Team:SDU-Denmark/project-m

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(Difference between revisions)
(1. Motivation)
(2. The real system)
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So the "real" system that we want to model is a bacterial pump as described by []. This is in principle just a small tube 15µm deep, 200µm wide and 15mm long, covered on the inside by a layer of flagellated bacteria. The bacterial layer described by [] 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 created flow from this carpet, it is important to understand the structure of the bacterial flagellum.
So the "real" system that we want to model is a bacterial pump as described by []. This is in principle just a small tube 15µm deep, 200µm wide and 15mm long, covered on the inside by a layer of flagellated bacteria. The bacterial layer described by [] 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 created flow from this carpet, it is important to understand the structure of the bacterial flagellum.
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This 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 touque creating part and the filament. For our pourpose is the filament the most interesting part. This is responsible for the conversion of the rotary motion into a linear thust. 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. A bacteria as E. coli typically has around 10 flagella.[cyber cell] These filaments is able to adopt a wide range of conformation under the induced torque. Numeric studies[2] and empiric results [1] suggests that this conformation is strongly on the hydrodynamic environment that surrounds the flagellum and the direction of rotation. When several flagella rotates counterclockwise the flagella tends to bundle together in a single helix structure, due to the hydrodynamic interactions[2]. <<random biokemi!>> at some point causes the flagella to turn clockwise instead. This induces a sequence of deformations that changes flagella structure and unravels the bundle. This is know as tumble mode.   
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This 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 touque creating part and the filament. For our pourpose is the filament the most interesting part. This is responsible for the conversion of the rotary motion into a linear thust. 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. A bacteria as E. coli typically has around 10 flagella.[cyber cell] These filaments are able to adopt a wide range of conformation under the induced torque. Numeric studies[2] and empiric results [1] suggests that this conformation is strongly on the hydrodynamic environment that surrounds the flagellum and the direction of rotation. When several flagella rotates counterclockwise the flagella tends to bundle together in a single helix structure, due to the hydrodynamic interactions[2]. <<random biokemi!>> at some point causes the flagella to turn clockwise instead. This induces a sequence of deformations that changes flagella structure and unravels the bundle. This is know as tumble mode.   
To be able to model the flow created by a bacterial carpet it is essential to know what kind of flowfield a single flagellum/bundle will create. This has primary been investigated by nurmerical approatch, where the flagella is modeled as semiflexibel hookian systems. Several studies [][] suggests that the flow created from a single flagellum is highly non-uniform, but to some degree circular symmetric at the end of the flagellum.(see figure XX and XX) When the flagella bundle together [] suggest that this symmetry becomes less clear and flow becomes even more complicated. The total movement of the bacteria in tumble mode is zero, so to a first approximation can the field here be thought as non existing.  
To be able to model the flow created by a bacterial carpet it is essential to know what kind of flowfield a single flagellum/bundle will create. This has primary been investigated by nurmerical approatch, where the flagella is modeled as semiflexibel hookian systems. Several studies [][] suggests that the flow created from a single flagellum is highly non-uniform, but to some degree circular symmetric at the end of the flagellum.(see figure XX and XX) When the flagella bundle together [] suggest that this symmetry becomes less clear and flow becomes even more complicated. The total movement of the bacteria in tumble mode is zero, so to a first approximation can the field here be thought as non existing.  

Revision as of 13:46, 16 October 2010