Publications by authors named "Emilie Bourgeois"

10 Publications

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Room-temperature control and electrical readout of individual nitrogen-vacancy nuclear spins.

Nat Commun 2021 Jul 20;12(1):4421. Epub 2021 Jul 20.

Institute for Materials Research (IMO), Hasselt University, Diepenbeek, Belgium.

Nuclear spins in semiconductors are leading candidates for future quantum technologies, including quantum computation, communication, and sensing. Nuclear spins in diamond are particularly attractive due to their long coherence time. With the nitrogen-vacancy (NV) centre, such nuclear qubits benefit from an auxiliary electronic qubit, which, at cryogenic temperatures, enables probabilistic entanglement mediated optically by photonic links. Here, we demonstrate a concept of a microelectronic quantum device at ambient conditions using diamond as wide bandgap semiconductor. The basic quantum processor unit - a single N nuclear spin coupled to the NV electron - is read photoelectrically and thus operates in a manner compatible with nanoscale electronics. The underlying theory provides the key ingredients for photoelectric quantum gate operations and readout of nuclear qubit registers. This demonstration is, therefore, a step towards diamond quantum devices with a readout area limited by inter-electrode distance rather than by the diffraction limit. Such scalability could enable the development of electronic quantum processors based on the dipolar interaction of spin-qubits placed at nanoscopic proximity.
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http://dx.doi.org/10.1038/s41467-021-24494-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292375PMC
July 2021

Relative Weight of Organic Waste Origin on Compost and Digestate 16S rRNA Gene Bacterial Profilings and Related Functional Inferences.

Front Microbiol 2021 14;12:667043. Epub 2021 May 14.

Univ Lyon, UMR Ecologie Microbienne (LEM), Université Claude Bernard Lyon 1, CNRS 5557, INRAE 1418, VetAgro Sup, Marcy L'Etoile, France.

Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products' bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated sludge supported a role in AD. Raw OW content in activated sludge was found to be a critical factor for predicting digestate bacterial contents. Composting generated highly predictable and specialized community patterns whatever the OW origin. AD and composting bacterial changes were driven by functional traits selected by physicochemical factors such as temperature and chemical pollutants.
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http://dx.doi.org/10.3389/fmicb.2021.667043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8160089PMC
May 2021

A Label-Free Diamond Microfluidic DNA Sensor Based on Active Nitrogen-Vacancy Center Charge State Control.

ACS Appl Mater Interfaces 2021 Apr 13;13(16):18500-18510. Epub 2021 Apr 13.

Department of Biomedical Technology, Faculty of Biomedical Engineering, Czech Technical University in Prague, Sítna sq. 3105, 27201 Kladno, Czech Republic.

We propose a label-free biosensor concept based on the charge state manipulation of nitrogen-vacancy (NV) quantum color centers in diamond, combined with an electrochemical microfluidic flow cell sensor, constructed on boron-doped diamond. This device can be set at a defined electrochemical potential, locking onto the particular chemical reaction, whilst the NV center provides the sensing function. The NV charge state occupation is initially prepared by applying a bias voltage on a gate electrode and then subsequently altered by exposure to detected charged molecules. We demonstrate the functionality of the device by performing label-free optical detection of DNA molecules. In this experiment, a monolayer of strongly cationic charged polymer polyethylenimine is used to shift the charge state of near surface NV centers from negatively charged NV to neutral NV or dark positively charged NV. Immobilization of negatively charged DNA molecules on the surface of the sensor restores the NV centers charge state back to the negatively charged NV, which is detected using confocal photoluminescence microscopy. Biochemical reactions in the microfluidic channel are characterized by electrochemical impedance spectroscopy. The use of the developed electrochemical device can also be extended to nuclear magnetic resonance spin sensing.
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http://dx.doi.org/10.1021/acsami.1c01118DOI Listing
April 2021

Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach.

Sci Total Environ 2021 May 26;767:145425. Epub 2021 Jan 26.

Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France. Electronic address:

The bTPMT (bacterial thiopurine S-methyltransferase), encoded by the tpm gene, can detoxify metalloid-containing oxyanions and xenobiotics. The hypothesis of significant relationships between tpm distribution patterns and chemical pollutants found in urban deposits was investigated. The tpm gene was found conserved among eight bacterial phyla with no sign of horizontal gene transfers but a predominance among gammaproteobacteria. A DNA metabarcoding approach was designed for tracking tpm-harboring bacteria among polluted urban deposits and sediments recovered for more than six years in a detention basin (DB). This DB recovers runoff waters and sediments from a zone of high commercial activities. The PCR products from DB samples led to more than 540,000 tpm reads after DADA2 or MOTHUR bio-informatic manipulations that were allocated to more than 88 and less than 634 sequence variants per sample. The tpm community patterns were significantly different between the recent urban deposits and those that had accumulated for more than 2 years in the DB, and between those of the DB surface and the DB settling pit. These groups of samples had distinct mixture of priority pollutants. Significant relationships between tpm ordination patterns, sediment accumulation time periods and location, and concentrations in PAH, chlorpyrifos, and 4-nonylphenols (NP) were observed. These correlations matched the higher occurrences of, among others, Aeromonas, Pseudomonas, and Xanthomonas tpm-harboring bacteria in recent urban DB deposits more contaminated with chrysene and alkylphenol ethoxylates. Highly significant drops in tpm reads allocated to Aeromonas species were recorded in the oldest DB sediments accumulating naphthalene and metallic pollutants. Degraders of urban pollutants such as P. aeruginosa and P. putida showed conserved distribution patterns over time but P. syringae phytopathogens were more abundant in the oldest sediments. TPMT-harboring bacteria can be used to assess the incidence of high risk priority pollutants on environmental systems.
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http://dx.doi.org/10.1016/j.scitotenv.2021.145425DOI Listing
May 2021

Photoelectrical imaging and coherent spin-state readout of single nitrogen-vacancy centers in diamond.

Science 2019 02;363(6428):728-731

Institute for Quantum Optics and IQST, Ulm University, Albert-Einstein-Allee 11, D-89081 Ulm, Germany.

Nitrogen-vacancy (NV) centers in diamond have become an important instrument for quantum sensing and quantum information science. However, the readout of NV spin state requires bulky optical setups, limiting fabrication of miniaturized compact devices for practical use. Here we realized photoelectrical detection of magnetic resonance as well as Rabi oscillations on a single-defect level. Furthermore, photoelectrical imaging of individual NV centers at room temperature was demonstrated, surpassing conventional optical readout methods by providing high imaging contrast and signal-to-noise ratio. These results pave the way toward fully integrated quantum diamond devices.
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http://dx.doi.org/10.1126/science.aav2789DOI Listing
February 2019

On the Possibility of Miniature Diamond-Based Magnetometers Using Waveguide Geometries.

Micromachines (Basel) 2018 Jun 1;9(6). Epub 2018 Jun 1.

Institut für Physik, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany.

We propose the use of a diamond waveguide structure to enhance the sensitivity of magnetometers relying on the detection of the spin state of nitrogen-vacancy ensembles in diamond by infrared optical absorption. An optical waveguide structure allows for enhanced optical path-lengths avoiding the use of optical cavities and complicated setups. The presented design for diamond-based magnetometers enables miniaturization while maintaining high sensitivity and forms the basis for magnetic field sensors applicable in biomedical, industrial and space-related applications.
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http://dx.doi.org/10.3390/mi9060276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187276PMC
June 2018

Incidence of hydrological, chemical, and physical constraints on bacterial pathogens, Nocardia cells, and fecal indicator bacteria trapped in an urban stormwater detention basin in Chassieu, France.

Environ Sci Pollut Res Int 2018 Sep 21;25(25):24860-24881. Epub 2018 Jun 21.

Université de Lyon, Lyon, France.

The nature and fate of urban contaminants washed by stormwater events and accumulating in a detention basin (DB) were investigated. Relations between bacterial and chemical contaminants of trapped urban sediments, and field parameters were analyzed. Fecal indicators and some pathogens known to be environmentally transmitted (Nocardia, Pseudomonas aeruginosa, and Aeromonas caviae) were tracked, and their persistence investigated. Six sampling campaigns were carried out over 3 years, using five sites including a settling chamber (SC). Aerosolized bacteria at these sites were also monitored. Deposits in the basin were made of fine particles and their content in chemical pollutants was found highly variable. High polycyclic aromatic hydrocarbon (PAH) contents were measured but only three pesticides, over 22, were detected. Deposits were significantly contaminated by fecal indicator bacteria (FIB), P. aeruginosa, A. caviae, and by Nocardia. Only A. caviae showed significant numbers in aerosolized particles recovered over the detention basin. Nocardia spp. cells heavily contaminated the SC. The efficacy of the detention basin at reducing bacterial counts per rain event and over time were estimated. A slight drop in the counts was monitored for fecal indicators but not for the other bacterial groups. Hydrodynamic parameters had a strong impact on the distribution and features of the deposits. Multiple factors impacted the fate of FIB, P. aeruginosa, A. caviae, and Nocardia cells, but in a group dependent manner. Nocardia counts were found positively correlated with volatile organic matter. FIB appeared highly efficient colonizers of the DB.
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http://dx.doi.org/10.1007/s11356-018-1994-2DOI Listing
September 2018

Refractive indices of layers and optical simulations of Cu(In,Ga)Se solar cells.

Sci Technol Adv Mater 2018 15;19(1):396-410. Epub 2018 May 15.

Laboratory for Thin films and Photovoltaics, Empa - Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland.

Cu(In,Ga)Se based solar cells have reached efficiencies close to 23%. Further knowledge-driven improvements require accurate determination of the material properties. Here, we present refractive indices for all layers in Cu(In,Ga)Se solar cells with high efficiency. The optical bandgap of Cu(In,Ga)Se does not depend on the Cu content in the explored composition range, while the absorption coefficient value is primarily determined by the Cu content. An expression for the absorption spectrum is proposed, with Ga and Cu compositions as parameters. This set of parameters allows accurate device simulations to understand remaining absorption and carrier collection losses and develop strategies to improve performances.
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http://dx.doi.org/10.1080/14686996.2018.1458579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954485PMC
May 2018

Molecular orientation of lead phthalocyanine on (100) oriented single crystal diamond surfaces.

Phys Chem Chem Phys 2015 Apr;17(15):9619-23

Institute for Materials Research (IMO), Hasselt University, Wetenschapspark 1, B-3590 Diepenbeek, Belgium.

Lead phthalocyanine (PbPc) thin films of 5 and 50 nm have been deposited on hydrogen and oxygen terminated single crystal diamond (SCD) using organic molecular beam deposition. Atomic force microscopy and X-ray diffraction (XRD) studies showed that PbPc grown on the hydrogen terminated SCD forms layers with a high degree of crystallinity, dominated by the monoclinic (320) orientation parallel to the diamond surface. The oxygen terminated diamond led to a randomly oriented PbPc film. Absorption and photocurrent measurements indicated the presence of both polymorphs of PbPc, however, the ratio differed depending on the termination of the SCD. Finally, polarized Raman spectroscopy was used to determine the orientation of the molecules of the thin film. The results confirmed the random orientation on the O-terminated diamond. On SCD:H, the PbPc molecules are lying down in accordance with the XRD results.
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http://dx.doi.org/10.1039/c5cp00174aDOI Listing
April 2015

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition.

Microb Biotechnol 2015 Jan 4;8(1):131-42. Epub 2014 Sep 4.

INRA, UMR1347 Agroécologie, Plateforme GenoSol, Dijon, France.

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.
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http://dx.doi.org/10.1111/1751-7915.12162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321379PMC
January 2015
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