On pairwise distances and median score of three genomes under DCJ

In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a resulting genome is called median genome). In contrast to the rearrangement distance between two genomes which can be computed in linear time, computing the median score for three genomes is NP-hard. This inspires a quest for simpler and faster approximations for the median score, the most natural of which appears to be the halved sum of pairwise distances which in fact represents a lower bound for the median score. In this work, we study relationship and interplay of pairwise distances between three genomes and their median score under the model of Double-Cut-and-Join (DCJ) rearrangements. Most remarkably we show that while a rearrangement may change the sum of pairwise distances by at most 2 (and thus change the lower bound by at most 1), even the most "powerful" rearrangements in this respect that increase the lower bound by 1 (by moving one genome farther away from each of the other two genomes), which we call strong, do not necessarily affect the median score. This observation implies that the two measures are not as well-correlated as one's intuition may suggest. We further prove that the median score attains the lower bound exactly on the triples of genomes that can be obtained from a single genome with strong rearrangements. While the sum of pairwise distances with the factor 2/3 represents an upper bound for the median score, its tightness remains unclear. Nonetheless, we show that the difference of the median score and its lower bound is not bounded by a constant.Comment: Proceedings of the 10-th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2012. (to appear

A Computational Method for the Rate Estimation of Evolutionary Transpositions

Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as transpositions, they are rarely observed and believed to constitute only a small fraction of genome rearrangements happening in the course of evolution. The analysis of transpositions is further obfuscated by intractability of the underlying computational problems. We propose a computational method for estimating the rate of transpositions in evolutionary scenarios between genomes. We applied our method to a set of mammalian genomes and estimated the transpositions rate in mammalian evolution to be around 0.26.Comment: Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), 2015. (to appear

Metrological characterization of the pulsed Rb clock with optical detection

We report on the implementation and the metrological characterization of a vapor-cell Rb frequency standard working in pulsed regime. The three main parts that compose the clock, physics package, optics and electronics, are described in detail in the paper. The prototype is designed and optimized to detect the clock transition in the optical domain. Specifically, the reference atomic transition, excited with a Ramsey scheme, is detected by observing the interference pattern on a laser absorption signal. \ The metrological analysis includes the observation and characterization of the clock signal and the measurement of frequency stability and drift. In terms of Allan deviation, the measured frequency stability results as low as $1.7\times 10^{-13} \ \tau^{-1/2}$, $\tau$ being the averaging time, and reaches the value of few units of $10^{-15}$ for $\tau=10^{4}$ s, an unprecedent achievement for a vapor cell clock. We discuss in the paper the physical effects leading to this result with particular care to laser and microwave noises transferred to the clock signal. The frequency drift, probably related to the temperature, stays below $10^{-14}$ per day, and no evidence of flicker floor is observed. \ We also mention some possible improvements that in principle would lead to a clock stability below the $10^{-13}$ level at 1 s and to a drift of few units of $10^{-15}$ per day

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Reagent precipitation of hardness ions by carbonate-containing builders

Phase composition of carbonate containing builders obtained by neutralization of proton containing reagents with sodium carbonate is investigated. Itis shown that the builders are a mixture consisting mainly of Na[2]CO[3] · NaHCO[3] · 2H[2]O, Na[2]CO[3] · H[2]O and salts of the corresponding acids. The mixture is able to reduce total water hardness with 3.9 to 1.6–1.7 mmol-eq·l{ -1}. It is found that the builders containing Na[2]CO[3] · NaHCO[3] · 2H[2]O, Na[2]CO[3] · H[2]O and CH[3]COONa · 3H[2]O remove hardness as well as Na[2]CO[3], Na[3]PO[4] ·12H[2]O and STPP at the same flow rate

Proton acceleration in analytic reconnecting current sheets

Particle acceleration provides an important signature for the magnetic collapse that accompanies a solar flare. Most particle acceleration studies, however, invoke magnetic and electric field models that are analytically convenient rather than solutions of the governing magnetohydrodynamic equations. In this paper a self-consistent magnetic reconnection solution is employed to investigate proton orbits, energy gains, and acceleration timescales for proton acceleration in solar flares. The magnetic field configuration is derived from the analytic reconnection solution of Craig and Henton. For the physically realistic case in which magnetic pressure of the current sheet is limited at small resistivities, the model contains a single free parameter that specifies the shear of the velocity field. It is shown that in the absence of losses, the field produces particle acceleration spectra characteristic of magnetic X-points. Specifically, the energy distribution approximates a power law ~ξ-3/2 nonrelativistically, but steepens slightly at the higher energies. Using realistic values of the “effective” resistivity, we obtain energies and acceleration times that fall within the range of observational data for proton acceleration in the solar corona

Towards the electron EDM search: Theoretical study of HfF+

We report first ab initio relativistic correlation calculations of potential curves for ten low-lying electronic states, effective electric field on the electron and hyperfine constants for the ^3\Delta_1 state of cation of a heavy transition metal fluoride, HfF^+, that is suggested to be used as the working state in experiments to search for the electric dipole moment of the electron. It is shown that HfF^+ has deeply bound ^1\Sigma^+ ground state, its dissociation energy is D_e=6.4 eV. The ^3\Delta_1 state is obtained to be the relatively long-lived first excited state lying about 0.2 eV higher. The calculated effective electric field E_eff=W_d|\Omega| acting on an electron in this state is 5.84*10^{24}Hz/(e*cm)Comment: 4 page

An adaptive prefix-assignment technique for symmetry reduction

This paper presents a technique for symmetry reduction that adaptively assigns a prefix of variables in a system of constraints so that the generated prefix-assignments are pairwise nonisomorphic under the action of the symmetry group of the system. The technique is based on McKay's canonical extension framework [J.~Algorithms 26 (1998), no.~2, 306--324]. Among key features of the technique are (i) adaptability---the prefix sequence can be user-prescribed and truncated for compatibility with the group of symmetries; (ii) parallelizability---prefix-assignments can be processed in parallel independently of each other; (iii) versatility---the method is applicable whenever the group of symmetries can be concisely represented as the automorphism group of a vertex-colored graph; and (iv) implementability---the method can be implemented relying on a canonical labeling map for vertex-colored graphs as the only nontrivial subroutine. To demonstrate the practical applicability of our technique, we have prepared an experimental open-source implementation of the technique and carry out a set of experiments that demonstrate ability to reduce symmetry on hard instances. Furthermore, we demonstrate that the implementation effectively parallelizes to compute clusters with multiple nodes via a message-passing interface.Comment: Updated manuscript submitted for revie