Publications

This list presents the publications, presentations, theses, and other scholarly activities from our lab. Please visit Dr. Özçelikkale's Institutional CV or Google Scholar Profile for detailed records.

• Mehrasa, “Development of 2D traction force microscopy on actuatable silicone elastomer substrates,” M.sc. Thesis, Middle East Technical University, Ankara, Turkey, 2025. [Online]. Available: https://open.metu.edu.tr/handle/11511/116091 (🎓 Thesis).            
• E. Dağıstan, P. Esmaeilzadeh, E. Büküşoğlu, and A. Özçelikkale, “Implementation of Microfluidic FRAP for Characterization of Nanoparticle Transport in Porous Biopolymer Networks,” in 19th Nanoscience and Nanotechnology Conference (NanoTR-19), Ankara, Turkey, Aug. 2025, pp. 444–444. [Online]. Available: https://drive.google.com/file/d/1OwEILS7TLr8A7pYpU6H78kAIUUV7L-LU/view (📢️ Conference Proceeding).      
• M. Fathi, A. Mehrasa, and A. Özçelikkale, “Engineering Actuatable Cell Culture Substrates with Embedded Nanoparticles for Probing Cellular Force Generation under Mechanical Stimulation,” in 19th Nanoscience and Nanotechnology Conference, Ankara, Turkey: Podium Presentation, Aug. 2025, p. 90. [Online]. Available: https://drive.google.com/file/d/1OwEILS7TLr8A7pYpU6H78kAIUUV7L-LU/view (📢️ Conference Proceeding).      
• H. B. Aydın, “Development of bioinspired hydrogel culture systems for in vitro recapitulation of 3d tumor microenvironment,” Master thesis, Middle East Technical University, 2025. [Online]. Available: https://open.metu.edu.tr/handle/11511/115693 (🎓 Thesis).            
• A. Akalın, E. Dağıstan, and A. Özçelikkale, “Microstructure-Level Investigation of Nanoparticle Transport in Collagen Hydrogels for Advancing Nanomedicine Design and Delivery Strategies,” in Advances in Computational Heat and Mass Transfer, ICCHMT 2025, Cham: Springer International Publishing Ag,  2025. (📢️ Conference Proceeding).  
• H. B. Aydin, A. Ozcelikkale, and A. Acar, “Exploiting Matrix Stiffness to Overcome Drug Resistance,” ACS Biomater. Sci. Eng., vol. 10, no. 8, pp. 4682–4700, Aug. 2024, doi: 10.1021/acsbiomaterials.4c00445. (📜 Journal Article).         
• Ildız, “Investigation of migration of breast cancer cells in relation to fibroblasts on a microfluidic system,” Master Thesis, Middle East Technical University, 2024. Accessed: Nov. 23, 2024. [Online]. Available: https://open.metu.edu.tr/handle/11511/111572 (🎓 Thesis).            
• M. Fathi, A. Mehrasa, and A. Ozcelikkale, “Prototyping of a Microfluidic Mechanochemical Gradient Chip by 3D Printed Molding for In Vitro Drug Testing,” in SB3C2024 Summer Biomechanics, Bioengineering and Biotransport Conference, Lake Geneva, WI, USA: Podium Presentation, Jun. 2024. (📢️ Conference Proceeding). 
• H. B. Aydin, H. Moon, B. Han, A. Ozcelikkale, and A. Acar, “Tumor-Microenvironment-on-Chip Platform for Assessing Drug Response in 3D Dynamic Culture,” in 3D Cell Culture: Methods and Protocols, Z. Sumbalova Koledova, Ed., New York, NY: Humana Press, New York, NY, 2024, pp. 265–278. doi: 10.1007/978-1-0716-3674-9_17. [📚 Book Chapter].              
• A. Akalın, “Modeling and characterization of fluid, macromolecule, and nanoparticle transport in fibrous collagen hydrogels,” M.Sc. Thesis, Middle East Technical University, Ankara, Turkey, 2023. (🎓 Thesis).            
• Dedekargınoğlu, “Rapid prototyping of microfluidic tissue culture systems via mask based photo polymerization,” M.Sc. Thesis, Middle East Technical University, Ankara, Turkey, 2023. (🎓 Thesis).        
• Dedekargınoğlu, C. Ildız, A. Acar, and A. Özçelikkale, “Rapid prototyping of microfluidic co-culture platform based on a 3D printing workflow for systematic investigation of tumor stromal interactions,” in 2nd MPS World Summit ALTEX Proceedings, in 1, vol. 11. Berlin, Germany: Poster Presentation, Jun. 2023, p. 200. (📢️ Conference Proceeding). 
• M. Fathi, B. Dedekargınoğlu, A. A. Akalın, and A. Ozcelikkale, “Parametric Design and Manufacturing of Mammary Carcinoma Chip by Stereolithography for Simulating Drug Transport Around the Tumor,” in 2nd MPS World Summit ALTEX Proceedings, in 1, vol. 11. Berlin, Germany: Poster Presentation, Jun. 2023, p. 235. (📢️ Conference Proceeding).             
• A. Akalın, B. Dedekargınoğlu, S. R. Choi, B. Han, and A. Ozcelikkale, “Predictive Design and Analysis of Drug Transport by Multiscale Computational Models Under Uncertainty,” Pharm Res, vol. 40, no. 2, pp. 501–523, Feb. 2023, doi: 10.1007/s11095-022-03298-8. (📜 Journal Article).         
• S. Farahani, “Development of a micro-well-based microfluidic 3d cell culture for cytotoxicity assays,” Master thesis, Middle East Technical University, 2023. Accessed: Nov. 23, 2024. [Online]. Available: https://open.metu.edu.tr/handle/11511/102777 (🎓 Thesis).            
• C. Açıkgöz, U. Dirmencioğlu, S. Farahani, A. Özçelikkale, and E. Yıldırım, “Capillary pressure barriers for spatial confinement in organ-on-a-chip devices,” İzmir, Türkiye: 5th NOVEL FLUIDIC TECHNOLOGIES WORKSHOP WITH AN EMPHASIS ON TISSUE ENGINEERING,  2023. [Online]. Available: https://www.yesilceliktaslab.com/5thnovelfluidicworkshop (📢️ Conference Proceeding).         
• Afthinos et al., “Migration and 3D Traction Force Measurements inside Compliant Microchannels,” Nano Lett., vol. 22, no. 18, pp. 7318–7327, Sep. 2022, doi: 10.1021/acs.nanolett.2c01261. (📜 Journal Article).           
• A. Akalın and A. Özçelikkale, “Modeling and Characterization of Nanomedicine Transport within Tumor Microenvironment across Scales,” in 16th Nanoscience and Nanotechnology Conference, Ankara, Turkey: Poster Presentation, Sep. 2022, p. 338. [Online]. Available: https://hdl.handle.net/11511/98956 (📢️ Conference Proceeding). 
• A. Akalın, B. Dedekargınoğlu, S. R. Choi, B. Han, and A. Ozcelikkale, “Predictive Design and Analysis of Drug Transport by Multiscale Computational Models Under Uncertainty,” Pharm Res, Jun. 2022, doi: 10.1007/s11095-022-03298-8. (📜 Journal Article).              
• Pathni et al., “Cytotoxic T Lymphocyte Activation Signals Modulate Cytoskeletal Dynamics and Mechanical Force Generation,” Frontiers in Immunology, vol. 13, 2022, doi: https://doi.org/10.3389/fimmu.2022.779888. (📜 Journal Article).         

• Dedekargınoğlu, A. A. Akalın, and A. Ozcelikkale, “Rapid Low-Cost Prototyping of Organ-on-Chip Platforms by 3D-Printed Microfluidics,” in 3rd Annual European Organ-on-Chip Society Meeting, Uppsala, Sweden (Online): Poster Presentation, Jul. 2021. (📢️ Conference Proceeding).

  Prior Research

  Research conducted by Dr. Özçelikkale before the lab's founding in 2021.

• H. Moon, A. Ozcelikkale, Y. Yang, B. D. Elzey, S. F. Konieczny, and B. Han, “An engineered pancreatic cancer model with intra-tumoral heterogeneity of driver mutations,” Lab Chip, Sep. 2020, doi: 10.1039/D0LC00707B. (📜 Journal Article).          
• Ozcelikkale and A. Upadhyaya, “Regulation of Cytoskeletal Dynamics during T Cell Activation by Substrate Stiffness,” in Bulletin of the American Physical Society, American Physical Society, Mar. 2018. Accessed: Jan. 12, 2018. [Online]. Available: https://meetings.aps.org/Meeting/MAR18/Session/R51.7 (📢️ Conference Proceeding).         
• Ozcelikkale et al., “Differential response to doxorubicin in breast cancer subtypes simulated by a microfluidic tumor model,” Journal of Controlled Release, vol. 266, no. Supplement C, pp. 129–139, Nov. 2017, doi: 10.1016/j.jconrel.2017.09.024. (📜 Journal Article).           
• Ozcelikkale, J. C. Dutton, F. Grinnell, and B. Han, “Effects of dynamic matrix remodelling on en masse migration of fibroblasts on collagen matrices,” Journal of The Royal Society Interface, vol. 14, no. 135, p. 20170287, Oct. 2017, doi: 10.1098/rsif.2017.0287. (📜 Journal Article). 
• Ozcelikkale, H. Moon, M. Linnes, and B. Han, “Cover Image, Volume 9, Issue 5,” WIREs Nanomed Nanobiotechnol, vol. 9, no. 5, pp. e1489-n/a, Sep. 2017, doi: 10.1002/wnan.1489. (📜 Journal Article).              
• Q. Wan et al., “Subcellular domain-dependent molecular hierarchy of SFK and FAK in mechanotransduction and cytokine signaling,” Scientific Reports, vol. 7, no. 1, p. 9033, Aug. 2017, doi: 10.1038/s41598-017-09495-5. (📜 Journal Article).              
• Y. Liang et al., “Enzyme-Induced Matrix Softening Regulates Hepatocarcinoma Cancer Cell Phenotypes,” Macromolecular Bioscience, vol. 17, no. 9, p. 1700117, 2017, doi: 10.1002/mabi.201700117. (📜 Journal Article). 
• Ozcelikkale, H. Moon, M. Linnes, and B. Han, “In vitro microfluidic models of tumor microenvironment to screen transport of drugs and nanoparticles,” Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, pp. e1460-n/a, 2017, doi: 10.1002/wnan.1460. (📜 Journal Article).              
• N. E. Clay et al., “Modulation of Matrix Softness and Interstitial Flow for 3D Cell Culture Using a Cell-Microenvironment-on-a-Chip System,” ACS Biomater. Sci. Eng., vol. 2, no. 11, pp. 1968–1975, Nov. 2016, doi: 10.1021/acsbiomaterials.6b00379. (📜 Journal Article).         
• S. Ghosh, A. Ozcelikkale, J. C. Dutton, and B. Han, “Role of intracellular poroelasticity on freezing-induced deformation of cells in engineered tissues,” Journal of The Royal Society Interface, vol. 13, no. 123, p. 20160480, Oct. 2016, doi: 10.1098/rsif.2016.0480. (📜 Journal Article). 
• Ozcelikkale, A. Conteh, M. Korc, and B. Han, “Role of Cancer-Associated Fibroblasts on Drug Response of Pancreatic Cancer Using Tumor-Microenvironment-on-Chip,” presented at the 2016 Controlled Release Society Annual Meeting and Exposition, Jul. 2016. (📢️ Conference Proceeding).   
• F. Li, T.-G. Cha, J. Pan, A. Ozcelikkale, B. Han, and J. H. Choi, “DNA Walker-Regulated Cancer Cell Growth Inhibition,” ChemBioChem, vol. 17, no. 12, pp. 1138–1141, Jun. 2016, doi: 10.1002/cbic.201600052. (📜 Journal Article).         
• Ozcelikkale and B. Han, “Thermal Destabilization of Collagen Matrix Hierarchical Structure by Freeze/Thaw,” PLoS ONE, vol. 11, no. 1, p. e0146660, Jan. 2016, doi: 10.1371/journal.pone.0146660. (📜 Journal Article).         
• V. Noe-Kim, A. Ozcelikkale, and B. Han, “An In Vitro Microfluidic Tumor Model to Mimic Ductal Carcinoma In Situ,” presented at the The Summer Biomechanics, Bioengineering, and Biotransport Conference, Jun. 2015. [Online]. Available: https://archive.sb3c.org/2015-proceedings/ (📢️ Conference Proceeding).   
• Ozcelikkale, “Freezing-Induced Deformation of Biomaterials in Cryomedicine,” Purdue University, West Lafayette, IN USA, 2015. (🎓 Thesis).            
• Ozcelikkale, F. Grinnell, and B. Han, “Spatiotemporal Cell-matrix Interactions during En Masse Migration of Fibroblasts on Collagen Matrices,” 2015. (📜 Journal Article).         
• Ozcelikkale, F. Grinnell, and B. Han, “Spatiotemporal Cell-Matrix Interactions During En Masse Migration of Fibroblasts on Collagen Matrices,” presented at the Summer Biomechanics, Bioengineering, and Biotransport Conference,  2015. [Online]. Available: https://archive.sb3c.org/2015-proceedings/ (📢️ Conference Proceeding).   
• Kwak, A. Ozcelikkale, C. S. Shin, K. Park, and B. Han, “Simulation of complex transport of nanoparticles around a tumor using tumor-microenvironment-on-chip,” Journal of Controlled Release, vol. 194, pp. 157–167, Nov. 2014, doi: 10.1016/j.jconrel.2014.08.027. (📜 Journal Article). 
• Ozcelikkale, K. Shin, V. Noe-Kim, C. S. Shin, K. Park, and B. Han, “Rapid Screening of Anti-cancer Drugs and Delivery Vehicles Using Tumor microenvironment-on-chip,” in 2014 Controlled Release Society Annual Meeting and Exposition, Chicago, IL, Jul. 2014. (📢️ Conference Proceeding).              
• Ozcelikkale, B. D. Elzey, T. L. Ratliff, and B. Han, “Development of Tumor-On-Chip Platform to Tumor Heterogeneity Induced Chemoresponse,” in Walther Cancer Foundation Symposium, South Bend, IN, Oct. 2013. (📢️ Conference Proceeding).          
• Z. Xu, A. Ozcelikkale, Y. L. Kim, and B. Han, “Spatiotemporal Characterization of Extracellular Matrix Microstructures in Engineered Tissue: A Whole-Field Spectroscopic Imaging Approach,” Journal of Nanotechnology in Engineering and Medicine, vol. 4, no. 1, Jul. 2013, doi: 10.1115/1.4024130. (📜 Journal Article). 
• Ozcelikkale, S. Ghosh, and B. Han, “Multifaceted transport characteristics of nanomedicine: Needs for characterization in dynamic environment,” Molecular Pharmaceutics, vol. 10, pp. 2111–2126, 2013. (📜 Journal Article).  
• Ozcelikkale, Y. Li, X. Xu, and B. Han, “Effects of Freezing on Collagen Nanoscale Structure in Engineered Tissues,” in ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology, Boston,  2013. [Online]. Available: https://doi.org/10.1115/NEMB2013-93125 (📢️ Conference Proceeding).   
• Seawright, A. Ozcelikkale, C. Dutton, and B. Han, “Role of Cells in Freezing-induced Cell-fluid-matrix Interactions within Engineered Tissues,” J Biomech Eng, vol. 135, p. 91001, 2013, doi: 10.1115/1.4024571. (📜 Journal Article). 
• Ozcelikkale and C. Sert, “Least-squares spectral element solution of incompressible Navier–Stokes equations with adaptive refinement,” Journal of Computational Physics, vol. 231, no. 9, pp. 3755–3769, May 2012, doi: 10.1016/j.jcp.2012.01.024. (📜 Journal Article).           
• Y. Kim, Z. Xu, A. Ozcelikkale, and B. Han, “Functional Imaging of Matrix Structure of Cryopreserved Engineered Tissues Using Back-Directional Gated Mesoscopic Imaging,” presented at the ASME 2012 Summer Bioengineering Conference,  2012. doi: 10.1115/SBC2012-80692. (📢️ Conference Proceeding). 
• Ozcelikkale and B. Han, “Nanoscale Fluid-Structure Interactions in Cytoplasm During Freezing,”  2012. doi: 10.1115/IMECE2012-88161. (📢️ Conference Proceeding). 
• Ozcelikkale and B. Han, “Nano-scale Fluid-Structure Interactions in Cytoplasm During Freezing,” in Proceedings of ASME 2012 International Mechanical Engineering Congress & Exposition,  2012. [Online]. Available: https://doi.org/10.1115/IMECE2012-88161 (📢️ Conference Proceeding).         
• Seawright, A. Ozcelikkale, C. Dutton, and B. Han, “Role of Cells in Freezing-Induced Cell-Fluid Matrix Interactions Within Engineered Tissues,” presented at the ASME 2012 Summer Bioengineering Conference,  2012. doi: https://doi.org/10.1115/SBC2012-80531. (📢️ Conference Proceeding).         
• Ozcelikkale and C. Sert, “h- and p-Adaptive Incompressible Flow Solutions on Cartesian Grids Using Least Squares Spectral Element Method,” presented at the ECCOMAS CFD 2010 Conference, Lisbon, Portugal, Jun. 2010. [Online]. Available: http://congress2.cimne.com/eccomas/proceedings/cfd2010/searchPapers.htm (📢️ Conference Proceeding).         
• Ozcelikkale, “Development of an Incompressible, Laminar Flow Solver Based on Least Squares Spectral Element Method with p-Type Adaptive Refinement Capabilities,” M.S. Thesis, Middle East Technical University, 2010. (🎓 Thesis).