Speaker
Description
Trypanosomes's mitochondrial genome (kinetoplast DNA, kDNA) is made of many interlinked DNA circles. In the case of Crithidia fasciculata, the kDNA consists of a network of about 5000 semi-flexible minicircles that form a chain-mail-like 2D network and a couple dozen interlaced maxicircles located at the network's border. In vivo it has a diameter of $d=1\mu m$ while, once extracted, presents a characteristic buckled shape with an intrinsic curvature and overall diameter of $d=5\mu m$. Understanding this unique structure can lead to cures for Trypanosomatid-transmitted diseases like sleeping sickness (Trypanosoma brucei), Chagas disease (Trypanosoma cruzi) and Leishmaniasis (Leishmania spp.) but also provide a cheap and natural playground to study 2D catenated materials and their applications. Experiments in these directions focus on atomic force microscopy with precision of a single molecule. For smaller resolutions, computational models are required.
I will present my results relative to coarse-grained simulations of kDNA. By properly tuning the number of beads and size of the network, it is possible to obtain timescales comparable to AFM experiments while retaining single-bead precision. This allows us to study both equilibrium properties like curvature, axis distributions and the role of the maxicircles in the network structure, and dynamical properties such as single-point and two-point Mean Squared Displacement to characterize diffusion and internal properties.\
| Role | Master/PhD student |
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