A subcellular biochemical model for T6SS dynamics reveals winning competitive strategies.

The type VI secretion system (T6SS) is a broadly distributed interbacterial weapon that can be used to eliminate competing bacterial populations. Although unarmed target populations are typically used to study T6SS function in vitro, bacteria most likely encounter other T6SS-armed competitors in nature. However, the connection between subcellular details of the T6SS and the outcomes of such mutually lethal battles is not well understood. Here, we incorporate biological data derived from natural competitors of Vibrio fischeri light organ symbionts to build a biochemical model for T6SS at the single-cell level, which we then integrate into an agent-based model (ABM). Using the ABM, we isolate and experiment with strain-specific physiological differences between competitors in ways not possible with biological samples to identify winning strategies for T6SS-armed populations. Through in vitro experiments, we discover that strain-specific differences exist in T6SS activation speed. ABM simulations corroborate that faster activation is dominant in determining survival during competition. Once competitors are fully activated, the energy required for T6SS creates a tipping point where increased weapon building and firing becomes too costly to be advantageous. Through ABM simulations, we identify the threshold where this transition occurs in the T6SS parameter space. We also find that competitive outcomes depend on the geometry of the battlefield: unarmed target cells survive at the edges of a range expansion where unlimited territory can be claimed. Alternatively, competitions within a confined space, much like the light organ crypts where natural V. fischeri compete, result in the rapid elimination of the unarmed population.

Regulation of the swimming kinematics of lampreys Petromyzon marinus across changes in viscosity.

The bodies of most swimming fishes are very flexible and deform as result of both external fluid dynamic forces and internal musculoskeletal forces. If fluid forces change, the body motion will also change unless the fish senses the change and alters its muscle activity to compensate. Lampreys and other fishes have mechanosensory cells in their spinal cords that allow them to sense how their body is bending. We hypothesized that lampreys (Petromyzon marinus) actively regulate body curvature to maintain a fairly constant swimming waveform even as swimming speed and fluid dynamic forces change. To test this hypothesis, we measured the steady swimming kinematics of lampreys swimming in normal water, and water in which the viscosity was increased by 10 or 20 times by adding methylcellulose. Increasing the viscosity over this range increases the drag coefficient, potentially increasing fluid forces up to 40%. Previous computational results suggested that if lampreys did not compensate for these forces, the swimming speed would drop by about 52%, the amplitude would drop by 39%, and posterior body curvature would increase by about 31%, while tail beat frequency would remain the same. Five juvenile sea lampreys were filmed swimming through still water, and midlines were digitized using standard techniques. Although swimming speed dropped by 44% from 1× to 10× viscosity, amplitude only decreased by 4%, and curvature increased by 7%, a much smaller change than the amount we estimated if there was no compensation. To examine the waveform overall, we performed a complex orthogonal decomposition and found that the first mode of the swimming waveform (the primary swimming pattern) did not change substantially, even at 20× viscosity. Thus, it appears that lampreys are compensating, at least partially, for the changes in viscosity, which in turn suggests that sensory feedback is involved in regulating the body waveform.

Eulerian simulation of complex suspensions and biolocomotion in three dimensions.

We present a numerical method specifically designed for simulating three-dimensional fluid-structure interaction (FSI) problems based on the reference map technique (RMT). The RMT is a fully Eulerian FSI numerical method that allows fluids and large-deformation elastic solids to be represented on a single fixed computational grid. This eliminates the need for meshing complex geometries typical in other FSI approaches and greatly simplifies the coupling between fluid and solids. We develop a three-dimensional implementation of the RMT, parallelized using the distributed memory paradigm, to simulate incompressible FSI with neo-Hookean solids. As part of our method, we develop a field extrapolation scheme that works efficiently in parallel. Through representative examples, we demonstrate the method's suitability in investigating many-body and active systems, as well as its accuracy and convergence. The examples include settling of a mixture of heavy and buoyant soft ellipsoids, lid-driven cavity flow containing a soft sphere, and swimmers actuated via active stress.