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Towards 3D characterisation of site-controlled InGaAs pyramidal QDs at the nanoscale.

ABSTRACT: In this work, we report an extensive investigation via transmission electron microscopy (TEM) techniques of InGaAs/GaAs pyramidal quantum dots (PQDs), a unique site-controlled family of quantum emitters that have proven to be excellent sources of single and entangled photons. The most striking features of this system, originating from their peculiar fabrication process, include their inherently 3-dimensional nature and their interconnection to a series of nanostructures that are formed alongside them, such as quantum wells and quantum wires. We present structural and chemical data from cross-sectional and plan view samples of both single and stacked PQDs structures. Our findings identify (i) the shape of the dot, being hexagonal and not triangular as previously assumed, (ii) the chemical distribution at the facets and QD area, displaying clear Indium diffusion, and (iii) a near absence of Aluminium (from the AlAs marker) at the bottom of the growth profile. Our results shed light on previously unreported structural and chemical features of PQDs, which is of extreme relevance for further development of this family of quantum emitters.

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Supplementary information

The online version contains supplementary material available at 10.1007/s10853-022-07654-2.

SUBMITTER: Holsgrove KM

PROVIDER: S-EPMC9463298 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Towards 3D characterisation of site-controlled InGaAs pyramidal QDs at the nanoscale.

Holsgrove Kristina M KM O'Reilly Tamsin I TI Varo Simone S Gocalinska Agnieszka A Juska Gediminas G Kepaptsoglou Demie M DM Pelucchi Emanuele E Arredondo Miryam M

Journal of materials science 20220830 34

In this work, we report an extensive investigation via transmission electron microscopy (TEM) techniques of InGaAs/GaAs pyramidal quantum dots (PQDs), a unique site-controlled family of quantum emitters that have proven to be excellent sources of single and entangled photons. The most striking features of this system, originating from their peculiar fabrication process, include their inherently 3-dimensional nature and their interconnection to a series of nanostructures that are formed alongside ...[more]

PMID: 36101839

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Project description:BACKGROUND: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. RESULTS: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. CONCLUSION: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structure-based P-site prediction method has been made available at (http://phos3d.mpimp-golm.mpg.de).

Dataset Information

Towards 3D characterisation of site-controlled InGaAs pyramidal QDs at the nanoscale.

Graphical abstract

Supplementary information

Publications

Towards 3D characterisation of site-controlled InGaAs pyramidal QDs at the nanoscale.

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