Fickian yet non-Gaussian behaviour: A dominant role of the intermittent dynamics

Acharya, Sayantan; Nandi, Ujjwal Kumar; Bhattacharyya, S. K.

doi:10.1063/1.4979338

Cited by 28 publications

(14 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While the MSD tells us the width of the distribution of step sizes for each lag time, it cannot tell us more. Indeed there has been a growing appreciation in the soft condensed matter community that the MSD can easily be over interpreted [61][62][63][64][65][66] (as recently reviewed in ref. 67 ) and this issue requires even greater care in biologically complex systems, such as ensembles of twitching P. aeruginosa.…”

Section: Solitary Twitchermentioning

confidence: 99%

Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms

Nagel

Greenberg

Shendruk

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Pseudomonas aeruginosa, like many bacilliforms, are not limited only to swimming motility but rather possess many motility strategies. in particular, twitching-mode motility employs hair-like pili to transverse moist surfaces with a jittery irregular crawl. twitching motility plays a critical role in redistributing cells on surfaces prior to and during colony formation. We combine molecular dynamics and rule-based simulations to study twitching-mode motility of model bacilliforms and show that there is a critical surface coverage fraction at which collective effects arise. Our simulations demonstrate dynamic clustering of twitcher-type bacteria with polydomains of local alignment that exhibit spontaneous correlated motions, similar to rafts in many bacterial communities. Active matter possesses the potential to bridge between physics and biology. Like living systems, manufactured active systems maintain far-from-equilibrium states by autonomously drawing energy from the surroundings to fuel non-thermal processes. Furthermore, active systems exhibit many of the characteristic traits of biological materials, such as spontaneous motion, self-organization and complex spatio-temporal dynamics. Communities of model bacteria, such as Pseudomonas aeruginosa, are excellent biological examples of out-of-equilibrium systems. These relatively simple living systems serve as a biophysical study of active matter in which collectivity arising from bio-mechanical action can perform essential biological roles. Theories and simulations have approached such bacterial systems by simplifying or omitting all but the most essential, lowest-order physical traits of these microbes, as well as biological complexities. From the very first considerations of active matter, self-propulsion and local alignment were identified as the fundamental components necessary for collective dynamics to emerge from active particles 1,2. Simulations of self-propelled rods and their continuum limit of active nematics have been particularly important to the field 3-14 , as recently reviewed in ref. 15. However, the universality of behaviors exhibited by active systems is still a matter of debate 16,17 and it cannot simply be taken for granted that the collective dynamics of Vicsek boids 1 , active Brownian particles 18-20 or self-propelled rods are directly inherited by microbial motility strategies. Indeed it is known that what might appear to be higher-order details can qualitatively alter the large-scale dynamics. For example, while self-propelled rods and other active colloids commonly exhibit pronounced clustering 21 , which can be explained by motility-induced phase separation or other theoretical approaches 22-24 , swimming microbes can behave as homogeneous fluids on the scales of mesoscale active turbulence 25 , with simulations suggesting that the details of hydrodynamic interactions are essential for differentiating these large-scale swimmer properties 20,26-28. Various modes of swimming motility, including but not limited to pushing, pulling, squi...

show abstract

Section: Solitary Twitchermentioning

confidence: 99%

Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms

Nagel

Greenberg

Shendruk

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…This phenomenon is commonly seen in crowded media in both synthetic and biological systems, and is a hallmark of dynamic heterogeneity [32][33][34][35][36]45,46 . However, in these systems, non-Gaussian transport is often transient and reverts to Gaussian at long enough times [47][48][49] . Conversely, we note the absence of a crossover to Gaussian transport in our systems at long lag times (100 s), suggesting that the dynamical processes governing transport in these networks have relaxation times longer than our measurement time scale.…”

mentioning

confidence: 99%

Subtle changes in crosslinking drive diverse anomalous transport characteristics in actin–microtubule networks

et al. 2021

View full text Add to dashboard Cite

show abstract

“…However, the physical origin of the non-Gaussianity in the displacement distribution remains an open question [79]. This has been rationalized with the hypothesis that a tracer can have a distribution of random diffusivities which can lead to a slower (or caged) and faster motion in a complex environment [80][81][82][83][84][85]. Still, a consensus is lacking on the physical picture of the anomalous diffusion and non-Gaussian distribution of passive tracer particles in a complex and crowded environment [1].…”

mentioning

confidence: 99%

Transport of probe particles in a polymer network: effects of probe size, network rigidity and probe–polymer interaction

et al. 2019

View full text Add to dashboard Cite

Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in the biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the probe particle in a polymer network on a diamond lattice which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and the probe size.In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to surrounding network. These observations go with general experimental findings. Surprisingly for a probe particle of size comparable to the mesh size, unrestricted motion engulfing large length scales has been observed.This happens with the more flexible polymer network, which is easily pushed by the bigger probe. Our study gives a general qualitative picture of transport of probes in gel like medium, as encountered in different contexts.

show abstract

Fickian yet non-Gaussian behaviour: A dominant role of the intermittent dynamics

Cited by 28 publications

References 29 publications

Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms

Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms

Subtle changes in crosslinking drive diverse anomalous transport characteristics in actin–microtubule networks

Transport of probe particles in a polymer network: effects of probe size, network rigidity and probe–polymer interaction

Contact Info

Product

Resources

About