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Modelling mycelium growth

  Why material science? Since material names are used to define periods of civilisations of the past (Stone Age, Bronze Age, etc ...), material science is considered, in my opinion, one of the species-defining endeavours. Civilizations that mastered smelting iron ended up victorious. All of a sudden, enemies had to deal with stronger swords and implantable shields. The same applies today, countries that managed to master silicon chip manufacturing ended up economically victorious. With the advent of biotechnology, largely with the help of artificial intelligence tools such as AlphaFold, there could be a promise of a new class of materials that are grown instead of manufactured. Bio-composite materials offer an alternative solution to create materials inspired by nature and can returned to it at the end of their lifespan. Such materials will tremendously accelerate reaching our sustainability goals. Mycelium Composites One such material is mycelium, which is considered nature's solu...
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Engineered Patterns in Biology I: Intro to Turing Pattern Formation

What is this post about? This post will cover an overview of pattern formation, specifically Turing pattern formation in a non-mathematical way. The whole point here is to appreciate the beauty of what can Turing's reaction-diffusion model describe. If you are excited enough about the topic and want to cover some technicalities, a subsequent post will cover my Master's thesis work on the design of genetic circuits from first principles that makes use of Turing's reaction-diffusion model. Pattern formation in Biology It is best to start by explaining pattern formation in biology. The easiest and most obvious way to see patterns is within animals. Zebras; fish; cheetahs are some of the few animal examples that exhibit pigment patterns on their skin [1]. If you accept the fact that pigments are no more than proteins expressed within a group of cells [2], one can reasonably ask the question: How can cells determine their relative position to other cells so they end up ex...
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PromAssist, synthetic biologists assistant

In previous posts , I briefly introduced the world of synthetic biology and designing of genetic circuits. The goal of competition such as iGEM is to encourage people designing creative solutions to real-world problems using synthetic biology with the hope of moving the field out of academia into industry, much like electronics. And much like electronics, iGEM is trying to develop a library of biological parts, analogous to electronic parts such as capacitors and resistors to build any circuit. If you have ever dabbled in electronics, you'd notice that not parts are created equally; Some capacitors have higher efficiencies than others which might suit a certain application more. In this post, I want to explore one of the most important "biological parts" in my opinion:   What are promoters Promoters are regions of DNA usually found upstream of a gene that act as a switch to express whatever gene is downstream of it. Since translating DNA to mRNA requires the help of RNA ...
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