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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Optimization of argon-air DBD plasma-assisted grafting of polyacrylic acid on electrospun POSS-PCUU(Pergamon-Elsevier Science Ltd, 2023) Salehi, Roya; Mahkam, Mehrdad; Siahpoush, Vahid; Rahbarghazi, Reza; l; Abbasi, Farhang; Gargari, Ziba Zakeri; Sokullu, Emel; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of MedicineIt is accepted that significant interfacial reactions take place in engineered tissues between biomaterial surfaces and the host's tissue in the body. The lack of appropriate functional groups limits long-term biocompatibility and successful biological response of biomaterials. Therefore, the cell-biomaterial affinity should be increased by functional groups grafting to the surface of biomaterials which provide the basic properties of the desired tissue. For the first time in this study, PAAc grafting was performed using two-step argon-air DBD plasma at atmospheric pressure in a few seconds of exposure time, to modify the surface of POSS-PCUU nanofibers to selectively in-crease their superficial properties while maintaining the required mechanical properties. The Response Surface Methodology was used for experimental design to optimize the operating conditions of carboxylic acid grafting at the electrospun POSS-PCUU surface. Nanofiber surface modification was confirmed using ATR-FTIR, FE-SEM, AFM, WCA, and tensile test. The grafting of PAAc to the nanofiber surface was proved by the presence of a broad hydroxyl band in ATR-FTIR spectrum, the morphological changes observed in the SEM and AFM images, and the reduction of the water contact angle. The stress-strain behavior at the optimum point also showed an acceptable reduction in tensile strength. Furthermore, the effects of two variables, plasma processing time and plasma copolymerization time were optimized and investigated using the CCD method at five levels of carboxylic acid grafting density. The grafting of PAAc onto the nanofiber surface (73.69 +/- 2.1 mu g/cm2) produced at reaction conditions displayed great agreement with the predicted results by the model. Results showed that the modified PAAc-POSS-PCUU nanofibers will be a desirable surface for the immobilization of various ECM proteins with high potential in small-diameter vascular graft applications.Publication Metadata only Geometrical optimization of spin clusters for the preservation of quantum coherence(American Physical Society, 2024) ; Department of Physics; Gassab, Lea; Pusuluk, Orhan; Müstecaplıoğlu, Özgür Esat; Department of Physics; ; Graduate School of Sciences and Engineering; College of Sciences;We investigate the influence of geometry on the preservation of quantum coherence in spin clusters subjected a thermal environment. Assuming weak interspin coupling, we explore the various buffer network configura yons that can be embedded in a plane. Our findings reveal that the connectivity of the buffer network is crucial indetermining the preservation duration of quantum coherence in an individual central spin. Specifically, we observe that the maximal planar graph yields the longest preservation time for a given number of buffer spins. Interestingly, our results demonstrate that the preservation time does not consistently increase with an increasing #umber of buffer spins. Employing a quantum master equation in our simulations, we further demonstrate that a Cetrahedral geometry comprising a four-spin buffer network provides optimal protection against environmental Tects.Publication Metadata only Metal-support interaction in PT nanodisk-carbon nitride catalyst: insight from theory and experiment(MDPI, 2024) Doustkhah, Esmail; Kotb, Ahmed; Assadi, Mohammad Hussein Naseef; Balkan, Timuçin; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM)Metal-support interaction plays a critical role in determining the eventual catalytic activity of metals loaded on supporting substrates. This interaction can sometimes cause a significant drop in the metallic property of the loaded metal and, hence, a drop in catalytic activity in the reactions, especially in those for which low charge carrier transfer resistance is a necessary parameter. Therefore, there should be a case-by-case experimental or theoretical (or both) in-depth investigation to understand the role of support on each metal. Here, onto a layered porous carbon nitride (g-CN), we grew single crystalline Pt nanodisks (Pt@g-CN) with a lateral average size of 21 nm, followed by various characterisations such as electron microscopy techniques, and the measurement of electrocatalytic activity in the O-2 reduction reaction (ORR). We found that intercalating Pt nanodisks in the g-CN interlayers causes an increase in electrocatalytic activity. We investigated the bonding mechanism between carbon support and platinum using density functional theory and applied the d-band theory to understand the catalytic performance. Analysis of Pt's density of states and electronic population across layers sheds light on the catalytic behaviour of Pt nanoparticles, particularly in relation to their thickness and proximity to the g-CN support interface. Our simulation reveals an optimum thickness of similar to 11 angstrom, under which the catalytic performance deteriorates.Publication Metadata only Can Nth order Born approximation be exact?(IOP Publishing Ltd, 2024) Loran, Farhang; Department of Mathematics; Mostafazadeh, Ali; Department of Mathematics; College of SciencesFor the scattering of scalar waves in two and three dimensions and electromagnetic waves in three dimensions, we identify a condition on the scattering interaction under which the Nth order Born approximation gives the exact solution of the scattering problem for some N >= 1.Publication Metadata only Conditions on detecting tripartite entangled state in psychophysical experiments(SPRINGER HEIDELBERG, 2024) Department of Physics; Gassab, Lea; Pedram, Ali; Müstecaplıoğlu, Özgür Esat; Department of Physics; Graduate School of Sciences and Engineering; College of SciencesThis paper explores the sensitivity of the human visual system to quantum entangled light. We examine the possibility of human subjects perceiving multipartite entangled state through psychophysical experiments. Our focus begins with a bipartite entangled state to make a comparative study with the literature by taking into account additive noise for false positive on bipartite entanglement perception by humans. After that, we limit our similar investigation to a tripartite entangled state for simplicity in higher dimensions. To model the photodetection by humans, we employ the probability of seeing determined for coherently amplified photons in Fock number states, including an additive noise. Our results indicate that detecting bipartite and tripartite entanglement with the human eye is possible for a certain range of additive noise levels and visual thresholds. Finally, we discuss several alternative amplification methods.Publication Metadata only Consistent treatment of quantum systems with a time-dependent Hilbert space(MDPI, 2024) Department of Mathematics; Mostafazadeh, Ali; Department of Mathematics; College of SciencesWe consider some basic problems associated with quantum mechanics of systems having a time-dependent Hilbert space. We provide a consistent treatment of these systems and address the possibility of describing them in terms of a time-independent Hilbert space. We show that in general the Hamiltonian operator does not represent an observable of the system even if it is a self-adjoint operator. This is related to a hidden geometric aspect of quantum mechanics arising from the presence of an operator-valued gauge potential. We also offer a careful treatment of quantum systems whose Hilbert space is obtained by endowing a time-independent vector space with a time-dependent inner product. © 2024 by the author.Publication Metadata only What is quantum in probabilistic explanations of the sure-thing principle violation?(Elsevier Ireland Ltd, 2024) Department of Physics; Mahalli, Nematollah Farhadi; Pusuluk, Orhan; Department of Physics; College of SciencesThe Prisoner's Dilemma game (PDG) is one of the simple test-beds for the probabilistic nature of the human decision-making process. Behavioral experiments have been conducted on this game for decades and show a violation of the so-called sure-thing principle, a key principle in the rational theory of decision. Quantum probabilistic models can explain this violation as a second-order interference effect, which cannot be accounted for by classical probability theory. Here, we adopt the framework of generalized probabilistic theories and approach this explanation from the viewpoint of quantum information theory to identify the source of the interference. In particular, we reformulate one of the existing quantum probabilistic models using density matrix formalism and consider different amounts of classical and quantum uncertainties for one player's prediction about another player's action in PDG. This enables us to demonstrate that what makes possible the explanation of the violation is the presence of quantum coherence in the player's initial prediction and its conversion to probabilities during the dynamics. Moreover, we discuss the role of other quantum information-theoretical quantities, such as quantum entanglement, in the decision-making process. Finally, we propose a three-choice extension of the PDG to compare the predictive powers of quantum probability theory and a more general probabilistic theory that includes it as a particular case and exhibits third-order interference. © 2024 Elsevier B.V.Publication Metadata only Silk as a biodegradable resist for field-emission scanning probe lithography(Institute of Physics (IOP) Publishing, 2020) Sadeghi, Sadra; Rangelow, Ivo W.; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; N/A; N/A; Department of Electrical and Electronics Engineering; Alaca, Burhanettin Erdem; Kumar, Baskaran Ganesh; Melikov, Rustamzhon; Doğru-Yüksel, Itır Bakış; Nizamoğlu, Sedat; Faculty Member; Other; PhD Student; PhD Student; Faculty Member; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştirmalari Merkezi (KUYTAM); N/A; N/A; N/A; N/A; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; 115108; N/A; N/A; N/A; 130295The patterning of silk allows for manufacturing various structures with advanced functionalities for optical and tissue engineering and drug delivery applications. Here, we propose a high-resolution nanoscale patterning method based on field-emission scanning probe lithography (FE-SPL) that crosslinks the biomaterial silk on conductive indium tin oxide (ITO) promoting the use of a biodegradable material as resist and water as a developer. During the lithographic process, Fowler-Nordheim electron emission from a sharp tip was used to manipulate the structure of silk fibroin from random coil to beta sheet and the emission formed nanoscale latent patterns with a critical dimension (CD) of similar to 50 nm. To demonstrate the versatility of the method, we patterned standard and complex shapes. This method is particularly attractive due to its ease of operation without relying on a vacuum or a special gaseous environment and without any need for complex electronics or optics. Therefore, this study paves a practical and cost-effective way toward patterning biopolymers at ultra-high level resolution.Publication Metadata only FRET lasing from self-assembled DNA tetrahedral nanostructures suspended in optofluidic droplet resonators(Springer, 2014) Jonas, A.; Liu, H.; Fan, C.; Chen, Q.; Fan, X.; Department of Physics; N/A; N/A; Kiraz, Alper; Özelci, Ersan; Aas, Mehdi; Faculty Member; PhD Student; PhD Student; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 22542; N/A; N/AWe demonstrate Förster resonance energy transfer (FRET) lasing from self-assembled tetrahedral DNA complexes labeled with Cy3 and Cy5 dyes and suspended as a gain medium in aqueous microdroplet cavities deposited on a superhydrophobic surface. Threshold fluence and differential efficiency are characterized for DNA complexes containing 1Cy3-3Cy5 and 3Cy3-1Cy5. We demonstrate that at a constant Cy5 concentration, average threshold fluence is reduced 3 to 8 times and average differential efficiency is enhanced 6 to 30 times for 3Cy3-1Cy5 as compared to 1Cy3-3Cy5. Using 3Cy3-1Cy5 nanostructures, FRET lasing is observed at very low concentrations down to ∼ 1 μM. This work shows that optofluidic microlasers based on droplet resonators can be combined with DNA nanotechnology to explore applications in bio/chemical sensing and novel photonic devices.Publication Metadata only Structural changes in a Schiff base molecular assembly initiated by scanning tunneling microscopy tip(Institute of Physics (IOP) Publishing, 2016) Tomak, A.; Bacaksiz, C.; Mendirek, G.; Sahin, H.; Hur, D.; Gorgun, K.; Senger, R. T.; Peeters, F. M.; Zareie, H. M.; N/A; Birer, Özgür; Researcher; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/AWe report the controlled self-organization and switching of newly designed Schiff base (E)-4-((4-(phenylethynyl) benzylidene) amino) benzenethiol (EPBB) molecules on a Au (111) surface at room temperature. Scanning tunneling microscopy and spectroscopy (STM/STS) were used to image and analyze the conformational changes of the EPBB molecules. The conformational change of the molecules was induced by using the STM tip while increasing the tunneling current. The switching of a domain or island of molecules was shown to be induced by the STM tip during scanning. Unambiguous fingerprints of the switching mechanism were observed via STM/STS measurements. Surface-enhanced Raman scattering was employed, to control and identify quantitatively the switching mechanism of molecules in a monolayer. Density functional theory calculations were also performed in order to understand the microscopic details of the switching mechanism. These calculations revealed that the molecular switching behavior stemmed from the strong interaction of the EPBB molecules with the STM tip. Our approach to controlling intermolecular mechanics provides a path towards the bottom-up assembly of more sophisticated molecular machines.