A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

I Dukovski, D Bajić, JM Chacón, M Quintin, JCC Vila… - Nature protocols, 2021 - nature.com
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

Cooperative self-organization of microorganisms

E Ben-Jacob, I Cohen, H Levine - Advances in Physics, 2000 - Taylor & Francis
In nature, microorganisms must often cope with hostile environmental conditions. To do so
they have developed sophisticated cooperative behaviour and intricate communication …

Reaction–diffusion modelling of bacterial colony patterns

M Mimura, H Sakaguchi, M Matsushita - Physica A: Statistical Mechanics …, 2000 - Elsevier
It is well known from experiments that bacterial species Bacillus subtilis exhibit various
colony patterns. These are essentially classified into five types in the morphological …

Could DNA uptake be a side effect of bacterial adhesion and twitching motility?

M Bakkali - Archives of Microbiology, 2013 - Springer
DNA acquisition promotes the spread of resistance to antibiotics and virulence among
bacteria. It is also linked to several natural phenomena including recombination, genome …

Universality in bacterial colonies

JA Bonachela, CD Nadell, JB Xavier… - Journal of Statistical …, 2011 - Springer
The emergent spatial patterns generated by growing bacterial colonies have been the focus
of intense study in physics during the last twenty years. Both experimental and theoretical …

Interactions of multiple biological fields in stored grain ecosystems

ZD Wu, Q Zhang, J Yin, XM Wang, ZJ Zhang, WF Wu… - Scientific Reports, 2020 - nature.com
Biological entities such as fungi in stored grain evolve and interact with the environment in
similar fashions as physical fields. An experiment was conducted to study the behavior of the …

Constructal pattern formation in stony corals, bacterial colonies and plant roots under different hydrodynamics conditions

AF Miguel - Journal of Theoretical Biology, 2006 - Elsevier
This paper explores a new application of the constructal theory, namely in describing and
predicting the formation of dissimilar patterns inside elements of the same species under …

Biofluiddynamics of lubricating bacteria

I Cohen, I Golding, IG Ron… - … methods in the applied …, 2001 - Wiley Online Library
Various bacterial strains exhibit colonial branching patterns during growth on thin poor
substrates. The growth can be either diffusion‐limited or kinetic‐limited, according to the …

Bacterial cooperative organization under antibiotic stress

E Ben-Jacob, I Cohen, I Golding, DL Gutnick… - Physica A: Statistical …, 2000 - Elsevier
Bacteria have developed sophisticated modes of cooperative behavior to cope with
unfavorable environmental conditions. Here we report the effect of antibiotic stress on the …

A defined medium to investigate sliding motility in a Bacillus subtilis flagella-less mutant

R Fall, DB Kearns, T Nguyen - BMC microbiology, 2006 - Springer
Background We have recently shown that undomesticated strains of Bacillus subtilis can
extensively colonize the surfaces of rich, semi-solid media, by a flagellum-independent …