The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Diamond-like carbon (DLC) is a metastable form of amorphous carbon with significant sp3 bonding. DLC is a semiconductor with a high mechanical hardness, chemical inertness, and optical transparency. This review will describe the deposition methods, deposition mechanisms, characterisation methods, electronic structure, gap states, defects, doping, luminescence, field emission, mechanical properties and some applications of DLCs. The films have widespread applications as protective coatings in areas, such as magnetic storage disks, optical windows and micro-electromechanical devices (MEMs).

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Diamond-like amorphous carbon

Transparent, conductive, and ultrathin graphene films, as an alternative to the ubiquitously employed metal oxides window electrodes for solid-state dye-sensitized solar cells, are demonstrated. These graphene films are fabricated from exfoliated graphite oxide, followed by thermal reduction. The obtained films exhibit a high conductivity of 550 S/cm and a transparency of more than 70% over 1000−3000 nm. Furthermore, they show high chemical and thermal stabilities as well as an ultrasmooth surface with tunable wettability.

Transparent, Conductive Graphene Electrodes for Dye-Sensitized Solar Cells

A review was presented to demonstrate a historical description of the synthesis of light-emitting conjugated polymers for applications in electroluminescent devices. Electroluminescence (EL) was first reported in poly(para-phenylene vinylene) (PPV) in 1990 and researchers continued to make significant efforts to develop conjugated materials as the active units in light-emitting devices (LED) to be used in display applications. Conjugated oligomers were used as luminescent materials and as models for conjugated polymers in the review. Oligomers were used to demonstrate a structure and property relationship to determine a key polymer property or to demonstrate a technique that was to be applied to polymers. The review focused on demonstrating the way polymer structures were made and the way their properties were controlled by intelligent and rational and synthetic design.

Synthesis of Light-Emitting Conjugated Polymers for Applications in Electroluminescent Devices

Synthetic Principles for Bandgap Control in Linear pi-Conjugated Systems.

We report the preparation of hard nitrogenated amorphous carbon films doped with as much as 20 at. % nitrogen. The nitrogen groups created by doping do not dramatically affect the film structure, but are found to break symmetry in ${\mathrm{sp}}^{2}$ domains causing the Raman-active G (``graphitic'') and D (``disordered'') bands to become ir active. Elemental analysis of the films together with the infrared spectra shows that about one in six of the carbons are replaced by nitrogen. Also observed in the infrared spectrum are nitrile (and possibly isonitrile) groups which demonstrate for the first time the existence of sp carbon in amorphous carbon films.

Symmetry breaking in nitrogen-doped amorphous carbon: Infrared observation of the Raman-active G and D bands.

We present a new method of electrochemical polymerization of poly(thiophene) using dithiophene as the starting material, from which we obtain a high-quality film with a sharp interband absorption edge. An in situ study of the absorption spectrum during the electrochemical doping process has been carried out. In the dilute regime, the results are in detailed agreement with charge storage via bipolarons; weakly confined soliton pairs with confinement parameter $\ensuremath{\gamma}\ensuremath{\cong}0.1\ensuremath{-}0.2$. At the highest doping levels, the data are characteristic of the free-carrier absorption expected for a metal. From a parallel electrochemical voltage spectroscopy study, we find evidence of charge injection near the band edge and charge removal from the bipolaron gap states. In the dilute regime, the position of the chemical potential is consistent with charge storage in weakly confined bipolarons. The high Coulombic recovery over a charge-discharge cycle indicates that poly (thiophene) may be an excellent cathode-active material in battery applications.

Charge storage in doped poly(thiophene): Optical and electrochemical studies

A nonvolatile magnetic random access memory (MRAM) is an array of individual magnetic memory cells. Each memory cell is a magnetic tunnel junction (MTJ) element and a diode electrically connected in series. Each MTJ is formed of a pinned ferromagnetic layer whose magnetization direction is prevented from rotating, a free ferromagnetic layer whose magnetization direction is free to rotate between states of parallel and antiparallel to the fixed magnetization of the pinned ferromagnetic layer, and an insulating tunnel barrier between and in contact with the two ferromagnetic layers. Each memory cell has a high resistance that is achieved in a very small surface area by controlling the thickness, and thus the electrical barrier height, of the tunnel barrier layer. The memory cells in the array are controlled by only two lines, and the write currents to change the magnetic state of an MTJ, by use of the write currents' inherent magnetic fields to rotate the magnetization of the free layer, do not pass through the tunnel barrier layer. All MTJ elements, diodes, and contacts are vertically arranged at the intersection regions of the two lines and between the two lines to minimize the total MRAM surface area. The power expended to read or sense the memory cell's magnetic state is reduced by the high resistance of the MTJ and by directing the sensing current through a single memory cell.

Magnetic memory array using magnetic tunnel junction devices in the memory cells

Light‐emitting diodes made with poly(2‐methoxy‐5(2′‐ethyl)hexoxy‐phenylenevinylene) (MEH‐ PPV) using indium‐tin‐oxide (ITO) as anode and Ca as cathode have been examined as they age during operation in a dry inert atmosphere. Two primary modes of degradation are identified. First, oxidation of the polymer leads to the formation of aromatic aldehyde, i.e., carbonyl which quenches the fluorescence. The concomitant chain scission results in reduced carrier mobility. ITO is identified as a likely source of oxygen. The second process involves the formation of localized electrical shorts which do not necessarily cause immediate complete failure because they can be isolated by self‐induced melting of the surrounding cathode metal. We have not identified the origin of the shorts, but once they are initiated, thermal runaway appears to accelerate their development. The ultimate failure of many MEH‐PPV devices occurs when the regions of damaged cathode start to coalesce.

Degradation and failure of MEH‐PPV light‐emitting diodes

In this work, the electrical admittance of this plane‐parallel resonator loaded on one face with a viscoelastic medium is described directly in terms of the physical properties of the system. This description is based on the detailed matrix equations for the piezoelectric quartz and includes the piezoelectric effect of the quartz transducer and the shear modulus and viscosity of the overlayer. This physically based analysis has proven invaluable in relating the admittance behavior directly to the materials’ properties. Initial comparisons of the theory with experimental data are given, including the appearance of even harmonics as described by Benes [E. Benes, J. Appl. Phys. 56, 608 (1984)] for the asymmetrically loaded resonator. Additionally, measurements on a series of perfluoropolyether fluids of differing molecular weights indicate that they cannot be described as simple viscous liquids in the MHz range. The assignment of a frequency‐dependent viscosity with a relaxation time proportional to the mole...

James H. Kaufman

Papers

Symmetry breaking in nitrogen-doped amorphous carbon: Infrared observation of the Raman-active G and D bands.

Charge storage in doped poly(thiophene): Optical and electrochemical studies

Magnetic memory array using magnetic tunnel junction devices in the memory cells

Degradation and failure of MEH‐PPV light‐emitting diodes

Physical description of a viscoelastically loaded AT‐cut quartz resonator