Compressed sensing quantum process tomography for superconducting quantum gates

We apply the method of compressed sensing (CS) quantum process tomography (QPT) to characterize quantum gates based on superconducting Xmon and phase qubits. Using experimental data for a two-qubit controlled-Z gate, we obtain an estimate for the process matrix $\chi$ with reasonably high fidelity compared to full QPT, but using a significantly reduced set of initial states and measurement configurations. We show that the CS method still works when the amount of used data is so small that the standard QPT would have an underdetermined system of equations. We also apply the CS method to the analysis of the three-qubit Toffoli gate with numerically added noise, and similarly show that the method works well for a substantially reduced set of data. For the CS calculations we use two different bases in which the process matrix $\chi$ is approximately sparse, and show that the resulting estimates of the process matrices match each ther with reasonably high fidelity. For both two-qubit and three-qubit gates, we characterize the quantum process by not only its process matrix and fidelity, but also by the corresponding standard deviation, defined via variation of the state fidelity for different initial states.Comment: 16 pages, 11 figure

Extraterrestrial Moessbauer Spectroscopy: More than Three Years of Mars Exploration and Developments for Future Missions

The NASA Mars Exploration Rovers (MER), Spirit and Opportunity, landed on the Red Planet in January 2004. Both rovers are equipped with a miniaturized Moessbauer spectrometer MIMOS II. Designed for a three months mission, both rovers and both Moessbauer instruments are still working after more than three years of exploring the Martian surface. At the beginning of the mission, with a landed intensity of the Moessbauer source of 150 mCi, a 30 minute touch and go measurement produced scientifically valuable data while a good quality Moessbauer spectrum was obtained after approximately eight hours. Now, after about five halflives of the sources have passed, Moessbauer integrations are routinely planned to last approx.48 hours. Because of this and other age-related hardware degradations of the two rover systems, measurements now occur less frequently, but are still of outstanding quality and scientific importance. Summarizing important Moessbauer results, Spirit has traversed the plains from her landing site in Gusev crater and is now, for the greater part of the mission, investigating the stratigraphically older Columbia Hills. Olivine in rocks and soils in the plains suggests that physical rather than chemical processes are currently active

LC-MS based quantification of 2’-ribosylated nucleosides Ar(p) and Gr(p) in tRNA

RNA nucleosides are often naturally modified into complex non-canonical structures with key biological functions. Here we report LC-MS quantification of the Ar(p) and Gr(p) 2'-ribosylated nucleosides in tRNA using deuterium labelled standards, and the first detection of Gr(p) in complex fungi

Human hippocampal theta power indicates movement onset and distance travelled

Theta frequency oscillations in the 6- to 10-Hz range dominate the rodent hippocampal local field potential during translational movement, suggesting that theta encodes self-motion. Increases in theta power have also been identified in the human hippocampus during both real and virtual movement but appear as transient bursts in distinct high- and low-frequency bands, and it is not yet clear how these bursts relate to the sustained oscillation observed in rodents. Here, we examine depth electrode recordings from the temporal lobe of 13 presurgical epilepsy patients performing a selfpaced spatial memory task in a virtual environment. In contrast to previous studies, we focus on movement-onset periods that incorporate both initial acceleration and an immediately preceding stationary interval associated with prominent theta oscillations in the rodent hippocampal formation. We demonstrate that movementonset periods are associated with a significant increase in both low (2–5 Hz)- and high (6–9 Hz)-frequency theta power in the human hippocampus. Similar increases in low- and high-frequency theta power are seen across lateral temporal lobe recording sites and persist throughout the remainder of movement in both regions. In addition, we show that movement-related theta power is greater both before and during longer paths, directly implicating human hippocampal theta in the encoding of translational movement. These findings strengthen the connection between studies of theta-band activity in rodents and humans and offer additional insight into the neural mechanisms of spatial navigation

Interactions among the A and T Units of an ECF-Type Biotin Transporter Analyzed by Site-Specific Crosslinking

Energy-coupling factor (ECF) transporters are a huge group of micronutrient importers in prokaryotes. They are composed of a substrate-specific transmembrane protein (S component) and a module consisting of a moderately conserved transmembrane protein (T component) and two ABC ATPase domains (A components). Modules of A and T units may be dedicated to a specific S component or shared by many different S units in an organism. The mode of subunit interactions in ECF transporters is largely unknown. BioMNY, the focus of the present study, is a biotin transporter with a dedicated AT module. It consists of the S unit BioY, the A unit BioM and the T unit BioN. Like all T units, BioN contains two three-amino-acid signatures with a central Arg residue in a cytoplasmic helical region. Our previous work had demonstrated a central role of the two motifs in T units for stability and function of BioMNY and other ECF transporters. Here we show by site-specific crosslinking of pairs of mono-cysteine variants that the Ala-Arg-Ser and Ala-Arg-Gly signatures in BioN are coupling sites to the BioM ATPases. Analysis of 64 BioN-BioM pairs uncovered interactions of both signatures predominantly with a segment of ∼13 amino acid residues C-terminal of the Q loop of BioM. Our results further demonstrate that portions of all BioN variants with single Cys residues in the two signatures are crosslinked to homodimers. This finding may point to a dimeric architecture of the T unit in BioMNY complexes

Upwelling on the continental slope of the Alaskan Beaufort Sea : storms, ice, and oceanographic response

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C00A13, doi:10.1029/2008JC005009.The characteristics of Pacific-born storms that cause upwelling along the Beaufort Sea continental slope, the oceanographic response, and the modulation of the response due to sea ice are investigated. In fall 2002 a mooring array located near 152°W measured 11 significant upwelling events that brought warm and salty Atlantic water to shallow depths. When comparing the storms that caused these events to other Aleutian lows that did not induce upwelling, interesting trends emerged. Upwelling occurred most frequently when storms were located in a region near the eastern end of the Aleutian Island Arc and Alaskan Peninsula. Not only were these storms deep but they generally had northward-tending trajectories. While the steering flow aloft aided this northward progression, the occurrence of lee cyclogenesis due to the orography of Alaska seems to play a role as well in expanding the meridional influence of the storms. In late fall and early winter both the intensity and frequency of the upwelling diminished significantly at the array site. It is argued that the reduction in amplitude was due to the onset of heavy pack ice, while the decreased frequency was due to two different upper-level atmospheric blocking patterns inhibiting the far field influence of the storms.The following grants provided support for this study: National Science Foundation grants OPP-0731928 (R.S.P.) and OPP-0713250 (R.S.P. and P.S.F.), Office of Naval Research grant N00014-07-1-1040 (D.J.T. and R.A.G.), Natural Sciences and Engineering Research Council of Canada (G.W.K.M.), Woods Hole Oceanographic Institution Arctic Initiative (J.Y.)

Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation

The Bacillus subtilis lysC lysine riboswitch modulates its own gene expression upon lysine binding through a transcription attenuation mechanism. The riboswitch aptamer is organized around a single five-way junction that provides the scaffold for two long-range tertiary interactions (loop L2–loop L3 and helix P2–loop L4)—all of this for the creation of a specific lysine binding site. We have determined that the interaction P2–L4 is particularly important for the organization of the ligand-binding site and for the riboswitch transcription attenuation control. Moreover, we have observed that a folding synergy between L2–L3 and P2–L4 allows both interactions to fold at lower magnesium ion concentrations. The P2–L4 interaction is also critical for the close juxtaposition involving stems P1 and P5. This is facilitated by the presence of lysine, suggesting an active role of the ligand in the folding transition. We also show that a previously uncharacterized stem–loop located in the expression platform is highly important for the riboswitch activity. Thus, folding elements located in the aptamer and the expression platform both influence the lysine riboswitch gene regulation

Structural Ordering of Disordered Ligand-Binding Loops of Biotin Protein Ligase into Active Conformations as a Consequence of Dehydration

Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of ∼3.5 Å in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action