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Infrared Beamline Emira Progress and Development
Ibraheem YOUSEFSESAME Synchrotron
Electro-Magnetic Infrared RAdiation
Summary of Recommendations
SAC 2012
1. Incorporate the complete drawings of the beamline into the general drawing.
2. Validation of extraction and implementation by technical director.
3. Ordering of microscope before end of 2012.
4. Preparation of the IR laboratory.
5. Completion of the TDR before June 2013.
6. Initiate studies in various scientific disciplines.
7. Organized a specialized workshop, with on hands experiments and data analysis.
8. Collaborations with local medical institutions.
Outline Preparation of the Infrared Laboratory
– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
Preparation of the Infrared Laboratory– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
FTIR Microscope
Delay on the microscope commissioning
1. Thermo Technician
2. Lab preparation
3. Lake of equipments
3 months of Delay due to the following reasons :
Final position…
FTIR microscope
location
View of the IR lab soon…
-The spectral range 11000 – 50 cm-1
-Resolution 0.1 cm-1
-Speed scanning at a resolution of 16 cm-1, 90 scan/s
- Two sources operating without water cooling system: for near / mid-infrared (wavelength range 20 000 - 2000 cm-1) and for the middle / far-infrared (wavelength range 9600 - 20 cm-1), including a system to automatically switch detectors team of software
FTIR Setup: Main Characteristics
Detectors:
1. TE Cooled DLaTGS Detector with KBr Window (12,500-350 cm-1)
2. DLaTGS Detector with Polyethylene Window (700-50 cm-1)
3. Room Temperature InGaAs Detector for NIR (12,000-3,800 cm-1)
4. 50um MCT-A Detector (11,400-700 cm-1)
5. MCT-B Detector (11,700-450 cm-1)
Commissioning of the Microscope
The calibration and Performance tests:
The calibration and Performance tests:
Performing FT-IR spectroscopy at SESAME…FT-IR Microscope is now available for users
Thermo Scientific Nicolet FT-IR Microscope
The Tabletop OpticalModule (TOM)
8700 FT-IR Spectrometer
Continuum Microscope
Call for proposals
Published online on 15 March 2013
Deadline was 15th of June 2013
Evaluation committee
Lisa Miller: Brookhaven National Laboratory, USA
Ulrich Schade: BESSY II, Germany
Lisa Vaccari: ELETTRA, Italy
Evaluation criteria
11 Proposals have been accepted
Accepted Proposals
Jordan
Pakistan
Egypt
Iran
Iraq
France
Jordan 45%
Pakistan18%
France 9%Iraq
9%Iran 9%
Egypt 9%
Fund for external proposals should be discussed!
Research fields of the proposals
Proposed Research fields
Pharmacy BiomedicalMarine ScienceBiologyMaterial ScienceEnvironmental Sceince
Biomedical Science
45%
Material Science
18%
Pharmacy 9%
Environment9%
Biology9%
Marine 9%
Current Studies and Collaborations
Fatemeh Elmi, assistant professor , University of Mazandaran, North Iran
Randa Mansour, PhD student at the faculty of Pharmacy, University of Jordan.
FTIR analysis of breast cancer from Iranian patients: collaboration with University of Mazandaran, Iran.
Red- Cancerous Breast tissuePurple- Normal Breast tissue
Lipids(CH2 & CH3)
Amide IAmide II
as CH3s CH3
as PO2 -
s PO2 -
Healthy region
Cancerous region
2. Chemical Maps are showing the distribution of some biochemical components inside the Breast Tissue.
Proteins Carbohydrates Lipids
Breast Cancer Investigation
EsterC=O
Study effects of pharmaceutical products on different skin layers with the asses of infrared microspectroscopy: collaboration the university of Jordan, Jordan.
Proteins Lipids
Sugar
Stratum corneum
Abso
rban
ce (A
bs)
0.00
0.20
0.40
Wavenumbers (cm-1)3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800
Position (micrometers)=19751 µm,680 µm
Abso
rban
ce (A
bs)
0.00
0.20
0.40
Wavenumbers (cm-1)3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800
Position (micrometers)=19751 µm,680 µm
Epidermis
DermisLipids(CH2 & CH3)
Amide I
Amide II
Sugar
Collaborations with local medical institutions
Used to cut the skin samplesVery useful for sample preparation in the FTIR measurements
Disadvantage:
Restricted access
Cryomicrotrome at the hospital of the university of Jordan
Collaborative projects with scientists from the Middle East:
FTIR analysis of breast cancer from Iranian patients: collaboration from Tehran University, Iran.
FTIR analysis of bacterial and marine micronutrients: Collaboration from the University of Pakistan
Study effects of pharmaceutical products on different skin layers with the asses of infrared microspectroscopy: collaboration the university of Jordan, Jordan.
Effect of environmental pollution on the edible, medicinal and aromatic plants grown in Jordan: faculty of pharmacy, university of Jordan, Jordan.
Investigation on diamond like carbon deposited on Si wafer using the FTIR microscope equipped with a grazing angle objective: collaboration with Ministry of Science & Technology. Baghdad, Iraq.
FTIR analysis on organic samples, which have promising pharmaceutical applications, combinatory analysis using powder diffraction: collaboration with Physics Division, National Research Center Cairo, Egypt.
23
Proposal for Research Project exploiting the new offline FTIR microscope at SESAME
Title: Fourier-transform infrared microspectroscopy as a tool to understand the biological response after minibeam radiation therapy (MBRT) irradiations in combination with chemotherapy drugs and contrast agents: an in vitro study
Participants :
1- From SESAME Synchrotron, Jordan.
Dr. Ibraheem Yousef: Infrared Beamline Emira.
Dr. Hafeez Hoorani: Scientific Director.
2- From CEA, France.
Dr. Immaculada Martínez-Rovira: Service Hospitalier Frédéric Joliot, Commissariat à l’énergie atomique
et aux énergies alternatives.
3- From CNRS, France.
Dr. Yolanda Prezado: Imagerie et Modélisation en Neurobiologie et Cancérologie, Centre National de la
Recherce Scientifique.
Dr. Olivier Seksek: Imagerie et Modélisation en Neurobiologie et Cancérologie, Centre National de la
Recherce Scientifique.
4- From Keele University, UK.
Dr. Josep Sulé-Suso: Institute for Science and Technology in Medicine, Guy Hilton Research Centre.
5- From Universitat Autònoma de Barcelona, Spain.
Dr. Silvia Gil: Department of Biology.
Dr. Manel Sabés, Department of Biology.
PROPOSAL SUBMITTED TO THE ESRF
Scientific Scope of the Project…
Exploit the new offline FTIR microscope to understand the biological effects occurring in extremely aggressive cancerous cells (glioma rat cells F98).
The idea is to evaluate by means of FTIR analysis, cells irradiated with minibeam radiation therapy (MBRT) in combination with drugs and contrast agents and compare its effect with respect to the absence of these elements.
In addition, this project will strength the scientific collaboration between SESAME and the ESRF facilities and indeed will promote the science program at SESAME. This will definitely help to develop more and enhance the collaboration and connections between the scientists of different countries and societies.
Open the door to the further understanding of the biological effects occurring when combining several innovative cancer treatment approaches (minibeams, chemotherapy drugs and contrast agents)
Work Plan, including proposed methods or techniques
1) MBRT measurements (at the ESRF):
Proposal has been already submitted
This experiment will be performed at the MRT station at
ID17 Biomedical Beamline.
2) FTIR microspectroscopic measurements at SESAME:
A new FTIR microscope will be installed on April of 2013 at
Emira. The microscope will be operating using the internal
source (conventional blackbody thermal source) until the
coupling with the synchrotron light in 2016.
Estimated Budget
Item Estimated project costs in €
Sample holder MirrIR CFR (3boxes of 25slides). The windows are necessary for FTIR measurements in the trans-reflection mode.
200
Sample holder CaF2 (130). The windows are necessary for FTIR measurements in the transmission mode.
1500
Radiochromic films (detector system), 1 box 600
Cell line Glioma F89 + cell culture reagents (medium, serum..) 2000
Chemotherapeutic drugs (Temozolomide and JAI-51) 1000
Contrast agents (Au and Gd) 1500
Miscellaneous consumables (basic chemicals, gloves…) 2000
Sub-total: € 8800
Item Estimated project costs in €
One week Beamtime at ESRF [travel and accommodation] 1500
One week Beamtime at SESAME [travel and accommodation] 1500
Local transportation institutes and laboratories 1500
Sub-total: € 4500
Total estimated project cost:
€ 13300 Euros
a) Equipment
b) Miscellaneous (including transport)
CNRS Funded the Project
Glioma Cells Chemo-drugs
Nanoparticles
FTIR transmission windows
Experiment allocated on the 5th of December 2013
Preparation of the Infrared Laboratory– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
Expected total number of participants:25 persons: 12 from the member countries and 13 from Jordan
Duration of the workshop (in actual working days):Three days
Two choices of preferred dates:•13-15 August 2013•26-28 August 2013
Place SESAME Synchrotron
Infrared Microspectroscopy Workshop
Applications and Data analysis
Description of the topics to be covered and reasons for their
special interest:
Introduction to synchrotron radiation
Synchrotron-based infrared microspectroscopy
Sample preparation and the successful IR microspectroscopy
experiment.
Applications:1. Biological and Biomedical fields2. Cultural heritage 3. Environmental science4. Material and surface science
Data analysis : Univariate and multivariate analytical approaches.
Preparation of the Infrared Laboratory– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
IR workshop Program 11th SESAME Users meeting
IR - Workshop
09:00 – 09:10
Welcome and introduction (Ibraheem Yousef)
09:10 –0 9:30 FTIR Microspectroscopy at SESAME (Ibraheem Yousef)
09:30 – 10:00 So You Think You Need a Synchrotron: How to Write a Successful Proposal for Synchrotron IR Experiments.
(Thomas Ellis) 10:00 – 10:30
Transflection-mode infrared microscopy: A valuable sampling methodology or a flawed technique? The answer depends on the question.
(Peter Gardner) 10:30 – 11:00 Coffee Break 11:00 – 11:20
FTIR as a tool to understand the biological response of tumoral cells after Minibeam Radiation Therapy (MBRT) irradiations in combination with chemotherapy drugs.
(Immaculada Martinez-Rovira) 11:20 – 11:40
Alternative diagnostic method for breast malignancy based on bio-molecular changes in malignant tissues using IR- Micro Spectroscopy: A Preliminary Study.
(Sohaila Rehman) 11:40- 12:00 Combined DFT, IR Deconvolution Analysis for Structural Investigation of
Copper –doped Lead Borate Glasses. (Amr Abdelghany)
12:00 – 13:00
Round table discussion
13:00 – 14:00 Lunch Break
Round Table Discussion...1. Number of participants: around 25.
2. Scientist attending the IR workshop show a lot of interest on performing experiments with the IR microscope.
3. Need of training for users not familiar with the microscope. Several options proposed:
1. Lectures at Jordan (and country member) universities.2. Organization of training course at SESAME with a hands on part.3. Online courses (link to several IR resources, for instance from the University of
Manchester, as proposed by Prof. Peter Gardner).
4. Need for a sample preparation lab at SESAME, specially for users travelling long distances.
5. Accessories that users requested:1. Optical microscope.2. Cryomicrotome.3. Tools to manipulate small samples.4. Electron microscope.
6. Need for help on writing proposals.
Some of the IR workshop participants
Preparation of the Infrared Laboratory– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
IAEA Fellowship at BESSY IIIRIS Beamline
The Mid-IR and far-IR spectra (2-5000 cm-1) of hydrate Nafion membranes of various Cation forms.
Contribute at the beamline activities, mainly a Local Contact.
THz Microspectroscopy with coherent synchrotron radiation, micro-cell ellipsometry and imaging, the infrared beamline IRIS of the Helmholtz-Zentrum Berlin in Germany, Fellowship, Sep-Dec 2012.
Aim: join and collaborate in the research activities at the infrared beamline IRIS, learning and acquiring more knowledge in “physics-oriented” experiments and application using the synchrotron infrared radiation.
• Pre-treatment of the membranes using special procedure of chemical solutions in order to prepare the samples and record the complete infrared spectra (2-5000 cm-1) of Nafion and PFIA membranes and its alki salts.
• The spectral features of PFIA that correlate with the corresponding cation in the terahertz region will be reported in our study for the first time.
Japan scientific program school (JSPS)
Eriobotrya japonica
Laurus nobilis
Rosmarinus officinalis
Pistacia atlantica
Invited talks and seminars• Conceptual design of the Infrared beamline EMIRA and the currant status at
SESAME. I. Yousef, Institute of Methods and Instrumentation for Synchrotron Radiation Research, BESSY II Synchrotron, Berlin (Germany), 2nd October (2012)
• An Infrared Synchrotron Radiation beamline Emira at the third generation
light source SESAME. I. Yousef, Spring-8 Synchrotron, Hyogo (Japan), 1st February (2013)
• Infrared Microspectroscopy and Beamline development Plans at SESAME. I.
Yousef, UVSOR Facility, Okazaki (Japan), 5th February (2013) • Synchrotron Infrared Microspectroscopy in Environmental Science:
Bioremediation. I. Yousef, the Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste (Italy), 25th April (2013)
• Applications of synchrotron infrared microspectroscopy. I. Yousef, The
Cyprus Institute, Nicosia (Cyprus), 14th May (2013)
• An Infrared Synchrotron Radiation beamline Emira at the third generation light source SESAME. I. Yousef, WIRMS Melbourne (Australia), 9th-14th November (2013)
Preparation of the Infrared Laboratory– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
Integrate the Beamline 3D drawings with SESAME general
drawing
Dipole chamber
M1 chamber
(M2-M3) chamber
Prote
ctio
n wal
l
Diamond window
Experimental station
Cylindrical mirrors Chamber
Branch 1
Branch 2
Technical Design Review (TDR)
Circular flange design (hits the magnet coils at the two edges)
Rectangular flange design (fits inside the colis 3mm far from the edges)
Valve will be replaced with VAT seriese 10 to fit with the space.
New valve VAT seriese 10 (smaller in width)
Port for diagnostics to be relocated at M1 exit port or removed.
Absorber position not fitting with new updates. Absorber length to be reduced to 70 mm
SRW Simulation for the new M1 position (in progress)
2D plan of the whole beamline are being currently produced…The 2D plan of each individual component of the beamline is currently being created by Akrum Homoud
Simulation and Design of an Infrared Beamline for
SESAME
Dipole chamber
M1 chamber
(M2-M3) chamber
Prote
ctio
n wal
l
Diamond window
Experimental station
Cylindrical mirrors Chamber
Branch 1
Branch 2
Technical specification of the beamline components for
Tender…• Is being currently prepared in collaboration with:
1) Eng. Firas Makahleh, the head of Vacuum and cooling group.
2) Eng. Maher Shehab, the head of mechanical engineering group.Detailed specification and Diagnostic for:
- Ion bumps- Bumps- Valves- bellows-Chamber materials
-Mechanical support of the chambers
Preparation of the Infrared Laboratory– FTIR microscope: installation and commissioning.– Call for proposals.– Collaborative projects and research studies.– Collaborations with local medical institutions.
Organize a specialized workshop
IR Workshop – 11th SESAME Users Meeting (summary and users recommendations)
Scientific research visits– BESSY II, Berlin – Germany.– UVSOR, Okazaki – Japan.– Invited talks and presentations.
Infrared Beamline– Incorporate the complete drawings of the beamline into the general drawing.– Completion of the Technical design review (TDR).– 2D Plan and drawings. – Tender of beamline components.
Plan 2014
Plan 2014• Perform experiments & data analysis of the first round of proposals
(11 experiments)
• 1st of January: Second announcement “Call for proposals”
• 1st of January – 1st of June: Tender and procurement of the beamline individual components
• 1st of March – 1st of July: Tender and procurement of the beamline mirrors
• From 1st July : Perform experiments & data analysis of the second round of proposals
• Install beamline components (if possible, depending on purchase process)
• Alignment of the beamline: mirrors (if possible, depending on purchase process)
Acknowledgments
• SESAME Synchrotron
Hafeez Hoorani, Firas Makahleh and Maher
Shehab
• SOLEIL Synchrotron
Paul Dumas and Stéphane Lefrançois
Thank you for your attention!
