Team:ZJU-China/Project

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      <h3>Overview</h3>
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<h4>Overview</h4>
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                <a  href="https://2011.igem.org/Team:ZJU-China/Project">Summary</a>
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        <a  href= "https://2011.igem.org/Team:ZJU-China/Project">Summary</a>
<a  href="https://2011.igem.org/Team:ZJU-China/Project/Stratifiedsystem">Background<br/></a>
<a  href="https://2011.igem.org/Team:ZJU-China/Project/Stratifiedsystem">Background<br/></a>
<a  href="https://2011.igem.org/Team:ZJU-China/Project/Result">Results<br/></a>
<a  href="https://2011.igem.org/Team:ZJU-China/Project/Result">Results<br/></a>
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<a  href="https://2011.igem.org/Team:ZJU-China/Modeling">|Biofilm formation<br/></a>
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<a  href="https://2011.igem.org/Team:ZJU-China/Modeling">Biofilm formation<br/></a>
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<a  href="https://2011.igem.org/Team:ZJU-China/Modeling/Biobrick">|Biobrick<br/></a>
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<a  href="https://2011.igem.org/Team:ZJU-China/Modeling/Biobrick">Biobrick<br/></a>
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         <a  href="#">Results<br/></a>
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  <div class="bigblock" id="m_biofilm"><div class="block" id="introduction">
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    <h3><font color="white">Introduction</font></h3>
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    <p id="intro"><strong>abstract:</strong>.................................</p>
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<h1>Project Abstract</h1>
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                <p>This model is used for simulating biofilm formation and the stratification of concentration of oxygen
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                    <h1>Introduction</h1>
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                    <p ><strong>Compartment:</strong>The biofilm itself is distinguished from the overlying water and the substratum to which it is attached. A mass-transport boundary layer separates the biofilm from the overlying water.</p>
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<p>Within each compartment are<strong> components</strong>: include different types of biomass ,substrates , products. biomass is often divided into active microbial species, inert cells, and extracellular polymeric substances(EPS).</p>
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<p >The components can undergo transformation, transport, and transfer <strong>processes</strong>. For
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example, substrate is consumed, and this leads to the synthesis of new active biomass.</p>
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<p>All process affecting each component in each compartment are mathematically linked together into a<strong> mass balance equation</strong> that contains rate terms and parameters for each process.
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</p>
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<p><strong>Model Selection:</strong>Many kinds of Mathematics models have been founded to describe a system of biofilm. Models
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of different dimensions (1d, 2d, 3d) focus on different properties of a biofilm. Since we care most
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about the oxygen concentration gradients perpendicular to the substratum, <strong>numerical
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1-dimensional dynamic model(N1)</strong> would be a proper choice for us.</p>
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            <h1>Compartment</h1>
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<p><strong>The biofilm:</strong>A biofilm is a gel-like aggregation of microorganisms and other particles embedded in
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extracellular polymeric substancs. A biofilm contains water inside it, but its main physical
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characteristic is that it is a solid phase. A biofilm normally is anchored to a solid surface called the
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substratum on one side and in contact with liquid on its other side. Frequently, a mass-transfer
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boundary layer is included between the bulk liquid and the biofilm itself. Thus, following figure
 +
illustrates a biofilm having four compartments: the substratum, the biofilm itself, the boundary
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layer, and the bulk liquid outside of the biofilm. While it is complex even for a homogeneous biofilm morphology, we assume the biofilm surface is flat and all material below the maximum biofilm thickness as part of the biofilm components, and they have a constant density.</p>
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<img src="http://ung.igem.org/wiki/images/0/02/Modeling-biofilm.jpg"  alt="biofilm" width="541" height="317" />
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<p><strong>the mass-transport boundary layer</strong>Experimental observations clearly indicate strong concentration gradients for solutes just
 +
outside the biofilm when these solutes are utilized or produced by the microorganisms in the
 +
biofilm. Consequently, the solute concentrations at the biofilm surface and in a completely
 +
mixed bulk liquid often are significantly different.So we introduce the mass-transport boundary layer,which is a hypothetical layer of liquid above the biofilm and
 +
in which all the resistance to mass transport of dissolved components outside the biofilm
 +
occurs.</p>
 +
<p><strong>The bulk liquid:</strong> In our experiments, the bulk liquid is large compared to the biofilm. So the simplest way seems to consider it as a boundary condition of the biofilm compartment and specify the concentrations of dissolved. However, dissolved components can exchange between the biofilm and the bulk liquid, and it has a profound impact on the concentrations in the bulk liquid. Thus we include the bulk liquid not only as a boundary condition, but also as a separate, completely mixed compartment, varying according to the inflow, outflow, and the exchanges with the biofilm.</p>
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<p><strong>The substratum:</strong> In our basic model, the substratum is a separate compartment and impermeable. So it does not have much effect on the biofilm system. However in some bioreactor, the substratum may be permeable, or include organic solids that are biodegraded by attached microorganisms.
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                <p><a name="jumptop" id="p_intro">&nbsp;Introduction&nbsp;</a>|<a id="p_model">&nbsp;Model&nbsp;</a>|<a id="p_simul">&nbsp;Simulation&nbsp;</a></p>
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            <div class="links"><a>link1</a> <a>link2</a> <a>link3</a></div>
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Revision as of 22:35, 5 October 2011

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Untitled Document

Overview

Summary Background
 Results
 Future Application

Modeling

Biofilm formation
 Biobrick
 Results

Results

Data page Parts

Project Abstract

This model is used for simulating biofilm formation and the stratification of concentration of oxygen

Introduction

Compartment:The biofilm itself is distinguished from the overlying water and the substratum to which it is attached. A mass-transport boundary layer separates the biofilm from the overlying water.

Within each compartment are components: include different types of biomass ,substrates , products. biomass is often divided into active microbial species, inert cells, and extracellular polymeric substances(EPS).

The components can undergo transformation, transport, and transfer processes. For example, substrate is consumed, and this leads to the synthesis of new active biomass.

All process affecting each component in each compartment are mathematically linked together into a mass balance equation that contains rate terms and parameters for each process.

Model Selection:Many kinds of Mathematics models have been founded to describe a system of biofilm. Models of different dimensions (1d, 2d, 3d) focus on different properties of a biofilm. Since we care most about the oxygen concentration gradients perpendicular to the substratum, numerical 1-dimensional dynamic model(N1) would be a proper choice for us.

Compartment

The biofilm:A biofilm is a gel-like aggregation of microorganisms and other particles embedded in extracellular polymeric substancs. A biofilm contains water inside it, but its main physical characteristic is that it is a solid phase. A biofilm normally is anchored to a solid surface called the substratum on one side and in contact with liquid on its other side. Frequently, a mass-transfer boundary layer is included between the bulk liquid and the biofilm itself. Thus, following figure illustrates a biofilm having four compartments: the substratum, the biofilm itself, the boundary layer, and the bulk liquid outside of the biofilm. While it is complex even for a homogeneous biofilm morphology, we assume the biofilm surface is flat and all material below the maximum biofilm thickness as part of the biofilm components, and they have a constant density.

biofilm

the mass-transport boundary layerExperimental observations clearly indicate strong concentration gradients for solutes just outside the biofilm when these solutes are utilized or produced by the microorganisms in the biofilm. Consequently, the solute concentrations at the biofilm surface and in a completely mixed bulk liquid often are significantly different.So we introduce the mass-transport boundary layer,which is a hypothetical layer of liquid above the biofilm and in which all the resistance to mass transport of dissolved components outside the biofilm occurs.

The bulk liquid: In our experiments, the bulk liquid is large compared to the biofilm. So the simplest way seems to consider it as a boundary condition of the biofilm compartment and specify the concentrations of dissolved. However, dissolved components can exchange between the biofilm and the bulk liquid, and it has a profound impact on the concentrations in the bulk liquid. Thus we include the bulk liquid not only as a boundary condition, but also as a separate, completely mixed compartment, varying according to the inflow, outflow, and the exchanges with the biofilm.

The substratum: In our basic model, the substratum is a separate compartment and impermeable. So it does not have much effect on the biofilm system. However in some bioreactor, the substratum may be permeable, or include organic solids that are biodegraded by attached microorganisms.

link1 link2 link3

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