Researcher: TRUE, Sedat
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Publication Metadata only Impact of the surface modifications and cell culture techniques on the biomechanical properties of PDMS in relation to cell growth behavior(Taylor & Francis, 2022) N/A; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; N/A; Aydemir, Duygu; TRUE, Sedat; Alaca, Burhanettin Erdem; Ulusu, Nuriye Nuray; Researcher; Master Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); NA; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; N/A; 115108; 6807PDMS is the most widely used material in the microfluidic systems because of its advantageous properties including ease of manufacture, low cost, transparency, and gas permeability. Although all biomaterials need to be sterilized for usage for in vitro or in vivo systems to avoid possible contaminants, none of them proved effective in providing the gold standards so far for PDMS sterilization. Therefore we evaluated the influence of both UV and ethanol sterilization of PDMS substrates on the cell behavior via investigating cell proliferation, oxidative stress and nutrient metabolism of 293 T cells growing on the PDMS first time in the literature. Modulus of elasticity and stress relaxation of UV-treated PDMS samples increased compared to the ethanol-treated ones leading to a state of surface stiffness preferable for cell growth and proliferation. Oxidative stress metabolism of cells growing on the UV-treated PDMS was more stable compared to the ethanol-treated samples. Trace element and mineral metabolism are not impaired in the cells growing on the UV-treated PDMS samples. First time in the literature, we showed that UV treatment is more suitable for the PDMS samples used in the cell culture experiments. [GRAPHICS] .Publication Metadata only Impact of PDMS surface treatment in cell-mechanics applications(Elsevier, 2020) N/A; N/A; Department of Mechanical Engineering; N/A; Department of Mechanical Engineering; TRUE, Sedat; Aydemir, Duygu; Salman, Naveed; Ulusu, Nuriye Nuray; Alaca, Burhanettin Erdem; Master Student; PhD Student; Other; Faculty Member; Faculty Member; Department of Mechanical Engineering; N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Health Sciences; College of Engineering; School of Medicine; College of Engineering; N/A; N/A; N/A; 6807; 115108As a widely used elastomer in cell mechanics studies, PDMS is exposed to a variety of surface treatments during cell culture preparation. Considering its viscoelastic nature in particular, effects of the aforementioned treatments on PDMS mechanical behaviour, especially at the relevant length scale of 100 mu m, received limited attention. This is despite the fact that significant errors were reported in the quantification of cellular traction forces as a result of minute changes in PDMS mechanical properties. Hence, the effects of plasma oxidation, sterilization and incubation on PDMS modulus of elasticity, relaxation modulus and Poisson's ratio are studied here through tension and stress relaxation tests, with the results of the latter interpreted via the linear viscoelastic formulation. It is observed that although significant deviations from the properties of untreated PDMS are measured through this cycle of surface treatment, properties of untreated PDMS are almost recovered following incubation in cell medium. For example, the modulus of elasticity of treated PDMS was found to be 6% smaller than that of the untreated PDMS. The corresponding deviation was <3% and <1% for the relaxation modulus and time-averaged Poisson's ratio, respectively. The rate of change of the Poisson's ratio with time was also found to be reduced at the end of incubation process in cell medium. As a result, viscoelastic properties of untreated PDMS can safely be used within the error margins provided by this work.Publication Metadata only Poisson's ratio of PDMS thin films(Elsevier Sci Ltd, 2018) Bayraktar, Halil; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; TRUE, Sedat; Aksoy, Bekir; Alaca, Burhanettin Erdem; Master Student; Master Student; Faculty Member; Department of Mechanical Engineering; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 115108Despite the fact that a small uncertainty in PDMS Poisson's ratio leads to significant errors in traction force microscopy, there is a clear lack of data for PDMS films at the scale of 100 mu m, a relevant size scale frequently employed in cell mechanics studies. Equally important is the need for consideration of the viscoelastic nature of PDMS, as no mechanical property - including Poisson's ratio - can be taken as a time-independent constant. The foremost challenge for addressing these issues is the difficulty of carrying out stress relaxation tests on miniature PDMS samples accompanied by non-contact strain measurement with a very high spatiotemporal resolution. This study introduces such a stress relaxation platform incorporating i) the proper means for the application of necessary boundary conditions, ii) a high-precision in load measurement, and iii) a non-contact, local strain measurement technique based on single particle tracking. During stretching, images were recorded at a rate of 18 Hz with a 40 mu m spatial resolution. Microsphere-embedded PDMS films as thin as 125 and 155 mu m were prepared to study the Poisson's ratio by a local strain microscope. After tracing the displacement of microspheres by a single particle tracking method and using a strain mapping, Poisson's ratio for 155-mu m-thick PDMS was found to decrease from 0.483 +/- 0.034 to 0.473 +/- 0.040 over a period of 20 min. For 125-mu m-thick PDMS, this reduction took place from 0.482 +/- 0.041 to 0.468 +/- 0.038. Moreover, a non-monotonic reduction was observed in both cases. This negative correlation between Poisson's ratio and relaxation time was found to be statistically significant for both thicknesses with p < 0.001. The viscoelastic behavior was further characterized through the Burgers model. With a measurement field of 597 x 550 mu m(2), this study emphasizes the importance of the local investigation of mechanical properties. Furthermore, the dependence of transverse strain on a film thickness difference of 30 mu m was measured to determine the sensitivity of local strain tracking. The inherent high resolution of the proposed approach enables one to measure deformations more precisely and to observe the temporal evolution of the Poisson's ratio that has not been observed before. In addition to the high-precision determination of PDMS Poisson's ratio, this work also offers a promising pathway for the accurate and time dependent determination of the mechanical properties of other soft materials, where similar ambiguities exist regarding the mechanical behavior.Publication Open Access Soft-tissue material properties and mechanogenetics during cardiovascular development(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Pekkan, Kerem; Siddiqui, Hummaira Banu; TRUE, Sedat; Lashkarinia, Seyedeh Samaneh; Faculty Member; Master Student; Researcher; Department of Mechanical Engineering; College of Engineering; Graduate School of Social Sciences and Humanities; 161845; N/A; N/A; N/ADuring embryonic development, changes in the cardiovascular microstructure and material properties are essential for an integrated biomechanical understanding. This knowledge also enables realistic predictive computational tools, specifically targeting the formation of congenital heart defects. Material characterization of cardiovascular embryonic tissue at consequent embryonic stages is critical to understand growth, remodeling, and hemodynamic functions. Two biomechanical loading modes, which are wall shear stress and blood pressure, are associated with distinct molecular pathways and govern vascular morphology through microstructural remodeling. Dynamic embryonic tissues have complex signaling networks integrated with mechanical factors such as stress, strain, and stiffness. While the multiscale interplay between the mechanical loading modes and microstructural changes has been studied in animal models, mechanical characterization of early embryonic cardiovascular tissue is challenging due to the miniature sample sizes and active/passive vascular components. Accordingly, this comparative review focuses on the embryonic material characterization of developing cardiovascular systems and attempts to classify it for different species and embryonic timepoints. Key cardiovascular components including the great vessels, ventricles, heart valves, and the umbilical cord arteries are covered. A state-of-the-art review of experimental techniques for embryonic material characterization is provided along with the two novel methods developed to measure the residual and von Mises stress distributions in avian embryonic vessels noninvasively, for the first time in the literature. As attempted in this review, the compilation of embryonic mechanical properties will also contribute to our understanding of the mature cardiovascular system and possibly lead to new microstructural and genetic interventions to correct abnormal development.