Team:SDU-Denmark/project-m

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(2. The real system)
(2. The real system)
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The "real" system that we want to model is a bacterial pump as described by M. J. Kim and K. S. Breuer  [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 1]]. This is in principle just a microscopic chamber with a flow channel 15µm deep, 200µm wide and 15mm long, covered on the inside by a layer of flagellated bacteria. The bacterial layer described by M. J. Kim and K. S. Breuer [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 1]] is very dense and uniform, with a spacing between each bacterium of less that 1µm and 80% of the bacteria adhered to the surface as single bacteria. To get a better understanding of the origin of the  flow created from the bacterial coating, it is important to understand the structure of the bacterial flagellum.
The "real" system that we want to model is a bacterial pump as described by M. J. Kim and K. S. Breuer  [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 1]]. This is in principle just a microscopic chamber with a flow channel 15µm deep, 200µm wide and 15mm long, covered on the inside by a layer of flagellated bacteria. The bacterial layer described by M. J. Kim and K. S. Breuer [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 1]] is very dense and uniform, with a spacing between each bacterium of less that 1µm and 80% of the bacteria adhered to the surface as single bacteria. To get a better understanding of the origin of the  flow created from the bacterial coating, it is important to understand the structure of the bacterial flagellum.
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The bacterial flagellum consists of 3 major parts, a rotary motor complex, a hook and a filament. The first part creates the rotary motion of the flagellum and the second part serves as a flexible coupling between the torque creating part and the filament. For our model the filament is the most interesting part. This is responsible for the conversion of the rotary motion into a linear thrust. The filament is a self-assembling polymeric structure composed of flagellin protein subunits. These are arranged in a circular way to create a hollow helical structure, with a typical width of 120-250Å and a length of 10-15µm.[[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 2]] A bacterium as ''E. coli'' typically has around 10 flagella [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 3]]. These filaments are able to adopt a wide range of conformations under the induced torque. Numeric studies[[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 4-5]] and empiric results [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 6]] suggest that the conformation is strongly dependent on the hydrodynamic environment that surrounds the flagellum and its rotational direction. When several flagella rotates counterclockwise the flagella tends to bundle together in a single helix structure, due to the hydrodynamic interactions [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 4]]. A phosphorylationcascade causes the flagella to turn clockwise at irregular intervals. This induces a sequence of deformations that changes the single helix structure of the flagella and unravels the bundle. This is known as tumble mode. <br> </p>
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The bacterial flagellum consists of 3 major parts, a rotary motor complex, a hook and a filament. The first part creates the rotary motion of the flagellum and the second part serves as a flexible coupling between the torque creating part and the filament. For our model the filament is the most interesting part. This is responsible for the conversion of the rotary motion into a linear thrust. The filament is a self-assembling polymeric structure composed of flagellin protein subunits. These are arranged in a circular way to create a hollow helical structure, with a typical width of 120-250Å and a length of 10-15µm [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 2]]. A bacterium as ''E. coli'' typically has around 10 flagella [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 3]]. These filaments are able to adopt a wide range of conformations under the induced torque. Numeric studies [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 4-5]] and empiric results [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 6]] suggest that the conformation is strongly dependent on the hydrodynamic environment that surrounds the flagellum and its rotational direction. When several flagella rotates counterclockwise the flagella tends to bundle together in a single helix structure, due to the hydrodynamic interactions [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 4]]. A phosphorylationcascade causes the flagella to turn clockwise at irregular intervals. This induces a sequence of deformations that changes the single helix structure of the flagella and unravels the bundle. This is known as tumble mode. <br> </p>
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[[Image:Team-SDU-Denmark-2010-The_real1.jpeg|thumb|center|550px|A, shows a shematic picture of molecular structure of a flagellum [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 7]]. B and C shows respectively the flagella of a bacteria stuck to a surface and flagella bundels of a moving bacteria[[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 6]].]]
[[Image:Team-SDU-Denmark-2010-The_real1.jpeg|thumb|center|550px|A, shows a shematic picture of molecular structure of a flagellum [[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 7]]. B and C shows respectively the flagella of a bacteria stuck to a surface and flagella bundels of a moving bacteria[[https://2010.igem.org/Team:SDU-Denmark/project-m#Litterature 6]].]]

Revision as of 12:25, 24 October 2010