Difference between revisions of "Team:Kent/Modeling"

Revision as of 10:39, 10 September 2015

iGEM Kent 2015

Modeling

Modeling is important as it allows us to describe the system mathematically. If we change some of the parameters in our system we can see how this will affect the system, this is especially important when the some of the parameters are unknown. The main aim of our model is to demonstrate the production of our nanowires in an interactive and interesting way.

More to come soon...

@@ Line 183: / Line 183: @@
 <p>
-Sivanathan, V., & Hochschild, A. (2012). Generating extracellular amyloid aggregates using E. coli cells. Genes & development, 26(23), 2659-2667.
+[1] Sivanathan, V., & Hochschild, A. (2012). Generating extracellular amyloid aggregates using E. coli cells. Genes & development, 26(23), 2659-2667.
-<br><br>
-Elowitz, M. B., Surette, M. G., Wolf, P. E., Stock, J. B., & Leibler, S. (1999). Protein Mobility in the Cytoplasm of Escherichia coli. Journal of bacteriology,181(1), 197-203.
+[2] Elowitz, M. B., Surette, M. G., Wolf, P. E., Stock, J. B., & Leibler, S. (1999). Protein Mobility in the Cytoplasm of Escherichia coli. Journal of bacteriology,181(1), 197-203.
-<br><br>
-Philipse, A. P. (2011). Notes on Brownian Motion. Utrecht University, Debye Institute, Van’t Hoff Laboratory.
+[3] Philipse, A. P. (2011). Notes on Brownian Motion. Utrecht University, Debye Institute, Van’t Hoff Laboratory.
-<br><br>
-Barlett, V. R., Hoyuelos, M., & Mártin, H. O. (2013). Monte Carlo simulation with fixed steplength for diffusion processes in nonhomogeneous media. Journal of Computational Physics, 239, 51-56.
+[4] Barlett, V. R., Hoyuelos, M., & Mártin, H. O. (2013). Monte Carlo simulation with fixed steplength for diffusion processes in nonhomogeneous media. Journal of Computational Physics, 239, 51-56.
-<br><br>
-Xue, W. F., Homans, S. W., & Radford, S. E. (2008). Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly. Proceedings of the National Academy of Sciences,105(26), 8926-8931.
+[5] Xue, W. F., Homans, S. W., & Radford, S. E. (2008). Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly. Proceedings of the National Academy of Sciences,105(26), 8926-8931.
-<br><br>
-Knowles, T. P., Waudby, C. A., Devlin, G. L., Cohen, S. I., Aguzzi, A., Vendruscolo, M., ... & Dobson, C. M. (2009). An analytical solution to the kinetics of breakable filament assembly. Science, 326(5959), 1533-1537.
+[6] Knowles, T. P., Waudby, C. A., Devlin, G. L., Cohen, S. I., Aguzzi, A., Vendruscolo, M., ... & Dobson, C. M. (2009). An analytical solution to the kinetics of breakable filament assembly. Science, 326(5959), 1533-1537.
+[7] Smith, J. F., Knowles, T. P., Dobson, C. M., MacPhee, C. E., & Welland, M. E. (2006). Characterization of the nanoscale properties of individual amyloid fibrils.Proceedings of the National Academy of Sciences, 103(43), 15806-15811.
+[8] Hall, D., & Edskes, H. (2004). Silent prions lying in wait: a two-hit model of prion/amyloid formation and infection. Journal of molecular biology, 336(3), 775-786.
+[9] Lomakin, A., Chung, D. S., Benedek, G. B., Kirschner, D. A., & Teplow, D. B. (1996). On the nucleation and growth of amyloid beta-protein fibrils: detection of nuclei and quantitation of rate constants. Proceedings of the National Academy of Sciences, 93(3), 1125-1129.
+[10] Scheibel, T., Parthasarathy, R., Sawicki, G., Lin, X. M., Jaeger, H., & Lindquist, S. L. (2003). Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition. Proceedings of the National Academy of Sciences, 100(8), 4527-4532.
+[11] vandenAkker, C. C., Engel, M. F., Velikov, K. P., Bonn, M., & Koenderink, G. H. (2011). Morphology and persistence length of amyloid fibrils are correlated to peptide molecular structure. Journal of the American Chemical Society,133(45), 18030-18033.
 </p>