13Natural biological structures are often complex and cannot be mapped directly to 14 genes, being therefore impossible to explore by traditional biological tools. In contrast, 15 digitizing these structures enables to explore their properties and behavior under specific 16 conditions, by means of computational manipulations, simulations, and analyses. We 17 describe a generic algorithm for the digitization and exploration of the complex structures 18 exhibited by common, interwoven bird nests. This algorithm takes as input computerized 19 tomographic scans of the studied Dead-Sea Sparrow (Passer moabiticus) nest, identifies and 20 isolates each branch entity within the three-dimensional data and finally extracts the 21 characteristics of each branch. The result is a reliable three-dimensional numerical model 22 of the nest that contains a complete geometric dataset per each of its components, e.g. 23 dimensions and contact points with neighboring components, as well as global properties, 24 e.g. density distribution and network structure. Based on these, we were able to simulate 25 various models of the nest construction process. Altogether, the described algorithm and 26 possible derivatives thereof could be a valuable tool in studying the structure-function 27 relationships of similarly complex biological objects. 28 29 Introduction
30The field of structural biology is concerned with the relationships between structure and 31 function of biological objects, mainly at the molecular level. Testing specific hypotheses 32 regarding these relationships is typically done by altering the structures using traditional 33 experimental techniques such as genetic mutations, and measuring the consequent behavior of 34 the object under study 1 . However, complex biological structures at the macro-scale level, such as 35 animal made structures, e.g termite mounds 2 , orb webs 3 , and bird nests 4 , that presumably have a 36 genetic basis, are challenging and often impossible to explore this way, since there is no simple 37 injective mapping between genotype and phenotype.
38While such macro-scale biological structures cannot be studied by traditional biological 39 tools, their structure-function relationships can be studied in-silico in digital formats. Digitizing 40 complex structures by converting the objects using three dimensional (3D) imaging techniques,