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International audience; The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds. Despite its size and economic importance, there is no reference genome sequence for the Compositae, which impedes research and improvement efforts. We report on progress toward sequencing the 3.5 Gb genome of cultivated sunflower (Helianthus annuus), the most important crop in the family. Our sequencing strategy combines whole-genome shotgun sequencing using the Solexa and 454 platforms with the generation of high-density genetic and physical maps that serve as scaffolds for the linear assembly of whole-genome shotgun sequences. The performance of this approach is enhanced by the construction of a sequence-based physical map, which provides unique sequence-based tags every 5-6 kb across the genome. Thus far, our physical map covers similar to 85% of the sunflower genome, and we have generated similar to 80x genome coverage with Solexa reads and 15.5x with 454 reads. Preliminary analyses indicated that similar to 78% of the sunflower genome consists of repetitive sequences. Nonetheless, similar to 76% of contigs >5 kb in size can be assigned to either the physical or genetic map or to both, suggesting that our approach is likely to deliver a highly accurate and contiguous reference genome for sunflower.

A nonblocking photonic switch can be used to implement a tapped delay line with a large number of adaptive weights and a wide range of time delays. An advantage of using optical tapped delay lines for adaptive filtering is that the operating frequency can be quite high, in the 10-100 GHz range. We present a sparse reconfigurable adaptive filter (SRAF) based on a photonic switch with an input/output connection architecture that can be represented by a matrix of adaptive weights. This unique parallel structure can be reconfigured in an adaptive manner to implement a sparse filter impulse response for use in many applications. We consider an adaptive algorithm for this filter that chooses the input and output delays using a cross-correlation-based approach and connects these delays by weights that are adapted using a gradient algorithm. An alternative adaptive algorithm is also considered that is based on a system identification formulation where the weights are first adapted, and then the appropriate delay combinations are chosen. A search algorithm for implementing the connection constraint required by the SRAF is also discussed whereby each input is connected to only one output at any moment. Computer simulation examples are presented to illustrate the behavior of the filter for a system identification model.

We describe the design and performance of a number of elements based on traveling-wave electroabsorption modulators (TW-EAMs) in optical time-division-multiplexing (OTDM) and wavelength-division-multiplexing (WDM) networks. The incorporation of traveling-wave (TW) electrode design into electroabsorption modulators (EAMs) relieves the resistance-capacitance (RC ) bandwidth limitation common to lumped components, enabling higher operation speed without shortening the device. As a result, high-speed operation can be combined with essential modulator characteristics such as modulation efficiency and extinction ratio. While significant modulation bandwidth has been achieved, a lesser known aspect is that the TW electrode also provides an extra dimension for improving and enabling functionalities beyond broadband modulation. This new dimension originates from the distributed effect of the TW design and its interactions with distinctive EAM properties. This paper reviews such developments in recent years with specific applications for optical signal processing in OTDM and WDM networks. The covered functionalities include various optical gating operations for OTDM, regenerative wavelength conversions for WDM, and clock recovery

A novel traveling-wave electroabsorption modulator (TWEAM) based on undercut-etching-active-region waveguide (UEAW) is proposed and demonstrated. By selectively wet-etching the InGaAsP from InP to reduce InGaAsP active region, the waveguide can reduce parasitic capacitance with high conductivity in n-InP and p-InP cladding layers. In comparison with conventional ridge-waveguide (RW) TWEAM, 3 dB lower optical-insertion-loss, at least 6 dB higher in radio-frequency-link gain (dc to 40 GHz), and faster electrooptical response (3-dB bandwidth of 25 GHz at 50 /spl Omega/-termination for UEAW and 15 GHz for RW) are obtained in UEAW-TWEAM. A 10-Gbs/s operation with low swing voltage of 0.6 V has been achieved in UEAW-TWEAM, a 3.2-dB enhancement over RW-TWEAM. It indicates the tradeoff in designing electroabsorption modulators can be greatly released.

High speeds, high external quantum efficiencies, narrow spectral linewidths, and convenience in coupling make resonant-cavity photodetectors (RECAP's) good candidates for telecommunication applications. In this paper, we present analytical expressions for the design of RECAP's with narrow spectral linewidths and high quantum efficiencies. We also present experimental results on a RECAP having an operating wavelength /spl lambda//sub 0//spl ap/1.3 /spl mu/m with a very narrow spectral response. The absorption takes place in a thin In/sub 0.53/Ga/sub 0.47/As layer placed in an InP cavity. The InP p-i-n structure was wafer bonded to a high-reflectivity GaAs/AlAs quarter-wavelength Bragg reflector. The top mirror consisted of three pairs of a ZnSe/CaF/sub 2/ quarter-wavelength stack (QWS). A spectral linewidth of 1.8 nm was obtained with an external quantum efficiency of 48%. We also demonstrate that the spectral response can be tailored by etching the top layer of the microcavity. The results are found to agree well with those obtained from analytical expressions derived on the assumption of linear-phase Bragg reflectors as well as detailed simulations performed using the transfer matrix method.

Silicon (Si) lasers have long been a goal for semiconductor scientists. A number of important breakthroughs in the past decade have focused attention on Si as a photonic platform. We first briefly study the fundamentals of carrier transition physics in crystalline Si, followed by the most recent progress in the fields of achieving lasing in Si or materials monolithically grown on Si. The hybrid Si platform, a novel III-V-on-Si hybrid integration approach, and the basics of hybrid lasers are then discussed in detail. Advanced hybrid Si lasers based on grating components and ring resonators are reviewed. Several demonstrated photonic integrated circuits on this hybrid Si platform are discussed, showing future possibilities for hybrid Si lasers to be high-performance light sources for Si photonics.

We report the large epitaxial transfer of 100 mm InP/InGaAs/InP wafers to Silicon-on-insulator (SOI) substrates through a low-temperature (300degC) O2 plasma- assisted wafer bonding process. Efficient vertical outgassing channels (VOCs) are developed to eliminate the fundamental obstacle of interfacial voids in bonding due to intrinsic chemical reactions. Generated gas species of H2O and H2 can quickly diffuse to VOCs, etched through-holes to buried oxide layer (BOX), and absorbed by the BOX layer owing to the open network structure and large gas permeability. The interfacial void density is reduced from 55,000 cm-2 down to 3 cm-2, more than five orders of magnitude reduction for appropriate design of VOCs. Uniform patterning of VOCs leads to a no outgassing "dead zone" across the entire bonding area, and decrease of the thermal mismatch-induced interfacial strain potentially as well, which both result in the wafer scale-independent bonding. The bonding strain is observed through X-ray rocking curve measurement conducted on both of a 2 times 2 cm2 bonded pair and 100 mm wafer-scale bonding sample. A variety of devices have been fabricated using this technique. As one example, hybrid silicon evanescent distributed feedback (DFB) lasers integrated with monitor photodiodes have been fabricated using this bonding technique. These highly single mode lasers may find applications in computer interconnects.

The rapid planning and deployment of reconfigurable all-optical carrier networks requires next-generation ROADM's that can support unlimited add-drop access with very high flexibility. We review a cost-effective multi-degree ROADM that can support up to 100% add-drop traffic capacity with unparalleled agility and minimal pre-planning. The ability of this ROADM to share, distribute and therefore minimize the need for local resources such as regeneration, wavelength-conversion, broadcast, and multicast cards, to the lowest possible required, is discussed for overall network level savings.

A nonblocking photonic switch can be used to implement a tapped delay line with a large number of coefficients and a wide range of time delays. In this paper, we present a sparse reconfigurable adaptive filter (SRAF) based on a photonic switch with an input/output connection architecture that can be represented by a matrix of adaptive weights. This unique parallel structure can be reconfigured in an adaptive manner to implement a sparse filter impulse response for a variety of applications. The appropriate choice of time delays is determined from a cross-correlation function between the filter input and a desired response signal that depends on the particular application. A computer simulation example illustrates the performance of the algorithm for modeling a bandpass filter characteristic.

As modulation bandwidths for semiconductor lasers continue to increase, distributed effects become more important. The velocity mismatch between the optical field and the microwave field has long been known to be an important limit to the bandwidth of modulators, but this effect has so far been ignored in lasers and amplifiers. However, with bandwidths above 40 GHz lasers are now operating in a regime where the wavelength of the microwave field is comparable to the length of the device. Consequently, we can no longer treat the device as a lumped element, but have to consider the propagation effects, i.e. velocity mismatch and microwave propagation loss. In this work we use a simple numerical model to investigate the bandwidth limits set by the velocity mismatch, and compare the performance to that of the ideal, velocity matched case.

Photodetectors with bandwidths beyond 100 GHz and detectors with 900 /spl Aring/ thick active layers exhibiting more than 90% quantum efficiency have been published. These devices makes it possible to implement ultra-high speed high efficiency digital receivers and mm-wave analog receivers. Photodetectors and optical receivers for digital communication systems above 10 Gbit/s will be discussed as well as mm-wave optical analog receivers for cellular communication systems and phased arrayed antennas.

In this paper microwave packages for very high speed analog and digital circuits are described. The microwave packages have excellent performance up to 40 GHz. Use of these packages is demonstrated with a 30 Gbit/s 4:1 multiplexer and a DC-26 GHz baseband AGC amplifier.

High speeds, high external quantum efficiencies, narrow spectral linewidths, and convenience in coupling make resonant-cavity photodetectors (RECAPs) good candidates for telecommunication applications. In this paper, we report a highly-efficient and wavelength-selective separate absorption and multiplication (SAM) avalanche photodiode (APD) with a thin (500 /spl Aring/) absorbing layer. The improved characteristics of the photodetector were obtained by placing the absorption and multiplication layers in a Fabry-Perot cavity. An external quantum efficiency of 77% was achieved with a spectral linewidth of less than 4 nm and an avalanche gain of more than 50. We also present the experimental results on a RECAP having an operating wavelength /spl lambda//sub 0//spl ap/1.3 /spl mu/m with a very narrow spectral response. The absorption takes place in a thin In/sub 0.53/Ga/sub 0.47/As layer placed in an InP cavity. The InP p-i-n structure was wafer bonded to a high-reflectivity GaAs-AlAs quarter-wavelength Bragg reflector. The top mirror consisted of three pairs of a ZnSe-CaF/sub 2/ quarter-wavelength stack (QWS). A spectral linewidth of 1.8 nm was obtained with an external quantum efficiency of 48%.

The first monolithically integrated attenuated counter-propagating optical phase-locked loop based coherent receiver is presented. A spurious-free dynamic range of 131.3 dB Hz 2/3 is measured in the detector shot-noise limit at 100 MHz, which is the highest reported for a single-chip device.

TBA and TBP are liquid organometallic sources that are a safer alternative to arsine and phosphine. Using TBA and TBP, we have successfully grown lattice matched In0.53Ga0.47As/InP single quantum well lasers emitting at 1.5 μm with a threshold current density of 220 A/cm2 for broad area devices 3.5 mm in length.

Hg 1-x Cd x Te has been grown on CdTe substrates by liquid-phase epitaxy (LPE) from: 1) Te-rich solution at atmospheric pressure in a slider system, 2) Hg-rich solution in a sealed tube dipping system, and 3) HgTe-rich solution in sealed tube tipping and sliding systems. For epitaxial layers grown from Te-rich solution at 500°C, the width of the graded composition region is 3 µm and the compositional variation across the layer and with depth into the layers is less than ±0.01 mole fraction CdTe. The graded composition region for layers grown from Hg-rich solution at 460°C is less than 3 µm; however, there is no uniform composition region because of CdTe depletion from the melt. The graded bandgap region for pseudobinary growth at 700°C is much wider (20 µm) than the other two cases; however, a region of uniform composition can be obtained by growing sufficiently thick layers (> 30 µm). Pseudobinary growth has the theoretical advantage that either p-type or n-type layers may be grown, whereas, only p-type layers may be grown from Te-rich solution at atmospheric pressure.

A detailed theory is presented for the writing and reading processes in the monolithic surface acoustic wave (SAW) storage cor- relator. Theoretical and experimental results are presented on the dependence of the conelation output on the duration of the acoustic, write, and read signals. The dependence of the output on the ampli- tudes of the acoustic, write, and read signals is also given. The theoreti- cal predictions me in good agreement with the experimental results in all of these cases. Suggestions are provided for the design of improved monolithic storage conelators.

Harmonic and intermodulation distortion are two crucial performance parameters of laser diodes in determining their utility in wide-bandwidth analog links. The multimode rate equations are solved numerically to give information on the bandwidth phase, harmonic, and intermodulation distortion of GaInAsP laser diodes at both small- and large-signal levels. The results of the theoretical analysis agree well with experimental results, and show that the effects of both spatial and spectral hole burning are necessary to create an accurate theoretical model that correctly predicts the modulation damping and distortion levels for a range of lateral cavity structures. Anomalous variations in the low-frequency harmonic and intermodulation curves at high modulation levels are explained with this model. The model can be used for any arbitrary input current waveform, and provides information on the output optical spectra which can be used to analyze the propagation of the waveform along an optical fiber. >