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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access On the capacity of diffusion-based molecular communications with SiNW FET-based receiver(Institute of Electrical and Electronics Engineers (IEEE), 2016) Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; College of EngineeringMolecular communication (MC) is a bio-inspired communication method based on the exchange of molecules for information transfer among nanoscale devices. Although MC has been extensively studied from various aspects, limitations imposed by the physical design of transceiving units have been largely neglected in the literature. Recently, we have proposed a nanobioelectronic MC receiver architecture based on the nanoscale field effect transistor-based biosensor (bioFET) technology, providing noninvasive and sensitive molecular detection at nanoscale while producing electrical signals at the output. In this paper, we derive analytical closed-form expressions for the capacity and capacity-achieving input distribution for a memoryless MC channel with a silicon nanowire (SiNW) FET-based MC receiver. The resulting expressions could be used to optimize the information flow in MC systems equipped with nanobioelectronic receivers.Publication Open Access 3D printed personalized magnetic micromachines from patient blood-derived biomaterials(American Association for the Advancement of Science (AAAS), 2021) Ceylan, Hakan; Doğan, Nihal Olcay; Yaşa, İmmihan Ceren; Department of Mechanical Engineering; Sitti, Metin; Musaoğlu, Miraç Nur; Kulalı, Zeynep Umut; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104; N/A; N/AWhile recent wireless micromachines have shown increasing potential for medical use, their potential safety risks concerning biocompatibility need to be mitigated. They are typically constructed from materials that are not intrinsically compatible with physiological environments. Here, we propose a personalized approach by using patient blood-derivable biomaterials as the main construction fabric of wireless medical micromachines to alleviate safety risks from biocompatibility. We demonstrate 3D printed multiresponsive microswimmers and microrollers made from magnetic nanocomposites of blood plasma, serum albumin protein, and platelet lysate. These micro-machines respond to time-variant magnetic fields for torque-driven steerable motion and exhibit multiple cycles of pH-responsive two-way shape memory behavior for controlled cargo delivery and release applications. Their proteinaceous fabrics enable enzymatic degradability with proteinases, thereby lowering risks of long-term toxicity. The personalized micromachine fabrication strategy we conceptualize here can affect various future medical robots and devices made of autologous biomaterials to improve biocompatibility and smart functionality.Publication Open Access Epithelial Wnt secretion drives the progression of inflammation-induced colon carcinoma in murine model(Cell Press, 2021) Değirmenci, Bahar; Dinçer, Cansu; Demirel, Habibe Cansu; Berkova, Linda; Moor, Andreas E.; Kahraman, Abdullah; Hausmann, George; Aguet, Michel; Valenta, Tomas; Basler, Konrad; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 245513Colon cancer is initiated by stem cells that escape the strict control. This process is often driven through aberrant activation of Wnt signaling by mutations in components acting downstream of the receptor complex that unfetter tumor cells from the need for Wnts. Here we describe a class of colon cancer that does not depend on mutated core components of the Wnt pathway. Genetically blocking Wnt secretion from epithelial cells of such tumors results in apoptosis, reduced expression of colon cancer markers, followed by enhanced tumor differentiation. In contrast to the normal colonic epithelium, such tumor cells autosecrete Wnts to maintain their uncontrolled proliferative behavior. In humans, we determined certain cases of colon cancers in which the Wnt pathway is hyperactive, but not through mutations in its core components. Our findings illuminate the path in therapy to find further subtypes of Wnt-dependent colon cancer that might be to Wnt secretion inhibitors.Publication Open Access Exciton recycling via InP quantum dot funnels for luminescent solar concentrators(Tsinghua University, 2021) Ow-Yang, Cleva W.; N/A; N/A; Department of Physics; Department of Electrical and Electronics Engineering; Jalali, Houman Bahmani; Sadeghi, Sadra; Toker, Işınsu Baylam; Han, Mertcan; Sennaroğlu, Alphan; Nizamoğlu, Sedat; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; N/A; 23851; 130295Luminescent solar concentrators (LSC) absorb large-area solar radiation and guide down-converted emission to solar cells for electricity production. Quantum dots (QDs) have been widely engineered at device and quantum dot levels for LSCs. Here, we demonstrate cascaded energy transfer and exciton recycling at nanoassembly level for LSCs. The graded structure composed of different sized toxic-heavy-metal-free InP/ZnS core/shell QDs incorporated on copper doped InP QDs, facilitating exciton routing toward narrow band gap QDs at a high nonradiative energy transfer efficiency of 66%. At the final stage of non-radiative energy transfer, the photogenerated holes make ultrafast electronic transitions to copper-induced mid-gap states for radiative recombination in the near-infrared. The exciton recycling facilitates a photoluminescence quantum yield increase of 34% and 61% in comparison with semi-graded and ungraded energy profiles, respectively. Thanks to the suppressed reabsorption and enhanced photoluminescence quantum yield, the graded LSC achieved an optical quantum efficiency of 22.2%. Hence, engineering at nanoassembly level combined with nonradiative energy transfer and exciton funneling offer promise for efficient solar energy harvesting.Publication Open Access Singularity links with exotic Stein fillings(Worldwide Center of Mathematics, 2014) Akhmedov, Anar; Department of Mathematics; Özbağcı, Burak; Faculty Member; Department of Mathematics; College of Sciences; 29746In [4], it was shown that there exist infinitely many contact Seifert fibered 3-manifolds each of which admits infinitely many exotic (homeomorphic but pairwise non-diffeomorphic) simply-connected Stein fillings. Here we extend this result to a larger set of contact Seifert fibered 3-manifolds with many singular fibers and observe that these 3-manifolds are singularity links. In addition, we prove that the contact structures induced by the Stein fillings are the canonical contact structures on these singularity links. As a consequence, we verify a prediction of András Némethi by providing examples of isolated complex surface singularities whose links with their canonical contact structures admitting infinitely many exotic simply-connected Stein fillings. Moreover, for infinitely many of these contact singularity links and for each positive integer n, we also construct an infinite family of exotic Stein fillings with fixed fundamental group ? ? ?n.Publication Open Access Comparison of the trifecta outcomes of robotic and open nephron-sparing surgeries performed in the robotic era of a single institution(SpringerOpen, 2015) Isik, Esin Ozturk; Mut, Tuna; Saglican, Yesim; Vural, Metin; Musaoğlu, Ahmet; N/A; N/A; Acar, Ömer; Onay, Aslıhan; Esen, Tarık; Faculty Member; Faculty Member; School of Medicine; 237530; N/A; 50536Purpose: In this study we aimed to report a comparative analysis between open and robotic nephron sparing surgeries (NSS) from a single institutional database. Methods: Patients who have undergone NSS during the robotic era of our institution were included in this study. Open (n = 74) and robotic (n = 59) groups were compared regarding trifecta outcome. Trifecta was defined as; warm ischemia time (WIT) <25 min, negative surgical margins and the absence of perioperative complications. Results: A total of 57 (77 %) and 45 (76 %) patients in the open and robotic groups, respectively achieved the trifecta outcome. Overall trifecta rate was 77 % (n = 102/133). The only statistically significant difference between trifecta positive and trifecta negative patients was the length of hospitalization (LOH). Except LOH; none of the tested parameters were shown to be predictive of trifecta outcome on univariate and multivariate analyses. Concerning trifecta positive patients; those in the open surgery group had larger tumors with a higher degree of morphometric complexity and were hospitalized for a longer period of time. Additionally, operative duration was significantly higher in the robotic group. Conclusions: In our cohort, no significant difference in achieving the trifecta outcome was reported after open and robotic NSS. Length of hospitalization was the only parameter that differed significantly between trifecta positive and trifecta negative patients. Surgical approach was not a significant predictor of simultaneous achievement of trifecta outcomes. Irrespective of the trifecta definition; larger and more complicated tumors were handled via open NSS.Publication Open Access Molecular dynamics study of orientation-dependent tensile properties of Si nanowires with native oxide: surface stress and surface energy effects(Institute of Electrical and Electronics Engineers (IEEE), 2021) Esfahani, Mohammad Nasr; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Zarepakzad, Sina; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; 115108; N/AMolecular dynamics (MD) simulations are employed to investigate the influence of native oxide layer on the mechanical properties of Si nanowires (NWs) through analyzing surface stress and surface energy effect. This work studies the tensile response of Si NWs along <100> and <110> crystal orientations. MD results are compared with the traditional core-shell model on the estimation of the modulus of elasticity of Si NWs with a native oxide layer. Density functional theory (DFT) methods are used to verify MD results on the surface energy calculations. Surface stress and surface elastic constants are studied for native oxide surface using MD simulations and compared with unreconstructed surfaces. In this work, the role of native oxide is addressed to understand the difference between experimental and computational findings on the modulus of elasticity of Si NWs.Publication Open Access Diversity in diffusion-based molecular communication channel with drift(Institute of Electrical and Electronics Engineers (IEEE), 2016) Department of Electrical and Electronics Engineering; Malak, Derya; Ramezani, Hamideh; Kocaoğlu, Murat; Akan, Özgür Barış; PhD Student; Department of Electrical and Electronics Engineering; College of EngineeringWe utilize the well known Additive Inverse Gaussian Noise (AIGN) communication channel to investigate the effect of diversity in diffusion-based molecular communication with drift, where the transmitter releases different types of molecules to the fluid medium by encoding the information onto the release time and type of molecules. The fluid channel imposes extra delay on the communication, and the receiver decodes the encoded information by solely utilizing the molecular arrival times. In this paper, simple receiver models based on maximum likelihood estimation (MLE) are investigated. Furthermore, upper and lower bounds on the capacity of AIGN communication channel with molecular diversity are derived.Publication Open Access Distinct chemical composition and enzymatic treatment induced human endothelial cells survival in acellular ovine aortae(BioMed Central, 2021) Rahbarghazi, Reza; Saberianpour, Shirin; Delkhosh, Aref; Amini, Hassan; Hassanpour, Mehdi; Heidarzadeh, Morteza; Sokullu, Emel; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of Medicine; N/A; 163024Objective: the current experiment aimed to assess the impact of detergents such as 3% Triton X-100, 1% peracetic acid, 1% Tween-20, and 1% SDS in combination with Trypsin–EDTA on acellularization of ovine aortae after 7 days. Results: Hematoxylin–Eosin staining showed an appropriate acellularization rate in ovine aortae, indicated by a lack of cell nuclei in the tunica media layer. DAPI staining confirmed the lack of nuclei in the vascular wall after being exposed to the combination of chemical and enzymatic solutions. Verhoeff-Van Gieson staining showed that elastin fibers were diminished in acellular samples compared to the control group while collagen stands were unchanged. CCK-8 survival assay showed enhanced viability in human umbilical vein endothelial cells 5 days after being cultured on decellularized samples compared to the cells cultured on a plastic surface (p < 0.05). SEM imaging showed flattening of endothelial cells on the acellular surface.Publication Open Access Soft-bodied adaptive multimodal locomotion strategies in fluid-filled confined spaces(American Association for the Advancement of Science (AAAS), 2021) Ren, Z.; Zhang, R.; Soon, R. H.; Liu, Z.; Hu, W.; Onck, P. R.; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; School of Medicine; College of Engineering; 297104Soft-bodied locomotion in fluid-filled confined spaces is critical for future wireless medical robots operating inside vessels, tubes, channels, and cavities of the human body, which are filled with stagnant or flowing biological fluids. However, the active soft-bodied locomotion is challenging to achieve when the robot size is comparable with the cross-sectional dimension of these confined spaces. Here, we propose various control and performance enhancement strategies to let the sheet-shaped soft millirobots achieve multimodal locomotion, including rolling, undulatory crawling, undulatory swimming, and helical surface crawling depending on different fluid-filled confined environments. With these locomotion modes, the sheet-shaped soft robot can navigate through straight or bent gaps with varying sizes, tortuous channels, and tubes with a flowing fluid inside. Such soft robot design along with its control and performance enhancement strategies are promising to be applied in future wireless soft medical robots inside various fluid-filled tight regions of the human body.