360 research outputs found
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
Disturbance of Thermodynamic Equilibrium of the Quartz-Water System and Silica Separation from the Liquid Phase at a Small Temperature Gradient
AbstractIn electric furnaces destined for experimental geochemical investigations, a small temperature gradient (TG) always exists, and it is difficult to avoid it. In our electric furnaces (from bottom to top) the temperature rises in the lower part (TG = 0.25°/cm) and falls in the upper part (TG = -0.16°/cm). Long-term runs with quartz and water at 300°C have shown the attainment of equilibrium at TG equal to -0.16°/cm. At TG equal to 0.25°/cm, the silica re- precipitated from the ampoule bottom onto its walls above the meniscus, and the aqueous silica concentration was reduced and became 300 times lower than quartz solubility. The obtained results were explained by the combined action of slow convection of water and thermal diffusion of silica. The efficient mechanism of fractionation revealed by us can be extended to other substances and has geochemical and technological importance
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
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
, being the averaging time, and
reaches the value of few units of for 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 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 level at 1 s and to a drift of few units
of per day
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
The quantum computer potential
The efficient system architecture of quantum computers has led to
improvements in various areas. This paper describes the concepts of quantum
computing and quantum computing applications. The current status of the
developments in quantum computing is presented
- …