Funded by the European Union

PhD Projects

The NanED project is devoted to the training of 15 PhD students in mastering  and developing innovative electron diffraction methods for crystal structure determination. Here their research projects are listed.

Research Theme 1

Electron nanocrystallography of heterometallic MOF

3D electron diffraction on heterometallic MOF synthesized by innovative mechanochemical methods. Solving the crystal structure of sub-micrometric beam sensitive crystal grains.

Objectives

Establish mechanochemical or solvothermal synthetic approaches that promote the formation of heterometallic systems. Establish a synergy between mechanochemistry and electron nanocrystallography. Design a protocol for crystallographic characterization of electron beam sensitive porous MOFs.

Expected results

Synthesis and structural characterization of new heterometallic MOFs. Optimal sample preparation and 3D ED data collection conditions for MOF. Direct observation on the Fourier map of guest molecules inside MOF channels.
  • Supervisor
    Dr. Mauro Gemmi
  • Hosting Institution
    • Istituto Italiano di Tecnologia, Pisa Italy
    • Enrolment in Doctoral degree: Università di Parma
  • Planned secondments
    • FZU: Dynamical refinement. Supervisor: P. Brázda.
    • UA: In-situ transmission electron microscopy Supervisor:  M. Batuk
    • Nanomegas: Commercial application of electron diffraction. Supervisor: S. Nicolopoulos
    • ThermoFisher: Direct experience on state of art TEM use.
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Research Theme 2

3D electron diffraction on organic nanocrystals

3D electron diffraction reveals the crystal structure of unexpected organic micro and nano crystals. How to fully characterize the standard yield of an organic chemical synthesis.

Objectives

Establish 3D ED data collection procedures suitable for very beam sensitive samples that guarantees quasi-kinematical ED intensities of structure solution quality. Test structure solution techniques on low quality and highly incomplete 3D ED data sets exploiting previous knowledge of the small molecules present in the crystal (simulated annealing). Develop merging strategies able to combine several partial 3D ED data sets from different crystals into one. Test dynamical refinement procedures on organic nanocrystals with the aim to distinguish between C, N and O and to determine the H positions.

Expected results

Define a procedure for data collection and analysis specific for organic beam sensitive nanocrystals able to deliver the crystal structure with accuracy comparable to x-ray diffraction. Structure solution of unknown organic structures
  • Supervisor
    Dr. Mauro Gemmi
  • Hosting Institution
    • Istituto Italiano di Tecnologia, Pisa Italy
    • Enrolment in Doctoral degree: Università di Parma
  • Planned secondments
    • SU: Cryo sample preparation Supervisor: H. Xu
    • UBA: cryo plunging sample preparation Supervisor:  E. van Genderen
    • Roche: 3D ED on polyphasic mixtures Supervisor: F. Stowasser
    • IUCr: syntax of Cif files Supervisor: B. McMahon
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Research Theme 3

In situ 3D electron diffraction for following reactions in gas and electrochemical environments

Making it possible to follow crystal structure changes during ongoing reactions

Objectives

Establish optimal collection procedures for in situ 3D ED data in gas and liquid electrochemical environments. Use the procedures to determine the intermediate structures during reactions of technologically relevant compounds, such as lithium battery cathode materials, perovskites for solid oxide fuel cells, thermochemical energy storage, chemical looping and CO2 capture

Expected results

A working methodology for future acquisition of in situ crystallographic data. Characterized structure evolution of relevant complex inorganic compounds during in situ reactions.
  • Supervisor
    Prof. Joke Hadermann
  • Hosting Institution
    Universiteit Antwerpen
  • Planned secondments
    • JGU: 3D ED on cement hydration Supervisor: U. Kolb.
    • CNRS: thin film preparation Supervisor:  A. David
    • DENS Solutions: Development of lab-on-a-chip optimized for 3D ED Supervisor: H. Perez
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Research Theme 4

Accurate structure refinement from 3D ED data

The limits of the possible accuracy of structure determination from 3D ED data will be explored, with particular emphasis on optimal incorporation of the treatment of the dynamical effects

Objectives

Test and optimize the dynamical refinement strategy for various types of materials and data collection methods. Generalize the dynamical refinement to include the effect of crystal imperfections, leading to the improvement of the fit to data from real crystal and to the accuracy of extracted structure models. Optimize the determination of absolute structure of non-centrosymmetric crystals, develop and verify the calculation of Flack parameter from 3D ED data.

Expected results

Software for the application of dynamical refinement to the most general range of experimental data. Computational method allowing to include and refine the effects of crystal imperfections in the calculation of diffraction intensities. A validated and reliable method of determination the absolute structure of non-centrosymmetric crystals, including the determination of Flack parameter for cases of potential inversion twinning.
  • Supervisor
    Dr. Lukas Palatinus
  • Hosting Institution
    • Institute of Physics of AS CR
    • Enrolment in Doctoral degree: Univerzita Karlova
  • Planned secondments
    • CNRS: 3D ED on thin films Supervisor: P. Boullay
    • UA: in situ 3D ED Supervisor: J. Hadermann
    • Elettra Sincrotrone Trieste: Synchrotron powder x-ray diffraction Supervisor: J. Plaisier
    • BASF: Electron diffraction on pharmaceutical Supervisor: P. Müller
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Research Theme 5

Charge density analysis from 3D ED data

Electron diffraction provides information about effects of bonding on the electrostatic potential. To extract this information, very accurate data collection and data processing work flows need to be developed.

Objectives

Optimize data collection and data reduction strategies necessary for obtaining data suitable for charge density studies, analyse the accuracy required to provide charge density refinement. Perform multipole refinements on a number of test samples from both organic and inorganic materials, compare the results with reference charge density studies from x-ray diffraction data. Apply the method to the analysis of interesting structures of organic and inorganic materials.

Expected results

A validated and optimized method for charge density studies from 3D ED data, which allows the study of bonding effects in all types of materials. Application of the method to real scientific problems, i.e. the characterization of interatomic interactions in specific compounds of scientific interest.
  • Supervisor
    Dr. Lukas Palatinus
  • Hosting Institution
    • Institute of Physics of AS CR
    • Enrolment in Doctoral degree: Univerzita Karlova
  • Planned secondments
    • IIT: Charge density study in organic materials Supervisor: M. Gemmi
    • Tescan: FIB sample preparation Supervisor: D. van der Wal
    • ULM: ePDF on disordered system Supervisor: T. Gorelik
    • IUCr: Syntax of CIF files Supervisor: B. McMahon
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Research Theme 6

Fine structure of 2D materials studied by 3D ED

Exploring the three-dimensional reciprocal space of a 2D crystal

Objectives

Developing the concepts of 3D ED for low-dimensional materials: optimizing data collection protocols from 2D crystals (step-wise scans, continuous rotation), experiments at different temperature; structure factor calculation for 2D crystals (including non-monoatomic layers, e.g. MoS2, Bi2Se3); development of models for out of plane atomic displacements in 2D crystals (layer corrugation) and calculation of their signature in 3D ED data; development of ED data collection procedures on 1D objects – fibrils, helical viruses; image / phase reconstruction algorithms for 1D objects.

Expected results

A complete methodology for structure characterization of 2D crystals by 3D ED. Structure reconstruction of 1D objects from 3D ED.
  • Supervisor
    Dr. Mauro Gemmi
  • Hosting Institution
    • Istituto Italiano di Tecnologia, Pisa - Italy
    • Enrolment in Doctoral degree: Università di Parma, Italy
  • Planned secondments
    • CNRS: 3D Ed on nanoparticles Supervisor: P. Boullay
    • UBA: Phasing from imaging Supervisor: JP. Abrahams
    • ASI: Single electron detectors Supervisor: J. Prangsma
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Research Theme 7

Quantitative analysis of ePDF

How to determine the structure of poorly crystalline material from its total electron scattering

Objectives

Optimizing the data collection protocol for ePDF: exposure series, camera length, diffraction pattern shift / mosaic data collection, energy filtering, effect of the acceleration voltage; robust algorithms for data denoising and background treatment; development of the models for the instrumental contribution into a PDF; partitioning of a PDF into the structural and instrumental contribution; refinement of ePDF; mathematical concepts for PDF for textured samples, PDF on 2D crystals and 2D amorphous materials, PDF on polycrystalline assembly of nanoparticles; mapping of nano crystalline / poorly crystalline / amorphous materials for heterogeneous mixed systems or samples with heterogeneous degree of crystallinity.

Expected results

A standard cross-TEM data collection and processing routine for ePDF; PDF methodology for textured amorphous / poorly crystalline materials; data collection protocols and processing routines for lateral mapping of heterogeneous amorphous materials.
  • Supervisor

    Dr. Cheuk-Wai Tai

  • Hosting Institution
    • Stockholm Universitet
  • Planned secondments
    • IIT: Fast 3D ED data collection
      Supervisor:       M. Gemmi
    • Eldico: Electron diffractometer design process
      Supervisor: G. Steinfeld
    • Rigaku: Testing an electron diffractometer on nanocrystals
      Supervisor: M. Benson
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Research Theme 8

Structural investigation of cement hydration mechanism by electron crystallography

Mapping cement chemistry at the nanoscale. Phase determination of the nanocrystals at every stage of cement hydration

Objectives

Set-up sample preparation strategies for hydrated samples. Establish data acquisition routines for the collection of 3D electron diffraction data optimized for diffuse scattering. Develop routines for combining simulation of diffuse scattering with quantitative analysis of diffuse streaks. Test the influence of different detectors, data acquisition routines and sample preparation strategies onto data quality and simulation analysis. Find solution strategies for problematic data sets.

Expected results

Development of an optimized sample preparation strategy for vacuum and beam sensitive material. Set-up of a structure solution strategy applicable to other material classes.
  • Supervisor
    Dr. Ute Kolb
  • Hosting Institution
    • Johannes Gutenberg Universitat Mainz
  • Planned secondments
    • UBA: Cryoplunging sample preparation Supervisor: E. van Genderen
    • UA: in-situ 3D Ed on cement Supervisor: J. Hadermann
    • BASF: TEM for characterizing solid state synthesis Supervisor: P. Müller
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Research Theme 9

Electron crystallographic applications for defect structures of nano crystals

What can we guess from the 3D reciprocal space reconstruction of a defective crystal?

Objectives

Establish crystal tracking routines for the collection of 3D electron diffraction data optimized for nano particles; develop routines for combining simulation of diffuse scattering with quantitative analysis of 3D diffuse scattering; determine the influence of inelastic scattering and beam damage onto the quantitative analysis of defects; test the use of in-situ sample holders.

Expected results

Development of an optimized tracking routine for particles of a few tens of nanometer. A structure solution strategy applicable to defects of different dimensionality.
  • Supervisor
    Dr. Ute Kolb
  • Hosting Institution
    • Johannes Gutenberg Universitat Mainz
  • Planned secondments
    • FZU: dynamical refinement on defective structure Supervisor: L. Palatinus
    • Eldico: Electron diffractometer design Supervisor: G. Steinfeld
    • CNRS: 3D ED to nanoparticles application Supervisor: P. Boullay
    • IUCr: syntax of cif files Supervisor: B. McMahon
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Research Theme 10

Development and application of electron crystallography methods for studying protein-ligand interactions

We will develop electron diffraction based methods for studying protein-ligand interactions in order to achieve structure-based drug discovery.

Objectives

Conduct a proof of principle study on resolving protein-ligand interactions by using 3D electron diffraction based methods. Develop protocols on sample handling, cryo-EM specimen preparation, data collection and processing, and structure refinement for studying protein-ligand interactions. Develop new software and hardware to improve throughput and reliability of 3D electron crystallography methods in order to realize fragment-based lead screening.

Expected results

Resolving a test case showing that 3D electron diffraction can be used for studying protein-ligand interactions. Solve a number of protein structures bond with different ligands. A dedicated specimen preparation method for handling protein crystals. The ability to perform fragment-based lead discovery.
  • Supervisor
    Dr. Hongji Xu
  • Hosting Institution
    • Stockholms Universitet
  • Planned secondments
    • UBA: 3D ED ab-initio phasing on proteins Supervisor: JP. Abrahams
    • FZU: Dynamical refinement on organics Supervisor:  P. Brázda
    • Astrazeneca: Protein ligand interaction Supervisor: H. Käck
    • eBIC: Single particle cryoEM Supervisor: P. Zhang
    • Thermo Fisher: State of art of cryo TEM
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Research Theme 11

Development of serial (rotation) electron diffraction and its application on MOFs and pharmaceutics

Serial (rotation) electron diffraction will enable automated high-throughput phase analysis and structure determination of beam sensitive samples. It will be applied for structural characterization of pharmaceutical compounds/polymorphs.

Objectives

Establish strategies and develop software for automation of serial (rotation) electron diffraction (SerialED/RED) data collection by combination of electron beam scanning and crystal tracking. Establish high-throughput protocols for data reduction and indexing that are optimised for electron diffraction data. Establish machine learning and clustering algorithms for phase analysis and structure determination. Develop new “crystalline sponges” based on metal-organic frameworks (MOFs) for structure analysis of molecules with nano-/pico gram quantity. Establish protocols for determination of phase analysis and structure determination of pharmaceutical compounds.

Expected results

SerialED/RED software for automation of SerialED/RED data collection will be developed and machine learning will be used for automation. Standard protocols for high-throughput phase analysis and structure determination will be established. Hierarchical clustering will be applied. New MOF crystalline sponges will be developed and applied for structure determination of organic molecules in nano-/pico gram quantity. Structures of several new pharmaceutical compounds/polymorphs will be developed.
  • Supervisor
    Dr. Xiaodong Zou
  • Hosting Institution
    • Stockholms Universitet
  • Planned secondments
    • IIT: Precession assisted 3D ED on organics Supervisor: E. Mugnaioli
    • JGU: 3D ED on defective materials Supervisor:  U. Kolb
    • STFC: 3D ED data reduction software Supervisor: D. Waterman
    • Astrazeneca: Role of solid-state chemistry in pharmaceutical development Supervisor: S. Norberg
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Research Theme 12

Electron crystallography of nanodomains in functional materials

Combining EM techniques to analyze the needle in the haystack.

Objectives

Preparation of ceramics with submicronic grains using micro-wave and SPS sintering. Development of a dedicated protocol for sample preparation to investigate submicronic grains in dense ceramics. Preparation of thin films and heterostuctures of transition metals oxides using pulsed laser deposition. Development of a dedicated protocol for sample preparation based on FIB technology to optimize 3D ED data collection on thin films. Determine the minimal beam size at which it is possible to collect 3D ED data suitable for the structure analysis of nanodomains. Compare structure obtained from 3D ED with atomic-scale structures obtained from electron microscopy images (HRTEM and/or STEM-HAADF).

Expected results

Standard protocols for the analysis of nanodomains and 2D materials by 3D ED, application of the developed protocols for the structure determination of low dimensional materials and ceramics of fundamental and industrial interest.
  • Supervisor
    Dr. Philippe Boullay
  • Hosting Institution
    • Centre National de la Recherche Scientifique - Laboratoire de Cristallographie et Science des Matériaux
    • Enrolment in Doctoral degree: Normandie Université
  • Planned secondments
    • FZU: Dynamical refinement. Supervisor: L. Palatinus
    • JGU: 3D ED on defective materials Supervisor: U. Kolb
    • TSC: FIB sample preparation Supervisor: D. van der Wal
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Research Theme 13

Electron crystallography of nanoparticles

Between particles and atoms: exploring the size limit of crystals

Objectives

Determine the minimal beam and crystal size at which it is possible to collect 3D ED data suitable for structure solutions and refinements. Develop a specific experimental set up for 3D ED data collection with parallel nanobeams. Compare the structure obtained from Rietveld refinement on powder x-ray data with dynamical refined structure from 3D ED data. From electron powder diffraction (ring patterns) of nanoparticles aggregates to 2D ePDF.

Expected results

Standard protocols for 3D ED analysis of nanoparticles. Standard protocols for ring patterns and ePDF data collection and analysis. Application of the developed protocols for the structure determination of nanoparticles of fundamental and industrial interest (thermoelectric, zeolites, energy materials).
  • Supervisor
    Dr. Philippe Boullay
  • Hosting Institution
    • Centre National de la Recherche Scientifique – Laboratoire de Cristallographie et Science des Matériaux
    • Enrolment in Doctoral degree: Normandie Université
  • Planned secondments
    • UA: In situ 3D ED and imaging Supervisor: J. Hadermann
    • ULM: TEM imaging on 2D materials Supervisor: U. Kaiser
    • Eettra Sincrotrone Trieste: Synchrotron powder x-ray diffraction Supervisor: J. Plaisier
    • Codex: marketing and commercial skills in an R&D lab Supervisor: S. Séguier
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Research Theme 14

Phasing of electron diffraction data

Combining cryo-EM and electron diffraction to see biological molecules in atomic detail

Objectives

Implement data collection strategies that allow experimental phasing of electron diffraction data by scanning crystals with a nano-beam (ptychography) and by measuring rotating crystals in imaging mode. Develop algorithms and software to exploit the unique information provided by these modes of data collection for determining phase probabilities of nano-crystal electron diffraction data. Specific problems in nanobeam diffraction: determine/refine beam location parameters; dealing with tilted crystals of limited thickness, resulting in moiré patterns. Specific problems in real space tomography: refining the shift parameters of image data obtained at different tilt angles; dealing with the focal gradient that will cause apparent phases differences between the top and bottom of the crystal. Extend the nano-beam diffraction method to non-crystalline samples of macromolecules.

Expected results

Protocols for data collection that allow retrieving phase information. Software for phasing nano-crystal data. Report on feasibility of phasing single molecule diffraction data.
  • Supervisor
    Prof. Jan Pieter Abrahams
  • Hosting Institution
    • Universitat Basel
  • Planned secondments
    • SU: TEM sample preparation for protein crystals Supervisor: H. Xu
    • ULM: Low voltage TEM imaging Supervisor:  U. Kaiser
    • ASI: Hybrid pixel detectors Supervisor: Prangsma
    • eBIC: TEM single molecule imaging Supervisor: P. Zhang
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Research Theme 15

Optimal data acquisition of biological samples

Boosting data quality of electron diffraction through novel technologies

Objectives

We will identify optimal data acquisition parameters for two types of data collection, specific for biological samples: rotation and nanobeam ED (optimization of serial ED is a task of ESR11). For both methods, we will consider the effects of the following beam parameters: di-/convergence angle, beam size, electron flux, illumination time. We will identify optimal detectors for combinations of beam parameters in rotation and nanobeam mode, comparing Eiger (Dectris/PSI), Jungfrau (PSI), Medipix3 and Timepix3 (both CERN/ASI). Where possible and appropriate, we will combine these tests with a range of relevant settings of a CEOS energy filter, in order to explore the effect of removal of inelastic scattering. Since there is theoretical proof that removal of inelastic scattering can increase the dynamic component of protein diffraction data, we will also include the effect of crystal thickness in this comparison.

Expected results

Protocols for optimal rotation data collection of biological samples. Protocols for optimal nanobeam data collection of biological samples.
  • Supervisor
    Prof. Jan Pieter Abrahams
  • Hosting Institution
    • Universitat Basel
  • Planned secondments
    • IIT: 3D ED data acquisition protocols on beam sensitive samples Supervisor: M. Gemmi
    • SU: Serial ED Supervisor:  X. Zou
    • STFC: 3D ED data reduction software Supervisor: D. Waterman
    • Roche: polymorphism in pharmaceuticals Supervisor: F. Stowasser
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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 956099.

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