Incoherent Noise and Quantum Information Processing

Incoherence in the controlled Hamiltonian is an important limitation on the precision of coherent control in quantum information processing. Incoherence can typically be modelled as a distribution of unitary processes arising from slowly varying experimental parameters. We show how it introduces artifacts in quantum process tomography and we explain how the resulting estimate of the superoperator may not be completely positive. We then go on to attack the inverse problem of extracting an effective distribution of unitaries that characterizes the incoherence via a perturbation theory analysis of the superoperator eigenvalue spectra.Comment: 15 pages, 5 figures, replaced with future JCP published versio

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling

Motivation: Recent advances in cell-free protein expression systems allow specific labeling of proteins with amino acids containing stable isotopes (¹⁵N, ¹³C and ²H), an important feature for protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. Given this labeling ability, we present a mathematical optimization framework for designing a set of protein isotopomers, or labeling schedules, to reduce the congestion in the NMR spectra. The labeling schedules, which are derived by the optimization of a cost function, are tailored to a specific protein and NMR experiment. Results: For 2D ¹⁵N-¹H HSQC experiments, we can produce an exact solution using a dynamic programming algorithm in under 2 h on a standard desktop machine. Applying the method to a standard benchmark protein, calmodulin, we are able to reduce the number of overlaps in the 500 MHZ HSQC spectrum from 10 to 1 using four samples with a true cost function, and 10 to 4 if the cost function is derived from statistical estimates. On a set of 448 curated proteins from the BMRB database, we are able to reduce the relative percent congestion by 84.9% in their HSQC spectra using only four samples. Our method can be applied in a high-throughput manner on a proteomic scale using the server we developed. On a 100-node cluster, optimal schedules can be computed for every protein coded for in the human genome in less than a month. Availability: A server for creating labeling schedules for ¹⁵N-¹H HSQC experiments as well as results for each of the individual 448 proteins used in the test set is available at http://nmr.proteomics.ics.uci.edu

The use of indigenous knowledge in development: problems and challenges

The use of indigenous knowledge has been seen by many as an alternative way of promoting development in poor rural communities in many parts of the world. By reviewing much of the recent work on indigenous knowledge, the paper suggests that a number of problems and tensions has resulted in indigenous knowledge not being as useful as hoped for or supposed. These include problems emanating from a focus on the (arte)factual; binary tensions between western science and indigenous knowledge systems; the problem of differentiation and power relations; the romanticization of indigenous knowledge; and the all too frequent decontextualization of indigenous knowledge

Comparison of dynamical decoupling protocols for a nitrogen-vacancy center in diamond

We perform a detailed theoretical-experimental study of the dynamical decoupling (DD) of the nitrogen-vacancy (NV) center in diamond. We investigate the DD sequences applied to suppress the dephasing of the electron spin of the NV center induced by the coupling to a spin bath composed of the substitutional nitrogen atoms. The decoupling efficiency of various DD schemes is studied, including both periodic and periodic pulse sequences. For ideal control pulses, we find that the DD protocols with the Carr-Purcell-Meiboom-Gill (CPMG) timing of the pulses provides best performance. We show that, as the number of control pulses increases, the decoupling fidelity scaling differs qualitatively from the predictions of the Magnus expansion, and explain the origin of this difference. In particular, more advanced symmetrized or concatenated protocols do not improve the DD performance. Next, we investigate the impact of the systematic instrumental pulse errors in different periodic and aperiodic pulse sequences. The DD protocols with the single-axis control do not preserve all spin components in the presence of the pulse errors, and the two-axis control is needed. We demonstrate that the two-axis control sequence with the CPMG timing is very robust with respect to the pulse errors. The impact of the pulse errors can be diminished further by symmetrizing this protocol. For all protocols studied here, we present a detailed account of the pulse error parameters which make strongest impact on the DD performance. In conclusion, we give specific recommendations about choosing the decoupling protocol for the system under investigation.Comment: 16 pages, 11 figure

Bang-Bang control of a qubit coupled to a quantum critical spin bath

We analytically and numerically study the effects of pulsed control on the decoherence of a qubit coupled to a quantum spin bath. When the environment is critical, decoherence is faster and we show that the control is relatively more effective. Two coupling models are investigated, namely a qubit coupled to a bath via a single link and a spin star model, yielding results that are similar and consistent.Comment: 10 pages, 4 figures, replaced with published versio

Towards a digital policing in developing nations : the Nigerian context

Technology-assisted living is a growing trend in most developing nations, particularly for young-aged demographic countries, as it presents a platform for personal development and knowledge management. However, this societyscaping trend has also introduced the myriad opportunity for the formation of complex crime, which is often beyond the (immediate) capability of the policing entity in developing nations. To address this lingering and futuristic problem, particularly in Nigeria, this study developed a context-based digital policing framework for the enhancement of the Nigerian Police. This Nigerian-context framework presents the viability and relevance of the digital policing mechanism in addressing challenges ravaging society. Furthermore, it also presents a modality for improving and enhancing the policing apparatus of the Nigerian society, as a model for other developing nations. The knowledge from the Nigerian-context of digital policing has both research and societal implications. In terms of research, it opens the community of security researchers into the contextual characteristics of digital policing as well as the probable research direction required to implement digital policing in developing nations. With respect to society, knowledge provides a substratum for the integration of the community-policing model.https://www.ijitee.orgpm2020Computer Scienc

Targeting Melanoma Metastasis and Immunosuppression with a New Mode of Melanoma Inhibitory Activity (MIA) Protein Inhibition

Melanoma is the most aggressive form of skin cancer, with fast progression and early dissemination mediated by the melanoma inhibitory activity (MIA) protein. Here, we discovered that dimerization of MIA is required for functional activity through mutagenesis of MIA which showed the correlation between dimerization and functional activity. We subsequently identified the dodecapeptide AR71, which prevents MIA dimerization and thereby acts as a MIA inhibitor. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy demonstrated the binding of AR71 to the MIA dimerization domain, in agreement with in vitro and in vivo data revealing reduced cell migration, reduced formation of metastases and increased immune response after AR71 treatment. We believe AR71 is a lead structure for MIA inhibitors. More generally, inhibiting MIA dimerization is a novel therapeutic concept in melanoma therapy

High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences

Probing Microsecond Time Scale Dynamics in Proteins by Methyl 1H Carr−Purcell−Meiboom−Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrCr

To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ H-1 Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [H-1, C-13]-D-glucose in similar to 100% D2O, which yields CHD2 methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using C-13 TOCSY NMR spectroscopy, as was recently demonstrated (Often, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure H-1 CPMG relaxation dispersion profiles for CHD2 methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-delta 1 and Thr-gamma 2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong C-13 scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone N-15 CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the H-1 line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 +/- 0.5) x 10(3) per second (i.e., tau(ex) = 64.7 +/- 1.9 mu s). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by H-1 CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone N-15 relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins