Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

VIP: An Experiment to Search for a Violation of the Pauli Exclusion Principle

The Pauli Exclusion Principle is a basic principle of Quantum Mechanics, and its validity has never been seriously challenged. However, given its fundamental standing, it is very important to check it as thoroughly as possible. Here we describe the VIP (VIolation of the Pauli exclusion principle) experiment, an improved version of the Ramberg and Snow experiment (E. Ramberg and G. Snow, {\it Phys. Lett. B} {\bf 238}, 438 (1990)); VIP has just completed the installation at the Gran Sasso underground laboratory, and aims to test the Pauli Exclusion Principle for electrons with unprecedented accuracy, down to $\beta^2/2 \approx 10^{-30} - 10^{-31}$. We report preliminary experimental results and briefly discuss some of the implications of a possible violation.Comment: Plenary talk presented by E. Milotti at Meson 2006, Cracow, 9-13 June 200

New experimental limit on the Pauli Exclusion Principle violation by electrons

The Pauli Exclusion Principle (PEP) is one of the basic principles of modern physics and, even if there are no compelling reasons to doubt its validity, it is still debated today because an intuitive, elementary explanation is still missing, and because of its unique stand among the basic symmetries of physics. The present paper reports a new limit on the probability that PEP is violated by electrons, in a search for a shifted K$_\alpha$ line in copper: the presence of this line in the soft X-ray copper fluorescence would signal a transition to a ground state already occupied by 2 electrons. The obtained value, ${1/2} \beta^{2} \leq 4.5\times 10^{-28}$, improves the existing limit by almost two orders of magnitude.Comment: submitted to Phys. Lett.

New experimental limit on Pauli Exclusion Principle violation by electrons (the VIP experiment)

The Pauli Exclusion Principle is one of the basic principles of modern physics and is at the very basis of our understanding of matter: thus it is fundamental importance to test the limits of its validity. Here we present the VIP (Violation of the Pauli Exclusion Principle) experiment, where we search for anomalous X-rays emitted by copper atoms in a conductor: any detection of these anomalous X-rays would mark a Pauli-forbidden transition. ] VIP is currently taking data at the Gran Sasso underground laboratories, and its scientific goal is to improve by at least four orders of magnitude the previous limit on the probability of Pauli violating transitions, bringing it into the 10**-29 - 10**-30 region. First experimental results, together with future plans, are presented.Comment: To appear in proceedings of the XLVI International Winter Meeting on Nuclear Physics, Bormio, Italy, January 20-26, 200

The VIP Experiment

The Pauli Exclusion Principle (PEP) is a basic principle of Quantum Mechanics, and its validity has never been seriously challenged. However, given its importance, it is very important to check it as thoroughly as possible. Here we describe the VIP (Violation of PEP) experiment, an improved version of the Ramberg and Snow experiment (Ramberg and Snow, Phys. Lett. B238 (1990) 438); VIP shall be performed at the Gran Sasso underground laboratories, and aims to test the Pauli Exclusion Principle for electrons with unprecedented accuracy, down to $\frac{\beta^2}{2} \sim 10^{-30}$Comment: 7 pages, 5 figures, PDF only, presented by Edoardo Milotti to the conference "Quantum Theory: reconsideration of foundations-3", Vaxjo (Sweden), June, 6-11 200

Testing the Pauli Exclusion Principle for Electrons

One of the fundamental rules of nature and a pillar in the foundation of quantum theory and thus of modern physics is represented by the Pauli Exclusion Principle. We know that this principle is extremely well fulfilled due to many observations. Numerous experiments were performed to search for tiny violation of this rule in various systems. The experiment VIP at the Gran Sasso underground laboratory is searching for possible small violations of the Pauli Exclusion Principle for electrons leading to forbidden X-ray transitions in copper atoms. VIP is aiming at a test of the Pauli Exclusion Principle for electrons with high accuracy, down to the level of 10$^{-29}$ - 10$^{-30}$, thus improving the previous limit by 3-4 orders of magnitude. The experimental method, results obtained so far and new developments within VIP2 (follow-up experiment at Gran Sasso, in preparation) to further increase the precision by 2 orders of magnitude will be presented.Comment: Proceedings DISCRETE 2012-Third Symposium on Prospects in the Physics of Discrete Symmetries, Lisbon, December 3-7, 201

High sensitivity tests of the Pauli Exclusion Principle with VIP2

The Pauli Exclusion Principle is one of the most fundamental rules of nature and represents a pillar of modern physics. According to many observations the Pauli Exclusion Principle must be extremely well fulfilled. Nevertheless, numerous experimental investigations were performed to search for a small violation of this principle. The VIP experiment at the Gran Sasso underground laboratory searched for Pauli-forbidden X-ray transitions in copper atoms using the Ramberg-Snow method and obtained the best limit so far. The follow-up experiment VIP2 is designed to reach even higher sensitivity. It aims to improve the limit by VIP by orders of magnitude. The experimental method, comparison of different PEP tests based on different assumptions and the developments for VIP2 are presented.Comment: 6 pages, 3 figures, Proceedings DISCRETE2014 Conferenc

Strong interaction studies with kaonic atoms

The strong interaction of antikaons (K-) with nucleons and nuclei in the low energy regime represents an active research field connected intrinsically with few-body physics. There are important open questions like the question of antikaon nuclear bound states - the prototype system being K-pp. A unique and rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions in low-lying states of light kaonic atoms like kaonic hydrogen isotopes. In the SIDDHARTA experiment at the electron-positron collider DA?NE of LNF-INFN we measured the most precise values of the strong interaction observables, i.e. the strong interaction on the 1s ground state of the electromagnetically bound K-p atom leading to a hadronic shift and a hadronic broadening of the 1s state. The SIDDHARTA result triggered new theoretical work which achieved major progress in the understanding of the low-energy strong interaction with strangeness. Antikaon-nucleon scattering lengths have been calculated constrained by the SIDDHARTA data on kaonic hydrogen. For the extraction of the isospin-dependent scattering lengths a measurement of the hadronic shift and width of kaonic deuterium is necessary. Therefore, new X-ray studies with the focus on kaonic deuterium are in preparation (SIDDHARTA2). Many improvements in the experimental setup will allow to measure kaonic deuterium which is challenging due to the anticipated low X-ray yield. Especially important are the data on the X-ray yields of kaonic deuterium extracted from a exploratory experiment within SIDDHARTA.Comment: Proc. Few Body 21, 4 pages, 2 figure

New experimental limit on Pauli Exclusion Principle violation by electrons (the VIP experiment)

The Pauli exclusion principle (PEP) represents one of the basic principles of modern physics and, even if there are no compelling reasons to doubt its validity, it still spurs a lively debate, because an intuitive, elementary explanation is still missing, and because of its unique stand among the basic symmetries of physics. A new limit on the probability that PEP is violated by electrons was estabilished by the VIP (VIolation of the Pauli exclusion principle) Collaboration, using the method of searching for PEP forbidden atomic transitions in copper. The preliminary value, {1/2}\beta^{2} \textless 4.5\times 10^{-28}, represents an improvement of about two orders of magnitude of the previous limit. The goal of VIP is to push this limit at the level of $10^{-30}$.Comment: submitted to Journal of Physics: Conference Series, by the Institute of Physic