An Efficient Algorithm For Chinese Postman Walk on Bi-directed de Bruijn Graphs

Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double stranded DNA string (SDDNA) containing all the k-long words in the reads seems to be a good heuristic to get close to the original genome. This problem is equivalent to finding a cyclic Chinese Postman (CP) walk on the underlying un-weighted bi-directed de Bruijn graph built from the reads. The Chinese Postman walk Problem (CPP) is solved by reducing it to a general bi-directed flow on this graph which runs in O(|E|2 log2(|V |)) time. In this paper we show that the cyclic CPP on bi-directed graphs can be solved without reducing it to bi-directed flow. We present a ?(p(|V | + |E|) log(|V |) + (dmaxp)3) time algorithm to solve the cyclic CPP on a weighted bi-directed de Bruijn graph, where p = max{|{v|din(v) - dout(v) > 0}|, |{v|din(v) - dout(v) < 0}|} and dmax = max{|din(v) - dout(v)}. Our algorithm performs asymptotically better than the bidirected flow algorithm when the number of imbalanced nodes p is much less than the nodes in the bi-directed graph. From our experimental results on various datasets, we have noticed that the value of p/|V | lies between 0.08% and 0.13% with 95% probability

Noninvasive Measurement of Dissipation in Colloidal Systems

According to Harada and Sasa [Phys. Rev. Lett. 95, 130602 (2005)], heat production generated in a non-equilibrium steady state can be inferred from measuring response and correlation functions. In many colloidal systems, however, it is a nontrivial task to determine response functions, whereas details about spatial steady state trajectories are easily accessible. Using a simple conditional averaging procedure, we show how this fact can be exploited to reliably evaluate average heat production. We test this method using Brownian dynamics simulations, and apply it to experimental data of an interacting driven colloidal system

Temperature-dependent Hall scattering factor and drift mobility in remotely doped Si:B/SiGe/Si heterostructures

Hall-and-Strip measurements on modulation-doped SiGe heterostructures and combined Hall and capacitance–voltage measurements on metal-oxide-semiconductor (MOS)-gated enhancement mode structures have been used to deduce Hall scattering factors, rH, in the Si1 – xGex two-dimensional hole gas. At 300 K, rH was found to be equal to 0.4 for x = 0.2 and x = 0.3. Knowing rH, it is possible to calculate the 300 K drift mobilities in the modulation-doped structures which are found to be 400 cm2 V – 1 s – 1 at a carrier density of 3.3 × 1011 cm – 2 for x = 0.2 and 300 cm2 V – 1 s – 1 at 6.3 × 1011 cm – 2 for x = 0.3, factors of between 1.5 and 2.0 greater than a Si pMOS control

Unexpected phase locking of magnetic fluctuations in the multi-k magnet USb

The spin waves in the multi-k antiferromagnet USb soften and become quasielastic well below the antiferromagnetic ordering temperature TN. This occurs without a magnetic or structural transition. It has been suggested that this change is in fact due to dephasing of the different multi-k components: a switch from 3-k to 1-k behavior. In this work, we use inelastic neutron scattering with tridirectional polarization analysis to probe the quasielastic magnetic excitations and reveal that the 3-k structure does not dephase. More surprisingly, the paramagnetic correlations also maintain the same clear phase correlations well above TN (up to at least 1.4TN)

Multi-k magnetic structures in USb_{0.9}Te_{0.1} and UAs_{0.8}Se_{0.2} observed via resonant x-ray scattering at the U M4 edge

Experiments with resonant photons at the U M4 edge have been performed on a sample of USb_{0.9}Te_{0.1}, which has an incommensurate magnetic structure with k = 0.596(2) reciprocal lattice units. The reflections of the form , as observed previously in a commensurate k = 1/2 system [N. Bernhoeft et al., Phys. Rev. B 69 174415 (2004)] are observed, removing any doubt that these occur because of multiple scattering or high-order contamination of the incident photon beam. They are clearly connected with the presence of a 3k configuration. Measurements of the reflections from the sample UAs_{0.8}Se_{0.2} in a magnetic field show that the transition at T* ~ 50 K is between a low-temperature 2k and high-temperature 3k state and that this transition is sensitive to an applied magnetic field. These experiments stress the need for quantitative theory to explain the intensities of these reflections.Comment: submitted to Phys. Rev.

The malleability of uranium: manipulating the charge-density wave in epitaxial films

We report x-ray synchrotron experiments on epitaxial films of uranium, deposited on niobium and tungsten seed layers. Despite similar lattice parameters for these refractory metals, the uranium epitaxial arrangements are different and the strains propagated along the a-axis of the uranium layers are of opposite sign. At low temperatures these changes in epitaxy result in dramatic modifications to the behavior of the charge-density wave in uranium. The differences are explained with the current theory for the electron-phonon coupling in the uranium lattice. Our results emphasize the intriguing possibilities of producing epitaxial films of elements that have complex structures like the light actinides uranium to plutonium.Comment: 6 pages, 6 figure

Effective Confinement as Origin of the Equivalence of Kinetic Temperature and Fluctuation-Dissipation Ratio in a Dense Shear Driven Suspension

We study response and velocity autocorrelation functions for a tagged particle in a shear driven suspension governed by underdamped stochastic dynamics. We follow the idea of an effective confinement in dense suspensions and exploit a time-scale separation between particle reorganization and vibrational motion. This allows us to approximately derive the fluctuation-dissipation theorem in a "hybrid" form involving the kinetic temperature as an effective temperature and an additive correction term. We show numerically that even in a moderately dense suspension the latter is negligible. We discuss similarities and differences with a simple toy model, a single trapped particle in shear flow

Triple-q octupolar ordering in NpO_2

We report the results of resonant X-ray scattering experiments performed at the Np M_4,5 edges in NpO_2. Below T_0 = 25 K, the development of long-range order of Np electric quadrupoles is revealed by the growth of superlattice Bragg peaks. The electronic transition is not accompanied by any measurable crystallographic distortion, either internal or external, so the symmetry of the system remains cubic. The polarization and azimuthal dependence of the intensity of the resonant peaks is well reproduced assuming Templeton scattering from a triple-q longitudinal antiferroquadrupolar structure. Electric quadrupole order in NpO_2 could be driven by the ordering at T_0 of magnetic octupoles of Gamma_5 symmetry, splitting the Np ground state quartet and leading to a singlet ground state with zero dipole magnetic moment.Comment: 4 Pages, 3 Figures, submitted to Phys. Rev. Lett. v2: resubmitted after referee report