User:Gavliegen/sandbox

= PHYMOT = The International Training Network (ITN) PHYMOT 'Physics of Microbial Motility' is funded by the European Union's Horizon 2020 research program under the Marie Sklodowska-Curie grant agreement no. 955910. PHYMOT is a Ph.D. training network program in the field of active matter, in particular, active biological matter at the microscale. Research in PHYMOT focuses on the motility of microorganisms like bacteria, marine- and freshwater flagellates, and trypanosomes.

The network started its action on Feb. 1st, 2021, and consists of 12 beneficiaries and 5 partner institutions coordinated by the Forschungszentrum Jülich. PHYMOT employs 15 early-stage researchers (ESRs) and provides a wide range of scientific and soft-skill training courses and exchange opportunities to them.

The PHYMOT consortium
PHYMOT consists of 12 beneficiaries and 5 partner organizations and is funded by the European Commission.


 * Beneficiaries
 * Forschungszentrum Jülich
 * Technical University of Denmark
 * ETH Zürich
 * Claude Bernard University Lyon 1
 * Sapienza University of Rome
 * University of Basel
 * University Würzburg
 * Synoptics
 * University of the Balearic Islands
 * University Cambridge
 * ESPCI Paris
 * LyncéeTec
 * Partner organisations
 * University of Warwick
 * CAIRN
 * Spanish National Research Council CSIC
 * Ben-Gurion University of the Negev
 * IFP Energies nouvelles

Objectives
PHYMOT's scientific objective is to understand the physics of cell motility, from single cells to collective behavior, and to acquire fundamental physical insight into the motile behavior of microbes as well as the interplay with their environment for sustainable applications in medicine and ecology.

PHYMOT's training activities provide the ESRs with a solid background in the physics and biology of microbial motility and equip the ESRs with state-of-the-art theoretical tools and experimental techniques.

Activities
PHYMOT offers its ESRs a range of specialized scientific training courses in hydrodynamics, biological aspects of microbial motility, microfluidics, advanced microscopy techniques, and soft skills courses like communication skills, management, entrepreneurship, and career development. In addition, training is provided by secondments and mini-projects.

Besides training for its ESRs, PHYMOT organizes workshops and conferences open to the whole scientific community.

Physics of microbial motility
Motile microorganisms are among the most important life-forms on earth, not only because of their abundance but also because of their vital functions, e.g., in symbiosis with mammals or in ecosystems. Swimming and microscopic fluid propulsion have been linked to the evolution of multicellularity, and in extant animals, the same organelles that propel eukaryotic microorganisms play fundamental roles in embryonic development. Unraveling the basic principles of these propulsion mechanisms is essential for the development of novel strategies in the treatment of diseases, to understand microbial transport like the migration of marine phytoplankton in aquatic environments, and ultimately to open avenues for the control of biological systems and the design of artificial nanomachines.

Motility encompasses diverse interconnected phenomena: the propulsion mechanism of an individual flagellum, steering and directed navigation by a cell, the emergence of cooperative and collective motion of many cells (e.g., swarming), the response to environmental stimuli (e.g., light, flows), and the effect of confinement (e.g., geometrical restrictions).

PHYMOT's research activity focuses on these three different aspects of microbial motility both by experimental investigations (microscopy, microfluidics, genetically modified microorganisms), theoretical studies (equilibrium and non-equilibrium statistical mechanics, hydrodynamics), and computer simulations (Brownian dynamics , Multi-particle collision dynamics )

<!-- Motility and sensing by single cells Microbial motility is governed by biological micromotors, the cellular structures that generate propulsion, from rotating passive flagellar filaments in bacteria to active beating of eukaryotic cilia and flagella. The latter, in particular, are organelles present also in humans, where they are linked to a variety of complex and poorly understood diseases. Through a combination of experimental and theoretical projects, PHYMOT will provide a novel perspective on the complex mechanism leading to ciliary beating, and the physical consequences of the ensuing micro-flows.

Collective cell motion From large-scale swarms in the ocean and increased antibiotic tolerance of biofilms to sperm bundling in mammalian fertilization, microorganisms often improve their evolutionary fitness by organizing into large assemblies and emerging collective behavior. The importance of group motility highlights the need to understand the basic interactions leading to collective dynamics, which can in turn open new avenues for controlling microbial growth in medical and industrial applications.

On the scale of two or a few microbes only, PHYMOT ESRs will unravel the interactions between the cells. More specifically, the goal is to resolve the role played by the flagella of planktonic and swarming cells compared to cell-cell scattering events.

Geometry and microbial motility Microbial dynamics is not only controlled by chemotaxis, fluid flow, or cell-cell interactions but also externally by the geometry of the environment — from the microscopic shape of confining surfaces to the spatial arrangement of obstacles. Paramount examples include the spontaneous accumulation of swimming microorganisms at boundaries, with potential knock-on effects on cell-cell interactions, as well as the emergent order in bacterial swarms induced by spatial confinement. Understanding the principles of geometric control of microbial motility opens an avenue for the development of ‘smart’ materials, from smart wound dressing to anti-biofouling coatings. Experiments will be conducted to advance the understanding of the geometric control of microbial activity. --!>

Experimental systems
PHYMOTs experimental groups study a variety of different systems: ciliated human epithelial cells, fresh and saltwater microorganisms, several bacterial species and also trypanosomes.

Experimental techniques
Experimental techniques that are used in the PHYMOT consortium are optical microscopy; optical manipulation; particle imaging; holographic microscopy; soft lithography; microfluidics; 3D printing and laser writing; two-photon polymerization; culturing of microorganisms; genetic manipulation; transcriptomic and proteomic analyses.

Theory & computer simulations
Theoretical studies rely on the framework of equilibrium and non-equilibrium statistical physics and hydrodynamics theory. Computer simulations will be done using coarse-grained methods like Brownian Dynamics, Dissipative Particle Dynamics, and Multiparticle Collision Dynamics.