Enumeration of distinct mechanically stable disk packings in small systems

We create mechanically stable (MS) packings of bidisperse disks using an algorithm in which we successively grow or shrink soft repulsive disks followed by energy minimization until the overlaps are vanishingly small. We focus on small systems because this enables us to enumerate nearly all distinct MS packings. We measure the probability to obtain a MS packing at packing fraction $\phi$ and find several notable results. First, the probability is highly nonuniform. When averaged over narrow packing fraction intervals, the most probable MS packing occurs at the highest $\phi$ and the probability decays exponentially with decreasing $\phi$. Even more striking, within each packing-fraction interval, the probability can vary by many orders of magnitude. By using two different packing-generation protocols, we show that these results are robust and the packing frequencies do not change qualitatively with different protocols.Comment: 4 pages, 3 figures, Conference Proceedings for X International Workshop on Disordered System

Waypoints Zemzev feedback space guidance for multi-spiral, long-duration low thrust transfers

LAUREA MAGISTRALEIl problema del controllo di traiettorie compiute da veicoli aerospaziali da una posizione e velocità iniziale arbitraria a una desiderata posizione finale è di fondamentale interesse come problema di controllo ottimo. L’obiettivo di questa tesi è di progettare una soluzione ottima in anello chiuso nell’ambito di trasferimenti orbitali di lunga durata con bassa spinta, considerando due diversi scenari (Terra-Marte e GTO-GEO). Sono presi in considerazione i trasferimenti a bassa spinta in quanto i motori a propulsione elettrica utilizzati richiedono una quantità di propellente minore e quindi minore massa al lancio e minori costi. E’ applicato un algoritmo di guida ZEMZEV che può essere facilmente implementato autonomamente a bordo. Quest’ultimo purtroppo non fornisce una soluzione ottima poiché durante l’intera missione alcune ipotesi sono violate. Un modo per migliorare le prestazioni è dividere il tempo totale di volo in più tratti, determinando un certo numero di waypoints con un metodo di ottimizzazione rigoroso e infine collegare i diversi tratti per dare origine all’intera traiettoria. Come riferimenti sono presi in considerazione le traiettorie ottime in anello aperto, generate da L.Ferrella and F.Topputo [1], su cui sono posizionati alcuni waypoints arbitrari attraverso cui la navicella deve passare grazie alla guida ZEMZEV. In seguito è impostato un problema di ottimizzazione parametrizzato rispetto alla posizione dei punti, per determinare un minimo set di waypoints necessari per avvicinarsi all’ottimalità. I risultati raggiunti sono migliori paragonati alla disposizione arbitraria dei punti quindi lo schema di guida utilizzato è capace di combinare la guida ottima in anello aperto con le capacità di targeting ZEMZEV. La stessa guida è applicata a casi più complessi – casi con un limite di spinta molto basso con conseguente controllo di traiettorie che possiedono più di 500 spirali. Infine il modello è simulato in uno scenario più realistico per verificare la robustezza del sistema utilizzando anche il metodo di Monte Carlo. La soluzione quasi-ottima dell’algoritmo ZEMZEV in questi trasferimenti orbitali (ambiente non lineare) è ampiamente verificata confrontandola con le soluzioni in anello aperto; si può quindi affermare che l’algoritmo può competere con queste ultime poiché rende il sistema più appropriato a gestire situazioni perturbate o con incertezza grazie alla retroazione in anello chiuso.The problem of controlling the trajectory of aerospace vehicles from an arbitrary initial position and initial velocity to a desired target position with constrained, free or pointed terminal velocity in a specific time is of fundamental interest as an optimal control problem. The purpose of this thesis is to design an optimized closed loop solution in low-thrust, long duration orbit transfer environment considering two different scenarios – Earth to Mars and GTO to GEO. Low-thrust transfers are taken into account because less fuel is required when using electric thrusters which results in less launch mass and less cost. The zero-effort-miss/zero-effort-velocity feedback guidance algorithm which has great potential for autonomous onboard implementation is applied. Unfortunately it does not give an optimal solution because during the entire mission some assumptions are violated. A way to improve the performances is to divide the total flight time into more segments, determining with a rigorous optimization method near-optimal waypoints to connect the different segments. Open loop energy-fuel-optimal trajectories generated by L.Ferrella and F.Topputo [1] are considered as reference where some arbitrary points are put to be targeted by ZEMZEV guidance. An accurate study is developed valuating performances which vary with the number of waypoints. Afterwards an optimization problem, parametrized with the position of the points is set in order to determine the minimum set of waypoints necessary for close-to-fuel-optimal waypoint space guidance. Improved results of optimization are figured out and compared with the random positioning reaching the conclusion that way-point guidance scheme is able to combine open-loop optimal guidance with ZEM/ZEV targeting capabilities. The same guidance is applied also to challenging cases – i.e. cases with a very low limit thrust which results in controlling a trajectory with more than 500 spirals. Finally the model is simulated in a more realistic scenario to verify the robustness of the system performing Monte Carlo analysis. By employing the zero-effort-miss/zero-effort-velocity algorithm in the highly nonlinear orbital transfer and comparing with corresponding open-loop optimal solutions, its near-optimality is further verified. Furthermore the algorithm can even compete with corresponding open-loop optimal solutions, while its feedback characteristics make it more suitable to deal with uncertainties and perturbations

Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods

Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda

Ecdysozoa is the recently recognized clade of molting animals that comprises the vast majority of extant animal species and the most important invertebrate model organisms—the fruit fly and the nematode worm. Evolutionary relationships within the ecdysozoans remain, however, unresolved, impairing the correct interpretation of comparative genomic studies. In particular, the affinities of the three Panarthropoda phyla (Arthropoda, Onychophora, and Tardigrada) and the position of Myriapoda within Arthropoda (Mandibulata vs. Myriochelata hypothesis) are among the most contentious issues in animal phylogenetics. To elucidate these relationships, we have determined and analyzed complete or nearly complete mitochondrial genome sequences of two Tardigrada, Hypsibius dujardini and Thulinia sp. (the first genomes to date for this phylum); one Priapulida, Halicryptus spinulosus; and two Onychophora, Peripatoides sp. and Epiperipatus biolleyi; and a partial mitochondrial genome sequence of the Onychophora Euperipatoides kanagrensis. Tardigrada mitochondrial genomes resemble those of the arthropods in term of the gene order and strand asymmetry, whereas Onychophora genomes are characterized by numerous gene order rearrangements and strand asymmetry variations. In addition, Onychophora genomes are extremely enriched in A and T nucleotides, whereas Priapulida and Tardigrada are more balanced. Phylogenetic analyses based on concatenated amino acid coding sequences support a monophyletic origin of the Ecdysozoa and the position of Priapulida as the sister group of a monophyletic Panarthropoda (Tardigrada plus Onychophora plus Arthropoda). The position of Tardigrada is more problematic, most likely because of long branch attraction (LBA). However, experiments designed to reduce LBA suggest that the most likely placement of Tardigrada is as a sister group of Onychophora. The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of the highly debated clade Mandibulata

Social Dreaming Matrix

The following is a report of the conference Social dreaming experience. It includes: an outline of the Social Dreaming model used at the conference, the methodology used to draw hypotheses, hypotheses and further questions about art therapy and the conference itself viewed as interacting systems. In the report I use the following abbreviations: SD for Social Dreaming, SDM for Social Dreaming Matrix, DRD for Dream Reflection Dialogue, DCR for Dream Creative Response, SS for System Synthesis

A resolution for the coiling direction paradox in Neogloboquadrina pachyderma.

We present new data on genotypic differences and biogeographic distribution of coiling types in the living planktonic foraminiferal morphospecies Neogloboquadrina pachyderma. The genetic evidence demonstrates that coiling direction in N. pachyderma is a genetic trait, heritable through time, and is not a morphological feature reflecting ecophenotypic variation. The two opposite coiling morphotypes appear to have diverged during the late Miocene, and they have distinctly different ecologies. In combination with fossil evidence, biogeography, and ecology the degree of genetic distinction between the two coiling types of N. pachyderma strongly implies that they should be considered different species. We propose the adoption of the widely recognized name N. incompta for the right coiling morphospecies. The genetic evidence also demonstrates a low level (<3%) of aberrant coiling associated with both morphotypes. The abundance of these aberrant specimens has no relationship with the environment. These findings have important consequences for the use of N. pachyderma and N. incompta as paleoceanographic signal carriers in polar and subpolar waters. Copyright 2006 by the American Geophysical Union

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses. © The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved