Interplay of active nematic defects and flow structures

Active nematics are a class of liquid crystals driven out-of-equilibrium by the intrinsic activity of the rod-like constituents. In bulk, global nematic order is destabilised via the coupled feedback between nematic deformations and active flows, facilitating a steady-state population of pairs of half-integer nematic topological defects and chaotic flows (active turbulence). When confined, active nematics can exhibit active turbulence if the activity is sufficient, or more ordered spatiotemporal flow field patterns with a reduced defect count, dependent on the confinement scale. Understanding these complex flow regimes have naturally favoured perspectives centred on the nematic defects, as their emergent steady-state presence is an evident feature of active nematics. Defect orientation, motility and flow generation has been employed to study quasi-particle like descriptions of larger scale flow structures [1]. Within this description, the production of active flows around defects has been studied [2], revealing that the flow-field solution around a +1/2 defect is associated with two vortices and a self-propulsion velocity, while the -1/2 defect is associated with six vortices and active flows tending to zero at their core. However, this viewpoint is necessarily an oversimplification since flows are not simply governed by defects – flows influence the defects in parallel. The reverse viewpoint, ‘how nematic defects respond to the structure of the flow field’, is therefore important for understanding the architecture of active flow patterns but has not received adequate attention. Through experiments of microtubule-kinesin based active nematics [3], and mesoscopic simulations [4], we explore how defects couple to the structure of the velocity field in 2D. We adopt a topological description of the velocity field, identifying the borders between rotationally dominated and strain-rate dominated regions. We establish the importance of these boundaries as paths for defect dynamics and categorize defect behaviours into two regimes associated with +1/2 defects tracing either one boundary or instantaneously traversing intersections. These results demonstrate that the ideal picture of two vortices associated with each of the +1/2 defects is not characteristic of active nematics. Through utilizing topological descriptions of structures in the director field and velocity field, we can provide a complementary perspective on active nematic flows and possible control mechanisms by manipulating either field.

References:
[1] S. Shankar and M. C. Marchetti, Phys Rev. X 9, 041047, (2019)
[2] L. Giomi et al., Phil. Trans. R. Soc. A. 372:20130365, (2014)
[3] J. Hardoüin et al. Nat. Commun. 13 (1), 6675, (2022)
[4] K. Thijssen et al. Soft Matter 16, 2065-2074, (2020)

May 22, 2023 Leave a Comment

First passage time statistics of non-Markovian walkers: Onsager’s regression hypothesis approach

How long does it take for a random walker to reach its destination? Such a question on “first passage time” is fundamental in stochastic process, and relevant to many practical applications.
While the problem for the Markovian case (memory free) is well documented in literature, the presence of memory effect makes the standard analysis intractable, leaving many open questions in non-Markovian cases. We propose a method to think about the first passage statistics based on the non-equilibrium statistical mechanics idea, i.e., Onsager’s regression hypothesis, and demonstrate that it enables us to calculate various quantities of interest for non-Markovian systems analytically.

This work is in collaboration with Y. Sakamoto (Aoyama Gakuin University)
Reference: https://arxiv.org/abs/2301.13466

May 15, 2023 Leave a Comment

Using movement data to analyze the effect of lockdowns and inform their implementation – the Italian case

While lockdowns are certainly effective in curbing the rise of infections, their imposition severely affects the life and health of citizens. For this reason, the extent of their deployment should be optimized both in time and space to minimize the number of people affected while guaranteeing the safety of the population. At the same time, contact-tracing initiatives can easily violate privacy laws, and are generally difficult to implement for a public administration. It is thus interesting to consider whether anonymized samples of social networks’ datasets still contain enough information to optimize the implementation of lockdowns. Starting from Facebook (FB) users’ movement data from META’s data for good program and publicly available data from the Italian Institute of Statistics (ISTAT), we show how a data-driven meta-population approach can be used to identify a spatial subdivision of a state that maximises movements within communities, while minimizing those outside of them. Specifically, we focus on the level of movements between provinces, administrative entities in between municipalities and regions. After verifying that FB movement data gives reasonable population density in each province, we show that a temporal clustering correctly identifies the first two national lockdowns without any prior information. Finally, by considering the most representative movement networks in both a lockdown and free-movement situation, we identify the optimal communities, i.e. macro regions that minimize the amount of traffic between them. Using two different approaches -modularity and resolution/relevance – gives largely comparable results, supporting the robustness of our findings.

May 8, 2023 Leave a Comment

Effect of bacterial diet on bacteriophage infection

Bacteria play a huge role in the human and natural world, for richer and for poorer. Their most well-known role being a pathogen. With the gradual reduction in antimicrobial efficacy, the promise of phage as a potential solution has gathered attention.
Bacteria are also able to rapidly develop resistances to bacteriophage through numerous pathways. Here I have investigated how the bacteria-bacteriophage system dynamics depends on environmental conditions. Escherichia coli, grown in a range of media with various carbon sources, were exposed to T1 bacteriophage. In all cases the bacteria developed a resistance to the phage at long times. However, the population dynamics of the system both post and during infection varied with both carbon source and the number of phage added. Long-read and short-read sequencing of surviving mutant bacteria was undertaken. These results suggest a coupling between carbon source and the progression of a bacterial populations response. These results contribute to the understanding of the dominant factors in the growth of phage which could result in significant differences between the rates of death and resistance development in vivo and in vitro due to differing environmental conditions.

May 1, 2023 Leave a Comment