Linear-time protein 3-D structure searching with insertions and deletions

<p>Abstract</p> <p>Background</p> <p>Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era.</p> <p>Results</p> <p>We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (<it>i.e.</it>, insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels <it>k </it>is bounded by a constant. Our algorithm solves the above problem for a query of size <it>m </it>and a database of size <it>N </it>in average-case <it>O</it>(<it>N</it>) time, whereas the time complexity of the previously best algorithm was <it>O</it>(<it>Nm</it>^<it>k</it>+1).</p> <p>Conclusions</p> <p>Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant.</p

Photo-enhanced antinodal conductivity in the pseudogap state of high-T-c cuprates

A major challenge in understanding the cuprate superconductors is to clarify the nature of the fundamental electronic correlations that lead to the pseudogap phenomenon. Here we use ultrashort light pulses to prepare a non-thermal distribution of excitations and capture novel properties that are hidden at equilibrium. Using a broadband (0.5-2 eV) probe, we are able to track the dynamics of the dielectric function and unveil an anomalous decrease in the scattering rate of the charge carriers in a pseudogap-like region of the temperature (T) and hole-doping (p) phase diagram. In this region, delimited by a well-defined T*(neq)(p) line, the photoexcitation process triggers the evolution of antinodal excitations from gapped (localized) to delocalized quasiparticles characterized by a longer lifetime. The novel concept of photo-enhanced antinodal conductivity is naturally explained within the singleband Hubbard model, in which the short-range Coulomb repulsion leads to a k-space differentiation between nodal quasiparticles and antinodal excitations. \ua9 2014 Macmillan Publishers Limited. All rights reserved

Biflorin: an o-naphthoquinone of clinical significance

Biflorin is an o-naphthoquinone with proven cytotoxic effects on tumor cells showing antimicrobial, antitumor and antimutagenic activities. Biflorin is an isolated compound taken from the roots of the plant Capraria biflora L. (Schrophulariaceae), indigenous of the West Indies and South America, which is located in temperate or tropical areas. This compound has shown to be strongly active against grampositive and alcohol-acid-resistant bacteria. It has been efficient in inhibiting the proliferation tumor cell lines CEM, HL-60, B16, HCT-8 and MCF-7. Recently, SK-Br3 cell line was treated with biflorin showing important cytotoxic effects. In this article, information related to the first structural characterization studies are presented, as well as the latest reports concerning the biological activity of this molecule

Imaging of stored charges in Si quantum dots by tapping and electrostatic force microscopy

We studied the charge storage and subsequent imaging of silicon quantum dots (SiQD) embedded in a \chem{SiO_2} film by using atomic-force microscopy (AFM) in tapping and electrostatic force microscopy (EFM) modes. The controllable deposition of both positive and negative localized charges in SiQD is described. The dynamics of the deposited charges is studied and the charge decay time constant is determined from the measurements. A simple analysis is presented to explain the contrast in tapping and EFM images and to quantify the total amount of stored charge

Local Community Detection Algorithm with Self-defining Source Nodes

Surprising insights in community structures of complex networks have raised tremendous interest in developing various kinds of community detection algorithms. Considering the growing size of existing networks, local community detection methods have gained attention in contrast to global methods that impose a top-down view of global network information. Current local community detection algorithms are mainly aimed to discover local communities around a given node. Besides, their performance is influenced by the quality of the source node. In this paper, we propose a community detection algorithm that outputs all the communities of a network benefiting from a set of local principles and a self-defining source node selection. Each node in our algorithm progressively adjusts its community label based on an even more restrictive level of locality, considering its neighbours local information solely. Our algorithm offers a computational complexity of linear order with respect to the network size. Experiments on both artificial and real networks show that our algorithm gains moreover networks with weak community structures compared to networks with strong community structures. Additionally, we provide experiments to demonstrate the ability of the self-defining source node of our algorithm by implementing various source node selection methods from the literature