ALBERT

Description: Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.

Description: Author(s): A. Cadien, Q. Y. Hu, Y. Meng, Y. Q. Cheng, M. W. Chen, J. F. Shu, H. K. Mao, and H. W. Sheng We report the first experimental observation of a liquid-liquid phase transition in the monatomic liquid metal cerium, by means of in situ high-pressure high-temperature x-ray diffraction experiments. At 13 GPa, upon increasing temperature from 1550 to 1900 K high-density liquid transforms to a low-... [Phys. Rev. Lett. 110, 125503] Published Thu Mar 21, 2013

Description: Author(s): C. X. Yu, C. Xue, J. Liu, X. Y. Hu, Y. Y. Liu, W. H. Ye, L. F. Wang, J. F. Wu, and Z. F. Fan In this article, multiple eigen-systems including linear growth rates and eigen-functions have been discovered for the Rayleigh-Taylor instability (RTI) by numerically solving the Sturm-Liouville eigen-value problem in the case of two-dimensional plane geometry. The system called the first mode has ... [Phys. Rev. E 97, 013102] Published Thu Jan 04, 2018

Description: An exact analytical solution is presented for the effective dynamic transverse shear modulus in a heterogeneous fluid-filled porous solid containing cylindrical inclusions. The complex and frequency-dependent properties of the dynamic shear modulus are caused by the physical mechanism of mesoscopic-scale wave-induced fluid flow whose scale is smaller than wavelength but larger than the size of pores. Our model consists of three phases: a long cylindrical inclusion, a cylindrical shell of poroelastic matrix material with different mechanical and/or hydraulic properties than the inclusion and an outer region of effective homogeneous medium of laterally infinite extent. The behavior of both the inclusion and the matrix is described by Biot's consolidation equations, whereas the surrounding effective medium which is used to describe the effective transverse shear properties of the inner poroelastic composite is assumed to be a viscoelastic solid whose complex transverse shear modulus needs to be determined. The determined effective transverse shear modulus is used to quantify the S -wave attenuation and velocity dispersion in heterogeneous fluid-filled poroelastic rocks. The calculation shows the relaxation frequency and relative position of various fluid saturation dispersion curves predicted by this study exhibit very good agreement with those of a previous 2-D finite-element simulation. For the double-porosity model (inclusions having a different solid frame than the matrix but the same pore fluid as the matrix) the effective shear modulus also exhibits a size-dependent characteristic that the relaxation frequency moves to lower frequencies by two orders of magnitude if the radius of the cylindrical poroelastic composite increases by one order of magnitude. For the patchy-saturation model (inclusions having the same solid frame as the matrix but with a different pore fluid from the matrix), the heterogeneity in pore fluid cannot cause any attenuation in the transverse shear modulus at all. A comparison with the case of spherical inclusions illustrates that the transverse shear modulus for the cylindrical inclusion exhibits more S -wave attenuation than spherical inclusions.

Description: Author(s): P. Androvitsaneas, A. B. Young, C. Schneider, S. Maier, M. Kamp, S. Höfling, S. Knauer, E. Harbord, C. Y. Hu, J. G. Rarity, and R. Oulton Quantum dots have long been considered systems that could deliver a significant advantage for practical quantum information applications. Their atomic dipolelike transitions and their compatibility to be integrated into a variety of photonic structures has highlighted this fact. Here, the authors measure an unexpectedly high single-photon level phase shift (~6 ∘ ), induced upon reflection from a singly negatively charged quantum dot incorporated in a low- Q -factor cavity ( Q ~290). This measurement provides the first evidence for a system with unit fidelity and a high efficiency in its interactions. The result opens a new road to realistic spin-photon entanglement devices, in a simple and easy to fabricate photonic structure. [Phys. Rev. B 93, 241409(R)] Published Tue Jun 21, 2016

Description: This paper is concerned with the issue of passivity analysis for switched generalized neural networks (SGNNs). Parametric uncertainty is considered and assumed to be time-variant and norm bounded. We first give the passivity condition for SGNNs without uncertainties, and then extend the result to the cases with time-varying parametric uncertainties both in network parameters and output matrices. By using the Lyapunov–Krasovskii functional and some analysis techniques, the passivity criteria are presented in terms of linear matrix inequalities. Two numerical examples are given to show the effectiveness of the theoretical results.

Description: Author(s): Dipanshu Bansal, Jiawang Hong, Chen W. Li, Andrew F. May, Wallace Porter, Michael Y. Hu, Douglas L. Abernathy, and Olivier Delaire The anharmonic phonon properties of SnSe in the P n m a phase were investigated with a combination of experiments and first-principles simulations. Using inelastic neutron scattering (INS) and nuclear resonant inelastic X-ray scattering (NRIXS), we have measured the phonon dispersions and density of st… [Phys. Rev. B 94, 054307] Published Tue Aug 09, 2016

Description: Motivation: How chromatin folds in three-dimensional (3D) space is closely related to transcription regulation. As powerful tools to study such 3D chromatin conformation, the recently developed Hi-C technologies enable a genome-wide measurement of pair-wise chromatin interaction. However, methods for the detection of biologically meaningful chromatin interactions, i.e. peak calling, from Hi-C data, are still under development. In our previous work, we have developed a novel hidden Markov random field (HMRF) based Bayesian method, which through explicitly modeling the non-negligible spatial dependency among adjacent pairs of loci manifesting in high resolution Hi-C data, achieves substantially improved robustness and enhanced statistical power in peak calling. Superior to peak callers that ignore spatial dependency both methodologically and in performance, our previous Bayesian framework suffers from heavy computational costs due to intensive computation incurred by modeling the correlated peak status of neighboring loci pairs and the inference of hidden dependency structure. Results: In this work, we have developed FastHiC, a novel approach based on simulated field approximation, which approximates the joint distribution of the hidden peak status by a set of independent random variables, leading to more tractable computation. Performance comparisons in real data analysis showed that FastHiC not only speeds up our original Bayesian method by more than five times, bus also achieves higher peak calling accuracy. Availability and Implementation: FastHiC is freely accessible at: http://www.unc.edu/~yunmli/FastHiC/ Contacts : yunli@med.unc.edu or ming.hu@nyumc.org Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Author(s): Y. W. Windsor, M. Ramakrishnan, L. Rettig, A. Alberca, E. M. Bothschafter, U. Staub, K. Shimamoto, Y. Hu, T. Lippert, and C. W. Schneider We employ resonant soft x-ray diffraction to individually study the magnetic ordering of the Mn and the Tm sublattices in single-crystalline films of orthorhombic ( o − ) TmMn O 3 . The same magnetic ordering wave vector of ( 0 q 0 ) with q ≈ 0.46 is found for both ionic species, suggesting that the familiar ant… [Phys. Rev. B 91, 235144] Published Fri Jun 26, 2015

Description: Author(s): C. Y. Hu and J. G. Rarity Giant optical Faraday rotation (GFR) and giant optical circular birefringence (GCB) induced by a single quantum-dot spin in an optical microcavity can be regarded as linear effects in the weak-excitation approximation if the input field lies in the low-power limit [Hu et al. , Phys. Rev. B 78 , 085307... [Phys. Rev. B 91, 075304] Published Tue Feb 10, 2015