Cellular Behaviors Underlying Disappearance of Myxococcus xanthus Fruiting Bodies

The soil bacterium Myxococcus xanthus is known as a social organism with many diverse behaviors under different conditions, behaviors which include swarming during predation, rippling, pulsing, and the formation of colonies known as fruiting bodies, or simply aggregates, when under nutritional stress. After initial aggregates have formed, some will destabilize and subsequently disappear, with a greater chance of this occurring for smaller aggregates.

In collaboration with the Welch Lab at Syracuse University, we identified behaviors at the cellular level that can result in coarsening. We analyzed movies of myxobacterial aggregation and coarsening that included fluorescent data of individually tracked cells. These tracked cells undergo quantifiable changes in their movement, reversing their direction of motion as well as entering or exiting a non-persistent motile state. By analyzing tracked cell data, we identified a bias in the duration a cell moves before changing its motile state when it is aligned with an aggregate. To test if this mechanism is a key factor in determining aggregate fate, we made a computational model of aggregate coarsening. By creating a database of cell behaviors at different local conditions within an experiment, simulated cells can then draw on these behaviors to accurately reproduce real cell behavior. The choice of which behavior a simulated cell chooses is determined by a K-nearest neighbors (KNN) search of the database using selected variables such as local cell density and alignment, as well as the orientation of cells to the nearest aggregate. By both changing the variables used in this search and breaking correlations by randomizing selected variables, we can measure the effects of these variables on the coarsening process.

Kinetic Boltzmann-type Model for Alignment of Self-Propelled Rods

Self-propelled rods are a facet of the field of active matter relevant to many physical systems ranging in scale from shaken granular media and bacterial alignment to the flocking dynamics of animals. We developed a model for nematic alignment of self-propelled rods interacting through binary collisions, avoiding phenomenological descriptions of rod interaction in favor of rigorously using a set of microscopic-level rules. Under the assumption that each collision results in a small change to a rod’s orientation, we derived the Fokker-Planck equation for the evolution of the kinetic density function. Using analytical and numerical methods, we studied the emergence of the nematic order from a homogeneous, uniform steady-state of the mean-field equation. We compared the level of orientational noise needed to destabilize this nematic order and compare our results to an existing phenomenological model that does not explicitly account for the physical collisions of rods. We showed the presence of an additional geometric factor in our equations reflecting a reduced collision rate between nearly-aligned rods reduces the level of noise at which nematic order is destroyed, suggesting that alignment that depends on purely physical collisions is less robust. We are developing further work for more general collision schemes and quantifying their accuracy using a combination of numerical solvers and agent-based simulations.

M A Perepelitsa*, I Timofeyev*, P Murphy*, and O Igoshin. Mean-field model for nematic alignment of self-propelled rods. Phys. Rev. E. 106, 034613 (2022) [arXiv link]

Doctoral Research

Diffusion with Spatially Dependent Switching Rates
Particles binding and unbinding within a spatially heterogeneous environment change diffusive states based on spatially changing rates. We have done a preliminary investigation into this phenomenon regarding cell polarization in a C. elegans zygote.

P Murphy*, P C Bressloff, and S D Lawley. Interaction Between Switching Diffusivities and Cellular Microstructure. Multiscale Model. Simul., 18(2), 572–588. (2020)

P C Bressloff*, S D Lawley*, and P Murphy*. Protein concentration gradients and switching diffusions. Phys. Rev. E. 99, 032409 (2019)

Age-Structured Gating

We investigated the effects of a cellular gate changing between open and closed conformational states where some memory of the occupation time of the current state is retained. This leads to diffusing particles experiencing a changing environment where the transition times are not necessarily exponentially distributed.

P C Bressloff*, S D Lawley*, and P Murphy*. Effective permeability of gap junctions with age-structured switching. SIAM J. Appl. Math. 80(1), 312–337 (2020)
P C Bressloff*, S D Lawley*, and P Murphy*. Diffusion in an age-structured randomly switching environment. J. Phys. A 51 315001 (2018)