Team:Macquarie Australia/Modeling

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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
 
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<h1><center>Modelling</h1>
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<center><h7> <p> Detail </p></h7>
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<br><br><br>
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One of the most important reactions on our earth is the photosynthetic energy harvesting reaction. Photosynthesis lets plants and cyanobacteria absorb energy from the sun and bind it chemically.
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<br><br>
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[Pathway]
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<br><br>
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The above chemical reaction is the basis for all higher living spices. The reaction takes place in a special organelle called chloroplast. Even the energy in fossil fuels, for example gasoline, is stored energy in plants, from million years ago.
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<br><br>
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[Pathway]
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<br>
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Figure1: Schematic picture of the chloroplast and thylakoid membrane, showing the four protein complexes involved in the photosynthetic light reactions: PSII, the Cyt b6f complex, PSI and ATP synthase.
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<br><br>
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In the above figure, the central part of the photosynthetic reaction is Photosystem II (PSII). In PSII, the electrons are removed from water molecules to create oxygen and protons. These protons are then directed through Photosystem I (PSI) to create carbohydrates from
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carbon dioxide.
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In artificial photosynthesis scientists try to mimic Photosystem II to split water into oxygen
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and hydrogen. The hydrogen can then be used as fuel.
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<br><br>
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Title - Artificial Photosynthesis
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<br><br>
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Artificial photosynthesis is the attempt to mimic the natural photosynthesis process whereby we aim to split water into hydrogen with help of energy from the sun. There are several different approaches to create artificial photosynthesis, but most of the methods have lots in common with the components of natural photosynthesis. That is, most systems have (i) an antenna for harvesting light, (ii) a reaction center for charge separation, (iii) catalysis and a (iv) membrane to separate the generated products. The reaction is very similar to natural
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photosynthesis but some reactants must be changed. The P700 molecule must be modified to
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build hydrogen instead of building sugar.
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<br><br>
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Title - Modelling Artificial Photosynthesis
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<br><br>
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Mathematical models attempting to model both natural photosynthesis and artificial photosynthesis have been developed.  However, the photosynthetic reaction shown above is a highly oversimplified version of events. As a result, the mathematical models attempting to describe either the natural or artificial photosynthetic systems are highly complicated. Firstly, the reaction does not occur spontaneously.  It must be catalysed. The organic molecule that does this is Chlorophyll, the focus of our project.
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<br><br>
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<b>Considerations for modelling photosynthesis include:</b>
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• The cellular components for where the reaction needs to take place must be first considered when developing the model and include:  the cytosol, the chloroplast ie the double layer membrane organelle where the reaction occurs and the inner membrane structures called the thylacoids.
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• The individual cycles of the photosynthetic  reaction must also be differentiated. This includes Photosystem I, Photosystem II and the Oxygen Evolving Complex
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<br><br>
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The focus of our project is modelling of events linked to PSII. This light absorbing complex we are constructing in E.coli is a large antenna, consisting of several hundreds of our light absorbing chlorophyll pigments. The role of our system we are developing is to simply capture the solar energy.
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<br><br>
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!align="center"|[[Team:Macquarie_Australia|Home]]
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!align="center"|[[Team:Macquarie_Australia/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Macquarie_Australia Official Team Profile]
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!align="center"|[[Team:Macquarie_Australia/Project|Project]]
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!align="center"|[[Team:Macquarie_Australia/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Macquarie_Australia/Modeling|Modeling]]
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!align="center"|[[Team:Macquarie_Australia/Notebook|Notebook]]
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!align="center"|[[Team:Macquarie_Australia/Safety|Safety]]
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!align="center"|[[Team:Macquarie_Australia/Attributions|Attributions]]
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For synthetic photosynthesis, other scientists have used Ruthenium(II, III) linked to a Manganese complex as the electron donor to replace the role of chlorophyll as shown in the figure below.
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If you choose to include a '''Modeling''' page, please write about your modeling adventures here. This is not necessary but it may be a nice list to include.
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<br><br>
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[Picture 2]
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<br>
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Figure 2 - The mathematical approach for modelling the photosynthesis of just PSII is to describe the electron and energy transitions. Attempts to model this are I
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<br><br>
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[picture 3]
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<br>
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Figure III: Detailed scheme of photosynthetic process in PSII. Chl- chlorophyll, Phe- primary electron acceptor. Qa- primary quinine acceptor, Qb-secondary quinon acceptor, kL rate constant of light reaction, k±i rate constant of the electron transfer, x±i, i = 1,2,3- rate constant of the deactivation from excited states, x24 and x25 rate constants of the electron exchange between molecule and the electron carriers
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<br><br>

Revision as of 05:00, 27 September 2013



Modelling

Detail




One of the most important reactions on our earth is the photosynthetic energy harvesting reaction. Photosynthesis lets plants and cyanobacteria absorb energy from the sun and bind it chemically.

[Pathway]

The above chemical reaction is the basis for all higher living spices. The reaction takes place in a special organelle called chloroplast. Even the energy in fossil fuels, for example gasoline, is stored energy in plants, from million years ago.

[Pathway]
Figure1: Schematic picture of the chloroplast and thylakoid membrane, showing the four protein complexes involved in the photosynthetic light reactions: PSII, the Cyt b6f complex, PSI and ATP synthase.

In the above figure, the central part of the photosynthetic reaction is Photosystem II (PSII). In PSII, the electrons are removed from water molecules to create oxygen and protons. These protons are then directed through Photosystem I (PSI) to create carbohydrates from carbon dioxide. In artificial photosynthesis scientists try to mimic Photosystem II to split water into oxygen and hydrogen. The hydrogen can then be used as fuel.

Title - Artificial Photosynthesis

Artificial photosynthesis is the attempt to mimic the natural photosynthesis process whereby we aim to split water into hydrogen with help of energy from the sun. There are several different approaches to create artificial photosynthesis, but most of the methods have lots in common with the components of natural photosynthesis. That is, most systems have (i) an antenna for harvesting light, (ii) a reaction center for charge separation, (iii) catalysis and a (iv) membrane to separate the generated products. The reaction is very similar to natural photosynthesis but some reactants must be changed. The P700 molecule must be modified to build hydrogen instead of building sugar.

Title - Modelling Artificial Photosynthesis

Mathematical models attempting to model both natural photosynthesis and artificial photosynthesis have been developed. However, the photosynthetic reaction shown above is a highly oversimplified version of events. As a result, the mathematical models attempting to describe either the natural or artificial photosynthetic systems are highly complicated. Firstly, the reaction does not occur spontaneously. It must be catalysed. The organic molecule that does this is Chlorophyll, the focus of our project.

Considerations for modelling photosynthesis include: • The cellular components for where the reaction needs to take place must be first considered when developing the model and include: the cytosol, the chloroplast ie the double layer membrane organelle where the reaction occurs and the inner membrane structures called the thylacoids. • The individual cycles of the photosynthetic reaction must also be differentiated. This includes Photosystem I, Photosystem II and the Oxygen Evolving Complex

The focus of our project is modelling of events linked to PSII. This light absorbing complex we are constructing in E.coli is a large antenna, consisting of several hundreds of our light absorbing chlorophyll pigments. The role of our system we are developing is to simply capture the solar energy.

For synthetic photosynthesis, other scientists have used Ruthenium(II, III) linked to a Manganese complex as the electron donor to replace the role of chlorophyll as shown in the figure below.

[Picture 2]
Figure 2 - The mathematical approach for modelling the photosynthesis of just PSII is to describe the electron and energy transitions. Attempts to model this are I

[picture 3]
Figure III: Detailed scheme of photosynthetic process in PSII. Chl- chlorophyll, Phe- primary electron acceptor. Qa- primary quinine acceptor, Qb-secondary quinon acceptor, kL rate constant of light reaction, k±i rate constant of the electron transfer, x±i, i = 1,2,3- rate constant of the deactivation from excited states, x24 and x25 rate constants of the electron exchange between molecule and the electron carriers

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