# Biomod/2013/NanoUANL/Nucleation

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Current revision (22:35, 12 October 2013) (view source) |
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\large F_{R} = \frac{F_{sample}}{F_{standard}} | \large F_{R} = \frac{F_{sample}}{F_{standard}} | ||

\end{equation} | \end{equation} | ||

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<p>where F<sub>sample</sub> is the OD<sub>600</sub>-normalized fluorescence emited by a sample, while F<sub>standard</sub> is the OD<sub>600</sub>-normalized fluorescence measurement for the corresponding standard culture (again, BBa_E1010 for RFP and BBa_E0040 for GFP).</p> | <p>where F<sub>sample</sub> is the OD<sub>600</sub>-normalized fluorescence emited by a sample, while F<sub>standard</sub> is the OD<sub>600</sub>-normalized fluorescence measurement for the corresponding standard culture (again, BBa_E1010 for RFP and BBa_E0040 for GFP).</p> | ||

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+ | <center>\(F_{R} - F_{Rst} = e^{C} \ e^{- \delta {t}} \)</center> | ||

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<div id="title"> | <div id="title"> | ||

<p><a name="Fixed_temperature_model"><h4>Fixed Temeperature Model <a href="#" class="btn btn-info">Back to top</a></h4><hr></p></div> | <p><a name="Fixed_temperature_model"><h4>Fixed Temeperature Model <a href="#" class="btn btn-info">Back to top</a></h4><hr></p></div> |

## Current revision

**Math Model**

Mathematical models that represent the dynamic behavior of biological systems are a quite prolific field of work and are pillar for Systems Biology. A number of deterministic and stochastic formalisms have been developed at different abstraction levels that range from the molecular to the population levels.

We present a model for the relation between time, temperature and the change in fluorescence (measured in Relative Fluorescent Units or RFUs) of an *E. coli* culture that harbors a genetic construction where a fluorescent protein is under control of a RNAT.

where F_{sample} is the OD_{600}-normalized fluorescence emited by a sample, while F_{standard} is the OD_{600}-normalized fluorescence measurement for the corresponding standard culture (again, BBa_E1010 for RFP and BBa_E0040 for GFP).

In Shah and Gilchrist, (2010), it was found that the probability of openness of a ribosome binding site (RBS) of an mRNA with respect to temperature, fits well into a logistic equation. However, the authors did not find significant differences in the behaviour of known RNATs and non-RNAT elements and admit that RBS openness cannot be assumed to be directly correlated to translational activity. Therefore, their RBS-melting probability equation would not be recommendable to be used directly in gene expression models for RNATs.

- ShahP ,Gilchrist MA(2010)Is Thermosensing Property of RNA Thermometers Unique?
*PLoS ONE*,5(7):e11308.doi:10.1371/journal.pone.0011308. - H. A. Von Fircks, T. Verwijst,(1993)Plant Viability as a Function of Temperature Stress(The Richards Function Applied to Data from Freezing Tests of Growing Shoots
*Plant Physio*,103(1):125–130. - Hoops S,
*et al.*(2010)COPASI–a COmplex PAthway SImulator*Bioinformatics*,22,3067-3074,2006,http://dx.doi.org/10.1093/bioinformatics/btl485 - COPASI Documentation 2.Steady State calculation(2013,May 16).Retrieved from http://www.copasi.org/tiki-integrator.php?repID=9&file=ch07s02.html
- Ting Chen,
*et al.*Modeling gene expression with differential equations (1999)*Pacic Symposium of Biocomputing* - Gaussian function(Consulted on 2013,September 27)Retrieved from http://uqu.edu.sa/files2/tiny_mce/plugins/filemanager/files/4282164/Gaussian%20function.pdf