Tomak, Aysel
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Tomak, A
Tomak, A.
Tomak, A.
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03.01. Department of Bioengineering
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Former Staff
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1NO POVERTY
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2ZERO HUNGER
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3GOOD HEALTH AND WELL-BEING
6
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4QUALITY EDUCATION
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5GENDER EQUALITY
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6CLEAN WATER AND SANITATION
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7AFFORDABLE AND CLEAN ENERGY
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8DECENT WORK AND ECONOMIC GROWTH
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
2
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10REDUCED INEQUALITIES
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11SUSTAINABLE CITIES AND COMMUNITIES
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
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13CLIMATE ACTION
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14LIFE BELOW WATER
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15LIFE ON LAND
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
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17PARTNERSHIPS FOR THE GOALS
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16
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339
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9
This researcher does not have a WoS ID.
Scholarly Output
20
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17
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42195/7980
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0
Supervised PhD Theses
1
WoS Citation Count
331
Scopus Citation Count
273
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0
WoS Citations per Publication
16.55
Scopus Citations per Publication
13.65
Open Access Source
14
Supervised Theses
1
| Journal | Count |
|---|---|
| Nanotechnology | 3 |
| RSC Advances | 2 |
| Nanotoxicology | 2 |
| Ceramics International | 1 |
| Ceramics - Silikaty | 1 |
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Now showing 1 - 10 of 20
Article Citation - WoS: 16Citation - Scopus: 18Bacterial Detection Using Bacteriophages and Gold Nanorods by Following Time-Dependent Changes in Raman Spectral Signals(Informa Healthcare, 2018) Moghtader, Farzaneh; Tomak, Aysel; Zareie, Hadi M.; Pişkin, ErhanThis study attemps to develop bacterial detection strategies using bacteriophages and gold nanorods (GNRs) by Raman spectral analysis. Escherichia coli was selected as the target and its specific phage was used as the bioprobe. Target bacteria and phages were propagated/purified by traditional techniques. GNRs were synthesized by using hexadecyltrimethyl ammonium bromide (CTAB) as stabilizer. A two-step detection strategy was applied: Firstly, the target bacteria were interacted with GNRs in suspensions, and then they were dropped onto silica substrates for detection. It was possible to obtain clear surface-enchanced Raman spectroscopy (SERS) peaks of the target bacteria, even without using phages. In the second step, the phage nanoemulsions were droped onto the bacterial-GNRs complexes on those surfaces and time-dependent changes in the Raman spectra were monitored at different time intervals upto 40 min. These results demonstrated that how one can apply phages with plasmonic nanoparticles for detection of pathogenic bacteria very effectively in a quite simple test.Article Citation - WoS: 12Citation - Scopus: 11Theoretical and Experimental Investigation of Conjugation of 1,6-Hexanedithiol on Mos2(IOP Publishing Ltd., 2018) Gül, Aytaç; Bacaksız, Cihan; Ünsal, Emre; Akbalı, Barış; Tomak, Aysel; Zareie, Hadi M.; Şahin, HasanWe report an experimental and theoretical investigation of conjugation of 1,6-Hexaneditihiol (HDT) on MoS2 which is prepared by mixing MoS2 structure and HDT molecules in proper solvent. Raman spectra and the calculated phonon bands reveal that the HDT molecules bind covalently to MoS2. Surface morphology of MoS2/HDT structure is changed upon conjugation of HDT on MoS2 and characterized by using Scanning Electron Microscope (SEM). Density Functional Theory (DFT) based calculations show that HOMO-LUMO band gap of HDT is altered after the conjugation and two-S binding (handle-like) configuration is energetically most favorable among three different structures. This study displays that the facile thiol functionalization process of MoS2 is promising strategy for obtaining solution processable MoS2.Review Citation - WoS: 69Nanoparticle-Protein Corona Complex: Understanding Multiple Interactions Between Environmental Factors, Corona Formation, and Biological Activity(TAYLOR & FRANCIS LTD, 2021) Tomak, Aysel; Tomak, Aysel; Çesmeli, Selin; Öksel Karakuş, Ceyda; Hanoglu, Bercem D.; Winkler, David; Oksel Karakus, CeydaThe surfaces of pristine nanoparticles become rapidly coated by proteins in biological fluids, forming the so-called protein corona. The corona modifies key physicochemical characteristics of nanoparticle surfaces that modulate its biological and pharmacokinetic activity, biodistribution, and safety. In the two decades since the protein corona was identified, the importance of nanoparticles surface properties in regulating biological responses have been recognized. However, there is still a lack of clarity about the relationships between physiological conditions and corona composition over time, and how this controls biological activities/interactions. Here we review recent progress in characterizing the structure and composition of protein corona as a function of biological fluid and time. We summarize the influence of nanoparticle characteristics on protein corona composition and discuss the relevance of protein corona to the biological activity and fate of nanoparticles. The aim is to provide a critical summary of the key factors that affect protein corona formation (e.g. characteristics of nanoparticles and biological environment) and how the corona modulates biological activity, cellular uptake, biodistribution, and drug delivery. In addition to a discussion on the importance of the characterization of protein corona adsorbed on nanoparticle surfaces under conditions that mimic relevant physiological environment, we discuss the unresolved technical issues related to the characterization of nanoparticle-protein corona complexes during their journey in the body. Lastly, the paper offers a perspective on how the existing nanomaterial toxicity data obtained from in vitro studies should be reconsidered in the light of the presence of a protein corona, and how recent advances in fields, such as proteomics and machine learning can be integrated into the quantitative analysis of protein corona components.Publication Gümüş Nanopartiküllerin Morfolojisinin Protein Etkileşimleri Üzerindeki Etkisi(2024) Öksel Karakuş, Ceyda; Tomak, AyselNanoteknolojideki gelişmelere paralel olarak biyomedikal uygulamalarda kullanılan nanopartiküllerin sayısında hızlı bir artış yaşanmıştır. Gümüş nanopartiküller, farklı metalik nanopartikül grupları arasında başta antibakteriyel etkinlik olmak üzere tıbbi uygulamaların gereksinimleriyle örtüşen çeşitli avantajlara sahip olmalari dolayısıyla öne çıkmakta ve yaygın olarak kullanılmaktadır. Gümüş nanopartikülleri avantajlı kılan yapı ve yüzey özellikleri biyolojik ortam etkileşimleri sonucunda değişiklik gösterebilmekte ve bu değişimler dolayısıyla biyolojik aktivite ve foksiyonellik gibi nanopartikül özellikleri de doğrudan etkilenmektedir. Nanopartiküllerin biyolojik ortamlarda değişen yüzey özelliklerinin en büyük nedeninin yüzeylerine tutunan proteinler olduğu bilinmektedir. Ancak nanopartiküllerin morfolojik özelliklerinin etraflarında oluşan bu protein halkasının bileşimine ve miktarına olan etkisi tam olarak aydınlatılmamıştır. Bu çalışmada, partikül morfolojisinin nanopartikül-protein etkileşimleri üzerine etkisi incelenmiştir. Bu amaçla küresel ve prizma-benzeri yapıya sahip gümüş nanopartikülleri detaylı olarak karakterize edilmiş ve yüzeylerine tutunan proteinler sodyum dodesil sülfat–poliakrilamid jel elektroforezi (SDS–PAGE) yöntemiyle analitik olarak tayin edilmiştir. Spesifik olarak, küresel ve prizmatik morfolojiye sahip gümüş nanopartikülleri protein eklentili hücre kültürü ortamı içerisinde farklı süre (15 dk, 2 sa ve 24 sa) ve sıcaklıklarda (22 oC ve 37 oC) inkübe edilmiş ve yüzeylerine tutunan proteinler tür ve miktar açısından karşılaştırılmıştır.Article Citation - WoS: 54Citation - Scopus: 53Nitrogen Doping for Facile and Effective Modification of Graphene Surfaces(Royal Society of Chemistry, 2017) Yanılmaz, Alper; Tomak, Aysel; Akbalı, Barış; Bacaksız, Cihan; Özçeri, Elif; Arı, Ozan; Senger, Ramazan Tuğrul; Selamet, Yusuf; Zareie, Hadi M.We report experimental and theoretical investigations of nitrogen doped graphene. A low-pressure Chemical Vapor Deposition (CVD) system was used to grow large-area graphene on copper foil, using ethylene as the carbon source. Nitrogen-doped graphene (N-graphene) was prepared by exposing the graphene transferred to different substrates to atomic nitrogen plasma. The effect of varying nitrogen flow rates on doping of graphene was investigated while keeping the power and time constant during the process. The N-graphene was characterized via Raman Spectroscopy, X-ray Photoelectron Spectroscopy (XPS), Scanning Tunneling Microscopy and Spectroscopy (STM and STS), and Fourier Transform Infrared spectroscopy (FTIR). Raman mapping of N-graphene was also performed to show homogeneity of nitrogen on the graphitic lattice. XPS results have revealed the presence of different nitrogen configurations in the graphitic lattice with similar doping concentrations. Density functional theory (DFT) based calculations showed that the periodic adsorption of N atoms predominantly occurs on top of the C atoms rather than through substitution of C in our N-graphene samples. Our results indicate a feasible procedure for producing N-graphene with homogenous and effective doping which would be valuable in electronic and optical applications.Doctoral Thesis Development of Plasmonic Nanostructures for Photothermal Therapy of Prostate and Breast Cancer(Izmir Institute of Technology, 2019) Tomak, Aysel; Bulmuş, Volga; Şahin, HasanThe aim of this thesis is to synthesize gold nanorods (AuNRs) and lipid-stabilized nanobubbles containing AuNRs and investigate the potential of these plasmonic nanostructures as photothermal therapy agents for breast and prostate cancer through in vitro cell culture experiments. For this aim, firstly, AuNRs were synthesized at varying aspect ratios (ARs) and characterized via several techniques including UV-Vis/NIR spectroscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), inductively coupled plasma-mass spectroscopy (ICP-MS), electrophoretic light scattering (ELS) and X-ray photoelectron spectroscopy (XPS). The surface of AuNRs was modified with a biocompatible polymer, poly(ethylene glycol) (PEG), via ligand exchange method. Cytotoxicity, cell uptake and photothermal effects of AuNRs were investigated via in vitro cell culture experiments using human prostate cancer (DU 145) and epithelial (RWPE-1), breast cancer (MCF7) and epithelial (MCF 10A) cell lines. It was concluded that AuNRs (AR=4.0) were superior than AuNRs (AR=7.0) in terms of cell viability and photothermal effect. Separately, a non-commercial antibody (Ab) targeting a specific sialic acid derivative on the plasma membrane of DU 145 and MCF7 cancer cells was conjugated to AuNRs. Conjugations were characterized with the same techniques and investigated via in vitro cytotoxicity and cell uptake experiments. The Ab-conjugated AuNRs displayed the capability of selective targeting prostate cancer cells. Additionally, lipid-stabilized AuNRs and lipid-stabilized nanobubbles containing AuNRs (AuNBs) were synthesized for the first time and characterized using UV-Vis/NIR spectroscopy, SEM, ICP-MS and ELS techniques. Lipid-stabilized AuNRs were successfully synthesized using varying lipid mixtures instead of cationic, toxic surfactant. Separately, AuNBs were synthesized by combining PEG modified AuNRs with DPPC: DSPE-PEG lipid film under sonication and gas stream. AuNBs showed the same or significantly lower toxicity depending on the cell types and the same photothermal effect with respect to AuNRs (AR=4.0) upon irradiation under laser at 808 nm.Article Citation - WoS: 3Citation - Scopus: 3Gold Nanorod Encapsulated Bubbles(Royal Society of Chemistry, 2015) Tomak, Aysel; Zareie, Hadi M.A simple method has been described for synthesizing gold nanorods (GNRs) encapsulated bubbles in a controlled manner. The method involves the use of nitrogen gas in the seed-mediated synthesis method routinely used for synthesis of GNRs. Control over the morphology of the nanostructures was achieved by nitrogen gas flow. The synthesized structures were examined by UV-Vis Spectroscopy, Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). New structures of this type could conceivably serve as plasmonic biosensors, nanodevices and photothermal theranostics with dual modality imaging functionality. © The Royal Society of Chemistry 2015.Article Citation - WoS: 36Citation - Scopus: 38Effect of Molecular Architecture on Cell Interactions and Stealth Properties of Peg(American Chemical Society, 2017) Özer, İmran; Tomak, Aysel; Zareie, Hadi M.; Baran, Yusuf; Bulmuş, VolgaPEGylation, covalent attachment of PEG to therapeutic biomolecules, in which suboptimal pharmacokinetic profiles limiting their therapeutic utility are of concern, is a widely applied technology. However, this technology has been challenged by reduced bioactivity of biomolecules upon PEGylation and immunogenicity of PEG triggering immune response and abrogating clinical efficacy, which collectively necessitate development of stealth polymer alternatives. Here we demonstrate that comb-shape poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA), a stealth polymer alternative, has a more compact structure than PEG and self-organize into nanoparticles in a molecular weight dependent manner. Most notably, we show that comb-shape POEGMA promotes significantly higher cellular uptake and exhibits less steric hindrance imposed on the conjugated biomolecule than PEG. Collectively, comb-shape POEGMA offers a versatile alternative to PEG for stealth polymer-biomolecule conjugation applications.Article Citation - WoS: 17Citation - Scopus: 22Protein Corona Formation on Silver Nanoparticles Under Different Conditions(Elsevier, 2022) Tomak, Aysel; Yılancıoğlu, Buket; Winkler, David; Öksel Karakuş, CeydaThe surfaces of nanoparticles become covered by biomolecules in biological fluids. This protein ‘corona’ modifies materials’ characteristics and biological activity. The composition of the protein corona is dynamic, abundant biomolecules that bind first are subsequently replaced by less abundant but more tightly bound ones. Here, we explore the formation of the silver nanoparticle protein corona on exposure to cell culture media containing 10 % fetal bovine serum supplemented Dulbecco's Modified Eagle's medium. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry analysis were used to monitor how different parameters such as incubation time, heating duration, cell culture medium, incubation temperature, and the number of washes affect the nanoparticle–protein corona complex. silver nanoparticles with and without bound proteins were characterized by electron microscopy, dynamic light scattering, and ultraviolet-visible-near-IR spectroscopy. The tetrazolium-based MTT assay was used to determine viability of A549 human lung adenocarcinoma cells treated with silver nanoparticles. Characterization of the nanoparticles before and after protein binding provided insights into their changing morphology on corona formation. Our results confirmed that the physiological environment directly affects protein corona formation on nanoparticle surfaces. In particular, incubation condition-dependent differences in the amount of bound proteins were observed. This work highlights the importance of environmental drivers of protein adsorption, which should be considered when predicting and/or controlling protein targets of silver nanoparticles.Article Citation - WoS: 2Citation - Scopus: 2Structural Changes in a Schiff Base Molecular Assembly Initiated by Scanning Tunneling Microscopy Tip(IOP Publishing Ltd., 2016) Tomak, Aysel; Bacaksız, Cihan; Mendirek, Gizem; Şahin, Hasan; Hür, Deniz; Görgün, Kamuran; Senger, Ramazan Tuğrul; Birer, Özgür; Peeters, François M.; Zareie, Hadi M.We 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.