SSB-51806 Physical Aspects of Synthetic Biology

Vak

Studiepunten 6.00

Language of instruction:

English

Assumed knowledge on:

SSB-50806 Introduction to Systems and Synthetic Biology; BIP-10803 Physics for Life Sciences, or equivalent.

Contents:

While systems biology aims at the full understanding of large systems by integrating more and more details into their models, synthetic biology seeks to engineer particular biological function with a certain known subsystem of reduced complexity. Through the rational design of reduced or 'minimal' systems the scientific community endeavours to achieve a desired specific behaviour and/or to uncover the design principles of natural biological systems. The most prominent representation of synthetic biology has so far been microbial engineering by recombinant DNA technology, employing modular concepts known from information technology. However, an additional route is to try to identify functional minimal modules that could then be combined in a bottom-up approach towards biology. Physical concepts are indispensable to understand the functioning of such minimal modules especially when spatial heterogeneity of the interacting components plays a role. Noise in biochemical networks can for example only be understood when the diffusion of individual components is taken into account. In this advanced course we aim to develop the necessary mathematical, physical and computational tools needed for rational engineering of minimal systems in synthetic biology. Among other topics, we will treat on stochastic processes and self- organization. Heterogeneity and variability are inherent features of biological and biochemical systems and thus need to be already considered at the design stage of synthetic systems. Further, the interpretation of experimental data often requires a detailed understanding of stochastic processes. Constructing biological systems beyond the single cell level entails knowledge of patterning processes, exhibiting emerging properties through self-organization by intercellular networks coupled via intracellular communication. In this course students will be able to practice their mathematical and analytical skills while designing biological models. A strong focus on scientific programming will enable students to train programming skills to a level that they can apply it in future research. Literature will be read and applied modelling methodologies will be practiced and possibly extended by the students.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- identify physical concepts that are important for understanding minimal systems in synthetic biology;
- identify functional minimal modules that could then be combined in a bottom-up approach towards synthetic biology;
- apply mathematical skills to solve physical models for simple geometries;
- use a programming language to set up a simple simulations;
- apply tools to validate simulations and models;
- evaluate models from the literature.

Activities:

- lectures;
- read and discuss literature;
- assignments;
- solve exercises;
- extensive practical's;
- computer programming.

Examination:

- exercises (30%);
- written exam with open questions (70%).

Literature:

Will be made available at the black board site of the course.