Umit Hakan Yildiz

Umit Hakan Yildiz
Izmir Institute of Technology · Department of Chemistry

PhD

About

57
Publications
6,041
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736
Citations
Additional affiliations
June 2014 - April 2015
Stanford University
Position
  • Post Doctoral Reseacher
January 2012 - present
January 2006 - present
Middle East Technical University

Publications

Publications (57)
Chapter
This review discusses biocompatible hydrogels and stimuli-responsive 3D networking polymeric materials and building blocks of nanopharmaceuticals. We aimed to outline the basics of gels and hydrogels, responsive behaviors, and applications such as therapeutic and drug carriers, bioimaging agents, biosensing elements. The review also covers signific...
Article
This study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing...
Article
Full-text available
The objective of this work is generation of propolis/polyvinyl alcohol (PVA) scaffold by electrospinning for 3D cell culture. Here, PVA used as co‐spinning agent since propolis alone cannot be easily processed by electrospinning methodology. Propolis takes charge in maximizing biological aspect of scaffold to facilitate cell attachment and prolifer...
Article
Full-text available
This study describes surface-assisted (SurfAst) urethane polymerization providing modular/post-functionalizable, bio-repellent, electroactive ~10 to 100 nm thick polyurethane (PU) interface on the gold surface. SurfAst is a functionalization methodology based on sequential incubation steps of alkane-diisocyanates and alkanediol monomers. The gold s...
Article
Full-text available
Acrylonitrile–butadiene–styrene (ABS) terpolymer was compounded with short carbon fiber (CF) and carbon nanotube (CNT) using a micro-extruder followed by the injection molding process. Composite samples were fabricated with loading ratios of 20 wt.% CF and 0.1, 0.5 and 1.0 wt.% of CNT. Mechanical, electrical, thermo-mechanical, thermal, melt-flow,...
Article
Full-text available
Polyamide 6 (PA) matrix was reinforced with Na-activated bentonite, amino functional silane treated bentonite and organo-modified clays at different concentrations. The preparation of composites was carried out using melt-blending method and the test samples were prepared by injection-molding process. Mechanical, thermal, structural and processing...
Patent
Full-text available
The invention relates to the fabrication of a single-chain conjugated polymer dot (Pdot) and the use of the fabricated single-chain conjugated Pdot as a biological probe.
Article
Natural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuronoxylan-based quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH a...
Article
This study presents a nonamplification-based nucleic acid assay for the detection of single-nucleotide polymorphism (SNP) associated with familial Mediterranean fever (FMF) besides polymerase chain reaction (PCR)-based methodologies. The major objective is to show the potential of the proposed assay for rapid screening of FMF in a Mediterranean reg...
Article
This study describes lipid bilayer-based sensor interface on SiO2 encapsulated graphene field effect transistors (GFET). The SiO2 layer was utilized as a lipid compatible surface that drives bilayer formation. The two types of surface morphologies i) wrinkled morphology by thermal evaporation (TE) and ii) flat morphology by pulsed electron depositi...
Article
The structural and optical changes resulting from the interaction between a polythiophene (PTAA) and a short unlabeled peptide were exploited to develop a sensitive bacterial detection method. The method itself targets the bacteria's surface protease activity and is sensitive enough to detect 1 CFU mL⁻¹ of E. coli in water within 6 hours. Abstract...
Article
E. coli and Salmonella are two of the most common bacterial pathogens involved in food and water borne related deaths. Hence, it is critical to develop rapid and sensitive detection strategies for near outbreak applications. We report a simple and specific assay to detect as low as 1 CFU/mL of E. coli in water within 6 hours by targeting the bacter...
Article
Full-text available
Over the past few decades, colorimetric assays have been developed for cost-effective and rapid on-site urinalysis. Most of these assays were employed for detection of biomarkers such as glucose, uric acid, ions, and albumin that are abundant in urine at µM to mM levels. In contrast, direct assaying of urinary biomarkers such as glycated proteins,...
Article
Full-text available
Conjugated polyelectrolytes (CPEs) have been widely used as reporters in colorimetric assays targeting nucleic acids. CPEs provide naked eye detection possibility by their superior optical properties however, as concentration of target analytes decrease, trace amounts of nucleic acid typically yield colorimetric responses that are not readily perce...
Article
Electrospun collagen is commonly used as a scaffold in tissue engineering applications since it mimics the content and morphology of native extracellular matrix (ECM) well. This report describes “toxic solvent free” fabrication of electrospun hybrid scaffold consisting of Collagen (Col) and Poly(l-lactide-co-ε-caprolactone) (PLLCL) for three-dimens...
Article
A flow-through colorimetric assay for detection of nucleic acids in plasma is reported. The proposed assay features an array of four polyvinylidene fluoride (PVDF) membranes impregnated with cationic poly (3-alkoxy-4-methylthiophene) (PT) as an optical reporter. The sensing strategy is based on monitoring the changes in optical properties of PT, up...
Article
Full-text available
This study reports on a handheld volatilome analyzer for selective determination of clinically relevant biomarkers in exhaled breath. The sensing platform is based on electrospun polymer nanofiber-multi walled carbon nanotube (MWCNT) sensing micro-channels. Polymer nanofibers of poly(vinylidene fluoride) (PVDF), polystyrene (PS), and poly(methyl me...
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Full-text available
The rapid developments in nanoscience, and its applications on biomedical areas have a large impact on drug delivery, tissue engineering, sensing, and diagnosis. Gold is widely investigated nanomaterial for the last couple of decades, since it has unique surface properties and very low toxicity to biological environment. In this work, we present a...
Article
Full-text available
Conductive polymer-electrospun polymer nanofiber network was combined to host iron oxide nanoparticles providing micrometer thick sensing interface. The sensor has fabricated as free-standing fabric exhibiting 10 to 100 KOhm base resistivity upon bias applied. The moving object has been sensed through the electrostatic interactions between fibers a...
Article
A luminescent paper device for visual detection of oxidative stress biomarker is reported. The assay platform consists of a polyvinylidene fluoride (PVDF) membrane impregnated with poly(3-alkoxy-4-methylthiophene) (PT) for colorimetric sensing. 8-hydroxy-2’-deoxyguanosine (8-OHdG), a biomarker associated with oxidative stress, is used as a model sy...
Article
A boron-dipyrromethene (BODIPY)-based fluorescent probe with a phosgene-specific reactive motif shows remarkable selectivity toward phosgene, in the presence of which the nonfluorescent dye rapidly transforms into a new structure and induces a fluorescent response clearly observable to the naked eye under ultraviolet light. Given that dynamic, we d...
Article
Poly(3-alkoxythiophene) (PT) with varying ratios of triethylamine and 1-methyl imidazole pendant groups and horizontally aligned single walled carbon nanotubes (SWCNT) are utilized in this study for volatile organic compounds (VOCs) classification. PTs with five different ratios of pendant groups are incorporated with SWCNT and are evaluated as che...
Article
The solvatochromic response of polydiacetylene (PDA) in the vapor phase is enabled upon incorporation with matrix polymers such as polyvinylpyrrolidone (PVP), polyethylene glycol (PEG), polyacrylic acid (PAA), and poly-4-vinylpyridine (P4VP). The matrix polymers provide a soft/gel-like framework for accommodating photopolymerized PDA, while facilit...
Article
Recent advances in clinical practice drive deoxyribonucleic acid (DNA) as an important class of biomarker. Monitoring the change in their concentration suggests the initiation and/or progression of various disorders. However, low quantity of DNA biomarkers in body fluids requires a delicate isolation methodology that provides efficient separation a...
Article
Here we report on the design and synthesis of cationic water soluble thiophene copolymers as reporters for colorimetric detection of microRNA (miRNA) in human plasma. Poly(3-alkoxythiophene) (PT) polyelectrolytes with controlled ratios of pendant groups such as triethylamine/1-methyl imidazole were synthesized for optimizing interaction with target...
Article
Full-text available
Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable chall...
Article
Full-text available
Timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods, such as enzyme linked immunosorbent assay (ELISA), culturing or polymerase chain reaction (PCR) require long assay times, and complex and expensive instruments, which are not adaptable to point-of-care...
Article
natural history, epidemiology and treatment of Hepatits B.•monitoring of therapy, cancer relationship and co-infections as well as the public health aspects of screening, diagnostics, cost-effective tools and assays for HBV•advances in nanotechnological tools for diagnosis of HBV and HBV co-infections.•impact of nanotechnology and nanomaterials on...
Article
A novel thymine-based surface chemistry suitable for label-free electrochemical DNA detection is described. It involves a simple two-step sequential process: immobilization of 9-mer thymine-terminated probe DNAs followed by backfilling with 9-mer thymine-based spacers (T9). As compared to commonly used organic spacer groups like 2-mercaptoethanol,...
Article
Submicrometer, porous polymeric vesicles, composed of an amphiphilic di-block copolymer, polystyrene-b-polyisocyanoalanine (2-thiophene-3-yl-ethyl) amide, are used to encapsulate an enzyme, alkaline phosphatase, and a fluorescent reporter polymer poly 1(3((4methylthiophen-3-yl)oxy) propyl) quinuclidin-1-ium. Passive diffusion of exogenously added a...
Article
Complex coacervates prepared from poly-aspartic acid (polyAsp) and poly-L-histidine (polyHis) were investigated as models of the metastable protein phases used in the formation of biological structures such as squid beak. When mixed, polyHis and polyAsp form coacervates whereas poly-L-glutamic acid (polyGlu) forms precipitates with polyHis. Layer-b...
Article
This letter demonstrates a biosensing platform for naked eye detection of miRNA, fabricated using a poly (vinylidene fluroide) thin paper impregnated with positively charged poly(3-alkoxy-4-methylthiophene) as luminescent reporters. The miRNA assay is based on the formation of a duplex and a triplex species between the "reporter and miRNA" and "rep...
Article
A facile method for assembly of biomimetic membranes serving as a platform for expression and insertion of membrane proteins is described. The membrane architecture was constructed in three steps: (i) assembly/printing of α-laminin peptide (P19) spacer on gold to separate solid support from the membrane architecture; (ii) covalent coupling of diffe...
Article
This contribution introduces a fluorescence assay for real-time determination of the activity of p97/VCP, a 540-kDa homo-hexameric enzyme, belonging to the AAA-ATPase family. A fluorescent reporter “poly 1-(3-((4-methylthiophen-3-yl)oxy)propyl)quinuclidin-1-ium” (poly PTQ) is used to monitor the hydrolysis of ATP to ADP by p97/VCP. The proposed ass...
Article
Cylindrical poly(styrene sulfonate) brushes were combined with a tetravalent double-DABCO based counterion. With increasing addition of counterion, hydrodynamic radius and radius of gyration decrease and AFMreveals a conformation change from wormlike to curled structures. Rg/Rh changes from 1.3 to 0.9. Above charge stoichiometry, brushes become int...
Article
We investigated the association of linear cationic model polyelectrolytes with oppositely charged pyrenetetrasulfonate in aqueous solution. Water soluble ionenes were prepared via Menschutkin reaction from 1-4-diazabicyclo[2.2.2 octane (DABCO) and dibromoalkenes. UV-Vis results revealed that PY molecules bind to ionenes in a cooperative process due...
Article
In this study, complexes of DNA with different organic di- and tetravalent counterions were systematically investigated in solution and on a surface. The complexation behavior was studied by dynamic light scattering, static light scattering, atomic force microscopy, analytical ultracentrifugation, and UV-vis spectroscopy. Results show that both div...
Article
A new polythiophene derivative was synthesized by both chemical and electrochemical oxidative polymerization of 1-(1-phenylethyl)-2,5-di(2-thienyl)-1H-pyrrole (PETPy). Of which the chemical method produces a polymer that is completely soluble in organic solvents. The structures of both the monomer and the soluble polymer were elucidated by nuclear...
Article
ABSTRACT Covalent Immobilization of Glucose Isomerase on Poly (2-hydroxyethyl methacrylate) Particles Yýldýz, Hakan Ümit M.S., Department of Chemistry Supervisor: Prof. Dr. Nesrin Hasýrcý July 2004, 54 pages In this study, poly (2-hydroxyethyl methacrylate), P(HEMA), particles were prepared by suspension polymerization of the monomer 2-hydroxyethyl...

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