Team:TU Delft-Leiden/Modeling/CodeRepository/StandardActivation

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      --><title>StandardActivation</title><meta name="generator" content="MATLAB 8.3"><link rel="schema.DC" href="http://purl.org/dc/elements/1.1/"><meta name="DC.date" content="2014-10-11"><meta name="DC.source" content="StandardActivation.m"><style type="text/css">
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  </style></head><body><div class="content"><h2>Contents</h2><div><ul><li><a href="#3">Parameters</a></li><li><a href="#4">Determine reporter protein (R) equilibrium concentration</a></li></ul></div><pre class="codeinput"><span class="keyword">function</span> RR = StandardActivation(beta,x)
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</pre><pre class="codeinput">R = zeros(size(x));
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RR =zeros(size(x));
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</pre><h2>Parameters<a name="3"></a></h2><pre class="codeinput">d_R = 4E-6; <span class="comment">%protein degradation rate</span>
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<span class="comment">% beta</span>
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<span class="comment">% beta(1) = K_d (Microscopic dissociation constant and also threshold value)</span>
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<span class="comment">% beta(2) = k1 (transcription rate active promoter)</span>
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<span class="comment">% beta(3) = k2 (transcription rate repressed promoter)</span>
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</pre><h2>Determine reporter protein (R) equilibrium concentration<a name="4"></a></h2><pre class="codeinput">    <span class="keyword">if</span> x &gt;= 0
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        R = (1/d_R).*((beta(2).*x + beta(1).*beta(3))./(beta(1) + x)); <span class="comment">%Concentration of R in equilibrium</span>
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        R0 = (beta(3)/d_R); <span class="comment">%Concentration of R in equilibrium without DNT</span>
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        RR = R./(R0);
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    <span class="keyword">else</span>
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        RR = 0;
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    <span class="keyword">end</span>
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</pre><pre class="codeinput"><span class="keyword">end</span>
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</pre><p class="footer"><br><a href="http://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2014a</a><br></p></div><!--
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##### SOURCE BEGIN #####
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function RR = StandardActivation(beta,x)
function RR = StandardActivation(beta,x)
R = zeros(size(x));
R = zeros(size(x));
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     end
end
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##### SOURCE END #####
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Revision as of 13:36, 11 October 2014

function RR = StandardActivation(beta,x)
R = zeros(size(x));
RR =zeros(size(x));

%% Parameters
d_R = 4E-6; %protein degradation rate

% beta
% beta(1) = K_d (Microscopic dissociation constant and also threshold value)
% beta(2) = k1 (transcription rate active promoter) 
% beta(3) = k2 (transcription rate repressed promoter)             


%% Determine reporter protein (R) equilibrium concentration
    if x >= 0 

        R = (1/d_R).*((beta(2).*x + beta(1).*beta(3))./(beta(1) + x)); %Concentration of R in equilibrium
        R0 = (beta(3)/d_R); %Concentration of R in equilibrium without DNT
        RR = R./(R0);

    else 
        RR = 0;
    end
end
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