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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access SimMBM channel simulator for media-based modulation systems(Institute of Electrical and Electronics Engineers (IEEE), 2021) Yiğit Zehra; Altunbaş, İbrahim; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Başar, Ertuğrul; Faculty Member; College of Engineering; 149116Media-based modulation (MBM), exploiting rich scattering properties of transmission environments via different radiation patterns of a single reconfigurable antenna (RA), has brought new insights into future communication systems. In this study, considering this innovative transmission principle, we introduce the realistic, two-dimensional (2D), and open-source SimMBM channel simulator to support various applications of MBM systems at sub-6 GHz frequency band in different environments.Publication Open Access Engineering human stellate cells for beta cell replacement therapy promotes in vivo recruitment of regulatory T cells(Elsevier, 2019) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Oran, Dilem Ceren; Lokumcu, Tolga; Bal, Tuğba; İnceoğlu, Yasemin; Albayrak, Özgür; Erkan, Murat Mert; Kurtoğlu, Metin; Can, Füsun; Önder, Tuğba Bağcı; Kızılel, Seda; Akolpoğlu, Mükrime Birgül; Faculty Member; Faculty Member; Master Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Health Sciences; College of Engineering; School of Medicine; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 103165; 184359; 28376; N/AType 1 diabetes (T1D) is an autoimmune disease characterized by destruction of pancreatic β cells. One of the promising therapeutic approaches in T1D is the transplantation of islets; however, it has serious limitations. To address these limitations, immunotherapeutic strategies have focused on restoring immunologic tolerance, preventing transplanted cell destruction by patients’ own immune system. Macrophage-derived chemokines such as chemokine-ligand-22 (CCL22) can be utilized for regulatory T cell (Treg) recruitment and graft tolerance. Stellate cells (SCs) have various immunomodulatory functions: recruitment of Tregs and induction of T-cell apoptosis. Here, we designed a unique immune-privileged microenvironment around implantable islets through overexpression of CCL22 proteins by SCs. We prepared pseudoislets with insulin-secreting mouse insulinoma-6 (MIN6) cells and human SCs as a model to mimic naive islet morphology. Our results demonstrated that transduced SCs can secrete CCL22 and recruit Tregs toward the implantation site in vivo. This study is promising to provide a fundamental understanding of SC-islet interaction and ligand synthesis and transport from SCs at the graft site for ensuring local immune tolerance. Our results also establish a new paradigm for creating tolerable grafts for other chronic diseases such as diabetes, anemia, and central nervous system (CNS) diseases, and advance the science of graft tolerance.Publication Open Access Synchronous and asynchronous response in dynamically perturbed proteins(American Chemical Society (ACS), 2021) Erkip, Albert; Erman, Batu; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Hacısüleyman, Aysima; Erman, Burak; Faculty Member; Graduate School of Sciences and Engineering; College of Engineering; N/A; 179997We present a dynamic perturbation-response model of proteins based on the Gaussian Network Model, where a residue is perturbed periodically, and the dynamic response of other residues is determined. The model shows that periodic perturbation causes a synchronous response in phase with the perturbation and an asynchronous response that is out of phase. The asynchronous component results from the viscous effects of the solvent and other dispersive factors in the system. The model is based on the solution of the Langevin equation in the presence of solvent, noise, and perturbation. We introduce several novel ideas: The concept of storage and loss compliance of the protein and their dependence on structure and frequency; the amount of work lost and the residues that contribute significantly to the lost work; new dynamic correlations that result from perturbation; causality, that is, the response of j when i is perturbed is not equal to the response of i when j is perturbed. As examples, we study two systems, namely, bovine rhodopsin and the class of nanobodies. The general results obtained are (i) synchronous and asynchronous correlations depend strongly on the frequency of perturbation, their magnitude decreases with increasing frequency, (ii) time-delayed mean-squared fluctuations of residues have only synchronous components. Asynchronicity is present only in cross correlations, that is, correlations between different residues, (iii) perturbation of loop residues leads to a large dissipation of work, (iv) correlations satisfy the hypothesis of pre-existing pathways according to which information transfer by perturbation rides on already existing equilibrium correlations in the system, (v) dynamic perturbation can introduce a selective response in the system, where the perturbation of each residue excites different sets of responding residues, and (vi) it is possible to identify nondissipative residues whose perturbation does not lead to dissipation in the protein. Despite its simplicity, the model explains several features of allosteric manipulation.Publication Open Access Observation of the correlations between pair wise interaction and functional organization of the proteins, in the protein ınteraction network of saccaromyces cerevisiae(World Academy of Science, Engineering and Technology (WASET), 2008) Haliloğlu, T.; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Keskin, Özlem; Faculty Member; College of Engineering; N/A; 26605Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.Publication Open Access Experimental verification of gap metric as a tool for model selection in multi-linear model-based control(Elsevier, 2004) Galan, O.; Romagnoli, J. A.; Palazoğlu, A.; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; College of Engineering; 108526A nonlinear system can be modeled using a set of linear models that cover the range of operation. A model-based control strategy then can be employed that uses the local models in a cooperative manner to control the nonlinear system. The decision of how many models are sufficient for effective control can be tackled by the use of the gap metric that quantifies the distance between two linear operators. A pH control experiment is used to demonstrate the effectiveness of gap metric as a tool for model selection.Publication Open Access Screening for selectivity(Nature Publishing Group (NPG), 2020) Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; College of Engineering; 40548Metal-organic frameworks are promising adsorbents for CO2 capture from flue gas, but many perform poorly when exposed to flue gas containing water. Now, a computational screening approach identifies MOFs with preserved CO2/N-2 selectivities in wet flue gas and experiments confirm their outstanding CO2 capture performance.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; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; 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 Androgen receptor-mediated transcription in prostate cancer(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Morova, Tunç; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Lack, Nathan Alan; Özturan, Doğancan; Faculty Member; PhD Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; 120842; N/AAndrogen receptor (AR)-mediated transcription is critical in almost all stages of prostate cancer (PCa) growth and differentiation. This process involves a complex interplay of coregulatory proteins, chromatin remodeling complexes, and other transcription factors that work with AR at cis-regulatory enhancer regions to induce the spatiotemporal transcription of target genes. This enhancer-driven mechanism is remarkably dynamic and undergoes significant alterations during PCa progression. In this review, we discuss the AR mechanism of action in PCa with a focus on how cis-regulatory elements modulate gene expression. We explore emerging evidence of genetic variants that can impact AR regulatory regions and alter gene transcription in PCa. Finally, we highlight several outstanding questions and discuss potential mechanisms of this critical transcription factor.Publication Open Access An integrated application of control performance assessment and root cause analysis in refinery control loops(Elsevier, 2020) Yağcı, Mehmet; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; College of Engineering; 108526Assessing the performance of control loops is an important component of Control Performance Monitoring (CPM) systems. Most of the industrial chemical processes have a large number of control loops interacting with each other in a complex way due to material and energy integration in the plant. A problem occurring in a certain control loop can easily upset the performance of the other control loops. Therefore, identification of the ""bad"" control loops causing a plant-wide disturbances is a crucial task. In this work, an integrated approach covering performance assessment and interaction analysis is proposed to detect the ""bad"" loops based on their performances. First, Minimum Variance Control (MVC) benchmark is used to screen-out the poor performing loops. Then, the spectral envelope method utilizing frequency analysis is used to identify the common oscillation periods among the loops under study. Finally, Granger causality is used to plot the interaction map between the loops. Even though these methods are well developed and used for several purposes separately, we present an integrated approach which focuses and analyzes the ""bad loops"". The developed approach has been tested in a refinery plant having 18 control loops. The results show that the proposed method is clearly able to identify and isolate the root-cause control loops. The validation of results and further improvements in the control loops under study have been given.Publication Open Access A review on computational modeling tools for MOF-based mixed matrix membranes(Multidisciplinary Digital Publishing Institute (MDPI), 2019) Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; College of Engineering; 40548Computational modeling of membrane materials is a rapidly growing field to investigate the properties of membrane materials beyond the limits of experimental techniques and to complement the experimental membrane studies by providing insights at the atomic-level. In this study, we first reviewed the fundamental approaches employed to describe the gas permeability/selectivity trade-off of polymer membranes and then addressed the great promise of mixed matrix membranes (MMMs) to overcome this trade-off. We then reviewed the current approaches for predicting the gas permeation through MMMs and specifically focused on MMMs composed of metal organic frameworks (MOFs). Computational tools such as atomically-detailed molecular simulations that can predict the gas separation performances of MOF-based MMMs prior to experimental investigation have been reviewed and the new computational methods that can provide information about the compatibility between the MOF and the polymer of the MMM have been discussed. We finally addressed the opportunities and challenges of using computational studies to analyze the barriers that must be overcome to advance the application of MOF-based membranes.