Studio MAKE in Conversation

CONVERSATION #4: Dr Chengzhi Peng and Dr Tsung-Hsien Wang with Sofia Maraki, January 2017

About the project

Bacteria ColonisationLed by Dr Tsung-Hsien Wang, Inspired by Nature is a five-week long project to explore the elements and rules of pattern-forming found in Nature.

Beginning with a small scale study, each student investigates a chosen topic of natural evolution through Rhino-Grasshopper based parametric modelling.

The goal is for each student to develop 3D parametric models that simulate the pattern-forming process or behaviour observed. The outcomes are expected to inform further Studio MAKE projects later in the semester.

Sofia Maraki is inspired by Bacteria Colonisation

CP: How did you choose this rather unusual topic of investigation?

Figure 1. Different types of bacteria colonisationSM: I started searching for microorganisms that form unusual patterns to create their colonies. I found that bacteria colonies create complex structures with a variety of different branching systems. The Paenibacillus vortex bacteria’s ability to rotate its branches around the centre of the colony piqued my interest for further exploration (Figure 1).

CP: What is the key question in your investigation?

SM: Considering the form of these patterns I was curious to understand how these colonies grow and to identify the mechanism. There was a need to clarify how they are in the beginning and how they come back when there is not any left space to grow.

THW: How did you translate the pattern-forming phenomena seen in the Paenibacillus vortex colonisation into a parametric logic?

SM: Since I understood that branches are the main way that these patterns are structured, I started creating different branching connections and I realised that the main parameter in this caseFigure 2. Paenibacillus vortex bacteria in relation with L-system would be the different growing generations. So I had to create a starting point and identify how the branches connect to each other as the colony grows. As shown in Figure 2, the logic was to create one angled and one straight branch followed by two angled branches.

CP: You seem to have adopted an abstraction strategy that combines the L-system (Lindenmayer system, first developed and introduced by Aristid Lindenmayer in 1968) and the Reaction-Diffusion system. Has this strategy worked in this project?

SM: The L-system branching growth was the first tool I used to create the colonies and it was very helpful in understanding the way they grow. This tool gave me the opportunity to identify how the branches will look, and also to create bending branches that are necessary for Paenibacillus vortex bacteria colonization (Figure 3). Following this process I designed different 2D generations, which in the next step became 3D. For the branch to interact with its neighbour, the Reaction-Diffusion method is required. The use of reaction diffusion can create different thicknesses in the branches and avoids overlapping.

THW: Is the combined L-system and Reaction-Diffusion system sufficient to simulate the colonisation pattern seen in Paenibacillus vortex?

SM: The combination of these two methods is ideal to simulate the colonisation pattern growth. The L-system can be the basis and reaction diffusion will solve some additional problems. However, reaction diffusion is more efficient in 3D growing patterns.

Figure 3. Four different generations of vortex bacteria colonisation diagram Figure 4. Four different generations of vortex bacteria colonisation rotated around the centre

CP: How does your abstraction and parameterisation reveal why the Paenibacillus vortex colonisation proceeds with a certain pattern? What are the benefits for the bacteria to behave in such a manner?

SM: Paenibacillus vortex colonisation forms patterns with complex architecture. The growing behaviour in the laboratory is very different of that in nature because, in the laboratory, bacteria have very limited space to spread. Therefore, when the first vortex bacteria reach the edge of the laboratory dish, they rotate so that the branches bend and the bacteria take advantage of the remaining space. This behaviour is beneficial for the colonies, as  they prolong their lifetime.

CP: Have you tried building physical models as material manifestation of the underlying pattern-forming principle found in the bacteria colonisation?

SM: During this project I created physical models of the branches and tried to make different combinations to create a 3D structure. I used the laser cutter to cut different generations of the same colony, and at the end I compose them to highlight the differences between each generation (Figure 5).

THW: How would you summarise the work-flow you have experimented with throughout the project?

Figure 5. 3D model fabrication experimentationSM: The workflow followed in this project was completely new to me and at the same time was very interesting because I discovered how different systems can be combined using the same parameters. The parametric tools helped me to give form to my thoughts and theories and, after testing them, they became reality. The most challenging part was the way that 2D drawings were converted into 3D objects. This transition required a detailed analysis of the previous procedure to lay new parameters related to the 2D growing system.

CP: Given that you had only five weeks from start to finish, you have been successful in showing us how you translate Paenibacillus vortex colonisation into a parametric model. Do you think this outcome can be further developed into an adaptive, pattern-forming production system mimicking how nature makes Paenibacillus vortex colonisation so socially dynamic?

SM: Due to the limitation of time I had to simplify some steps and make some assumptions. I think that an area that can be further developed is reaction diffusion in 3D form. Using reaction diffusion in 3D forms will give better results and the mimicking system will be more accurate. This tool will give the project a more adaptive character. Since the bacteria grows in any direction they simultaneously interact with each other and with the environment (Figure 6).

Sofia Maraki completed her MSc in Architecture at the University of Patras in Greece in December 2015. During her study at Patras, she discovered a new passion in architecture and new technologies in the design process. In her 4th year of studies, she participated in the architectural completion ‘D3 Housing Tomorrow’. Her team’s proposal on constructing a network of housing on planet Mars was later exhibited in the US.