Introduction of metrics for switching dynamic evaluation expressed by DNA based biological systems

Domen Gostinčar (2010) Introduction of metrics for switching dynamic evaluation expressed by DNA based biological systems. EngD thesis.

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Abstract

Due to minimization of computer structures and associated problems, we are forced to seek alternative solutions for a processing platform of the future. One such solution is to use biological systems as the building blocks of computer systems. With biological systems, proteins, created by use of DNA chains, are used to carry information. The desire to lower development costs of such systems leads us to mathematical models, used to simulate the operation of biological structures. Both deterministic and stochastic models exist, the latter being more suitable for simulating the operation of a single cell. The paper presents in greater detail the mathematical models used to simulate the operation of biological systems, the use of the chemical master equation and a way of solving the latter by means of the stochastic simulation algorithm. Metrics for assessing the dynamics of a biological system are defined and then applied to a model of an actual system, with the intent of assessing the suitability of the bacteriophage as a basis for implementing a toggle-switch with a biological structure. Results show that the bacteriophage is not suitable for this task. A suggested solution is to equalize gene properties, while maintaining the chemical diversity of the information carrying proteins.

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