Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
76 results
Search Results
Publication Metadata only Extracellular matrix sulfation in the tumor microenvironment stimulates cancer stemness and invasiveness(Wiley, 2024) Arlov, Oystein; Cunningham, Katherine; Vunjak-Novakovic, Gordana; Department of Chemical and Biological Engineering; Kızılel, Seda; Kuşoğlu, Alican; Örnek, Deniz; Dansık, Aslı; Özkan, Sena Nur; Sarıca, Sevgi; Yangın, Kardelen; Özdinç, Şevval; Solcan, Nuriye; Doğanalp, Efe Can; Karaoğlu, İsmail Can; Solaroğlu, İhsan; Bulutay, Pınar; Fırat, Pınar Arıkan; Erus, Suat; Tanju, Serhan; Dilege, Şükrü; Tunçbağ, Nurcan; Öztürk, Ece; Uzun, Ceren; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Health Sciences; Graduate School of Sciences and Engineering; School of MedicineTumor extracellular matrices (ECM) exhibit aberrant changes in composition and mechanics compared to normal tissues. Proteoglycans (PG) are vital regulators of cellular signaling in the ECM with the ability to modulate receptor tyrosine kinase (RTK) activation via their sulfated glycosaminoglycan (sGAG) side chains. However, their role on tumor cell behavior is controversial. Here, it is demonstrated that PGs are heavily expressed in lung adenocarcinoma (LUAD) patients in correlation with invasive phenotype and poor prognosis. A bioengineered human lung tumor model that recapitulates the increase of sGAGs in tumors in an organotypic matrix with independent control of stiffness, viscoelasticity, ligand density, and porosity, is developed. This model reveals that increased sulfation stimulates extensive proliferation, epithelial-mesenchymal transition (EMT), and stemness in cancer cells. The focal adhesion kinase (FAK)-phosphatidylinositol 3-kinase (PI3K) signaling axis is identified as a mediator of sulfation-induced molecular changes in cells upon activation of a distinct set of RTKs within tumor-mimetic hydrogels. The study shows that the transcriptomic landscape of tumor cells in response to increased sulfation resembles native PG-rich patient tumors by employing integrative omics and network modeling approaches.Publication Metadata only Rapid and accurate screening of the COF space for natural gas purification: COFInformatics(American Chemical Society, 2024) Department of Chemical and Biological Engineering; Aksu, Gökhan Önder; Keskin, Seda; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of EngineeringIn this work, we introduced COFInformatics, a computational approach merging molecular simulations and machine learning (ML) algorithms, to evaluate all synthesized and hypothetical covalent organic frameworks (COFs) for the CO2/CH4 mixture separation under four different adsorption-based processes: pressure swing adsorption (PSA), vacuum swing adsorption (VSA), temperature swing adsorption (TSA), and pressure-temperature swing adsorption (PTSA). We first extracted structural, chemical, energy-based, and graph-based molecular fingerprint features of every single COF structure in the very large COF space, consisting of nearly 70,000 materials, and then performed grand canonical Monte Carlo simulations to calculate the CO2/CH4 mixture adsorption properties of 7540 COFs. These features and simulation results were used to develop ML models that accurately and rapidly predict CO2/CH4 mixture adsorption and separation properties of all 68,614 COFs. The most efficient separation process and the best adsorbent candidates among the entire COF spectrum were identified and analyzed in detail to reveal the most important molecular features that lead to high-performance adsorbents. Our results showed that (i) many hypoCOFs outperform synthesized COFs by achieving higher CO2/CH4 selectivities;(ii) the top COF adsorbents consist of narrow pores and linkers comprising aromatic, triazine, and halogen groups;and (iii) PTSA is the most efficient process to use COF adsorbents for natural gas purification. We believe that COFInformatics promises to expedite the evaluation of COF adsorbents for CO2/CH4 separation, thereby circumventing the extensive, time- and resource-intensive molecular simulations.Publication Metadata only Targeting cancer cells via tumor-homing peptide CREKA functional PEG nanoparticles(Elsevier, 2016) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Okur, Aysu Ceren; Erkoç, Pelin; Kızılel, Seda; Master Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 28376Targeting cell microenvironment via nano-particle based therapies holds great promise for treatment of various diseases. One of the main challenges in targeted delivery of nanoparticles for cancer therapy includes reduced localization of delivery vehicles at tumor site. The therapeutic efficacy of drugs can be improved by recruiting delivery vehicles towards specific region of tumorigenesis in the body. Here, we demonstrate an effective approach in creating PEG particles via water-in-water emulsion technique where tumor-homing peptide CREKA was used for functionalization. Simultaneous conjugation of laminin peptide IKVAV into hydrogel network and influence of altered combinations of ligands on intracellular uptake of anticancer drugs by HeLa cells were investigated. CREKA conjugated hydrogel nanoparticles were more effective to improve apoptotic effects of the model drug Doxorubicin (DOX) compared to that of particles conjugated with other peptides. Fluorescence intensity analysis on confocal micrographs suggested significantly higher cellular uptake of CREKA conjugated PEG particles than internalization of nanoparticles in other groups. We observed that fibrin binding ability of PEG particles could be increased up to 94% through CREKA conjugation. Our results suggest the possibility of cancer cell targeting via CREKA-functional PEG nanoparticles.Publication Metadata only Versatile liquid-core optofluidic waveguides fabricated in hydrophobic silica aerogels by femtosecond-laser ablation(Elsevier, 2015) Yalizay, Berna; Morova, Yagiz; Dincer, Koray; Jonas, Alexandr; Akturk, Selcuk; N/A; Department of Chemical and Biological Engineering; Department of Physics; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Physics; Graduate School of Sciences and Engineering; College of Engineering; College of Science; N/A; 29633; 22542We report on the fabrication and characterization of versatile light waveguides exploiting filaments of a polar liquid confined within hydrophobic silica aerogels. Aerogels are highly porous materials with extremely low refractive index which makes them suitable as rigid cladding of liquid-core optofluidic waveguides based on total internal reflection of light. In this article, we introduce a new microfabrication technique that allows direct and precise processing of monolithic silica aerogels by ablation with femtosecond laser pulses. Using fast scanning of the focused laser ablation beam synchronized with the motion of the processed aerogel sample, we created high-quality straight microchannels of similar to 5 mm length with controlled cross-sections inside monolithic aerogels. After the ablation, we filled the channels with high-refractive index ethylene glycol, forming multimode liquid core - solid cladding optofluidic waveguides. Subsequently, we carried out light-guiding experiments to measure overall optical attenuation of these waveguides. The characterization of waveguide transmission yielded values of propagation losses lower than 10 dB cm(-1), demonstrating that the liquid-core waveguides with laser-ablated aerogel cladding represent an attractive alternative in optofluidic applications targeting controlled routing of light along arbitrary three-dimensional paths.Publication Metadata only MOF materials as therapeutic agents, drug carriers, imaging agents and biosensors in cancer biomedicine: recent advances and perspectives(Elsevier, 2021) Bieniek, Adam; Terzyk, Artur P.; Wisniewski, Marek; Roszek, Katarzyna; Kowalczyk, Piotr; Sarkisov, Lev; Kaneko, Katsumi; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548We summarize recent advances in application of MOFs as therapeutic agents, drug carriers, imaging agents and biosensors in cancer biomedicine. A holistic perspective is adopted to produce a comprehensive, critical and readable document useful to a broad community in chemistry, material science, medical fields etc. None of the previous articles adopted a holistic approach focusing on a specific disease or area, such as cancer. MOFs have a tremendous potential in cancer diagnostics and treatment. Although a new field, the amount of literature and data accumulated in this area is vast, quickly growing and requires some systematization and processing. We propose a broad overview of MOF-related literature in the treatment and diagnosis of cancer. In our study, we set: (i) to consolidate the most important and up to date information from the field of MOFs applications in medicine, particularly in anticancer therapy; and to reflect these developments in one, comprehensive study, (ii) to highlight new and emerging topics in the field, (iii) to tabulate the large number of the application examples and case studies to make the information more accessible and easy to follow, (iv) and finally, to broadly reflect on the potential of MOFs in application to cancer treatment, including the existing challenges and emerging opportunities.Publication Metadata only Mesenchymal Stem Cells (MSCs) Improve Beta Cell Function within Biomimetic PEG Hydrogels(Mary Ann Liebert, Inc., 2015) Karaoz, E.; Department of Chemical and Biological Engineering; N/A; Kızılel, Seda; Bal, Tuğba; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 28376; 353534N/APublication Metadata only Separation of CO2 mixtures using zn(bdc)(ted)0.5 membranes and composites: a molecular simulation study(amer Chemical Soc, 2011) N/A; Department of Chemical and Biological Engineering; Eruçar, İlknur; Keskin, Seda; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 260094; 40548We used grand canonical Monte Carlo and equilibrium molecular dynamics simulations to compute adsorption isotherms and self-diffusivities of CH4/H-2 mixtures in a nanoporous metal organic framework Zn(bdc)(ted)(0.5) in our recent study (J. Phys. Chem. C 2010, 114, 13047). in this work, we extended our calculations to CO2/CH4 and CO2/H-2 mixtures by computing adsorption selectivity, diffusion selectivity, and permeation selectivity of Zn(bdc)(ted)(0.5) for these gas mixtures. Performance of several composite membranes including Zn(bdc)(ted)(0.5) as filler particles in polymer matrices was also examined for separation of CO2 from CH4 and H-2 using a combination of atomistic and continuum modeling. Results showed that adding even a small volume fraction of Zn(bdc)(ted)(0.5) into polymers can significantly enhance the gas permeability and carry the polymer/Zn(bdc)(ted)(0.5) composite membranes above the current upper bound established for pure polymer membranes.Publication Metadata only Prediction of O-2/N-2 selectivity in metal-organic frameworks via high-throughput computational screening and machine learning(American Chemical Society (ACS), 2022) Orhan, İbrahim B.; Le, Tu C.; Babarao, Ravichandar; N/A; Department of Chemical and Biological Engineering; Harman, Hilal Dağlar; Keskin, Seda; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 40548Machine learning (ML), which is becoming an increasingly popular tool in various scientific fields, also shows the potential to aid in the screening of materials for diverse applications. In this study, the computation-ready experimental (CoRE) metal-organic framework (MOF) data set for which the O-2 and N-2 uptakes, self-diffusivities, and Henry's constants were calculated was used to fit the ML models. The obtained models were subsequently employed to predict such properties for a hypothetical MOF (hMOF) data set and to identify structures having a high O-2/N-2 selectivity at room temperature. The performance of the model on known entries indicated that it would serve as a useful tool for the prediction of MOF characteristics with r(2) correlations between the true and predicted values typically falling between 0.7 and 0.8. The use of different descriptor groups (geometric, atom type, and chemical) was studied; the inclusion of all descriptor groups yielded the best overall results. Only a small number of entries surpassed the performance of those in the CoRE MOF set; however, the use of ML was able to present the structure-property relationship and to identity the top performing hMOFs for O-2/N-2 separation based on the adsorption and diffusion selectivity.Publication Metadata only Tuning structural characteristics of red mud by simple treatments(Elsevier Sci Ltd, 2016) Soyer-Uzun, Sezen; N/A; Department of Chemical and Biological Engineering; Öztulum, Samira Fatma Kurtoğlu; Uzun, Alper; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; 384798; 59917Red mud (RM) is a hazardous waste produced vastly by aluminum industry worldwide. Because of its rich metal oxide content, it has potential to be utilized in various applications, such as ceramics production, construction, and catalysis. Here, we investigated the structural modification of RM by simple acid treatments using HCl and H2SO4 at different molarities, and at different digestion temperatures followed by calcinations at various temperatures. Structures before and after these treatments were characterized in deep detail by combining electron microscopy, diffraction, and spectroscopy complemented by thermal analysis and mass spectrometry to elucidate any changes in morphology, structure, and chemical composition introduced by these treatments. Results showed that acid treatments tremendously affect chemical composition; for instance, amount of Fe2O3 changes from 37 to 46 wt%, while that of minor components, such as Na2O, varies from approximately 9 wt% to trace amounts. Moreover, data also illustrated that high acid digestion temperature (220 degrees C) leads to significant improvements in surface area, from 17 m(2)/g to values exceeding 200 m(2)/g. Results presented here provide a guideline for modifying RM by simple treatments to tune its structural characteristics, potentially offering opportunities for its utilization as cost effective and environmentally friendly solutions to various applications.Publication Metadata only Impregnation of Ru(cod)(tmhd)(2) into PDMS film in supercritical carbon dioxide(Trans Tech Publications Ltd, 2012) Ge, Minglan; Ding, Fuchen; Department of Chemical and Biological Engineering; Erkey, Can; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 29633Metallopolymer nanocomposites has attracted much attention recently. The impregnation of organometallic compound from the supercritical solution into the polymer matrix has several advantages. The impregnation process isotherm of bis(2,2,6,6-tetramethy1-3,5-heptanedionato) (1,5-cyclooctadiene) ruthenium (II) (Ru(cod)(tmhd)(2)) into polydimethylsiloxane (PDMS) film in supercritical carbon dioxide (scCO(2)) was investigated. The experiments for determining the isotherm were carried out at 40 degrees C and 10.34 MPa. It was found that the impregnation isotherm is linear up to the saturation concentration of the precursor in scCO(2) fluid phase. The slope of the linear curve defined equilibrium partition coefficient K provides a measure of the partitioning of Ru(cod)(tmhd)(2) between the PDMS film and scCO(2) fluid phase and it is constant under the same conditions. It showed that K is mainly govered by the density of scCO(2) and does not change much with temperature at a constant density of scCO(2).