Ö. Zeynep Güner-Yılmaz | Computational Structural Biology & Biomaterials

Research on computational structural biology (MCG, ANM, shortest paths) and biomaterial innovations for drug delivery, tissue engineering, and wound dressing

Curriculum Vitae

Education

Ph.D. in Chemical Engineering – Istanbul Technical University, 2020–Present
Research Focus: Computational Structural Biology, Protein Dynamics

M.Sc. in Biomedical Engineering – Boğaziçi University, 2020
Thesis: Functionalization of Carbon Nanotubes for Drug Delivery in Cancer Therapy

B.Sc. in Chemical Engineering – Istanbul Technical University, 2018
Graduation Project: Investigation of Pectin Drug Systems with Molecular Dynamics Simulation Methods and Experiments

Honors and Scholarships

YÖK 100/2000 Priority Area Ph.D. Scholarship May 2021 – Ongoing

TÜBİTAK 1004 Project – NANOSIS (20AG029) March 2021 – Ongoing

TÜBİTAK 2250 – Graduate Scholarship Performance Program Feb-Jul 2024

EMBO Integrative Modelling of Protein Interactions – Reg Fee Waiver 17-22 Sept 2023

TÜBİTAK 1004 Project Research Scholarship Jul-Nov2017

Research Experience

ITU-BAP (Istanbul Technical University Scientific Research Projects)

Development of Hyaluronic Acid-Modified Hydrogel Formulations (2024, Ended)

Researcher
Developed and characterized hydrogel formulations for biomedical applications, focusing on the addition of hyaluronic acid for enhanced properties.

Investigation of Protein Adsorption Capacities and Performance of Single-Walled Carbon Nanotubes with Different Surface Chemistries (2024, Ended)

Researcher
Examined the protein adsorption capacities and performance of single-walled carbon nanotubes (SWCNTs) with various surface modifications, and performed rheological studies to analyze their flow properties and mechanical performance in hydrogels.

Application of Mixed Resolution Elastic Network Model in Structure-Based Drug Design (2021-Ongoing)

Researcher
Utilizing a mixed-resolution elastic network model for structure-based drug design, specifically applied to optimize interactions within supramolecular systems.

ILAP 3 Project: Development of Injectable Hydrogels for Osteoarthritis Treatment (2024-Ongoing)
Researcher
Focusing on the development of injectable hydrogels for osteoarthritis treatment, including material selection, in vitro evaluation, and computational modeling to optimize hydrogel properties for enhanced therapeutic efficacy.

TÜBİTAK (Scientific and Technological Research Council of Turkey)

Development of Sensor-Integrated Wound Dressings for Monitoring and Treatment of Venous Ulcers, TÜBİTAK 1004 Project (2021-2025, Ended)

Project Assistant
Project No: 20AG029
Worked on developing sensor-integrated wound dressings to monitor and treat venous ulcers, focusing on real-time treatment effectiveness.

Industry Collaborated Projects

BSH – Preparation and Characterization of Antibacterial Composites (2020, Ended)

Researcher
Worked on the preparation and characterization of polypropylene-based composites, using modified zeolite as an additive

Publications

2024

  • Aydın, B., Güner-Yılmaz, ÖZ, Yılmaz, A., Kilic-Cevirgel, S., Karaoglu, İ.C.,  Bozoglu, S., İzbudak, B, Kurkcuoglu, O, Bal-Öztürk, A.,  Karatepe, N., Güner, F.S. 2024. Mitoxantrone release from Fmoc-protected amino acids coated magnetic carbon nanotubes: Computational and experimental study for cancer treatment, Journal of Drug Delivery Science and Technology, 101, 106291, ISSN 1773-2247 https://doi.org/10.1016/j.jddst.2024.106291
  • Kocaaga B, Öztürk Y, Kurçin HC, Güner Yılmaz ÖZ, Kurkcuoglu O, Tatlier M, Özdemir İ, Kervancioglu Demirci E, Kotil T, Solakoğlu S, Aksu B, Batirel S, Bal-Öztürk A, Güner FS. 2024. Developing multifunctional pectin-based hydrogel for wound dressing: In silico, in vitro and in vivo evaluation, European Polymer Journal, 216, 113280. https://doi.org/10.1016/j.eurpolymj.2024.113280
  • Güner Yılmaz ÖZ, Yılmaz A, Bozoglu S, Karatepe N, Batirel S, Sahin A, Güner FS. 2024. Single-Walled (Magnetic) Carbon Nanotubes in a Pectin Matrix in the Design of an Allantoin Delivery System, ACS Omega, 9(9) 10069-10079. https://doi.org/10.1021/acsomega.3c03619
  • Murat FS, Güner Yılmaz ÖZ, Bozoglu S, Batirel S, Baysak, E, Hizal G, Karatepe N, Güner FS. 2024. Non-Covalent Functionalization of Magnetic Carbon Nanotubes with Fmoc Amino Acid-Modified Polyethylene Glycol, ChemNanoMat, https://doi.org/10.1002/cnma.202400028
  • Güner-Yılmaz ÖZ, Kurkcuoglu O, Using Truncated Structures in Molecular Dynamics Simulations to Investigate Protein-Ligand Interactions: A Case Study with Triose Phosphate Isomerase, The International Society of Quantum Biology and Pharmacology Presiden’s Meeting, Atina-Yunanistan, 19-23 May 2024
  • Güner-Yılmaz ÖZ, Alp CN, Kurkcuoglu O, Proteinlerde Bilgi Akışının k-En Kısa Yollar ile Öngörülmesi için Bir Program, 35. Ulusal Kimya Kongresi, 9-12 Eylül 2024.
  • Murat FS, Güner Yılmaz ÖZ, Bozoglu S, Batirel S, Baysak, E, Hizal G, Karatepe N, Güner FS, Manyetik Karbon Nanotüplerin Fmoc Amino Asitle Modifiye Edilmiş Polietilen Glikol ile Kovalent Olmayan Yöntemle Fonksiyonelleştirilmesi, 35. Ulusal Kimya Kongresi, 9-12 Eylül 2024

2021

  • Guner OZ, Kocaagaa B, Batirel S, Kurkcuoglu O, Guner FS. “2-Thiobarbituric Acid Addition Improves Structural Integrity and Controlled Drug Delivery of Biocompatible Pectin Hydrogels”, International Journal of Polymeric Materials and Polymeric Biomaterials, 2021. 70(10), 703-711. https://doi.org/10.1080/00914037.2020.1760272
  • Yeniyurt, Y.; Kilic, S.; Güner-Yılmaz, Ö.Z.; Bozoglu, S.; Meran, M.; Baysak, E.; Kurkcuoglu, O.; Hizal; G.; Karatepe, N.; Batirel, S.; Güner, F.S. 2021. Fmoc-PEG Coated Single-Wall Carbon Nanotube Carriers by Non-covalent Functionalization: An Experimental and Molecular Dynamics Study. Frontiers in Bioengineering and Biotechnology, 9, 648366. https://doi.org/10.3389/fbioe.2021.648366
  • Güner ÖZ, Aydın B., Karaoglu, IC, Bozoglu S, Kurkcuoglu, O., Karatepe N, Güner FS, Mitoxantrone-Loaded Magnetic Single-Walled Carbon Nanotubes as Nanocarriers for Cancer Treatment, First Global Nanobio E-Conference, Tampa, FL,13-20 March 2021.
  • Güner-Yılmaz, Ö.Z., Yılmaz, A., Bozoğlu, S., Yavuz, N., Güner, F.S., Yara Örtüsü Uygulamaları için Tek Duvarlı Karbon Nanotüp Katkılı Pektin Hidrojeller, 14. Ulusal Kimya Mühendisliği Kongresi, Konya Teknik Üniversitesi, 10-12 Haziran 2021.

2017

Güner, Ö.Z., Kacaaga, B., Güner, F.S., Development of Sulfide-Bridged Pectin Based Drug Carrier Hydrogels: Crosslinker Effect, Advanced Polymers via Macromolecular Engineering (APME 2017), Ghent-Belçika, May 21-25, 2017.

2023

  • Guner-Yılmaz OZ, Kurkcuoglu O, Akten ED. (2023) Tunnel-like region observed as a potential allosteric site in Staphylococcus aureus Glyceraldehyde-3-phosphate dehydrogenase. Arch Biochem Biophys. 752:109875. https://doi.org/10.1016/j.abb.2023.109875
  • Güner Yılmaz ÖZ, Güner FS. 2023. Hyaluronic Acid-Enriched Pectin-Based Hydrogel Films for Wound Healing. ITU ARI-Bulletin of the Istanbul Technical University, 55(1), Special issue: In memoriam to the late Prof. Dr. Yusuf Yağcı.
  • Güner-Yılmaz ÖZ, Akten ED, Kurkcuoglu O, Investigating Potential Allosteric Communication Paths in S.aureus GAPDH using Residue Interaction Networks, 19th Asian Chemical Congress, İstanbul-Türkiye,9-14July 2023
  • Güner-Yılmaz ÖZ, Yılmaz A, Akbıyıkoğulları K, Kocaağa B, Hooshmand S, Zabara MA, Alp Yürüm A, Bayazıt MK, Batırel S, Yavuz R, Karatepe K, Güner FS, Nanopartikül Katkılı Özel Tasarım Yara Örtüsü: Grafen Oksit ve Modifiye Grafen Oksit Katkılı Doğal Hidrojellerin Potansiyel Kullanımı, 15. Ulusal Kimya Mühendisliği Kongresi,Çanakkale 18 Mart Üniversitesi, 4-7 Eylül 2023.
  • Güner-Yılmaz ÖZ, Akten ED, Kürkçüoğlu Ö, Rezidü Etkileşim Ağları Kullanarak S. aureus GAPDH Enziminde Potansiyel Allosterik İletişim Yollarının Araştırılması, 15. Ulusal Kimya Mühendisliği Kongresi,Çanakkale 18 Mart Üniversitesi, 4-7 Eylül 2023.
  • Akbıyıkoğulları K, Güner-Yılmaz ÖZ, Yılmaz H, Güner FS, BSA ile Kaplanmış h-BN Nanopartikülleri: Kanser Tedavisinde Potansiyel Bir Taşıyıcı Sistem, 15. Ulusal Kimya Mühendisliği Kongresi,Çanakkale 18 Mart Üniversitesi, 4-7 Eylül 2023.
  • Yolaçan H, Karakaş E, Kaçan E, Akbıyıkoğulları K, Güner-Yılmaz ÖZ, Yılmaz A, Aliari M, Kocaağa B, Sirkecioğlu A, Güner FS, Kontrollü Aktif Molekül Salimi Yapabilen Zif-8 Nanopartikülü Katkili Pektin Hidrojel, 15. Ulusal Kimya Mühendisliği Kongresi,Çanakkale 18 Mart Üniversitesi, 4-7 Eylül 2023

2020

2018

2016

  • Güner, Ö.Z., Arabacıoglu-Kocaaga, B., Güner, F.S., Synthesis and Characterization of Pectin Based Hydrogel Films: Effect of pH and Drug Loading Method on Drug Release Kinetics, 46th IUPAC World Polymer Congress (MACRO 2016), Istanbul-Turkey, July 17-21, 2016.
  • Güner, Ö.Z., Kocaaga, B., Güner, F.S., Pektin Temelli Hidrojel Filmlerde Sentez Yönteminin ve pH’ın İlaç Salım Kinetiğine Etkisi, 12. Ulusal Kimya Mühendisliği Kongresi, İzmir Yüksek Teknoloji Enstitüsü, (23-26 Eylül 2016).