1. Infrared Beamline Emira Progress and Development Ibraheem YOUSEF SESAME Synchrotron ibraheem.yousef@sesame.org.jo Electro-Magnetic Infrared RAdiation

2. 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.

3. 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

4.  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

5. FTIR Microscope

6. Delay on the microscope commissioning 1.Thermo Technician 2.Lab preparation 3.Lake of equipments 3 months of Delay due to the following reasons :

7. Final position…

8. FTIR microscope location View of the IR lab soon…

9. -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

10. 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)

11. Commissioning of the Microscope The calibration and Performance tests:

13. Performing FT-IR spectroscopy at SESAME… FT-IR Microscope is now available for users Thermo Scientific Nicolet FT-IR Microscope The Tabletop Optical Module (TOM) 8700 FT-IR Spectrometer Continuum Microscope

14. Call for proposals Published online on 15 March 2013 Deadline was 15 th of June 2013

15. Evaluation committee Lisa Miller: Brookhaven National Laboratory, USA Ulrich Schade: BESSY II, Germany Lisa Vaccari: ELETTRA, Italy

16. Evaluation criteria

17. 11 Proposals have been accepted Jordan 45% Pakistan 18% France 9% Iraq 9% Iran 9% Egypt 9% Fund for external proposals should be discussed!

18. Research fields of the proposals Material Science 18% Pharmacy 9% Environment 9% Biology 9% Marine 9%

19. 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.

20. FTIR analysis of breast cancer from Iranian patients: collaboration with University of Mazandaran, Iran. Red- Cancerous Breast tissue Purple- Normal Breast tissue Lipids (CH2 & CH3) Amide I Amide II as CH3 s CH3 as PO 2 - s PO 2 - 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 Ester C=O

21. 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 Epidermis Dermis Lipids (CH2 & CH3) Amide I Amide II Sugar

22. Collaborations with local medical institutions Used to cut the skin samples Very useful for sample preparation in the FTIR measurements Disadvantage: Restricted access Cryomicrotrome at the hospital of the university of Jordan

23. 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

24. 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

25. 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)

26. 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.

27. Estimated Budget ItemEstimated 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 ItemEstimated 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)

28. CNRS Funded the Project Glioma Cells Chemo-drugs Nanoparticles FTIR transmission windows Experiment allocated on the 5 th of December 2013

29.  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

30. 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

31. 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 fields 2.Cultural heritage 3. Environmental science 4.Material and surface science  Data analysis : Univariate and multivariate analytical approaches.

32.  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

33. IR workshop Program

34. 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. 1.Need for help on writing proposals.

35. Some of the IR workshop participants

36.  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

37. IAEA Fellowship at BESSY II IRIS 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.

38. 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.

40. Japan scientific program school (JSPS) Eriobotrya japonica Laurus nobilis Rosmarinus officinalis Pistacia atlantica

41. 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), 2 nd 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), 5 th February (2013) Synchrotron Infrared Microspectroscopy in Environmental Science: Bioremediation. I. Yousef, the Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste (Italy), 25 th April (2013) Applications of synchrotron infrared microspectroscopy. I. Yousef, The Cyprus Institute, Nicosia (Cyprus), 14 th May (2013) An Infrared Synchrotron Radiation beamline Emira at the third generation light source SESAME. I. Yousef, WIRMS Melbourne (Australia), 9 th -14 th November (2013)

42.  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

43. Integrate the Beamline 3D drawings with SESAME general drawing Dipole chamber M 1 chamber (M 2 -M 3 ) chamber Protection wall Diamond window Experimental station Cylindrical mirrors Chamber Branch 1 Branch 2

44. Technical Design Review (TDR)

45. 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)

46. 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)

47. 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

48. Simulation and Design of an Infrared Beamline for SESAME Dipole chamber M 1 chamber (M 2 -M 3 ) chamber Protection wall Diamond window Experimental station Cylindrical mirrors Chamber Branch 1 Branch 2

49. 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

50.  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

51. Plan 2014 Perform experiments & data analysis of the first round of proposals (11 experiments) 1 st of January: Second announcement “Call for proposals” 1 st of January – 1 st of June: Tender and procurement of the beamline individual components 1 st of March – 1 st of July: Tender and procurement of the beamline mirrors From 1 st 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)

52. Acknowledgments SESAME Synchrotron Hafeez Hoorani, Firas Makahleh and Maher Shehab SOLEIL Synchrotron Paul Dumas and Stéphane Lefrançois

53. Thank you for your attention!