Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination detection are challenged by the enormous number of possible topologies, even for a moderate number of taxa. If, however, the detection analysis is conducted independently between each putative recombinant sequence and a set of reference parentals, potential recombinations between the recombinants are neglected. In this context, a recombination hotspot can be inferred in phylogenetic analyses if we observe several consecutive breakpoints. We developed a distance measure between unrooted topologies that closely resembles the number of recombinations. By introducing a prior distribution on these recombination distances, a Bayesian hierarchical model was devised to detect phylogenetic inconsistencies occurring due to recombinations. This model relaxes the assumption of known parental sequences, still common in HIV analysis, allowing the entire dataset to be analyzed at once. On simulated datasets with up to 16 taxa, our method correctly detected recombination breakpoints and the number of recombination events for each breakpoint. The procedure is robust to rate and transition∶transversion heterogeneities for simulations with and without recombination. This recombination distance is related to recombination hotspots. Applying this procedure to a genomic HIV-1 dataset, we found evidence for hotspots and de novo recombination

Atmospheric re-entry stability analysis of the space vehicle SARA

The aim of this paper is to present a re-entry stability analysis for the uncontrolled, non-winged, blunted cone space vehicle SARA (Atmospheric Re-entry Satellite) by taking into account a ballistic trajectory. The SARA project is a cooperation between Brazilian Space Agency (AEB) and Institute of Aeronautics and Space (IAE) to develop and construct a recoverable space vehicle to perform microgravity experiments. The Brazilian suborbital rocket VS-40 provides the insertion of the SARA capsule into microgravity environment reaching altitudes above 190 km. The analyzes presented in this work focuses on two configurations for SARA being the first, a blunted cone without aps (aero-breaking) and, the second, a blunted cone with aps. The work shows in details the re-entry stability analysis and co-simulation methodology including Newton's impact method modeling (NIM) and Computational Fluid Dynamics (CFD) software

Elastic deformation modeling of the VS-40M suborbital rocket with SARA payload

The aim of this paper is to present the flight dynamics analysis developed to the suborbital rocket VS-40 with SARA (Atmospheric Reentry Satellite) payload by taking into account the elasticity of the launcher in the equations of dynamics. The way to include structural dynamics in such an approach is the main topic of this paper. In order to include the flexibility in the overall dynamic analysis of the launcher, a mathematical model of a fully flexible structure subjected to thrust, aerodynamic and gravity forces is presented. By opportunely writing the translational, rotational and flexible dynamic equations, it is possible to obtain a fully non-linear system of equations of motion where the roles of the macro dynamics (representative of the translational and rotational flight mechanics of the launcher) and the micro dynamics (elastic vibrations) can be clearly appreciated. The elastic displacement of the launcher is represented through the modal superposition technique whereas the micro dynamics effects are obtained via Galeerkin approach. The consistency of the results, modal parameters and the trajectory of the launcher are checked by comparison with its rigid body trajectory obtained from a qualified trajectory code