scholarly journals Lane formation and critical coarsening in a model of bacterial competition

2019 ◽  
Vol 99 (4) ◽  
Author(s):  
Takuro Shimaya ◽  
Kazumasa A. Takeuchi
Keyword(s):  
Bacterial Competition ◽  
Lane Formation

Effect of external magnetic field on lane formation in driven pair-ion plasmas

2021 ◽  
Vol 87 (2) ◽  
Author(s):  
Swati Baruah ◽  
U. Sarma ◽  
R. Ganesh
Keyword(s):  
Magnetic Field ◽  
External Magnetic Field ◽  
Field Strength ◽  
Electric Field ◽  
Electric Field Strength ◽  
Coupling Parameter ◽  
Critical Parameters ◽  
Coulomb Coupling ◽  
Lane Formation ◽  
Parameter Values

Lane formation dynamics in externally driven pair-ion plasma (PIP) particles is studied in the presence of external magnetic field using Langevin dynamics (LD) simulation. The phase diagram obtained distinguishing the no-lane and lane states is systematically determined from a study of various Coulomb coupling parameter values. A peculiar lane formation-disintegration parameter space is identified; lane formation area extended to a wide range of Coulomb coupling parameter values is observed before disappearing to a mixed phase. The different phases are identified by calculating the order parameter. This and the critical parameters are calculated directly from LD simulation. The critical electric field strength value above which the lanes are formed distinctly is obtained, and it is observed that in the presence of the external magnetic field, the PIP system requires a higher value of the electric field strength to enter into the lane formation state than that in the absence of the magnetic field. We further find out the critical value of electric field frequency beyond which the system exhibits a transition back to the disordered state and this critical frequency is found as an increasing function of the electric field strength in the presence of an external magnetic field. The movement of the lanes is also observed in a direction perpendicular to that of the applied electric and magnetic field directions, which reveals the existence of the electric field drift in the system under study. We also use an oblique force field as the external driving force, both in the presence and absence of the external magnetic field. The application of this oblique force changes the orientation of the lane structures for different applied oblique angle values.

scholarly journals Emerging and divergent roles of pyrophosphorylated nucleotides in bacterial physiology and pathogenesis

2021 ◽  
Vol 17 (5) ◽  
pp. e1009532
Author(s):  
N. Y Elizabeth Chau ◽  
Shehryar Ahmad ◽  
John C. Whitney ◽  
Brian K. Coombes
Keyword(s):  
Pathogenic Bacteria ◽  
Second Messengers ◽  
Protein Family ◽  
Bacterial Toxin ◽  
Bacterial Physiology ◽  
Bacterial Competition ◽  
Reactive Nitrogen Intermediates ◽  
Host Infection ◽  
The Complement System

Bacteria inhabit diverse environmental niches and consequently must modulate their metabolism to adapt to stress. The nucleotide second messengers guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) (collectively referred to as (p)ppGpp) are essential for survival during nutrient starvation. (p)ppGpp is synthesized by the RelA-SpoT homologue (RSH) protein family and coordinates the control of cellular metabolism through its combined effect on over 50 proteins. While the role of (p)ppGpp has largely been associated with nutrient limitation, recent studies have shown that (p)ppGpp and related nucleotides have a previously underappreciated effect on different aspects of bacterial physiology, such as maintaining cellular homeostasis and regulating bacterial interactions with a host, other bacteria, or phages. (p)ppGpp produced by pathogenic bacteria facilitates the evasion of host defenses such as reactive nitrogen intermediates, acidic pH, and the complement system. Additionally, (p)ppGpp and pyrophosphorylated derivatives of canonical adenosine nucleotides called (p)ppApp are emerging as effectors of bacterial toxin proteins. Here, we review the RSH protein family with a focus on its unconventional roles during host infection and bacterial competition.

scholarly journals Lane Formation Beyond Intuition Towards an Automated Characterization of Lanes in Counter-flows

2020 ◽  
Vol 5 ◽  
Author(s):  
Luca Crociani ◽  
Giuseppe Vizzari ◽  
Andrea Gorrini ◽  
Stefania Bandini
Keyword(s):  
Clustering Algorithm ◽  
Variable Density ◽  
Automatic Identification ◽  
Computing Power ◽  
Dbscan Clustering ◽  
Significant Difference ◽  
Lane Formation ◽  
Human Coder ◽  
Behavioural Dynamics

Pedestrian behavioural dynamics have been growingly investigated by means of (semi)automated computing techniques for almost two decades, exploiting advancements on computing power, sensor accuracy and availability, computer vision algorithms. This has led to a unique consensus on the existence of significant difference between unidirectional and bidirectional flows of pedestrians, where the phenomenon of lane formation seems to play a major role. The collective behaviour of lane formation emerges in condition of variable density and due to a self-organisation dynamic, for which pedestrians are induced to walk following preceding persons to avoid and minimize conflictual situations. Although the formation of lanes is a well-known phenomenon in this field of study, there is still a lack of methods offering the possibility to provide an (even semi-) automatic identification and a quantitative characterization. In this context, the paper proposes an unsupervised learning approach for an automatic detection of lanes in multi-directional pedestrian flows, based on the DBSCAN clustering algorithm. The reliability of the approach is evaluated through an inter-rater agreement test between the results achieved by a human coder and by the algorithm.

scholarly journals Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

2017 ◽  
Author(s):  
Alex Bishara ◽  
Eli L. Moss ◽  
Ekaterina Tkachenko ◽  
Joyce B. Kang ◽  
Soumaya Zlitni ◽  
...  
Keyword(s):  
Hematopoietic Cell Transplantation ◽  
Susceptibility Testing ◽  
Mobile Element ◽  
Strain Level ◽  
Short Read Sequencing ◽  
Bacterial Competition ◽  
Structural Differences ◽  
Stool Samples ◽  
Metagenomic Approach

AbstractAlthough shotgun short-read sequencing has facilitated the study of strain-level architecture within complex microbial communities, existing metagenomic approaches often cannot capture structural differences between closely related co-occurring strains. Recent methods, which employ read cloud sequencing and specialized assembly techniques, provide significantly improved genome drafts and show potential to capture these strain-level differences. Here, we apply this read cloud metagenomic approach to longitudinal stool samples from a patient undergoing hematopoietic cell transplantation. The patient’s microbiome is profoundly disrupted and is eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allows us to predict that particular mobile element integrations result in increased antibiotic resistance, which we further support using in vitro antibiotic susceptibility testing. Thus, we find read cloud sequencing to be useful in identifying strain-level differences that underlie differential fitness.

Simulating pedestrian flow by an improved two-process cellular automaton model

2017 ◽  
Vol 28 (02) ◽  
pp. 1750016 ◽  
Author(s):  
Cheng-Jie Jin ◽  
Wei Wang ◽  
Rui Jiang ◽  
Li-Yun Dong
Keyword(s):  
Cellular Automaton ◽  
Critical Density ◽  
Maximum Flow ◽  
Cellular Automaton Model ◽  
Open Boundary ◽  
Flow Density ◽  
Open Boundary Conditions ◽  
Pedestrian Flow ◽  
Exchange Rule ◽  
Lane Formation

In this paper, we study the pedestrian flow with an Improved Two-Process (ITP) cellular automaton model, which is originally proposed by Blue and Adler. Simulations of pedestrian counterflow have been conducted, under both periodic and open boundary conditions. The lane formation phenomenon has been reproduced without using the place exchange rule. We also present and discuss the flow-density and velocity-density relationships of both uni-directional flow and counterflow. By the comparison with the Blue-Adler model, we find the ITP model has higher values of maximum flow, critical density and completely jammed density under different conditions.

Erratum: Dynamics of Lane Formation in Driven Binary Complex Plasmas [Phys. Rev. Lett.102, 085003 (2009)]

2009 ◽  
Vol 102 (14) ◽  
Author(s):  
K. R. Sütterlin ◽  
A. Wysocki ◽  
A. V. Ivlev ◽  
C. Räth ◽  
H. M. Thomas ◽  
...  
Keyword(s):  
Binary Complex ◽  
Lane Formation ◽  
Complex Plasmas

scholarly journals The evolution of tit-for-tat in bacteria via the type VI secretion system

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
William P. J. Smith ◽  
Maj Brodmann ◽  
Daniel Unterweger ◽  
Yohan Davit ◽  
Laurie E. Comstock ◽  
...  
Keyword(s):  
Animal Behavior ◽  
Evolutionary Game ◽  
Secretion System ◽  
Evolutionary Strategy ◽  
Type Vi Secretion System ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Bacterial Competition ◽  
Type Vi Secretion ◽  
Tit For Tat

Abstract Tit-for-tat is a familiar principle from animal behavior: individuals respond in kind to being helped or harmed by others. Remarkably some bacteria appear to display tit-for-tat behavior, but how this evolved is not understood. Here we combine evolutionary game theory with agent-based modelling of bacterial tit-for-tat, whereby cells stab rivals with poisoned needles (the type VI secretion system) after being stabbed themselves. Our modelling shows tit-for-tat retaliation is a surprisingly poor evolutionary strategy, because tit-for-tat cells lack the first-strike advantage of preemptive attackers. However, if cells retaliate strongly and fire back multiple times, we find that reciprocation is highly effective. We test our predictions by competing Pseudomonas aeruginosa (a tit-for-tat species) with Vibrio cholerae (random-firing), revealing that P. aeruginosa does indeed fire multiple times per incoming attack. Our work suggests bacterial competition has led to a particular form of reciprocation, where the principle is that of strong retaliation, or ‘tits-for-tat’.

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