Estimating true evolutionary distances under the DCJ model

Motivation: Modern techniques can yield the ordering and strandedness of genes on each chromosome of a genome; such data already exists for hundreds of organisms. The evolutionary mechanisms through which the set of the genes of an organism is altered and reordered are of great interest to systematists, evolutionary biologists, comparative genomicists and biomedical researchers. Perhaps the most basic concept in this area is that of evolutionary distance between two genomes: under a given model of genomic evolution, how many events most likely took place to account for the difference between the two genomes? Results: We present a method to estimate the true evolutionary distance between two genomes under the ‘double-cut-and-join' (DCJ) model of genome rearrangement, a model under which a single multichromosomal operation accounts for all genomic rearrangement events: inversion, transposition, translocation, block interchange and chromosomal fusion and fission. Our method relies on a simple structural characterization of a genome pair and is both analytically and computationally tractable. We provide analytical results to describe the asymptotic behavior of genomes under the DCJ model, as well as experimental results on a wide variety of genome structures to exemplify the very high accuracy (and low variance) of our estimator. Our results provide a tool for accurate phylogenetic reconstruction from multichromosomal gene rearrangement data as well as a theoretical basis for refinements of the DCJ model to account for biological constraints. Availability: All of our software is available in source form under GPL at http://lcbb.epfl.ch Contact: [email protected]

Effect of microstructures on the electron-phonon interaction in the disordered metals Pd60_{60}Ag40_{40}

Using the weak-localization method, we have measured the electron-phonon scattering times $\tau_{ep}$ in Pd$_{60}$Ag$_{40}$ thick films prepared by DC- and RF-sputtering deposition techniques. In both series of samples, we find an anomalous $1/\tau_{ep} \propto T^2\ell$ temperature and disorder dependence, where $\ell$ is the electron elastic mean free path. This anomalous behavior cannot be explained in terms of the current concepts for the electron-phonon interaction in impure conductors. Our result also reveals that the strength of the electron-phonon coupling is much stronger in the DC than RF sputtered films, suggesting that the electron-phonon interaction not only is sensitive to the total level of disorder but also is sensitive to the microscopic quality of the disorder.Comment: accepted for publication in Phys. Rev.

Energy Dissipation and Regularity for a Coupled Navier-Stokes and Q-Tensor System

We study a complex non-newtonian fluid that models the flow of nematic liquid crystals. The fluid is described by a system that couples a forced Navier-Stokes system with a parabolic-type system. We prove the existence of global weak solutions in dimensions two and three. We show the existence of a Lyapunov functional for the smooth solutions of the coupled system and use the cancellations that allow its existence to prove higher global regularity, in dimension two. We also show the weak-strong uniqueness in dimension two

Estimating true evolutionary distances under the DCJ model

Motivation: Modern techniques can yield the ordering and strandedness of genes on each chromosome of a genome; such data already exists for hundreds of organisms. The evolutionary mechanisms through which the set of the genes of an organism is altered and reordered are of great interest to systematists, evolutionary biologists, comparative genomicists and biomedical researchers. Perhaps the most basic concept in this area is that of evolutionary distance between two genomes: under a given model of genomic evolution, how many events most likely took place to account for the difference between the two genomes

Anti-pancreatic cancer potential of secalonic acid derivatives from endophytic fungi isolated from Ocimum basilicum.

The word endophyte means "in the plant" and refers to all microorganisms that live in the intercellular spaces of stems, petioles, roots and leaves of plants causing no apparent symptoms of disease. Seven endophytic fungi were isolated from the medicinal plant of Ocimum basilicum L. The fungal strain, labeled as 2L, was cultivated at large scale on the potato dextrose agar semi solid medium and was extracted with ethyl acetate. Normal phase silica gel column chromatography of the ethyl acetate extract afforded ergosterol (1), secalonic acid A (2) and secalonic acid D (3). The structures of these compounds (1-3) were elucidated unequivocally by UV, IR, MS, a series of 1D & 2D NMR analyses. The cytotoxicity of these compounds was evaluated by the MTT assay against human pancreatic cancer cell line. Secalonic acid A (2) and secalonic acid D (3) exhibited significant anti-pancreatic cancer activity with IC 50 values of 7.3 and 1.6 µM, respectively

J/psi D*D* vertex from QCD sum rules

We calculated the strong form factor and coupling constant for the $J/\psi D^* D^*$ vertex in a QCD sum rule calculation. We performed a double Borel sum rule for the three point correlation function of vertex considering both $J/\psi$ and $D^*$ mesons off--shell. The form factors obtained are very different, but they give the same coupling constant.Comment: 7 pages and 4 figures, replaced version accepted for publication in Phys. Lett.

D∗DsKD^* D_s K and Ds∗DKD_s ^* D K vertices in a QCD Sum Rule approach

We calculate the strong form factors and coupling constants of $D^* D_s K$ and $D_s^* D K$ vertices using the QCD sum rules technique. In each case we have considered two different cases for the off-shell particle in the vertex: the ligthest meson and one of the heavy mesons. The method gives the same coupling constant for each vertex. When the results for different vertices are compared, they show that the SU(4) symmetry is broken by around 40%.Comment: 10 pages, 8 figures. Submitted to Phys. Lett.

Uniqueness of Self-Similar Asymptotically Friedmann-Robertson-Walker Spacetime in Brans-Dicke theory

We investigate spherically symmetric self-similar solutions in Brans-Dicke theory. Assuming a perfect fluid with the equation of state $p=(\gamma-1)\mu (1 \le \gamma<2)$, we show that there are no non-trivial solutions which approach asymptotically to the flat Friedmann-Robertson-Walker spacetime if the energy density is positive. This result suggests that primordial black holes in Brans-Dicke theory cannot grow at the same rate as the size of the cosmological particle horizon.Comment: Revised version, 4 pages, no figures, Revtex, accepted for publication in Physical Review

Surface and capillary transitions in an associating binary mixture model

We investigate the phase diagram of a two-component associating fluid mixture in the presence of selectively adsorbing substrates. The mixture is characterized by a bulk phase diagram which displays peculiar features such as closed loops of immiscibility. The presence of the substrates may interfere the physical mechanism involved in the appearance of these phase diagrams, leading to an enhanced tendency to phase separate below the lower critical solution point. Three different cases are considered: a planar solid surface in contact with a bulk fluid, while the other two represent two models of porous systems, namely a slit and an array on infinitely long parallel cylinders. We confirm that surface transitions, as well as capillary transitions for a large area/volume ratio, are stabilized in the one-phase region. Applicability of our results to experiments reported in the literature is discussed.Comment: 12 two-column pages, 12 figures, accepted for publication in Physical Review E; corrected versio

Global Solutions for Incompressible Viscoelastic Fluids

We prove the existence of both local and global smooth solutions to the Cauchy problem in the whole space and the periodic problem in the n-dimensional torus for the incompressible viscoelastic system of Oldroyd-B type in the case of near equilibrium initial data. The results hold in both two and three dimensional spaces. The results and methods presented in this paper are also valid for a wide range of elastic complex fluids, such as magnetohydrodynamics, liquid crystals and mixture problems.Comment: We prove the existence of global smooth solutions to the Cauchy problem for the incompressible viscoelastic system of Oldroyd-B type in the case of near equilibrium initial dat