Bootstrap tomography of high-precision pulses for quantum control

Long-time dynamical decoupling and quantum control of qubits require high-precision control pulses. Full characterization (quantum tomography) of imperfect pulses presents a bootstrap problem: tomography requires initial states of a qubit which can not be prepared without imperfect pulses. We present a protocol for pulse error analysis, specifically tailored for a wide range of the single solid-state electron spins. Using a single electron spin of a nitrogen-vacancy (NV) center in diamond, we experimentally verify the correctness of the protocol, and demonstrate its usefulness for quantum control tasks

Dynamical control of electron spin coherence in a quantum dot

We investigate the performance of dynamical decoupling methods at suppressing electron spin decoherence from a low-temperature nuclear spin reservoir in a quantum dot. The controlled dynamics is studied through exact numerical simulation, with emphasis on realistic pulse delays and long-time limit. Our results show that optimal performance for this system is attained by a periodic protocol exploiting concatenated design, with control rates substantially slower than expected from the upper spectral cutoff of the bath. For a known initial electron spin state, coherence can saturate at long times, signaling the creation of a stable ``spin-locked'' decoherence-free subspace. Analytical insight on saturation is obtained for a simple echo protocol, in good agreement with numerical results.Comment: 4 pages, 4 figures with 3 of them in colo

Suppression of electron spin decoherence in a quantum dot

The dominant source of decoherence for an electron spin in a quantum dot is the hyperfine interaction with the surrounding bath of nuclear spins. The decoherence process may be slowed down by subjecting the electron spin to suitable sequences of external control pulses. We investigate the performance of a variety of dynamical decoupling protocols using exact numerical simulation. Emphasis is given to realistic pulse delays and the long-time limit, beyond the domain where available analytical approaches are guaranteed to work. Our results show that both deterministic and randomized protocols are capable to significantly prolong the electron coherence time, even when using control pulse separations substantially larger than what expected from the {\em upper cutoff} frequency of the coupling spectrum between the electron and the nuclear spins. In a realistic parameter range, the {\em total width} of such a coupling spectrum appears to be the physically relevant frequency scale affecting the overall quality of the decoupling.Comment: 8 pages, 3 figures. Invited talk at the XXXVII Winter Colloquium on the Physics of Quantum Electronics, Snowbird, Jan 2007. Submitted to J. Mod. Op

Long-time electron spin storage via dynamical suppression of hyperfine-induced decoherence in a quantum dot

The coherence time of an electron spin decohered by the nuclear spin environment in a quantum dot can be substantially increased by subjecting the electron to suitable dynamical decoupling sequences. We analyze the performance of high-level decoupling protocols by using a combination of analytical and exact numerical methods, and by paying special attention to the regimes of large inter-pulse delays and long-time dynamics, which are outside the reach of standard average Hamiltonian theory descriptions. We demonstrate that dynamical decoupling can remain efficient far beyond its formal domain of applicability, and find that a protocol exploiting concatenated design provides best performance for this system in the relevant parameter range. In situations where the initial electron state is known, protocols able to completely freeze decoherence at long times are constructed and characterized. The impact of system and control non-idealities is also assessed, including the effect of intra-bath dipolar interaction, magnetic field bias and bath polarization, as well as systematic pulse imperfections. While small bias field and small bath polarization degrade the decoupling fidelity, enhanced performance and temporal modulation result from strong applied fields and high polarizations. Overall, we find that if the relative errors of the control parameters do not exceed 5%, decoupling protocols can still prolong the coherence time by up to two orders of magnitude.Comment: 16 pages, 10 figures, submitted to Phys. Rev.

Communications Biophysics

Contains reports on four research projects.National Institutes of Health (Grant MH-04737-03)National Science Foundation (Grant G-16526)National Aeronautics and Space Administration (Grant NsG-496

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

In primates and other animals, reverse transcription of mRNA followed by genomic integration creates retroduplications. Expressed retroduplications are either “retrogenes” coding for functioning proteins, or expressed “processed pseudogenes,” which can function as noncoding RNAs. To date, little is known about the variation in retroduplications in terms of their presence or absence across individuals in the human population. We have developed new methodologies that allow us to identify “novel” retroduplications (i.e., those not present in the reference genome), to find their insertion points, and to genotype them. Using these methods, we catalogued and analyzed 174 retroduplication variants in almost one thousand humans, which were sequenced as part of Phase 1 of The 1000 Genomes Project Consortium. The accuracy of our data set was corroborated by (1) multiple lines of sequencing evidence for retroduplication (e.g., depth of coverage in exons vs. introns), (2) experimental validation, and (3) the fact that we can reconstruct a correct phylogenetic tree of human subpopulations based solely on retroduplications. We also show that parent genes of retroduplication variants tend to be expressed at the M-to-G1 transition in the cell cycle and that M-to-G1 expressed genes have more copies of fixed retroduplications than genes expressed at other times. These findings suggest that cell division is coupled to retrotransposition and, perhaps, is even a requirement for it

MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains

<p>Abstract</p> <p>Background</p> <p>Many protein interactions, especially those involved in signaling, involve short linear motifs consisting of 5-10 amino acid residues that interact with modular protein domains such as the SH3 binding domains and the kinase catalytic domains. One straightforward way of identifying these interactions is by scanning for matches to the motif against all the sequences in a target proteome. However, predicting domain targets by motif sequence alone without considering other genomic and structural information has been shown to be lacking in accuracy.</p> <p>Results</p> <p>We developed an efficient search algorithm to scan the target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder. The integration is performed using naïve Bayes and a training set of validated experiments.</p> <p>Conclusions</p> <p>By integrating a variety of biologically relevant features to predict domain targets, we demonstrated a notably improved prediction of modular protein domain targets. Combined with emerging high-resolution data of domain specificities, we believe that our approach can assist in the reconstruction of many signaling pathways.</p

Leading-Order Actions of Goldstino Fields

This paper starts with a self-contained discussion of the so-called Akulov-Volkov action S_AV, which is traditionally taken to be the leading-order action of Goldstino field. Explicit expressions for S_AV and its chiral version S_AV^ch are presented. We then turn to the issue on how these actions are related to the leading-order action S_NL proposed in the newly proposed constrained superfield formalism. We show that S_NL may yield S_AV/S_AV^ch or a totally different action S_KS, depending on how the auxiliary field in the former is integrated out. However, S_KS and S_AV/S_AV^ch always yield the same S-matrix elements, as one would have expected from general considerations in quantum field theory.Comment: Minor changes, version to appear in European Physical Journal