the wave energy.Comment: 21 pages. (to appear in J. Biol. Phys.

Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth

Blood vessels form either when dispersed endothelial cells (the cells lining the inner walls of fully-formed blood vessels) organize into a vessel network (vasculogenesis), or by sprouting or splitting of existing blood vessels (angiogenesis). Although they are closely related biologically, no current model explains both phenomena with a single biophysical mechanism. Most computational models describe sprouting at the level of the blood vessel, ignoring how cell behavior drives branch splitting during sprouting. We present a cell-based, Glazier-Graner-Hogeweg-model simulation of the initial patterning before the vascular cords form lumens, based on plausible behaviors of endothelial cells. The endothelial cells secrete a chemoattractant, which attracts other endothelial cells. As in the classic Keller-Segel model, chemotaxis by itself causes cells to aggregate into isolated clusters. However, including experimentally-observed adhesion-driven contact inhibition of chemotaxis in the simulation causes randomly-distributed cells to organize into networks and cell aggregates to sprout, reproducing aspects of both de novo and sprouting blood-vessel growth. We discuss two branching instabilities responsible for our results. Cells at the surfaces of cell clusters attempting to migrate to the centers of the clusters produce a buckling instability. In a model variant that eliminates the surface-normal force, a dissipative mechanism drives sprouting, with the secreted chemical acting both as a chemoattractant and as an inhibitor of pseudopod extension. The branching instabilities responsible for our results, which result from contact inhibition of chemotaxis, are both generic developmental mechanisms and interesting examples of unusual patterning instabilities.Comment: Thoroughly revised version, now in press in PLoS Computational Biology. 53 pages, 13 figures, 2 supporting figures, 56 supporting movies, source code and parameters files for computer simulations provided. Supporting information: http://www.psb.ugent.be/~romer/ploscompbiol/ Source code: http://sourceforge.net/projects/tst