Phototactic Behaviour of Active Fluids: Effects of Light Perturbation on Diffusion Coefficient of Bacterial Suspensions

2019 ◽  
Author(s):  
Thomas Vourc’h ◽  
Julien Léopoldès ◽  
Hassan Peerhossaini
Keyword(s):  
Collective Motion ◽  
Linear Response Theory ◽  
Directed Movement ◽  
Bacterial Response ◽  
Light Gradient ◽  
Average Motion ◽  
Typical Time ◽  
External Stresses ◽  
Light Stimuli ◽  
Phototactic Behaviour

Abstract Active fluids refer to the fluids that contain self-propelled particles such as bacteria or micro-algae, whose properties differ fundamentally from the passive fluids. Such particles often exhibit an intermittent motion; with high-motility “run” periods separated by low-motility “tumble” periods. The average motion can be modified with external stresses, such as nutrient or light gradient, leading to a directed movement called chemotaxis and phototaxis, respectively. Using cyanobacterium Synechocystis sp.PCC 6803, a model micro-organism to study photosynthesis, we track the bacterial response to light stimuli, under isotropic and non-isotropic conditions. In particular, we investigate how the intermittent motility is influenced by illumination. We find that just after a rise in light intensity, the probability to be in the run state increases. This feature vanishes after a typical time of about 1 hour, when initial probability is recovered. Our results are well described by a model based on the linear response theory. When the perturbation is anisotropic, the characteristic time of runs is longer whatever the direction, similar to what is observed with isotropic conditions. Yet we observe a collective motion toward the light source (phototaxis) and show that the bias emerges because of more frequent runs towards the light.

scholarly journals Light Control of the Diffusion Coefficient of Active Fluids

2020 ◽  
Vol 142 (3) ◽  
Author(s):  
Thomas Vourc'h ◽  
Julien Léopoldès ◽  
Hassan Peerhossaini
Keyword(s):  
Linear Response ◽  
Characteristic Time ◽  
Collective Motion ◽  
Linear Response Theory ◽  
Directed Movement ◽  
Bacterial Response ◽  
Average Motion ◽  
External Stresses ◽  
Light Stimuli ◽  
Intermittent Motion

Abstract Active fluids refer to the fluids that contain self-propelled particles such as bacteria or microalgae, whose properties differ fundamentally from the passive fluids. Such particles often exhibit an intermittent motion, with high-motility “run” periods broken by low-motility “tumble” periods. The average motion can be modified with external stresses, such as nutrient or light gradients, leading to a directed movement called chemotaxis and phototaxis, respectively. Using cyanobacterium Synechocystis sp. PCC 6803, a model microorganism to study photosynthesis, we track the bacterial response to light stimuli, under isotropic and nonisotropic (directional) conditions. In particular, we investigate how the intermittent motility is influenced by illumination. We find that just after a rise in light intensity, the probability to be in the run state increases. This feature vanishes after a typical characteristic time of about 1 h, when initial probability is recovered. Our results are well described by a mathematical model based on the linear response theory. When the perturbation is anisotropic, we observe a collective motion toward the light source (phototaxis). We show that the bias emerges due to more frequent runs in the direction of the light, whereas the run durations are longer whatever the direction.

scholarly journals An Early Response to Environmental Stress Involves Regulation of OmpX and OmpF, Two Enterobacterial Outer Membrane Pore-Forming Proteins

2007 ◽  
Vol 51 (9) ◽  
pp. 3190-3198 ◽  
Author(s):  
Myrielle Dupont ◽  
Chloë E. James ◽  
Jacqueline Chevalier ◽  
Jean-Marie Pagès
Keyword(s):  
Outer Membrane ◽  
Early Response ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Membrane Pore ◽  
Bacterial Response ◽  
External Stresses ◽  
Resistant Strains ◽  
Pore Forming Proteins

ABSTRACT Bacterial adaptation to external stresses and toxic compounds is a key step in the emergence of multidrug-resistant strains that are a serious threat to human health. Although some of the proteins and regulators involved in antibiotic resistance mechanisms have been described, no information is available to date concerning the early bacterial response to external stresses. Here we report that the expression of ompX, encoding an outer membrane protein, is increased during early exposure to drugs or environmental stresses. At the same time, the level of ompF porin expression is noticeably affected. Because of the role of these proteins in membrane permeability, these data suggest that OmpF and OmpX are involved in the control of the penetration of antibiotics such as β-lactams and fluoroquinolones through the enterobacterial outer membrane. Consequently, the early control of ompX and ompF induced by external stresses may represent a preliminary response to antibiotics, thus triggering the initial bacterial line of defense against antibiotherapy.

scholarly journals Formation, collective motion, and merging of macroscopic bacterial aggregates

2022 ◽  
Vol 18 (1) ◽  
pp. e1009153
Author(s):  
George Courcoubetis ◽  
Manasi S. Gangan ◽  
Sean Lim ◽  
Xiaokan Guo ◽  
Stephan Haas ◽  
...  
Keyword(s):  
Cell Density ◽  
Collective Motion ◽  
Bacterial Species ◽  
Aggregate Size ◽  
Enterobacter Cloacae ◽  
Soft Agar ◽  
Culture Dish ◽  
Directed Movement ◽  
Collective Behaviors ◽  
Bacterial Aggregates

Chemotactic bacteria form emergent spatial patterns of variable cell density within cultures that are initially spatially uniform. These patterns are the result of chemical gradients that are created from the directed movement and metabolic activity of billions of cells. A recent study on pattern formation in wild bacterial isolates has revealed unique collective behaviors of the bacteria Enterobacter cloacae. As in other bacterial species, Enterobacter cloacae form macroscopic aggregates. Once formed, these bacterial clusters can migrate several millimeters, sometimes resulting in the merging of two or more clusters. To better understand these phenomena, we examine the formation and dynamics of thousands of bacterial clusters that form within a 22 cm square culture dish filled with soft agar over two days. At the macroscale, the aggregates display spatial order at short length scales, and the migration of cell clusters is superdiffusive, with a merging acceleration that is correlated with aggregate size. At the microscale, aggregates are composed of immotile cells surrounded by low density regions of motile cells. The collective movement of the aggregates is the result of an asymmetric flux of bacteria at the boundary. An agent-based model is developed to examine how these phenomena are the result of both chemotactic movement and a change in motility at high cell density. These results identify and characterize a new mechanism for collective bacterial motility driven by a transient, density-dependent change in motility.

scholarly journals Fast, high-throughput measurement of collective behaviour in a bacterial population

2014 ◽  
Vol 11 (98) ◽  
pp. 20140486 ◽  
Author(s):  
R. Colin ◽  
R. Zhang ◽  
L. G. Wilson
Keyword(s):  
Collective Motion ◽  
Fluid Flows ◽  
Collective Behaviour ◽  
Coarse Grained ◽  
High Time Resolution ◽  
Bacterial Survival ◽  
Bacterial Populations ◽  
Bacterial Response ◽  
Fast Screening ◽  
Swimming Bacteria

Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards ‘a better life’. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for bacterial survival and virulence. Both single-cell and macroscopic assays have investigated bacterial behaviours. However, theories that relate the two scales have previously been difficult to test directly. We present an image analysis method, inspired by light scattering, which measures the average collective motion of thousands of bacteria simultaneously. Using this method, a time-varying collective drift as small as 50 nm s −1 can be measured. The method, validated using simulations, was applied to chemotactic Escherichia coli bacteria in linear gradients of the attractant α-methylaspartate. This enabled us to test a coarse-grained minimal model of chemotaxis. Our results clearly map the onset of receptor methylation, and the transition from linear to logarithmic sensing in the bacterial response to an external chemoeffector. Our method is broadly applicable to problems involving the measurement of collective drift with high time resolution, such as cell migration and fluid flows measurements, and enables fast screening of tactic behaviours.

scholarly journals Using activity and sociability to characterize collective motion

2018 ◽  
Vol 373 (1746) ◽  
pp. 20170015 ◽  
Author(s):  
David J. T. Sumpter ◽  
Alex Szorkovszky ◽  
Alexander Kotrschal ◽  
Niclas Kolm ◽  
James E. Herbert-Read
Keyword(s):  
Poecilia Reticulata ◽  
Collective Motion ◽  
Movement Ecology ◽  
Simulation Studies ◽  
Evolutionary Perspective ◽  
Theme Issue ◽  
Directed Movement ◽  
Wide Range ◽  
Group Members ◽  
Main Factors

A wide range of measurements can be made on the collective motion of groups, and the movement of individuals within them. These include, but are not limited to: group size, polarization, speed, turning speed, speed or directional correlations, and distances to near neighbours. From an ecological and evolutionary perspective, we would like to know which of these measurements capture biologically meaningful aspects of an animal's behaviour and contribute to its survival chances. Previous simulation studies have emphasized two main factors shaping individuals' behaviour in groups; attraction and alignment. Alignment responses appear to be important in transferring information between group members and providing synergistic benefits to group members. Likewise, attraction to conspecifics is thought to provide benefits through, for example, selfish herding. Here, we use a factor analysis on a wide range of simple measurements to identify two main axes of collective motion in guppies ( Poecilia reticulata ): (i) sociability, which corresponds to attraction (and to a lesser degree alignment) to neighbours, and (ii) activity, which combines alignment with directed movement. We show that for guppies, predation in a natural environment produces higher degrees of sociability and (in females) lower degrees of activity, while female guppies sorted for higher degrees of collective alignment have higher degrees of both sociability and activity. We suggest that the activity and sociability axes provide a useful framework for measuring the behaviour of animals in groups, allowing the comparison of individual and collective behaviours within and between species. This article is part of the theme issue ‘Collective movement ecology’.

Distributed Coordination of Simulated Robots Based on Self-Organization

2006 ◽  
Vol 12 (3) ◽  
pp. 289-311 ◽  
Author(s):  
Gianluca Baldassarre ◽  
Domenico Parisi ◽  
Stefano Nolfi
Keyword(s):  
Collective Motion ◽  
Distributed Coordination ◽  
Coordination Problem ◽  
Motion Direction ◽  
Robust Solution ◽  
Average Motion ◽  
Common Task ◽  
Under Construction ◽  
Organizing Principles ◽  
Self Organizing

Distributed coordination of groups of individuals accomplishing a common task without leaders, with little communication, and on the basis of self-organizing principles, is an important research issue within the study of collective behavior of animals, humans, and robots. The article shows how distributed coordination allows a group of evolved, physically linked simulated robots (inspired by a robot under construction) to display a variety of highly coordinated basic behaviors such as collective motion, collective obstacle avoidance, and collective approach to light, and to integrate them in a coherent fashion. In this way the group is capable of searching and approaching a lighted target in an environment scattered with obstacles, furrows, and holes, where robots acting individually fail. The article shows how the emerged coordination of the group relies upon robust self-organizing principles (e.g., positive feedback) based on a novel sensor that allows the single robots to perceive the group's “average” motion direction. The article also presents a robust solution to a difficult coordination problem, which might also be encountered by some organisms, caused by the fact that the robots have to be capable of moving in any direction while being physically connected. Finally, the article shows how the evolved distributed coordination mechanisms scale very well with respect to the number of robots, the way in which robots are assembled, the structure of the environment, and several other aspects.

scholarly journals Formation, collective motion, and merging of macroscopic bacterial aggregates

2021 ◽  
Author(s):  
James Q Boedicker ◽  
George Courcoutbetis ◽  
Manasi Gangan ◽  
Sean Lim ◽  
Xiaokan Guo ◽  
...  
Keyword(s):  
Cell Density ◽  
Collective Motion ◽  
Aggregate Size ◽  
Enterobacter Cloacae ◽  
Soft Agar ◽  
Culture Dish ◽  
Directed Movement ◽  
Collective Behaviors ◽  
Chemical Gradients ◽  
Bacterial Aggregates

Chemotactic bacteria form emergent spatial patterns of variable cell density within cultures that are initially spatially uniform. These patterns are the result of chemical gradients that are created from the directed movement and metabolic activity of billions of cells. A recent study on pattern formation in wild bacterial isolates has revealed unique collective behaviors of the bacteria Enterobacter cloacae . As in other bacteria species, Enterobacter cloacae form macroscopic aggregates. Once formed, these bacterial clusters can migrate several millimeters, sometimes resulting in the merging of two or more clusters. To better understand these phenomena, we examine the formation and dynamics of thousands of bacterial clusters that form within a 22 cm square culture dish filled with soft agar over two days. At the macroscale, the aggregates display spatial order at short length scales, and the migration of cell clusters is superdiffusive, with a merging acceleration that is correlated with aggregate size. At the microscale, aggregates are composed of immotile cells surrounded by low density regions of motile cells. The collective movement of the aggregates is the result of an asymmetric flux of bacteria at the boundary. An agent based model is developed to examine how these phenomena are the result of both chemotactic movement and a change in motility at high cell density. These results identify and characterize a new mechanism for collective bacterial motility driven by a transient, density-dependent change in motility.

THE TRANSPORT COEFFICIENTS OF LARGE SCALE NUCLEAR COLLECTIVE MOTION

2008 ◽  
Vol 17 (01) ◽  
pp. 60-71
Author(s):  
FEDIR IVANYUK
Keyword(s):  
Large Scale ◽  
Collective Motion ◽  
Transport Coefficients ◽  
Harmonic Approximation ◽  
Linear Response Theory ◽  
Many Body ◽  
Collective Variables ◽  
Angular Rotation ◽  
Shell Effects ◽  
Deformation Parameters

An approach to the description of slow collective motion at finite excitations based on the linear response theory and locally harmonic approximation is discussed. The method relies on the assumption that the nuclear many-body Hamiltonian can be approximated by a one-body Hamiltonian which in parametric way depends on the collective variables (deformation parameters) and allows for the account of the shell effects, pairing correlation, angular rotation. Special attention is paid to the removal of spurious contributions caused by the violation of the conservation laws. As an application of the theory, the microscopic transport coefficient are used for the description of reaction 18O + 208 Pb within the Langevin approach.

Low-Frequency Collective Motions in Proteins

2003 ◽  
Vol 02 (02) ◽  
pp. 163-169 ◽  
Author(s):  
Dimitri Antoniou ◽  
Steven D. Schwartz
Keyword(s):  
Molecular Dynamics ◽  
Linear Response ◽  
Collective Motion ◽  
Interatomic Potential ◽  
Low Frequency ◽  
Linear Response Theory ◽  
Density Fluctuations ◽  
Dynamics Simulation ◽  
Collective Motions ◽  
Theoretical Predictions

There are several kinds of low-frequency collective motions in proteins, which are believed to have a significant effect on their properties. We propose that a new kind of global collective motion in proteins are density fluctuations, which are slowly-varying, long-lived, propagating disturbances. These can be studied using the linear response formalism, which is a dynamical approximation that uses the full anharmonic interatomic potential. We have performed a molecular dynamics simulation of a realistic protein and have found results that are consistent with the theoretical predictions of linear response theory.

Quasi-Periodic Oscillations in Dwarf Novae

1979 ◽  
Vol 46 ◽  
pp. 77-88
Author(s):  
Edward L. Robinson
Keyword(s):  
Binary Systems ◽  
Outer Edge ◽  
Light Curves ◽  
Close Binary ◽  
Bright Spot ◽  
Dwarf Novae ◽  
Periodic Oscillations ◽  
High Frequencies ◽  
Short Period ◽  
Typical Time

Three distinct kinds of rapid variations have been detected in the light curves of dwarf novae: rapid flickering, short period coherent oscillations, and quasi-periodic oscillations. The rapid flickering is seen in the light curves of most, if not all, dwarf novae, and is especially apparent during minimum light between eruptions. The flickering has a typical time scale of a few minutes or less and a typical amplitude of about .1 mag. The flickering is completely random and unpredictable; the power spectrum of flickering shows only a slow decrease from low to high frequencies. The observations of U Gem by Warner and Nather (1971) showed conclusively that most of the flickering is produced by variations in the luminosity of the bright spot near the outer edge of the accretion disk around the white dwarf in these close binary systems.

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