Orchard Networks are Trees with Additional Horizontal Arcs

Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely...

Rearranging Phylogenetic Networks

Heading in the right direction? Using head moves to traverse phylogenetic network space

Head moves are a type of rearrangement moves for phylogenetic net-works. They have primarily been studied as part of other types of moves, such as rSPR moves. Here, we study head moves as a type of moves on themselves. We show that the tiers (k > 0) of phylogenetic network space are connected by local head moves. Then, we show tail moves...

Maximal Operators Defined by Rearrangement Invariant Banach Function Spaces

In this thesis we study the boundedness of a generalization of the Hardy-Littlewood maximal operator, involving rearrangement invariant Banach function space and indices of the spaces.<br/> We first consider a classical proof of boundedness of the Hardy-Littlewood maximal operator on rearrangement invariant Banach function spaces. After...

Rearrangement operations on unrooted phylogenetic networks

Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been...

Understanding and Attenuating Simulator Sickness when Driving in Urban Environments: Final Thesis

A necessity in driving simulation testing is to understand and attenuate simulator sickness in urban environments to reduce the number of undesired drop-outs. This final thesis explains a 6 degree-of-freedom simulator sickness prediction model based on observer theory including the visual system. The model incorporates state-of-the-art knowledge...

Exploring the Tiers of Rooted Phylogenetic Network Space Using Tail Moves

Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rooted Nearest Neighbour Interchange (rNNI) and rooted Subtree Prune and Regraft (rSPR). Recently, these moves were generalized to rooted phylogenetic networks, which are a more suitable representation of reticulate evolutionary histories, and...

Initial porosity of random packing: Computer simulation of grain rearrangement

The initial porosity of clastic sediments is poorly defined. In spite of this, it is an important parameter in many models that describe the diagenetic processes taking place during the burial of sediments and which are responsible for the transition from sand to sandstone. Diagenetic models are of importance to predict the sub-seismic...