Researcher

@bue.edu.eg

Ext. 74014

PERSONAL STATEMENT

​

Spectroscopist and Materials Scientist with 18+ years of experience combining advanced experimental characterization and quantum-mechanical atomistic simulations. Core expertise spans vibrational spectroscopy (FTIR, Raman, UV/Vis/NIR, synchrotron microspectroscopy) and density functional theory (DFT) modeling to investigate atomic-scale and electronic interactions. Research portfolio covers polymeric nanocomposites, optoelectronics, environmental remediation, biochemical systems, and cultural heritage—with a strong emphasis on structure–property relationships and molecular-level understanding rather than synthesis alone. Proven ability to bridge experimental characterization and theoretical computation to solve complex materials problems. Skilled in scientific consultancy and research mentorship. Seeking to contribute this broad analytical and computational skill set to multidisciplinary research at NTRC.

​

EDUCATION

PhD Cairo University, Molecular Biophysics - June 2016

Dissertation: “Biophysical Properties and Molecular Structural Studies on Collagen Blends as Meshes for Hernia Repair”

MSc Ain Shams University, Biophysics - October 2010

Thesis: “Preparation and Characterization of Chitosan Blends to be used as Biosensors for the Amino Acid Glycine”

BSc Ain Shams University, Biophysics - June 2006

Graduated Very Good with Honors

EMPLOYMENT RECORD

​

• Associate Professor of Applied Spectroscopy (from 01-2023): Spectroscopy Department, Physics Research Institute, National Research Centre, Cairo, Egypt.

• Infrared Beamline Scientist (from 12-2019 to 07-2023): Synchrotron-light for Experimental Science and Applications in the Middle East (SESAME), Jordan.

• Postdoctoral Researcher (from 06-2016 to 12-2019): Spectroscopy Department, Physics Research Institute, National Research Centre, Cairo, Egypt.

• Assistant Researcher (from 03-2013 to 06-2016): Spectroscopy Department, Physics Research Institute, National Research Centre, Cairo, Egypt.

• Research Assistant (from 09-2011 to 03-2013): Spectroscopy Department, Physics Research Institute, National Research Centre, Cairo, Egypt.

• Physicist (from 08-2007 to 09-2011): Spectroscopy Department, Physics Research Institute, National Research Centre, Cairo, Egypt

• Teaching Assistant (from 02-2007 to 07-2008): Physics Department, Misr International University, Cairo, Egypt.

RESEARCH EXPERIENCE

• Spectroscopic Analysis (Qualitative & Quantitative): Proficient in UV/Vis/NIR spectroscopy, as well as FTIR microspectroscopy using both globar and synchrotron radiation sources.

​

• Consultancy & Technical Support: Active member of the Molecular Modeling and Spectroscopy Laboratory, Centre of Excellence for Advanced Science, National Research Centre. Provide professional scientific and technical consultations in vibrational spectroscopy to diverse industries, including oil, petrochemicals, glass, safety, food, textiles, pharmaceuticals, and paper.

​

• Cultural Heritage Materials Analysis: Extensive experience in FTIR and Raman microspectroscopic analysis of archaeological and historical artefacts, including Coptic icons, archaeological wood, ceramics, pottery, textiles, paintings, as well as human and animal skeletal remains.

​

• Material Synthesis & Characterization: Preparation and characterization of a wide range of materials for various applications, including biomaterials, polymeric nanocomposites, graphene nanocomposites, hydrogels, and nanoparticles.

• Environmental Remediation: Preparation and characterization of microspheres specifically designed for the remediation of heavy metals (e.g., lead and cadmium) from aquatic environments.

​

• Optoelectronic & Energy Storage Materials: Investigation of surface, electronic, and optical properties of polymeric nanocomposites for applications in sensors, optoelectronics, and energy storage devices.

​

• Biochemical Interactions: Study of biochemical interactions based on biomaterials and amino acids using a combination of vibrational spectroscopy and molecular modeling techniques.

​

• Computational & Theoretical Modeling: Investigation of electronic properties and quantitative structure-activity relationships (QSAR) of biomaterials, polymeric nanocomposites, and graphenebased structures using ab initio molecular modeling calculations, as well as molecular docking in drug design.

​​

​

TECHNICAL EXPERIENCE

• Operating FTIR Spectrometers: Bruker VERTEX 80 coupled with Hyperion 3000 IR microscope; Thermo Scientific Nicolet 8700 coupled with Nicolet Continuum XL IR microscope; Bruker VERTEX 70 FTIR spectrometer; and Bruker ALPHA II FTIR spectrometer.

​

• Operating UV-VIS-NIR Spectrophotometers: JASCO V-570 and V-670, and Agilent Cary 100.

• Operating WITec Raman Confocal Microscope alpha300 R.

​

• Operating ISS Inc. Alba v5 Time-Resolved Confocal Microscope with Single-Molecule Sensitivity.

• Experience working in a laboratory environment with excellent hands-on skills using different laboratory equipment, instruments and tools.

PUBLICATIONS

​

Book chapter

Refaat, A., Elhaes, H., and Ibrahim, M.A., chapter titled “Design and Implementation of Green Route Using Biopolymers and Water Hyacinth for Wastewater Treatment” accepted for publication in the e-book series on materials titled “Advances in Material Research and Technology” in the Volume: Advances in Green Materials Engineering, edited by: Shadia Jamil Ikhmayies; which will be published by Springer Publisher.

​

Journal Publications

​

1. Alqahtani, H., Gomaa, I. & Refaat, A. Electronic landscape remodeling in 2D HAT dimers: How Bpin and cyano mono-functionalization dictate reactivity and stability from first principles. MRS Advances 11, 75–82 (2026). https://doi.org/10.1557/s43580-025-01472-9

​

2. Atwa, D.M., Hussein, R.K., Mohamed, I.F., Ibrahim, S., Abdullah, E., Omar, G., Ibrahim, M.A., & Refaat, A. Structural and Chemical Degradation of Archeological Wood: Synchrotron XRD and FTIR Analysis of a 26th Dynasty Egyptian Polychrome Wood Statuette. Polymers 18, 258 (2026). https://doi.org/10.3390/polym18020258

3. Alqahtani, H., Gomaa, I., & Refaat, A. Electronic landscape remodeling in 2D HAT dimers: How Bpin and cyano mono-functionalization dictate reactivity and stability from first principles. MRS Advances 11, 75–82 (2026). https://doi.org/10.1557/s43580-025-01472-9

4. El-Sayed, N.M. & Refaat, A. In silico assessment of CNTs, GQDs and GO as modulators of amyloid-β aggregation. Next Materials 10, 101375 (2026). https://doi.org/10.1016/j.nxmate.2025.101375

5. Alqahtani, H., Gomaa, I., Refaat, A., Mansour, M.S.A., Alsaiari, R.A., & Rizk, M.A. FirstPrinciples Modeling of Nitazoxanide Analogues as Prospective PFOR-Targeted Antibacterials. Int. J. Mol. Sci. 26, 11578 (2025). https://doi.org/10.3390/ijms262311578

6. Sabry, N.M., Bassem, S.M., Temraz, T.A., Abdel-Gawad, F.Kh., Refaat, A., Elhaes, H., & Ibrahim, M.A. Spectroscopic analyses for possible transport of polyaromatic hydrocarbons onto fish in Mediterranean Sea. Sci. Rep. 15, 33807 (2025). https://doi.org/10.1038/s41598-025-98472- 4

7. Dehkordi, M.H., Kamel, G., Rozatian, A.S.H., Madani, F.S., Noohi, S., Refaat, A., Nokandeh, J, & Emami, M. Revealing sassanid dyeing practices through synchrotron FTIR. Sci. Rep. 15, 41318 (2025). https://doi.org/10.1038/s41598-025-25106-0

8. Mohsen, E., El Fishawy, A.M., Salama, A., Elgohary, R., Refaat, A., Elgamal, A.M., Younis, I.Y., & Kamal, R.M. Unveiling the gastroprotective effect of the ethyl acetate fraction of Cordia africana Lam. roots against ethanol-induced gastric ulcer and Helicobacter pylori. J Ethnopharmacol. 348, 119841 (2025). https://doi.org/10.1016/j.jep.2025.119841

​

9. Ibrahim, S., Grenni, P., Mancini, L., Voltolini, M., Abdel-Fatah, H.M.K., Refaat, A., & Atwa, D.M. Multifactorial Analysis of Wood Deterioration in Ancient Egypt: A Case Study of Khufu’s Second Solar Boat. Appl. Sci. 15, 3952 (2025). https://doi.org/10.3390/app15073952

10. Alqahtani, H., Refaat, A., & Islam Gomaa. Functionalized 2D Hexaazatriphenylene as Hydrogen Storage Platform: A DFT-Guided Design Approach. Curr. Anal. Chem, (2025). http://dx.doi.org/10.2174/0115734110412198250904142334. In press

11. Salama, A., El-Kassaby, M.I., Refaat, A., & Mohasib, R.M. GC–MS and Molecular Docking Analyses of Phytochemicals from Calendula officinalis L. Hexane Extract and Evaluation of its Antioxidant and Wound Healing Properties in Rats. Egypt. J. Chem. 67(13), 1037-1058 (2024). https://doi.org/10.21608/ejchem.2024.328645.10642

12. Badry, R., Elhaes, H., Ibrahim, A.M., Refaat, A., & Ibrahim, M.A. Investigating the electronic properties and reactivity of polyaniline emeraldine base functionalized with metal oxides. Sci. Rep. 14, 27024 (2024). https://doi.org/10.1038/s41598-024-72435-7

13. Refaat, A., Ibrahim, M. A., Shehata, D., Elhaes, H., Ibrahim, A., Mamatkulov, K., & Arzumanyan, G. Design, characterization and implementation of cost-effective sodium alginate/water hyacinth microspheres for remediation of lead and cadmium from wastewater. Int. J. Biol. Macromol. 277(Pt 1), 133765 (2024). https://doi.org/10.1016/j.ijbiomac.2024.133765

14. Atta, D., Refaat, A., Ashery, A., & Ibrahim, M. Graphene oxide: Synthesis and laser spectroscopy approach. Optical Materials: X 22, 100302 (2024). https://doi.org/10.1016/j.omx.2024.100302

15. Sherif, S., Sameh, A., Salah, S.M., Omar, A., Elhaes, H, Ibrahim, A., Refaat, A., & Ibrahim, M.A. DFT and QSAR study of Catechol-O-methyltransferase (COMT) as inhibitors for Parkinson’s disease treatment. Opt. Quant. Electron. 56, 633 (2024). https://doi.org/10.1007/s11082-023- 06125-5

​

16. Elhaes, H., Ezzat, H.A., Ibrahim, A., Samir, M., Refaat, A., & Ibrahim, M.A. Spectroscopic, Hartree–Fock and DFT study of the molecular structure and electronic properties of functionalized chitosan and chitosan-graphene oxide for electronic applications. Opt. Quant. Electron. 56, 458 (2024). https://doi.org/10.1007/s11082-023-05978-0

17. Refaat, A. & Ibrahim, M. Microspectroscopic, DFT and QSAR Study of PVP/CaCO3 Blends as Potential Bone-Remineralization Membranes. Egypt. J. Chem. 67(2), 29-41 (2024). https://doi.org/10.21608/ejchem.2023.214822.8072

18. Refaat, A., Elhaes, H., & Ibrahim, M.A. Effect of alkali metals on physical and spectroscopic properties of cellulose. Sci. Rep. 13(1), 21649 (2023). https://doi.org/10.1038/s41598-023-48850- 7

19. Tiama, T.M., Elhaes, H., Ibrahim, M.A., Refaat, A., El-Mansy, M.A.M., & Sabry, N.M. Molecular and biological activities of metal oxide-modified bioactive glass. Sci. Rep. 13(1), 10637 (2023). https://doi.org/10.1038/s41598-023-37017-z

20. Ezzat, H.A., Hegazy, M.A., Ghoneim, R., Zahran, H.Y., Yahia, I.S., Elhaes, H., Refaat, A., & Ibrahim, M.A. DFT and QSAR studies of PTFE/ZnO/SiO2 nanocomposite. Sci. Rep. 13(1), 9696 (2023). https://doi.org/10.1038/s41598-022-19490-0

21. Ibrahim, M., & Refaat, A. Recent Advances in Sensors. Egypt. J. Chem. 66(11), 685–700 (2023). https://doi.org/10.21608/ejchem.2023.214821.8071

22. Elhaes, H., Abdel-Salam, A.I., Gomaa, I., Ibrahim, A., Yahia, I.S., Zahran, H.Y., Ezzat, H.A., Zahran, M., Abdel-wahab, M.Sh., Refaat, A., & Ibrahim, M.A. Facile synthesis, structural, morphological and electronic investigation of Mn2O3 nano-rice shape and Mn2O3-rGO hybrid nanocomposite. Opt. Quant. Electron. 55, 947 (2023). https://doi.org/10.1007/s11082-023-05002- 5

23. Omar, A., Badry, R., Hegazy, M.A., Yahia, I.S., Elhaes, H., Zahran, H.Y., Ibrahim, M.A., Refaat, A. Enhancing the optical properties of chitosan, carboxymethyl cellulose, sodium alginate modified with nano metal oxide and graphene oxide. Opt. Quant. Electron. 54, 806 (2022). https://doi.org/10.1007/s11082-022-04107-7

24. Refaat, A. & Kamel, G. Synchrotron radiation infrared microspectroscopy: Insights on biomedicine. Applied Spectroscopy Reviews 58(8), 525-544 (2023). https://doi.org/10.1080/05704928.2022.2052308

​

25. Ezzat, H.A., Elhaes, H., Refaat, A., Abdel-Aal, M.S., & Ibrahim, M.A. Molecular Modeling Analyses and Vibrational Characteristics for Nitromethane. Egypt. J. Chem. 64(1), 75-84 (2021). https://doi.org/10.21608/ejchem.2020.35452.2736

26. Refaat, A., Elhaes, H., Ammar, N.S., Ibrahim, H.S., Ibrahim, M. Green Route for the Removal of Pb from Aquatic Environment. Comb. Chem. High Throughput Screen. 23(7), 587-598 (2020). https://doi.org/10.2174/1386207323666200127123349

27. Bayoumy, A.M., Refaat, A., Yahia, I.S., Zahran, H.Y., Elhaes, H., Ibrahim, M.A., & Shkir, M. Functionalization of graphene quantum dots (GQDs) with chitosan biopolymer for biophysical applications. Opt. Quant. Electron. 52, 16 (2020). https://doi.org/10.1007/s11082-019-2134-z

28. Refaat, A., Ibrahim, M.A., Elhaes, H., Badry, R., Ezzat, H., Yahia, I.S., Zahran, H.Y., & Shkir, M. Geometrical, vibrational and physical properties of polyvinyl chloride nanocomposites: Molecular modeling approach. Journal of Theoretical and Computational Chemistry 18(8), 1950037 (2019). https://doi.org/10.1142/S0219633619500378

29. Refaat, A., Atta, D., Osman, O., Mahmoud, A.A., El-Kohadary, S., Malek, W., Ferretti, M., Elhaes, H., & Ibrahim, M. Analytical and computational study of three coptic icons in Saint Mercurius Monastery, Egypt. Biointerface Res. Appl. Chem. 9(6), 4685-4698 (2019). http://dx.doi.org/10.33263/BRIAC96.685698

30. Nematov, D., Burhonzoda, A., Khusenov, M., Kholmurodov, K., Doroshkevych, A., Doroshkevych, N., Zelenyak, T., Majumder, S., Refaat, A., & Ibrahim, M.A. Molecular dynamics simulations of the DNA radiation damage and conformation behavior on a zirconium dioxide surface. Egypt. J. Chem. 62, 149–161 (2019).

​

31. El Gabaly, S.G., Youssif, G.M., Bayoumy, A.M., Ezzat, H., Elhaes, H., Refaat, A., & Ibrahim, M.A. Modeling the Effect of Functional Groups on the Electronic Properties of Benzene; Pyridine and Pyrimidine. Egypt. J. Chem. The First International Conference on Molecular Modeling and Spectroscopy: 1-11 (2019). https://doi.org/10.21608/ejchem.2019.12903.1807

32. Ibrahim, M.A., Elhaes, H., El-Khodary, S.A., Morsy, M. Refaat, A., Yahia, I.S., & Zahran, H.Y. Molecular modeling analyses for the effect of alkali metal oxides on graphene. Biointerface Res. Appl. Chem. 8(5), 3522-3525 (2018).

33. Badry, R., Omar, A., Mohammed, H., Mohamed, D.A.A., Elhaes, H., Refaat, A., & Ibrahim, M. Effect of alkaline elements on the structure and electronic properties of glycine. Biointerface Res. Appl. Chem. 8(6): 3682–3687 (2018).

34. Badry, R., Ghanem, A.S.A.-E., Ahmed, H., Fahmy, A., Elhaes, H., Refaat, A., & Ibrahim, M. Effect of Li, Na, K, Be, Mg and Ca on the electronic properties, geometrical parameters of carboxylic acids. Biointerface Res. Appl. Chem. 8(6), 3657-3660 (2018).

35. Badry, R., Shaban, H., Elhaes, H., Refaat, A., & Ibrahim, M. Molecular modeling analyses of polyaniline substituted with alkali and alkaline earth elements. Biointerface Res. Appl. Chem. 8(6), 3719–3724 (2018).

36. Ragab, T.I.M., El-Bassyouni, G.T., Helmy, W.A., Taie, H.A.A., Refaat, A., Ibrahim, M.A., Abd El-Hmeed, E., & Esawy, M.A. Evaluation of Multifunction Bioactivities of Extracted Chitosan and their UV/Ozone Derivatives. Journal of Applied Pharmaceutical Science 8(10), 053-062 (2018). http://dx.doi.org/10.7324/JAPS.2018.81008

37. Ragab, T.I.M., Shalaby, A.G., El Awdan, S.A., Refaat, A., & Helmy, W.A. New applied pharmacological approach/trend on utilization of agro-industrial wastes. Environ. Sci. Pollut. Res. 25, 26446–26460 (2018). https://doi.org/10.1007/s11356-018-2631-9

38. Refaat, A., Youness, R.A., Taha, M.A., & Ibrahim, M. Effect of zinc oxide on the electronic properties of carbonated hydroxyapatite. J. Mol. Struct. 1147, 148-154 (2017). https://doi.org/10.1016/j.molstruc.2017.06.091

39. Elhaes, H., Abd-El-Aal, M., Refaat, A., & Ibrahim, M. Metal Interaction with Organic Acids: Semiempirical Molecular Modeling Approach. Australian Journal of Basic and Applied Sciences 5(6), 44-50 (2011).

40. Ibrahim, M., Mahmoud, A.A., Osman, O., Refaat, A., El-Sayed, E.M. Molecular spectroscopic analysis of nano-chitosan blends as biosensor. Spectrochim. Acta A 77(4), 802–806 (2010). https://doi.org/10.1016/j.saa.2010.08.007

​

​

PRESENTATIONS AND INVITED LECTURES

Paper Presentations:

​

• “Assessing Structural and Chemical Deterioration in Archaeological Wood: A Synchrotron XRD and FTIR Study of a Polychrome Wooden Statuette from 26th Dynasty Egypt” – The 20th International Conference of Arab Chemists Union (ICACU), April 2026.

• “Design, characterization and implementation of cost-effective sodium alginate/water hyacinth microspheres for remediation of lead and cadmium from wastewater” – Workshop titled: Ecofriendly Cost-effective Microspheres for Multiple Applications, October 2024.

• “Microspectroscopic, DFT and QSAR Study of PVP/CaCO3 Blends as Potential Bone Remineralization Membranes” – The 5 th Hybrid International Conference on Molecular Modeling and Spectroscopy, September 2023.

• “DFT Study of the Effect of Potassium on the Electronic Properties and Molecular Electrostatic Potential of Cellulose” – The 5th Hybrid International Conference on Molecular Modeling and Spectroscopy, September 2023.

​

• “Effect of Lithium as a Monovalent Alkali Metal on the Electronic Properties of Cellulose – DFT Approach” – The 5th Hybrid International Conference on Molecular Modeling and Spectroscopy, September 2023.

• “DFT/B3LYP Hybrid Functional Study of the Electronic Properties of Hydrated and NonHydrated Sodium-Substituted Cellulose” – The 5th Hybrid International Conference on Molecular Modeling and Spectroscopy, September 2023.

• “Modified Chitosan Blends as Biosensor for Amino Acids” – The 1 st International Conference on Molecular Modeling and Spectroscopy, February, 2019.

• “Modeling and Spectroscopic Analyses of Coptic Icons” – The 1 st International Conference on Molecular Modeling and Spectroscopy, February, 2019.

​​

Invited Lectures: 

• “Application of Biomaterials in Environment and Drug Delivery Systems” – The 6th Hybrid International Conference on Molecular Modeling and Spectroscopy, December 2024.

• “Integration between Cultural Heritage and Spectroscopy: Spectroscopic Analyses of Icons of Historical and Artistic Value” – Interdisciplinary Workshop titled: Archaeology and Environment: Ancient Border Communities Between Sand and Waterways, November 2024.

​

​

​PROFESSIONAL SERVICE

 ​

Conference Board Member;

​

• The 5 th International Conference on Molecular Modeling and Spectroscopy, 17-19 September 2023,

at National Research Centre, Cairo, Egypt.

• The 1st International Conference on Molecular Modeling and Spectroscopy, 19-22 February 2019

at National Research Centre, Cairo, Egypt.​

​

Conference Co-Organizer;

​

• The 4th International Conference on Advanced Materials and Their Applications, 23-25 September 2025,

at National Research Centre, Cairo, Egypt.

• The 6 th International Conference on Molecular Modeling and Spectroscopy, 17-19 September 2024,

Dahab, South Sinai, Egypt.

• The 4th Hybrid International Conference on Molecular Modeling and Spectroscopy, 18-20 December 2022,

at National Research Centre, Cairo, Egypt.

• The 7th International Conference on Optical Spectroscopy, Laser and their Applications, 18-20 October 2016

at National Research Centre, Cairo, Egypt.

• The 6th International Conference on Optical Spectroscopy, Laser and their Applications, 07-09 April 2015

at National Research Centre, Cairo, Egypt.

• The 5th National Conference on Optical Spectroscopy, Laser and Their Applications, 23-27 March 2014

at National Research Centre, Cairo, Egypt.

​

​​

Peer-Reviewed Articles for Journals:​

​

• Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

• In Silico Research in Biomedicine • Clinical and Experimental Pharmacology and Physiology

• Ceramics International

• Applied Physics A

• Biointerface Research in Applied Chemistry

• Egyptian Journal of Chemistry • NRIAG Journal of Astronomy and Geophysics

• Letters in Applied NanoBioScience

​

COMMUNITY SERVICE

​

Training group of Physics Research Institute, National Research Centre, Cairo, Egypt

Training and teaching Vibrational Spectroscopy techniques and their applications to undergraduates and industry.

​LANGUAGES

English: Fluent both written and spoken (IELTS overall band score of 7.5 and CEFR level C1)

Arabic: Native language.

PERSONAL SKILLS

Excellent communication skills – Teamwork – Time management – Problem solving – Flexibility – Project management – Writing, planning and executing research proposals and projects.

​

COMPUTER SKILLS

​

• ISS, Inc. VistaVision 4.2.313 software package for confocal microscopy, instrument control, data acquisition, and data processing.

• Thermo Scientific OMNIC™ software for FTIR data acquisition and analysis.

• Thermo Scientific Atlμs™ FTIR mapping software.

• Thermo Scientific TQ Analyst™ quantitative analysis software.

• Bruker OPUS software for FTIR microspectroscopy data acquisition and analysis.

• Agilent Cary WinUV software for UV-Vis-NIR data acquisition and analysis.

• JASCO Spectra Manager™ software for FTIR and UV-Vis-NIR data acquisition and analysis.

• WITec Suite FIVE software for Raman data acquisition and analysis.

• Origin and OriginPro software for scientific graphing and data analysis.

• PeakFit® peak separation and analysis software.

• SigmaPlot® software for scientific graphing.

• The Unscrambler X multivariate data analysis software.

• Molecular Modeling and Computational Chemistry software packages: Gaussian (03, 09 and 16), GaussView, ORCA, Multiwfn, Chemcraft, Avogadro, Turbomole, Spartan Wavefunction, GaussSum, PyMOL, SwissPDB, Autodock, Autodock Vina and BIOVIA Discovery Studio.

• Full use of Microsoft Windows and Microsoft office.

• Excellent Internet search skills

​

​