Team:British Columbia/modeling equ
From 2010.igem.org
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- | <div id="news" style="height: | + | <div id="news" style="height:1250px;"> <br/> |
<h3>Variables:</h3> | <h3>Variables:</h3> | ||
<p><b> | <p><b> | ||
- | z</b> = depth of biofilm structure | + | z</b> = depth of the biofilm structure |
<br></br><b> | <br></br><b> | ||
- | x </b>= depth of phage-infested layer | + | x </b>= depth of the phage-infested layer |
+ | <br></br><b> | ||
+ | ε </b>= portion of the biofilm population susceptible to phage infection | ||
<br></br><b> | <br></br><b> | ||
B<sub>T</sub> </b>= total biofilm bacteria population | B<sub>T</sub> </b>= total biofilm bacteria population | ||
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B<sub>i</sub></b> = infected biofilm bacteria subpopulation | B<sub>i</sub></b> = infected biofilm bacteria subpopulation | ||
<br></br><b> | <br></br><b> | ||
- | B<sub>L</sub></b> = bacteria | + | B<sub>L</sub></b> = bacteria subpopulation infected with phage in latent phase |
<br></br><b> | <br></br><b> | ||
- | B<sub>l</sub> </b>= bacteria | + | B<sub>l</sub> </b>= bacteria subpopulation infected with phage in lytic cycle |
<br></br><b> | <br></br><b> | ||
P</b> = phage particle population | P</b> = phage particle population | ||
<br></br><b> | <br></br><b> | ||
- | r<sub>in</sub> </b>= diffusion rate of phage particles into biofilm structure | + | r<sub>in</sub> </b>= diffusion rate of phage particles into the biofilm structure |
<br></br><b> | <br></br><b> | ||
[DspB]</b> = extracellular DspB concentration (inside biofilm) | [DspB]</b> = extracellular DspB concentration (inside biofilm) | ||
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<h3>Parameters:</h3><p><b> | <h3>Parameters:</h3><p><b> | ||
- | A</b> = cross-sectional area of biofilm container | + | A</b> = cross-sectional area of the biofilm container |
<br></br><b> | <br></br><b> | ||
D</b> = maximum biofilm thickness; related to K | D</b> = maximum biofilm thickness; related to K | ||
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d </b>= diameter of a biofilm bacterium | d </b>= diameter of a biofilm bacterium | ||
<br></br><b> | <br></br><b> | ||
- | α</b> = EPS occupancy constant | + | α</b> = EPS occupancy constant (corrects for the space EPS occupies around a bacterium) |
<br></br><b> | <br></br><b> | ||
- | K </b>= carrying capacity of biofilm | + | K </b>= carrying capacity of the biofilm |
<br></br><b> | <br></br><b> | ||
- | p </b>= portion of | + | p </b>= portion of the bacteria in the infected subpopulation that are infected by phage in latent phase |
<br></br><b> | <br></br><b> | ||
- | ρ </b>= bacterial growth rate | + | ρ </b>= bacterial growth rate of the total population (T), and the uninfected (u) and infected (i) subpopulations |
<br></br><b> | <br></br><b> | ||
- | λ </b>= lysis rate | + | λ </b>= host lysis rate |
<br></br><b> | <br></br><b> | ||
- | π</b> = rate at which phage switches from latent to lytic phase | + | π</b> = rate at which phage switches from latent to lytic phase in its host cell after infection |
<br></br><b> | <br></br><b> | ||
- | κ </b>= portion of phage particles | + | κ</b>= portion of phage particles successfully infecting a host cell |
<br></br><b> | <br></br><b> | ||
η</b> = phage half-life | η</b> = phage half-life | ||
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R</b> = number of phage particles released per lysis | R</b> = number of phage particles released per lysis | ||
<br></br><b> | <br></br><b> | ||
- | δ</b> = phage and DspB | + | δ</b> = percentage of phage and DspB diffusing out of the system (mechanical removal from biofilm) |
<br></br><b> | <br></br><b> | ||
- | Y</b> = | + | Y</b> = diffusion linear proportionality constant |
<br></br><b> | <br></br><b> | ||
- | S </b>= amount of DspB | + | S </b>= amount of DspB enzyme released per lysis |
<br></br><b> | <br></br><b> | ||
σ </b>= rate of AIP production | σ </b>= rate of AIP production | ||
<br></br><b> | <br></br><b> | ||
- | γ </b>= rate of AIP degradation and/or mechanical removal from system | + | γ</b>= rate of AIP degradation and/or mechanical removal from the system |
+ | <br></br><b> | ||
+ | [AIP]<sub>thres</sub></b>= threshold level of AIP concentration above which phage and DspB production are activated | ||
<br></br><b> | <br></br><b> | ||
- | [AIP]<sub> | + | [AIP]<sub>max</sub></b>= maximum level of AIP concentration inside the biofilm |
<br></br><b> | <br></br><b> | ||
- | r<sub>out</sub> </b>= diffusion rate of phage particles out of biofilm | + | r<sub>out</sub> </b>= diffusion rate of phage particles out of the biofilm and towards boundary layer |
<br></br><b> | <br></br><b> | ||
- | r<sub>max</sub></b> = max diffusion rate of phage particles into biofilm | + | r<sub>max</sub></b> = max diffusion rate of phage particles into the biofilm |
<br></br><b> | <br></br><b> | ||
- | r<sub>min</sub></b> = min diffusion rate of phage particles into biofilm | + | r<sub>min</sub></b> = min diffusion rate of phage particles into the biofilm, <i>i.e.</i> base rate |
<br></br></p> | <br></br></p> | ||
Latest revision as of 00:33, 26 October 2010
Summary of Equations
Variables:
z = depth of the biofilm structure
x = depth of the phage-infested layer
ε = portion of the biofilm population susceptible to phage infection
BT = total biofilm bacteria population
Bu = uninfected biofilm bacteria subpopulation
Bi = infected biofilm bacteria subpopulation
BL = bacteria subpopulation infected with phage in latent phase
Bl = bacteria subpopulation infected with phage in lytic cycle
P = phage particle population
rin = diffusion rate of phage particles into the biofilm structure
[DspB] = extracellular DspB concentration (inside biofilm)
[AIP] = extracellular AIP concentration (inside biofilm)
Parameters:
A = cross-sectional area of the biofilm container
D = maximum biofilm thickness; related to K
d = diameter of a biofilm bacterium
α = EPS occupancy constant (corrects for the space EPS occupies around a bacterium)
K = carrying capacity of the biofilm
p = portion of the bacteria in the infected subpopulation that are infected by phage in latent phase
ρ = bacterial growth rate of the total population (T), and the uninfected (u) and infected (i) subpopulations
λ = host lysis rate
π = rate at which phage switches from latent to lytic phase in its host cell after infection
κ= portion of phage particles successfully infecting a host cell
η = phage half-life
R = number of phage particles released per lysis
δ = percentage of phage and DspB diffusing out of the system (mechanical removal from biofilm)
Y = diffusion linear proportionality constant
S = amount of DspB enzyme released per lysis
σ = rate of AIP production
γ= rate of AIP degradation and/or mechanical removal from the system
[AIP]thres= threshold level of AIP concentration above which phage and DspB production are activated
[AIP]max= maximum level of AIP concentration inside the biofilm
rout = diffusion rate of phage particles out of the biofilm and towards boundary layer
rmax = max diffusion rate of phage particles into the biofilm
rmin = min diffusion rate of phage particles into the biofilm, i.e. base rate