R&D Program at Quantum Wave Electron Microscopy Unit
T. Shintake, OIST 2011.10.11

We are going to develop“New Atomic Resolution Electron Microscope”.
For biological sample: DNA, Ion-channel, surface
structure of cells, and Membrane protein
crytallorappy..
For material research: Li-ion battery, catalysis, ..

2011 at OISTLaboratory
ReviewJanuary 19, 2010

1

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

OIST International Graduate University

Life Sciences, the Physical Sciences, and Mathematics.
To lay the foundation for the Graduate University, 44 Research Units.
220 Researchers.
2011 at OISTLaboratory
ReviewJanuary 19, 20102Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

X-ray FEL v.s. Electron Microscope
X-ray FEL (SACLA at SPring-8,or LCLS at Stanford)

Electron Microscope (SEM orTEM)

Very large scale machine

Small scale machine(1 ~ 3 m high, 1 ~ 10 M$)( > 1 km, 400 M$ cost)

Short pulse (<100 femt-sec),
intense X-ray flux (1010
photons /shot) illumination onsample.

Very weak electron beam.
Image accumulation before
sample is damaged (10 sec)

Image taking before sample isexploded.

We need to care about vibration.

Flying sample ( virus, nanocrystal)

Electron to sample interaction is
not clean event, there are many
“multiple collisions” and “nonelastic collisions”

We do not need to care aboutvibration.
X-ray photon and electron
collision is based on “cleanevent”, single scattering.
2011 at OISTLaboratory
ReviewJanuary 19, 2010

 energy filtering is important.
3

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

We want to see 3D DNA image
2 nm
computer model of DNA
Gif animation image
copied from Wikipedia

2011 at OISTLaboratory
ReviewJanuary 19, 2010

4

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Electron microscope image
Of DNA.
Double helix can not be seen.

2011 at OISTLaboratory
ReviewJanuary 19, 2010

5

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

2011 at OISTLaboratory
ReviewJanuary 19, 2010

6

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

SEM with Atomic Resolution
TEM
Transmission Electron Microscope

SEM
Scanning Electron Microscope
Gun

Gun

SEM++
~1Å
Surface View
Low Sample Damage

Beam Scan
Specimen

Specimen
Objective Lens

Copied from Wikipedia

S-TEM~ 10 Å
surface view

Screen& Camera
Copied from Wikipedia~ 0.1 Å for non biological sample
with CS correction.
~ 5 Å for biological sample

Sample Damage

2011 at OISTLaboratory
ReviewJanuary 19, 2010

7Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Bio-imaging with conventional TEM
In order to reduce multiple scattering, sample has been
made thinner and thinner, and also electron beamenergy has been raised to 300 kV, 1 MeV, even higher.
de’Broglie wavelength is about 0.01 Å.
Resolution of TEM was limited by spherical aberrationin objective lens. (CS correction technique improved
resolution, energy filtering improved contrast)

Contrast is low for biological sample  use staining
technique (uranium, gold)  artifact problem
Sevier same damage  cryo-sample  artifactproblem
2011 at OISTLaboratory
ReviewJanuary 19, 2010

8Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Let’s think to go lower beam energy.
Low energy electron does not go through sample.
It is OK if we can observe the surface structure likeSEM.
Sample damage becomes lower  we do not need tocool down or free the sample  raw bio-sample can beobserved (we may use fully hydrated sample)  lessartifacts.

We have to take “reflection signal” from the surface,
thus the object lens can not be placed (no physicalroom), TEM optics can not be applied.
“Remove Objective Lens”  lens less microscopy
2011 at OISTLaboratory
ReviewJanuary 19, 2010

9

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Remove lens2011 at OISTLaboratory
ReviewJanuary 19, 201010

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Holography

2011 at OISTLaboratory
ReviewJanuary 19, 201011

Tsumoru Shintakeshintake@spring8.or.jp
shintake@oist.jp

Diffraction Imaging in X-FELs
Pattern made by FIB on SiN4 membrane.
Illuminated by FEL beam at FLASH.
25 fs, 4 x1013 W/cm-2 pulse,Chapman, Barty and Bogan 2006
12
containing 10 photons
at 32 nm wavelength
Phase retrieved image as D.

scale-bar 1 micron2011 at OISTLaboratory
ReviewJanuary 19, 2010

12

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

鳥の羽、干渉実験

2011 at OISTLaboratory
ReviewJanuary 19, 201013

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

2011 at OISTLaboratory
ReviewJanuary 19, 201014

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Heavy atom (Au) diffracts large number of photons.

Shintake, T. 2008. Possibility of single biomolecular imaging withcoherent amplification of weak scattering X-ray photons.
Physical Review E 78: 041906
2011 at OISTLaboratory
ReviewJanuary 19, 201015

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Diffraction Electron Interference

2011 at OISTLaboratory
ReviewJanuary 19, 201016

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

To reduce sample damage  lower electron energy
For atomic resolution microscopy, a prove wave has to be 1Å orshorter wavelength.

X-ray of １Å has 12 keV quantum energy (energy transfer isquantized at 12 keV)Electron of 1Å de’Broglie wave has only 150 eV kinetic
energy.

Energy deposition of 150 eV single electron absorption is 80
times smaller than 12 keV single photon absorption.
150 eV is 2000 times lower than 300 keV TEM.

2011 at OISTLaboratory
ReviewJanuary 19, 201017

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Low energy electron reduces sample damage.
LEEP: Low Energy Electron Point Source Microscope

DNA molecule was exposed oncoherent low energyelectrons.
10 eV~ 300 eV, 200 nA
DNA survived for a hour.
106 electrons/A2
at 260 eV damage started.
Matthias Germann, et al.
"Non-destructive Imaging of Individual
Bio-Molecules“, Nature 2009
＠Institute of Physics,
University of Zurich2011 at OISTLaboratory
ReviewJanuary 19, 201018

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

LEED : Low Energy Electron Diffraction
LEED provides surface
structure information
through Braggs
diffraction.

LEED-Gun
SPECS Inc.

LEED pattern of a Si(100) surface.
2011 at OISTLaboratory
ReviewJanuary 19, 201019

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Proof of Principle Experiment2011 at OISTLaboratory
ReviewJanuary 19, 201020

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Diffraction Electron Detector

2011 at OISTLaboratory
ReviewJanuary 19, 201021

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Testing at SII Nanotech. 2011 Feb.

Diffraction from HOPG
(graphne)2011 at OISTLaboratory
ReviewJanuary 19, 201022

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Finding Problems  Cure
Diffraction from HOPG (Graphene) is not clear
enough to go holography.
Contamination of carbon on electron beam
results in poor diffraction.
Improve vacuum condition by ion-cleanerneed space in front side transmission typewill be better, less charge up, lesscontamination in backside.
Resolution of MCP+P34 phosphor is poor andnoisy.  Maybe it is due to secondary electron
generation from energy filter grid  grid lessdesign and CCD type detector.

2011 at OISTLaboratory
ReviewJanuary 19, 201023Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Solution and Direction
Change: Reflection type  Transmission typeThis is mathematically simpler and easier.
Less path length in the sample material
Lower multiple reflections.
It requests a little higher electron energy

Need to care sample damage by cryo-system.
It requests new configuration of SEM
Custom design  Need extra cost.
Need to cool sample (electron energy is higher)
Cryo-sample holder cost.

2011 at OISTLaboratory
ReviewJanuary 19, 201024

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

R&D Program

2011

Proof ofPrinciple Test
Using Gemini
SEM at SIIHOPG, Au base2011 at OISTLaboratory
ReviewJanuary 19, 2010

2012

2013

2014

2015

First Dedicated Machine
Proof ofPrinciple Test
Using Merline
SEM at OISTDNA, TMVFor Biology

Reading DNA

25

Protein NasnoCrystal

Bio-cellTsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Proposal: New Project by Mitarai&Shintake Unit2011 at OISTLaboratory
ReviewJanuary 19, 201026

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

Under Sea “Element Map”
Searching Minor Metals
Minor metals: Ni、Cr、Co、Mn、W、Mo、Rare earth: Sc, Y, La, Ce, Pr, Nd, Sm, Eu We detect by X-ray fluorescence (XRF)

Searching petroleum
far future, we go Natural energy
but Short term (~30 years), we still relyon petroleum (probably, not nuclear energy).
 Seep gas (CH4, CnHn) detection
by photo-absorption analyzer.
 Map with GPS
2011 at OISTLaboratory
ReviewJanuary 19, 201027

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp

We need efforts to teat CO2
Directly feed exhaust gas to bio-reactor ?

Oil FieldPowerPlant
Or, send back CO2 to deep sea water?
3000 m deep, form CO2 lake.

2011 at OISTLaboratory
ReviewJanuary 19, 201028

Tsumoru Shintake
shintake@spring8.or.jp
shintake@oist.jp