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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Database for CO2 separation performances of MOFs based on computational materials screening(American Chemical Society (ACS), 2018) Eruçar, İlknur; Department of Chemical and Biological Engineering; Altıntaş, Çiğdem; Avcı, Gökay; Harman, Hilal Dağlar; Azar, Ayda Nemati Vesali; Velioğlu, Sadiye; Keskin, Seda; Researcher; Post Doctorate Student; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40548Metal-organic frameworks (MOFs) are potential adsorbents for CO2 capture. Because thousands of MOFs exist, computational studies become very useful in identifying the top performing materials for target applications in a time-effective manner. In this study, molecular simulations were performed to screen the MOF database to identify the best materials for CO2 separation from flue gas (CO2/N-2) and landfill gas (CO2/CH4) under realistic operating conditions. We validated the accuracy of our computational approach by comparing the simulation results for the CO2 uptakes, CO2/N-2 and CO2/CH4 selectivities of various types of MOFs with the available experimental data. Binary CO2/N-2 and CO2/CH4 mixture adsorption data were then calculated for the entire MOF database. These data were then used to predict selectivity, working capacity, regenerability, and separation potential of MOFs. The top performing MOF adsorbents that can separate CO2/N-2 and CO2/CH4 with high performance were identified. Molecular simulations for the adsorption of a ternary CO2/N-2/CH4 mixture were performed for these top materials to provide a more realistic performance assessment of MOF adsorbents. The structure-performance analysis showed that MOFs with Delta Q(st)(0) > 30 kJ/mol, 3.8 angstrom < pore-limiting diameter < 5 angstrom, 5 angstrom < largest cavity diameter < 7.5 angstrom, 0.5 < phi < 0.75, surface area < 1000 m(2)/g, and rho > 1 g/cm(3) are the best candidates for selective separation of CO2 from flue gas and landfill gas. This information will be very useful to design novel MOFs exhibiting high CO2 separation potentials. Finally, an online, freely accessible database https://cosmoserc.ku.edu.tr was established, for the first time in the literature, which reports all of the computed adsorbent metrics of 3816 MOFs for CO2/N-2, CO2/CH4, and CO2/N-2/CH4 separations in addition to various structural properties of MOFs.Publication Open Access In situ formation of copper phosphate on hydroxyapatite for wastewater treatment(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Rahmani, Fatemeh; Ghadi, Arezoo; Khaksar, Samad; Doustkhah, Esmail; PhD Student; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM)Here, we control the surface activity of hydroxyapatite (HAp) in wastewater treatment which undergoes peroxodisulfate (PDS) activation. Loading the catalytically active Cu species on HAp forms a copper phosphate in the outer layer of HAp. This modification turns a low active HAp into a high catalytically active catalyst in the dye degradation process. The optimal operational conditions were established to be [Cu-THAp](0) = 1 g/L, [RhB](0) = 20 mg/L, [PDS](0) = 7.5 mmol/L, and pH = 3. The experiments indicate that the simultaneous presence of Cu-THAp and PDS synergistically affect the degradation process. Additionally, chemical and structural characterizations proved the stability and effectiveness of Cu-THAp. Therefore, this work introduces a simple approach to water purification through green and sustainable HAp-based materials.Publication Open Access Plasmon-coupled photocapacitor neuromodulators(American Chemical Society (ACS), 2020) Ülgüt, Burak; Çetin, Arif E.; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Melikov, Rustamzhon; Srivastava, Shashi Bhushan; Karatüm, Onuralp; Doğru-Yüksel, Itır Bakış; Jalali, Houman Bahmani; Sadeghi, Sadra; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Nizamoğlu, Sedat; PhD Student; Researcher; PhD Student; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 40319; 130295Efficient transduction of optical energy to bioelectrical stimuli is an important goal for effective communication with biological systems. For that, plasmonics has a significant potential via boosting the light-matter interactions. However, plasmonics has been primarily used for heat-induced cell stimulation due to membrane capacitance change (i.e., optocapacitance). Instead, here, we demonstrate that plasmonic coupling to photocapacitor biointerfaces improves safe and efficacious neuromodulating displacement charges for an average of 185% in the entire visible spectrum while maintaining the faradic currents below 1%. Hot-electron injection dominantly leads the enhancement of displacement current in the blue spectral window, and the nanoantenna effect is mainly responsible for the improvement in the red spectral region. The plasmonic photocapacitor facilitates wireless modulation of single cells at three orders of magnitude below the maximum retinal intensity levels, corresponding to one of the most sensitive optoelectronic neural interfaces. This study introduces a new way of using plasmonics for safe and effective photostimulation of neurons and paves the way toward ultrasensitive plasmon-assisted neurostimulation devices.Publication Open Access Nonlinear nanomechanical mass spectrometry at the single-nanoparticle level(American Chemical Society (ACS), 2019) Yüksel, Mert; Orhan, Ezgi; Yanık, Cenk; Arı, Atakan B.; Hanay, M. Selim; Department of Electrical and Electronics Engineering; Demir, Alper; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 3756Nanoelectromechanical systems (NEMS) have emerged as a promising technology for performing the mass spectrometry of large biomolecules and nanoparticles. As nanoscale objects land on NEMS sensors one by one, they induce resolvable shifts in the resonance frequency of the sensor proportional to their weight. The operational regime of NEMS sensors is often limited by the onset of nonlinearity, beyond which the highly sensitive schemes based on frequency tracking by phase-locked loops cannot be readily used. Here, we develop a measurement architecture with which to operate at the nonlinear regime and measure frequency shifts induced by analytes in a rapid and sensitive manner. We used this architecture to individually characterize the mass of gold nanoparticles and verified the results by performing independent measurements of the same nanoparticles based on linear mass sensing. Once the feasibility of the technique is established, we have obtained the mass spectrum of a 20 nm gold nanoparticle sample by individually recording about 500 single-particle events using two modes working sequentially in the nonlinear regime. The technique obtained here can be used for thin nanomechanical structures that possess a limited dynamic range.Publication Open Access Nanoscale communication with molecular arrays in nanonetworks(Institute of Electrical and Electronics Engineers (IEEE), 2012) Galmes, Sebastia; Atakan, Barış; Akan, Özgür Barış; PhD Student; Faculty Member; College of EngineeringMolecular communication is a promising nanoscale communication paradigm that enables nanomachines to exchange information by using molecules as communication carrier. Up to now, the molecular communication channel between a transmitter nanomachine (TN) and a receiver nanomachine (RN) has been modeled as either concentration channel or timing channel. However, these channel models necessitate exact time synchronization of the nanomachines and provide a relatively low communication bandwidth. In this paper, the Molecular ARray-based COmmunication (MARCO) scheme is proposed, in which the transmission order of different molecules is used to convey molecular information without any need for time synchronization. The MARCO channel model is first theoretically derived, and the intersymbol interference and error probabilities are obtained. Based on the error probability, achievable communication rates are analytically obtained. Numerical results and performance comparisons reveal that MARCO provides significantly higher communication rate, i.e., on the scale of 100 Kbps, than the previously proposed molecular communication models without any need for synchronization. More specifically, MARCO can provide more than 250 Kbps of molecular communication rate if intersymbol time and internode distance are set to 2 mu s and 2 nm, respectively.Publication Open Access Characterizing the cellular response to nitrogen-doped carbon nanocups(Multidisciplinary Digital Publishing Institute (MDPI), 2019) Griffith, Amber S.; Zhang, Thomas D.; Burkert, Seth C.; Adıgüzel, Zelal; Star, Alexander; Saunders, William S.; Department of Molecular Biology and Genetics; Ayhan, Ceyda Açılan; Faculty Member; Department of Molecular Biology and Genetics; School of MedicineCarbon nanomaterials, specifically, carbon nanotubes (CNTs) have many potential applications in biology and medicine. Currently, this material has not reached its full potential for application due to the potential toxicity to mammalian cells, and the incomplete understanding of how CNTs interface with cells. The chemical composition and structural features of CNTs have been shown to directly affect their biological compatibility. The incorporation of nitrogen dopants to the graphitic lattice of CNTs results in a unique cup shaped morphology and minimal cytotoxicity in comparison to its undoped counterpart. In this study, we investigate how uniquely shaped nitrogen-doped carbon nanocups (NCNCs) interface with HeLa cells, a cervical cancer epithelial cultured cell line, and RPE-1 cells, an immortalized cultured epithelial cell line. We determined that NCNCs do not elicit a cytotoxic response in cells, and that they are uptaken via endocytosis. We have conjugated fluorescently tagged antibodies to NCNCs and shown that the protein-conjugated material is also capable of entering cells. This primes NCNCs to be a good candidate for subsequent protein modifications and applications in biological systems.Publication Open Access Combining a nanoparticle-mediated immunoradiotherapy with dual blockade of LAG3 and TIGIT improves the treatment efficacy in anti-PD1 resistant lung cancer(BioMed Central, 2022) Hu, Yun; Paris, Sebastien; Bertolet, Genevieve; Barsoumian, Hampartsoum B.; He, Kewen; Chen, Dawei; Wasley, Mark; Da Silva, Jordan; Mitchell, Joylise A.; Voss, Tiffany A.; Masrorpour, Fatemeh; Leyton, Claudia Kettlun; Yang, Liangpeng; Leuschner, Carola; Puebla-Osorio, Nahum; Gandhi, Saumil; Quynh-Nhu Nguyen; Cortez, Maria Angelica; Welsh, James W.; Sezen, Duygu; Faculty Member; School of Medicine; 170535Background: while improvements in immunoradiotherapy have significantly improved outcomes for cancer patients, this treatment approach has nevertheless proven ineffective at controlling the majority of malignancies. One of the mechanisms of resistance to immunoradiotherapy is that immune cells may be suppressed via the myriad of different immune checkpoint receptors. Therefore, simultaneous blockade of multiple immune checkpoint receptors may enhance the treatment efficacy of immunoradiotherapy. Methods: we combined NBTXR3-enhanced localized radiation with the simultaneous blockade of three different checkpoint receptors: PD1, LAG3, and TIGIT, and tested the treatment efficacy in an anti-PD1-resistant lung cancer model in mice. 129 Sv/Ev mice were inoculated with fifty thousand alpha PD1-resistant 344SQR cells in the right leg on day 0 to establish primary tumors and with the same number of cells in the left leg on day 4 to establish the secondary tumors. NBTXR3 was intratumorally injected into the primary tumors on day 7, which were irradiated with 12 Gy on days 8, 9, and 10. Anti-PD1 (200 mu g), alpha LAG3 (200 mu g), and alpha TIGIT (200 mu g) were given to mice by intraperitoneal injections on days 5, 8, 11, 14, 21, 28, 35, and 42. Results: this nanoparticle-mediated combination therapy is effective at controlling the growth of irradiated and distant unirradiated tumors, enhancing animal survival, and is the only one that led to the destruction of both tumors in approximately 30% of the treated mice. Corresponding with this improved response is robust activation of the immune response, as manifested by increased numbers of immune cells along with a transcriptional signature of both innate and adaptive immunity within the tumor. Furthermore, mice treated with this combinatorial therapy display immunological memory response when rechallenged by the same cancer cells, preventing tumor engraftment. Conclusion: our results strongly attest to the efficacy and validity of combining nanoparticle-enhanced radio-therapy and simultaneous blockade of multiple immune checkpoint receptors and provide a pre-clinical rationale for investigating its translation into human patients.Publication Open Access High-yield production of biohybrid microalgae for on-demand cargo delivery(Wiley, 2020) Akolpoğlu, Mukrime Birgul; Bozüyük, Uğur; Ceylan, Hakan; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Kızılel, Seda; Doğan, Nihal Olcay; Sitti, Metin; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; College of Engineering; Graduate School of Sciences and Engineering; School of Medicine; 28376; N/A; 297104Biohybrid microswimmers exploit the swimming and navigation of a motile microorganism to target and deliver cargo molecules in a wide range of biomedical applications. Medical biohybrid microswimmers suffer from low manufacturing yields, which would significantly limit their potential applications. In the present study, a biohybrid design strategy is reported, where a thin and soft uniform coating layer is noncovalently assembled around a motile microorganism.Chlamydomonas reinhardtii(a single-cell green alga) is used in the design as a biological model microorganism along with polymer-nanoparticle matrix as the synthetic component, reaching a manufacturing efficiency of approximate to 90%. Natural biopolymer chitosan is used as a binder to efficiently coat the cell wall of the microalgae with nanoparticles. The soft surface coating does not impair the viability and phototactic ability of the microalgae, and allows further engineering to accommodate biomedical cargo molecules. Furthermore, by conjugating the nanoparticles embedded in the thin coating with chemotherapeutic doxorubicin by a photocleavable linker, on-demand delivery of drugs to tumor cells is reported as a proof-of-concept biomedical demonstration. The high-throughput strategy can pave the way for the next-generation generation microrobotic swarms for future medical active cargo delivery tasks.Publication Open Access A radioenhancing nanoparticle mediated immunoradiation improves survival and generates long-term antitumor immune memory in an anti-PD1-resistant murine lung cancer model(BioMed Central, 2021) Hu, Yun; Paris, Sebastien; Barsoumian, Hampartsoum; Abana, Chike O.; He, Kewen; Wasley, Mark; Masrorpour, Fatemeh; Chen, Dawei; Yang, Liangpeng; Dunn, Joe D.; Gandhi, Saumil; Nguyen, Quynh-Nhu; Cortez, Maria Angelica; Welsh, James W.; Sezen, Duygu; Faculty Member; School of Medicine; 170535Background: combining radiotherapy with PD1 blockade has had impressive antitumor effects in preclinical models of metastatic lung cancer, although anti-PD1 resistance remains problematic. Here, we report results from a triple-combination therapy in which NBTXR3, a clinically approved nanoparticle radioenhancer, is combined with high-dose radiation (HDXRT) to a primary tumor plus low-dose radiation (LDXRT) to a secondary tumor along with checkpoint blockade in a mouse model of anti-PD1-resistant metastatic lung cancer. Methods: mice were inoculated with 344SQR cells in the right legs on day 0 (primary tumor) and the left legs on day 3 (secondary tumor). Immune checkpoint inhibitors (ICIs), including anti-PD1 (200 mu g) and anti-CTLA4 (100 mu g) were given intraperitoneally. Primary tumors were injected with NBTXR3 on day 6 and irradiated with 12-Gy (HDXRT) on days 7, 8, and 9; secondary tumors were irradiated with 1-Gy (LDXRT) on days 12 and 13. The survivor mice at day 178 were rechallenged with 344SQR cells and tumor growth monitored thereafter. Results: NBTXR3 + HDXRT + LDXRT + ICIs had significant antitumor effects against both primary and secondary tumors, improving the survival rate from 0 to 50%. Immune profiling of the secondary tumors revealed that NBTXR3 + HDXRT + LDXRT increased CD8 T-cell infiltration and decreased the number of regulatory T (Treg) cells. Finally, none of the re-challenged mice developed tumors, and they had higher percentages of CD4 memory T cells and CD4 and CD8 T cells in both blood and spleen relative to untreated mice. Conclusions: NBTXR3 nanoparticle in combination with radioimmunotherapy significantly improves anti-PD1 resistant lung tumor control via promoting antitumor immune response.Publication Open Access Liquid crystal eastomer actuated reconfigurable microscale kirigami metastructures(Wiley, 2021) Zhang, Mingchao; Shahsavan, Hamed; Guo, Yubing; Pena-Francesch, Abdon; Zhang, Yingying; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Programmable actuation of metastructures with predesigned geometrical configurations has recently drawn significant attention in many applications, such as smart structures, medical devices, soft robotics, prosthetics, and wearable devices. Despite remarkable progress in this field, achieving wireless miniaturized reconfigurable metastructures remains a challenge due to the difficult nature of the fabrication and actuation processes at the micrometer scale. Herein, microscale thermo-responsive reconfigurable metasurfaces using stimuli-responsive liquid crystal elastomers (LCEs) is fabricated as an artificial muscle for reconfiguring the 2D microscale kirigami structures. Such structures are fabricated via two-photon polymerization with sub-micrometer precision. Through rationally designed experiments guided by simulations, the optimal formulation of the LCE artificial muscle is explored and the relationship between shape transformation behaviors and geometrical parameters of the kirigami structures is build. As a proof of concept demonstration, the constructs for temperature-dependent switching and information encryption is applied. Such reconfigurable kirigami metastructures have significant potential for boosting the fundamental small-scale metastructure research and the design and fabrication of wireless functional devices, wearables, and soft robots at the microscale as well.