Electromagnetic modelling of a terahertz-frequency quantum-cascade laser integrated with dual diagonal feedhorns

We present an electromagnetic model of a THz QCL, integrated with a micro-machined waveguide and dual diagonal feedhorns, enabling simultaneous access to both facets of the QCL. A hybrid finite-element/Fourier transform approach enables analysis of both the near and far-fields in agreement with experimental observations. The far-field pattern shows enhancement of the beam profile when compared with an unmounted QCL, in terms of beam divergence and side-lobe suppression ratio

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

FMRI resting slow fluctuations correlate with the activity of fast cortico-cortical physiological connections

Recording of slow spontaneous fluctuations at rest using functional magnetic resonance imaging (fMRI) allows distinct long-range cortical networks to be identified. The neuronal basis of connectivity as assessed by resting-state fMRI still needs to be fully clarified, considering that these signals are an indirect measure of neuronal activity, reflecting slow local variations in de-oxyhaemoglobin concentration. Here, we combined fMRI with multifocal transcranial magnetic stimulation (TMS), a technique that allows the investigation of the causal neurophysiological interactions occurring in specific cortico-cortical connections. We investigated whether the physiological properties of parieto-frontal circuits mapped with short-latency multifocal TMS at rest may have some relationship with the resting-state fMRI measures of specific resting-state functional networks (RSNs). Results showed that the activity of fast cortico-cortical physiological interactions occurring in the millisecond range correlated selectively with the coupling of fMRI slow oscillations within the same cortical areas that form part of the dorsal attention network, i.e., the attention system believed to be involved in reorientation of attention. We conclude that resting-state fMRI ongoing slow fluctuations likely reflect the interaction of underlying physiological cortico-cortical connections

Electromagnetic-field analysis of diagonal-feedhorn antennas for terahertz-frequency quantum-cascade laser integration

We present an electromagnetic-field analysis of a terahertz-frequency quantum-cascade laser (THz QCL) integrated with a mechanically micro-machined waveguide cavity and diagonal feedhorn. A hybrid finite-element/Fourier transform approach enables analysis of both the near-field and far-field regions and is shown to agree well with experimental observations. The far-field antenna patterns show enhancement of the beam profile when compared with an unmounted QCL, in terms of beam divergence and side-lobe suppression ratio. Furthermore, we demonstrate integration of the QCL with dual diagonal feedhorns, enabling simultaneous access to both facets of the QCL, underpinning future integration with a satellite-based receiver and frequency-stabilization subsystem

Quantum‐Cascade Laser emission at 3.5 THz from dual diagonal feedhorns

The LOCUS satellite (Linking Observations of Climate, the Upper Atmosphere and Space weather) is a proposed mission to explore and observe key gas species within the upper atmosphere using a novel terahertz-frequency (THz) heterodyne spectrometer, in which the emission spectra are simultaneously recorded in four channels in the 0.8–4.7 THz band [1]. THz quantum-cascade lasers (QCLs) will be exploited as local oscillators for the first time in space because they are powerful, yet compact THz sources, providing > 1 mW continuous-wave output at key LOCUS frequencies (3.5 and 4.7 THz). Furthermore, they have been integrated successfully into precision-micro-machined waveguide blocks and operated in space-qualified Stirling-cycle cryo-coolers (~60 K) [2]. A key development challenge will be stabilising the emission frequency of the QCL by locking it to a stable reference oscillator. In this paper, we present a new QCL dual-feedhorn integration technique, which advances this goal by enabling access to radiation emitted from both facets of the QCL simultaneously. In this configuration, the THz emission may be coupled simultaneously to a mixer and to a stabilisation subsystem. Figure 1(a) shows the integration of a 3.5 THz QCL into a precision micro-machined channel in a copper block. A second, symmetrical copper block is placed on top of this to form a rectangular waveguide around the QCL, with a diagonal feedhorn at either end. Figure 1(b) shows the simulated far-field beam pattern for a single feedhorn at 3.5 THz, in which the maximum collected power is represented in the bright central area. Figure 1(c) shows the experimental results for the dual-feedhorn waveguide block, in which the radiation from each horn is reflected onto the same plane, and measured using a raster-scanned Golay-cell detector. Good agreement with the simulated single-feedhorn emission has been observed, with similar beam width and side-lobe content. In conclusion, the integration of a 3.5-THz QCL into a dual-feedhorn waveguide block has been demonstrated. This opens the way towards simultaneous integration of the QCL with a frequency stabilisation system and a supra-THz mixer

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement

Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models

The cerebellum has long been considered to undergo supervised learning, with climbing fibers acting as a ‘teaching’ or ‘error’ signal. Purkinje cells (PCs), the sole output of the cerebellar cortex, have been considered as analogs of perceptrons storing input/output associations. In support of this hypothesis, a recent study found that the distribution of synaptic weights of a perceptron at maximal capacity is in striking agreement with experimental data in adult rats. However, the calculation was performed using random uncorrelated inputs and outputs. This is a clearly unrealistic assumption since sensory inputs and motor outputs carry a substantial degree of temporal correlations. In this paper, we consider a binary output neuron with a large number of inputs, which is required to store associations between temporally correlated sequences of binary inputs and outputs, modelled as Markov chains. Storage capacity is found to increase with both input and output correlations, and diverges in the limit where both go to unity. We also investigate the capacity of a bistable output unit, since PCs have been shown to be bistable in some experimental conditions. Bistability is shown to enhance storage capacity whenever the output correlation is stronger than the input correlation. Distribution of synaptic weights at maximal capacity is shown to be independent on correlations, and is also unaffected by the presence of bistability

Early anthropogenic transformation of the Danube-Black Sea system

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 2 (2012): 582, doi:10.1038/srep00582.Over the last century humans have altered the export of fluvial materials leading to significant changes in morphology, chemistry, and biology of the coastal ocean. Here we present sedimentary, paleoenvironmental and paleogenetic evidence to show that the Black Sea, a nearly enclosed marine basin, was affected by land use long before the changes of the Industrial Era. Although watershed hydroclimate was spatially and temporally variable over the last ~3000 years, surface salinity dropped systematically in the Black Sea. Sediment loads delivered by Danube River, the main tributary of the Black Sea, significantly increased as land use intensified in the last two millennia, which led to a rapid expansion of its delta. Lastly, proliferation of diatoms and dinoflagellates over the last five to six centuries, when intensive deforestation occurred in Eastern Europe, points to an anthropogenic pulse of river-borne nutrients that radically transformed the food web structure in the Black Sea.This study was supported by grants OISE 0637108, EAR 0952146, OCE 0602423 and OCE 0825020 from the National Science Foundation and grants from the Woods Hole Oceanographic Institution

3.5 THz quantum-cascade laser emission from dual diagonal feedhorns

Antenna-pattern measurements obtained from a double-metal supra-terahertz-frequency (supra-THz) quantum cascade laser (QCL) are presented. The QCL is mounted within a mechanically micro-machined waveguide cavity containing dual diagonal feedhorns. Operating in continuous-wave mode at 3.5 THz, and at an ambient temperature of ∼60 K, QCL emission has been directed via the feedhorns to a supra-THz detector mounted on a multi-axis linear scanner. Comparison of simulated and measured far-field antenna patterns shows an excellent degree of correlation between beamwidth (full-width-half-maximum) and sidelobe content and a very substantial improvement when compared with unmounted devices. Additionally, a single output has been used to successfully illuminate and demonstrate an optical breadboard arrangement associated with a future supra-THz Earth observation space-borne payload. Our novel device has therefore provided a valuable demonstration of the effectiveness of supra-THz diagonal feedhorns and QCL devices for future space-borne ultra-high-frequency Earth-observing heterodyne radiometers