Periodic Reporting for period 1 - LODIS (Looking Through Disorder) Reporting period: 2016-03-01 to 2018-02-28 Summary of the context and overall objectives of the project "When we fabricate optical systems today, we often want a high degree of order and we see disorder as adverse to obtaining such desired properties. Low tolerances are for example required for optical communications cables, DVDs and medical equipment to function properly. Nature sees it differently, though! Here, the tuning of disorder is what makes some of the most vivid colours in nature able to exist. The colouration principle is called structural colour and is based on interference of light with structures having features smaller than one millonth of a meter! The principle is for example seen in soap bubble, where the thin film of the bubble interferes with light. Shining blue butterflies (try searching ""Morpho rhetenor""), bird feathers in all appearances imaginable and much more can be created by controlling interference in a partially disordered system. If we can copy how nature so effortlessly incorporates disorder in its designs, we would be able to fabricate advanced optical systems much more easily, since we could interplay with manufacturing uncertainty instead of spending intense effort in trying to avoid it.The objective of this fellowship is to investigate how colours that arise by interference are influenced by disorder and how we can understand them mathematically. This is done by focusing on a few specific examples and analysing the structures that give rise to colours in detail, by imaging their nanostructures using electron microscopy. We then creating computational tools to describe the optical effects arising from the disordered nanostructures such that we can gain a better understanding of these specific systems and try to generalising them to other systems in nature. By advancing the understanding of nature's nanofabrication, we will be able to understand nature better and to mimic its design principles better, in the long run leading to nanotechnology that is more fault tolerant and easier to produce." Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far Optical appearance of bacterial colonies:As you can read about below, one of the most important aspects of the fellowship was the investigation of optical properties in bacterial colonies. Here, we looked at rod-shaped bacteria with a diameter of roughly 400nm that self-organised into very ordered - but not fully ordered - colonies that made them interfere with light. By measuring the striking metallic green, red and blue colours of these we were able to infer a lot about how the bacteria pack. Furthermore, we could change the colour of the colonies through genetic manipulation.Eggstraordinary colouration:The constant arms race between parasite birds (suck as cuckoos) and host birds leads to constant improvements in mimicking eggs and detecting these imitations. This has lead to cuckoo eggs with egg shells where the size of air inclusions that generate diffuse scattering has been optimized. We will report on this in a future publication, and also show how a pigment is reintroduced in a branch of the phylogenetic tree where it hasn't been observed for millions of years.Defect in coloured cellulose nanocrystal systems:We developed a so-called hyperspectral imaging system on our microscope to investigate colour defects in photonic films obtained by self-assembly of cellulose nano-crystals (CNC). This analysis combined advanced structural and optical measurements with simulation tools in order to classify which type of defect we were looking at. We were amazed about how much more information we could get from looking at spectral changes rather than looking at colour changes, and these signatures allowed us to pinpoint types of defect formations with great accuracy. The results will help future fabrication of defect-free structurally coloured materials made from wood pulp or cotton.Review of disorder in structurally coloured systems in nature:An extensive literature study and classification of work done within disorder in natural photonic systems was carried out. The results were published as a book chapter (Photonics in Nature: From Order to Disorder, http://dx.doi.org/10.1007/978-3-319-74144-4_3 ). The literature study served as a base for a lot of the work in the fellowship. It is furthermore our hope that the increased focus on the topic will lay the ground for further work in understanding disorder.The colour of 'raspberry' colloids helps understand how they pack:At University of Cambridge, a new type of hard spheres with smaller dimples on them (hence the name 'raspberry' colloids) were recently synthesised. What is so unusual for these sub-micrometre structures is how their unique morphology prevents salt-induced colloidal aggregation and facilitates tight packing of the colloids. The packing lead to appearance of structural colour, and in this fellowship, we also assisted on understanding the self-assembly through optical measurements. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) "A very important outcome of the fellowship is the work on the genetic manipulation of structural colour in bacterial colonies.This work describes the genetic pathways that regulate structural colouration in colonies of a novel Flavobacterium strain. We show that we control the colour and scattering properties, and therefore the appearance) of the living organism by modifying their genes. We believe that our result are original and they will bring significant change to the fields of natural science and technology for two main reasons: 1- Fundamental novelty: While a lot of research has focused on the optical characterization of structurally coloured organisms, there are no studies investigating the genetic pathways underpinning structural colouration in any living organism. 2- High application potential: We envision the use of such bacterial colonies as photonic bio-materials (or as a bio-mimetic template) that can be readily optimized for pigments. Such pigments change colouration under external stimuli and can interface with other living tissues, thereby adapting to variable environments. This work created the realisation of a spin off company aimed at the production of structural colors.Another important contribution is the review book chapter on disorder of nano- and microstructures in structurally coloured systems in nature. We believe the understanding of disorder in nanostructures is important for optical components, since it is an inherent part of all large-scale (in-vivo and ""in-lab"") nanofabrication. With this review, we try to engage a larger part of the biological sciences community in the continuing research on these systems.From a more technical viewpoint, a manuscript is in preparation on the in-depth understanding of the optical properties of the Flavobacterium colonies described above. This novel understanding will make it easier to relate optical responses to the order-disorder relation of the self-assembly of the bacterial colonies, and can also help giving insight to the unanswered question of which function colour could have in this biological system. We will also make the tools we use for the analysis openly available." Several different structurally coloured bacteria colonies investigated in this fellowship
