Gul, A, Bacaksiz, C, Unsal, E, Akbali, B, Tomak, A, Zareie, HM & Sahin, H 2018, 'Theoretical and experimental investigation of conjugation of 1,6-hexanedithiol on MoS2', MATERIALS RESEARCH EXPRESS, vol. 5, no. 3.View/Download from: Publisher's site
Moghtader, F, Tomak, A, Zareie, HM & Piskin, E 2018, 'Bacterial detection using bacteriophages and gold nanorods by following time-dependent changes in Raman spectral signals', ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY, vol. 46, pp. 122-130.View/Download from: Publisher's site
Ozer, I, Tomak, A, Zareie, HM, Baran, Y & Bulmus, V 2017, 'Effect of Molecular Architecture on Cell Interactions and Stealth Properties of PEG.', Biomacromolecules, vol. 18, no. 9, pp. 2699-2710.View/Download from: Publisher's site
PEGylation, 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.
Yanilmaz, A, Tomak, A, Akbali, B, Bacaksiz, C, Ozceri, E, Ari, O, Senger, RT, Selamet, Y & Zareie, HM 2017, 'Nitrogen doping for facile and effective modification of graphene surfaces', RSC Advances, vol. 7, no. 45, pp. 28383-28392.View/Download from: Publisher's site
© The Royal Society of Chemistry 2017. 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.
Kiymaz, D, Yagmurcukardes, M, Tomak, A, Sahin, H, Senger, RT, Peeters, FM, Zareie, HM & Zafer, C 2016, 'Controlled growth mechanism of poly (3-hexylthiophene) nanowires', NANOTECHNOLOGY, vol. 27, no. 45.View/Download from: Publisher's site
Moghtader, F, Congur, G, Zareie, HM, Erdem, A & Piskin, E 2016, 'Impedimetric detection of pathogenic bacteria with bacteriophages using gold nanorod deposited graphite electrodes', RSC ADVANCES, vol. 6, no. 100, pp. 97832-97839.View/Download from: Publisher's site
Tomak, A, Bacaksiz, C, Mendirek, G, Sahin, H, Hur, D, Gorgun, K, Senger, RT, Birer, O, Peeters, FM & Zareie, HM 2016, 'Structural changes in a Schiff base molecular assembly initiated by scanning tunneling microscopy tip', NANOTECHNOLOGY, vol. 27, no. 33.View/Download from: Publisher's site
Barlas, FB, Ag Seleci, D, Ozkan, M, Demir, B, Seleci, M, Aydin, M, Tasdelen, MA, Zareie, HM, Timur, S, Ozcelik, S & Yagci, Y 2014, 'Folic acid modified clay/polymer nanocomposites for selective cell adhesion', Journal of Materials Chemistry B, vol. 2, no. 37, pp. 6412-6412.View/Download from: Publisher's site
Coutts, MJ, Zareie, HM, Cortie, MB & McDonagh, AM 2014, 'Charging of gold/metal oxide/gold nanocapacitors in a scanning electron microscope', NANOTECHNOLOGY, vol. 25, no. 15.View/Download from: Publisher's site
Ayas, S, Cinar, G, Ozkan, AD, Soran, Z, Ekiz, O, Kocaay, D, Tomak, A, Toren, P, Kaya, Y, Tunc, I, Zareie, H, Tekinay, T, Tekinay, AB, Guler, MO & Dana, A 2013, 'Label-Free Nanometer-Resolution Imaging of Biological Architectures through Surface Enhanced Raman Scattering', Scientific Reports, vol. 3, no. 1, pp. 1-8.View/Download from: Publisher's site
Label free imaging of the chemical environment of biological specimens would readily bridge the
supramolecular and the cellular scales, if a chemical fingerprint technique such as Raman scattering can be
coupled with super resolution imaging. We demonstrate the possibility of label-free super-resolution
Raman imaging, by applying stochastic reconstruction to temporal fluctuations of the surface enhanced
Raman scattering (SERS) signal which originate from biomolecular layers on large-area plasmonic surfaces
with a high and uniform hot-spot density (.1011/cm2
, 20 to 35 nm spacing). A resolution of 20 nm is
demonstrated in reconstructed images of self-assembled peptide network and fibrilated lamellipodia of
cardiomyocytes. Blink rate density is observed to be proportional to the excitation intensity and at high
excitation densities (.10 kW/cm2
) blinking is accompanied by molecular breakdown. However, at low
powers, simultaneous Raman measurements show that SERS can provide sufficient blink rates required for
image reconstruction without completely damaging the chemical structure
Moghaddam, MJ, Yang, W, Bojarski, B, Gengenbach, TR, Gao, M, Zareie, HM & McCall, MJ 2013, 'Azide photochemistry for facile modification of graphitic surfaces: preparation of DNA-coated carbon nanotubes for biosensing (vol 23, 425503, 2012)', NANOTECHNOLOGY, vol. 24, no. 37.View/Download from: Publisher's site
Moghaddam, MJ, Yang, W, Bojarski, B, Gengenbach, T, Gao, M, Zareie, HM & Mccall, M 2012, 'Azide Photochemistry For Facile Modification Of Graphitic Surfaces: Preparation Of DNA-coated Carbon Nanotubes For Biosensing', Nanotechnology, vol. 23, no. 42, pp. 1-12.View/Download from: Publisher's site
A facile, two-step method for chemically attaching single-stranded DNA to graphitic surfaces, represented here by carbon nanotubes, is reported. In the first step, an azide-containing compound, N-5-azido-nitrobenzoyloxy succinimide (ANB-NOS), is used to
Sevimli, S, Inci, F, Zareie, HM & Bulmus, V 2012, 'Well-defined Cholesterol Polymers With Ph-controlled Membrane Switching Activity', Biomacromolecules, vol. 13, no. 10, pp. 3064-3075.View/Download from: Publisher's site
Cholesterol has been used as an effective component of therapeutic delivery systems because of its ability to cross cellular membranes. Considering this, well-defined copolymers of methacrylic acid and cholesteryl methacrylate, poly(methacrylic acid-co-c
Coutts, MJ, Zareie, HM, Cortie, MB, Phillips, M, Wuhrer, R & McDonagh, AM 2010, 'Exploiting Zinc Oxide Re-Emission To Fabricate Periodic Arrays', ACS Applied Materials & Interfaces, vol. 2, no. 6, pp. 1774-1779.View/Download from: Publisher's site
The synthesis of hexagonal ring-shaped structures of zinc oxide using nanosphere lithography and metal/metal oxide sputtering is demonstrated. This synthesis exploits the surface re-emission of zinc oxide to deposit material in regions lying out of the l
Rawling, T, Austin, CE, Zareie, HM & McDonagh, AM 2010, 'Thin Films Of A Dimeric Ruthenium Phthalocyanine Complex On Gold', Inorganic Chemistry Communications, vol. 13, no. 1, pp. 208-210.View/Download from: Publisher's site
Thin films of a new dimeric ruthenium phthalocyanine complex bearing a thioester-functionalized axial ligand were formed on gold surfaces. Characterization of the thin films by laser ablation-inductively coupled-mass spectrometry and scanning tunneling m
Wong, LC, Sevimli, S, Zareie, HM, Davis, T & Bulmus, V 2010, 'Pegylated Functional Nanoparticles From A Reactive Homopolymer Scaffold Modified By Thiol Addition Chemistry', Macromolecules, vol. 43, no. 12, pp. 5365-5375.View/Download from: Publisher's site
Well-defined reactive polymer scaffolds are useful building blocks for a variety of biomedicine and nanotechnology applications. In this study, we have converted a RAFT-synthesized thiol-functional homopolymer scaffold (poly(pyridyl disulfide ethyl metha
Rawling, T, Austin, CE, Hare, DJ, Doble, PA, Zareie, HM & McDonagh, AM 2009, 'Thin films of Ruthenium Phthalocyanine complexes', Nano Research, vol. 2, pp. 678-687.View/Download from: Publisher's site
Four new ruthenium phthalocyanine complexes bearing axial ligands with thioacetate groups that facilitate thin film formation on gold surfaces are presented. Scanning tunnelling microscopy (STM) images and surface coverage data obtained by solution inductively coupled plasma mass spectrometry (ICP-MS) experiments show that peripheral and axial ligand substituents on the complexes have a significant effect on their surface coverage. A laser ablation ICP-MS technique that provides information about thin films across macro-sized areas is described here for the first time. Using the technique, the maximum surface coverage of a ruthenium phthalocyanine complex was found to occur within one minute of gold substrate immersion in the complexcontaining solution.
Eggers, P, Zareie, HM, Paddon-Row, MN & Gooding, JJ 2009, 'Structure and Properties of Redox Active Self-Assembled Monolayers Formed from Norbornylogous Bridges', Langmuir, vol. 25, no. 18, pp. 11090-11096.View/Download from: Publisher's site
Three different length rigid norbornylogous bridges with terminal ferrocene moieties were synthesized. Pure self-assembled monolayers (SAMs) of the norbornylogous bridges and SAMs with the bridges diluted using either hydroxyl-terminated or methyl-terminated diluents were formed for each length of norbornylogous bridge. The SAMs were imaged with scanning tunneling micrsocopy (STM) and the electrochemical properties were Investigated. It was found that SAMs composed of only norbornylogous bridges were crystalline-like, while in mixed SAMs, where the norbornylogous bridge was diluted, the ferrocene stood above the surface of the diluent because of the rigidity of the norbornylogous bridges and were homogeneously distributed across the surface. Further. the rate of electron transfer of the norbornylogous bridges was observed to be similar to an alkanethiol-derived ferrocene whose construct was designed to be as close as possible to that of the norbornylogous bridge. Finally, the rate of electron transfer for the norbornylogous bridges in a diluted SAM was slower With it hydroxyl-terminated diluent. than with a methyl-terminated diluent.
Liu, J, Yang, W, Zareie, HM, Gooding, JJ & Davis, T 2009, 'pH-Detachable Polymer Brushes Formed Using Titanium-Diol Coordination Chemistry and Living Radical Polymerisation (RAFT)', Macromolecules, vol. 42, no. 8, pp. 2931-2939.View/Download from: Publisher's site
pH-detachable poly(styrene) brushes formed on indium-tin oxide (ITO) glass substrates using metal complex chemistry and reversible addition-fragmentation chain transfer (RAFT) polymerization was described. These pH-detachable polymeric brushes were generated using both "graft-from" and "graft-to" methodologies. The methodologies involved either the surface self-assembly of catechol-functional RAFT agents (graft-from) or catechol-terminal polymer chains (graft-to) onto the ITO substrate via titanium-diol coordination. The stepwise functionalization of the ITO glass surfaces was characterized successfully using X-ray photoelectron spectroscopy (XPS) and contact angle measurement. Poly(styrene) brushes generated using the "graft-from" method were denser than those generated using the "graft-to" method, as exemplified by atom force microscopy (AFM) and quantified using cyclic voltammetry. Poly(styrene) brushes assembled using both methods could be detached easily by manipulating the pH of the brush environment. Cyclic voltammetry was utilized to calculate precisely the surface coverage of the RAFT functionality and polymeric brush density.
Shon, H, Vigneswaran, S, Kandasamy, JK, Zareie, HM, Kim, JB, Cho, DL & Kim, JH 2009, 'Preparation and Characterisation of Titanium Dioxide (TiO2) from Sludge produced by TiCl4 Flocculation with FeCl3, Al2(SO4)3 and Ca(OH)2 Coagulant Aids in Wastewater', Separation Science and Technology, vol. 44, no. 7, pp. 1525-1543.View/Download from: Publisher's site
In this study, TiCl4 coagulant together with coagulant aids such as FeCl3, Al2(SO4)3, and Ca(OH)2 were investigated to improve the photoactivity of titanium dioxide (TiO2) produced from sludge and to increase the resulting low pH value. After TiCl4 flocculation with three coagulant aids, the settled floc (sludge) was incinerated at 600Â°C to produce TiO2 doped with Fe, Al, and Ca elements. Fe-, Al-, and Ca-doped TiO2 was characterized in terms of structural, chemical, and photo-electronic properties. All the coagulant aids used together with Ti-salt flocculation effectively increased the pH values. The surface area of TiO2-WO (without any coagulant aids), Fe/TiO2, Al/TiO2, and Ca/TiO2 was 122 m2/g, 77 m2/g, 136 m2/g and 116 m2/g, respectively. The TiO2-WO, Fe/TiO2, Al/TiO2, and Ca/TiO2 was found to be of anatase phase. The XRD pattern on the Fe/TiO2 included an additional peak of hematite (Î±-Fe2O3). The majority of gaseous acetaldehyde with TiO2-WO and Ca/TiO2 for photocatalytic activity was completely removed within 40 minutes under UV irradiation.
Shon, H, Vigneswaran, S, Zareie, HM, Ben Aim, R, Lee, E, lee, J, Cho, J & Kim, IS 2009, 'Physico-chemical pretreatment to Seawater Reverse Osmosis (SWRO): Organic Characterization and Membrane Autopsy', Desalination, vol. 236, no. 1 - 3, pp. 282-290.View/Download from: Publisher's site
In this study, different pretreatment methods such as microfiltration (MF), ultrafiltration (UF), nanofiltration (NF), powdered activated carbon (PAC) adsorption and ferric chloride (FeCl3) flocculation were evaluated in terms of their capability in removing seawater organic matter (SWOM) and the characteristics of the foulants on the seawater reverse osmosis (SWRO) membranes. A detailed experiment with a crossflow SWRO filtration unit was conducted with SR membrane (MWCO 100 Da) at 60 bar with seawater (conductivity = 48.9 mS/cm) drawn from south-western Korea. The SWOM removal by UF, NF, PAC adsorption and FeCl3 flocculation was 20.3, 28.9, 46 and 23.3%, respectively. SWOM used in this study predominantly consisted of small size organic matter (<1000 Da). A large amount of the hydrophobic fraction present in SWOM was removed by PAC adsorption. The SDI5min significantly decreased from 12.7 (without any pretreatment) to 3.2 (MF), 1.3 (UF), 1.0 (NF) and 4.4 (PAC adsorption). RO filtration of seawater with and without pretreatment showed significant flux decline (normalized flux decline (J/J0) = 0.17 ± 0.02) within 20-h operation. The elemental analyses made on the RO surface after direct RO filtration showed that the relative fraction of the carbon decreased, while sodium (Na), magnesium (Mg), chlorine (Cl) and iron (Fe) elements were found in the foulants extracted from the fouled membrane surface. The average roughness of the clean membrane surface was 41.5 nm. After MF and UF pretreatment, the roughness slightly increased to 54.8 and 55.6 nm, respectively. On the other hand, without any pretreatment, with PAC adsorption and with FeCl3 flocculation, the roughness increased up to 69.7, 66.4 and 110 nm, respectively. It can be concluded that the pretreatment by MF and UF could relatively preserve the RO membrane surface.
West, PJ, Zareie, HM & McDonagh, AM 2008, 'Synthesis and characterization of anthracene-2,6-dithioacetate: a rigid, conjugated molecule for the formation of monolayers on gold', Australian Journal Of Chemistry, vol. 61, no. 10, pp. 758-761.View/Download from: Publisher's site
The synthesis and characterization of a new photoswitchable anthracene compound, anthracene-2,6-dithioacetate, is presented. The compound dimerizes in solution on irradiation with UV light, and thin films can be formed on gold surfaces from both the monomer and photodimer.
Wong, L, Boyer, C, Jia, Z, Zareie, HM, Davis, TP & Bulmus, V 2008, 'Synthesis of versatile thiol-reactive polymer scaffolds via RAFT polymerization', Biomacromolecules, vol. 9, no. 7, pp. 1934-1944.View/Download from: Publisher's site
Well-defined polymer scaffolds convertible to (multiffunctional polymer structures via selective and efficient modifications potentially provide an easy, versatile, and useful approach for a wide variety of applications. Considering this, a homopolymer s
Zareie, HM, Boyer, C, Bulmus, V, Nateghi, E & Davis, T 2008, 'Temperature-responsive self-assembled monolayers of oligo(ethylene glycol): Control of biomolecular recognition', Acs Nano, vol. 2, no. 4, pp. 757-765.View/Download from: Publisher's site
Self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-tethered molecules on gold are important for various biorelevant applications ranging from biomaterials to bioanalytical devices, where surface resistance to nonspecific protein adsorption
Natural lithography was used to prepare arrays of nanoscale capacitors on silicon. The capacitance was verified by a novel technique based on the interaction of a charged substrate with the electron beam of a scanning electron microscope. The nanocapacit
Lucas, NT, Zareie, HM & McDonagh, AM 2007, 'Self-organization of a Discotic Coordination Complex Bearing Orthogonal Discotic Ligands', ACS Nano, vol. 1, no. 4, pp. 348-354.View/Download from: Publisher's site
McDonagh, AM, Zareie, HM, Ford, M, Barton, C, Ginic-markovic, M & Matisons, J 2007, 'Ethynylbenzene monolayers on gold A metal-molecule binding motif derived from a hydrocarbon', Journal Of The American Chemical Society, vol. 129, no. 12, pp. 3533-3538.View/Download from: Publisher's site
Exposure of a Au(111) surface to ethynylbenzene in solution leads to the formation of a bound monolayer. A chemisorption process occurs to give a stable layer consisting of oxygen-containing hydrocarbon species. Ethynylbenzene itself does not oxidize under the deposition conditions indicating that the gold surface facilitates the oxidation process. Calculations show that ethynylbenzene and its oxidation products phenylacetic acid and phenylxirane have positive bending energies to the gold surface. 1,4- Diethynylbenzene also bind to Au (111) and anchors gold nanoparticles deposited from solution to form dense, semiregular arrays.
Veal, TD, Piper, L, Phillips, M, Zareie, HM, Lu, H, Schaff, W & Mcconville, C 2007, 'Doping-dependence of subband energies in quantized electron accumulation at InN surfaces', Physica Status Solidi A-Applications And Materials Science, vol. 204, no. 2, pp. 536-542.View/Download from: Publisher's site
Electron tunnelling spectroscopy is used to investigate the quantized electron accumulation at the surfaces of wurtzite InN with different doping levels. The tunnelling spectra of InN-oxide-tip junctions recorded in air at room temperature exhibit a simi
A method is described for assembling gold nanorods, end-to-end, into long chains attached on top of a mixed self-assembled monolayer that has been functionalized with streptavidin. Methods to prepare chains Of nanorods in colloidal suspension have been reported by others, but our protocol offers a way to directly form such structures on a substrate. The rods are spaced ~~5 nm apart i the resulting chains, which extend for over a micrometer in length. The assembly and morphology of the nanorods structures were characterised by surface plasmon resonance spectroscopy as well as by scanning electron microscopy and scanning probe microscopy. Strcutures of this type could concievably serve as plasmonic waveguides in future nanodevices.
Chan, Y, Bulmus, V, Zareie, HM, Byrne, F, Barner, L & Kavallaris, M 2006, 'Acid-cleavable polymeric core-shell particles for delivery of hydrophobic drugs', Journal of Controlled Release, vol. 115, no. 2, pp. 197-207.View/Download from: Publisher's site
Here we describe the combined use of acid-labile microgel approach and RAFT-mediated seeded despersion polymerisation technique to prepare an acid-cleavable core-shell like polymeric colloidal system for the delivery of hydrophobic drugs at slightly acidic sites. A new bisacrylate acetal crosslinker was copolymerised with n-butyl acrylate (BA) in the presence of a RAFT agent using a dispersion polymerisation technique, which yieled crosslinked spherical particles with the size ranging between 150 and 500 nm. The particles were cleaved in a pH-dependent manner similar to the acid-labile hydrolysis behaviour of the crosslinker. In order to mask the hydrophobic surface of the particles, polyethelene glycol acrylate (PEG-A) was grafted onto poly(BA) seed particles via the RAFT agent groups on the particle surface. The acidic-site selective delivery protential of the poly(BA)-g-poly(PEG-A) particles was assessed in-vitro using a lipophilic flueorescent dye as a model hydrophobic drug. Ca. 73% and 34% of the total dye loaded in the paerticles was found to be released at pH 5.0 and 7.4 in 24h, respectively. Thegrowth of human neuroblastoma cells was not affected by the incubation with the core-shell particles and their cleavage by-products upto 3 mg/ml concentration. The physiocochemical and the functional features support the potential value of the acid-cleavable poly(BA) core-poly(PEG-A) shell particles as carriers for the delivery of hydrophobic drugs at acidic sites.
Veal, TD, Piper, L, Phillips, M, Zareie, HM, Lu, H, Schaff, W & Mcconville, C 2006, 'Scanning tunnelling spectroscopy of quantized electron accumulation at InxGa1-xN surfaces', Physica Status Solidi A-Applications And Materials Science, vol. 203, no. 1, pp. 85-92.View/Download from: Publisher's site
Electron tunnelling spectroscopy has been used to investigate quantized levels in electron accumulation layers at InGaN surfaces. The tunnelling spectra exhibit a plateau in the normalized conductance which widens with increasing Ga-content, correspondin
Zareie, HM, Barber, J & McDonagh, AM 2006, 'Structural changes in self-assembled monolayers initiated by ultraviolet light', Journal Of Physical Chemistry B, vol. 110, no. 32, pp. 15951-15954.View/Download from: Publisher's site
Self-assembled monolayers of 2-anthracenethiol and 2-naphthalenethiol on gold (111) were irradiated with low-power UV light. Scanning tunneling microscope images recorded in situ show unusual structural changes. In the case of 2-anthracenethiol, structur
Zareie, HM, McDonagh, AM, Edgar, JA, Ford, M, Cortie, MB & Phillips, M 2006, 'Controlled assembly of 1,4-phenylenedimethanethiol molecular nanostructures', Chemistry Of Materials, vol. 18, no. 9, pp. 2376-2380.View/Download from: Publisher's site
We present here the first high-resolution scanning tunneling microscope images showing that 1,4phenylenedimethanethiol forms mono- and multilayers on gold(1 11) substrates under particular solution-deposition conditions. The high-resolution images show t
Cortie, MB, Zareie, HM, Ekanayake, SR & Ford, M 2005, 'Conduction, storage, and leakage in particle-on-SAM nanocapacitors', IEEE Transactions On Nanotechnology, vol. 4, no. 4, pp. 406-414.View/Download from: Publisher's site
Individual gold nanoparticles exhibit discrete capacitances of the order of 1 aF, and they can be tethered to a conductive substrate using a bi-functional monolayer of a suitable organic molecule. However the conduction, retention and leakage of charge b
Drozdowicz-Tomsia, K, Goldys, EM, Motlan, M, Zareie, HM & Phillips, M 2005, 'Growth-temperature-dependent cathodoluminescence properties of GaSb/GaAs quantum-dot multilayer structures', Applied Physics Letters, vol. 86, no. 17, pp. 1-3.
Multilayer GaSb/GaAs quantum-dot (QD) structures grown by atmospheric-pressure metalorganic chemical vapor deposition on semi-insulating GaAs (100) substrates with varying growth temperature of the confinement layers are studied by the cathodoluminescenc
Kang, S, Ma, H, Kang, M, Kim, K, Jen, AK, Zareie, HM & Sarikaya, M 2004, 'Ordered Self-assembly And Electronic Behavior Of C-60-anthrylphenylacetylene Hybrid', Angewandte Chemie-international Edition, vol. 43, no. 12, pp. 1512-1516.View/Download from: Publisher's site
A functional hybrid molecule, C60-MPAA, has been designed and synthesized by taking advantage of the excellent physical and chemical properties of C60 and nanoscale ordering of anthryl-based self-assembled monolayers (SAMs). The SAM of C60-MPAA exhibits stable and highly ordered 2D arrays that form an oblique lattice at room temperature and exhibit interesting electronic properties.
Phillips, M, Zareie, HM, Gelhausen, O, Drago, M, Schmidtling, T & Richter, W 2004, 'Scanning tunnelling and cathodoluminescence spectroscopy of indium nitride', Journal of Crystal Growth, vol. 269, no. 1, pp. 106-110.View/Download from: Publisher's site
ndium nitride epilayers grown by metalorganic vapor-phase epitaxy have been studied by cathodoluminescence (CL) spectroscopy, scanning tunneling microscopy and scanning tunneling spectroscopy (STS). A broad CL emission peak centered at 0.8 eV was observed at 80 K. This peak was attributed to an excitonic radiative recombination mechanism as its emission intensity exhibited a super-linear dependence on beam current with a power-law exponent of m=2. A large spatial variation in the CL emission intensity was ascribed to the presence of threading dislocations, which act as non-radiative recombination centers. A surface band gap of not, vert, similar1.4 eV was estimated from STS IV curves.
Xia, N, Shumaker-Parry, JS, Zareie, HM, Campbell, CT & Castner, D 2004, 'A Streptavidin Linker Layer That Functions After Drying', Langmuir, vol. 20, no. 9, pp. 3710-3716.View/Download from: Publisher's site
The ability of streptavidin (SA) to simultaneously bind four biotins is often used in linker layers, where a biotinylated molecule is linked to a biotin-functionalized surface via SA. For biosensor and array applications, it is desirable that the SA link
Zareie, HM, Shumaker-Parry, JS, Aebersold, R & Campbell, CT 2004, 'Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy', Analytical Chemistry, vol. 76, no. 4, pp. 918-929.View/Download from: Publisher's site
We present two strategies for microspotting 10 × 12 arrays of double-stranded DNAs (dsDNAs) onto a gold-coated glass slide for high-throughput studies of protein-DNA interactions by surface plasmon resonance (SPR) microscopy. Both methods use streptavidin (SA) as a linker layer between a biotin-containing mixed self-assembled monolayer (SAM) and biotinylated dsDNAs to produce arrays with high packing density. The primary mixed SAM is produced from biotin- and oligo(ethylene glycol)-terminated thiols bonded as thiolates onto the gold surface. In the first method, a robotic microspotter is used to deliver nanoliter droplets of dsDNA solution onto a uniform layer of this SA (~2 × 1012 SA/cm2). SPR microscopy shows a density of (5-6) × 1011 dsDNA/cm2 (0.2-0.3 dsDNA/SA) in the array elements. The second method uses instead a microspotted array of this SA linker layer, onto which the microspots of dsDNA are added with spatial registry. SPR microscopy before addition of the dsDNA shows a SA coverage of 2 × 1012 SA/cm2 within the spots and a dsDNA density of 8.5 ± 3.5 × 1011 dsDNA/cm2 (0.3-0.7 dsDNA/SA, depending on the length of dsDNA) after dsDNA spotting. We demonstrate the ability to simultaneously monitor protein binding with the SPR microscope in many 200-m spots with 1-s time resolution and sensitivity to <1 pg of protein.
Zareie, HM, Wacker, JL, Fong, H, Sarikaya, M & Muchowski, PJ 2004, 'Hsp70 and Hsp40 attenuate formation of spherical and annular polyglutamine oligomers by partitioning monomer', Nature Structural & Molecular Biology, vol. 11, no. 12, pp. 1215-1222.
Protein conformational changes that result in misfolding, aggregation and amyloid fibril formation are a common feature of many neurodegenerative disorders. Studies with ?-amyloid (A?), ?-synuclein and other amyloid-forming proteins indicate that the assembly of misfolded protein conformers into fibrils is a complex process that may involve the population of metastable spherical and/or annular oligomeric assemblies. Here, we show by atomic force microscopy that a mutant huntingtin fragment with an expanded polyglutamine repeat forms spherical and annular oligomeric structures reminiscent of those formed by A? and ?-synuclein. Notably, the molecular chaperones Hsp70 and Hsp40, which are protective in animal models of neurodegeneration, modulate polyglutamine aggregation reactions by partitioning monomeric conformations and disfavoring the accretion of spherical and annular oligomers.
Jen, AK, Ma, H, Luo, JD, Liu, S, Haller, M, Jang, SW, Dalton, L, Zareie, HM, Reed, BW & Sarikaya, M 2003, 'Nanoscale Architectural Control Of Organic Functional Materials For Photonics And Molecular Electronics.', Abstracts Of Papers Of The American Chemical Society, vol. 225, pp. 1-1.
Ma, H, Kang, S, Kim, M, Kim, K, Zin, M, Zareie, HM, Sarikaya, M & Jen, AK 2003, 'Functional Self-assemblies With Nanoscale Ordering For Molecular Electronics And Biomaterials.', Abstracts Of Papers Of The American Chemical Society, vol. 226, pp. 1-1.
Ma, H, Kim, K, Li, H, Horwitz, J, Zin, M, Zareie, HM, Sarikaya, M & Jen, AK 2003, 'Effects Of Molecular Architecture, W-functional Groups And Hydrogen-bonding On The Nanoscopic Features Of Highly-ordered Self-assemblies.', Abstracts Of Papers Of The American Chemical Society, vol. 226, pp. 1-2.
Tamerler, C, Dincer, S, Heidel, D, Zareie, HM & Sarikaya, M 2003, 'Biomimetic Multifunctional Molecular Coatings Using Engineered Proteins', Progress In Organic Coatings, vol. 47, no. 3-4, pp. 267-274.View/Download from: Publisher's site
A molecular biomimetics approach is presented in developing polypeptide-based coatings for inorganic surfaces. In general, inorganic surface-binding polypeptides are genetically engineered using cell surface and phage display technologies. These peptides contain short amino acid sequences, known to bind specifically to selected inorganics. Based on the sequences of the polypeptides that were recently selected by this (e.g. Au, Pt and Pd) and other groups, one may find certain specificity, e.g. hydrophobic and hydroxyl amino acids, common among noble metal-binders. We show that an engineered gold-binding protein self-assembles onto gold surface forming monomolecular and highly structured crystallographic domains. The protein-based molecular films could provide robust templates for potential utility in practical nanotechnological and bionanotechnological applications.
Zareie, HM & Lukins, PB 2003, 'Atomic-resolution STM structure of DNA and localization of the retinoic acid binding site', Biochemical and Biophysical Research Communication, vol. 303, no. 1, pp. 153-159.View/Download from: Publisher's site
Single-molecule imaging by scanning tunnelling microscopy (STM) yields the atomic-resolution (0.6 Å) structure of individual B-type DNA molecules. The strong correlation between these STM structures and those predicted from the known base sequence indicates that sequencing of single DNA molecules using STM may be feasible. There is excellent agreement between the STM and X-ray structures, but subtle differences exist due to radial distortions. We show that the interactions of other molecules with DNA, their binding configurations, and the structure of these complexes can be studied at the single-molecule level. The anti-cancer drug retinoic acid (RA) binds selectively to the minor groove of DNA with up to 6 RA molecules per DNA turn and with the plane of the RA molecule approximately parallel to the DNA symmetry axis. Similar studies for other drug molecules will be valuable in the a priori evaluation of the effectiveness of anti-cancer drugs.
Zareie, HM, Gokmen, V & Javadipour, I 2003, 'Investigating Network, Branching, Gelation And Enzymatic Degradation In Pectin By Atomic Force Microscopy', Journal Of Food Science And Technology-mysore, vol. 40, no. 2, pp. 169-172.
The molecular structures of pectin networks and gels have been imaged using atomic force microscopy (AFM). All the samples were deposited from aqueous solution onto the surface of freshly cleaved mica, air dried, and then imaged under butanol. The intera
Zareie, HM, Ma, H, Reed, BW, Jen, AK & Sarikaya, M 2003, 'Controlled Assembly of Conducting Monomers for Molecular Electronics', Nano Letters, vol. 3, no. 2, pp. 139-142.View/Download from: Publisher's site
We report controlled self-assemblies of two molecules as crystalline arrays on gold substrates at room temperature. The size, shape, orientation, and ordered assemblies of molecular wires can be engineered through a delicate interplay of the intermolecular - stacking and chemisorptive substrate-linker interactions. In particular, the molecule based on a fused aromatic, anthracene, forms an ordered 2D stacked array. Through scanning tunneling spectroscopy, we demonstrate changes in the electronic behavior of single molecules that form into superlattices. The ability to assemble predictable 2D crystals and understand the order-related electronic behavior of single molecular components could allow for the future design of nanopatterned arrays as a controlled platform toward further miniaturization of electronic devices.
David, G, Ozer, F, Simionescu, BC, Zareie, HM & Piskin, E 2002, 'Microemulsion photopolymerization of methacrylates stabilized with sodium dodecyl sulfate and poly(N-acetylethylenimine) macromonomers', European Polymer Journal, vol. 38, no. 1, pp. 73-78.View/Download from: Publisher's site
Methyl methacrylate and butyl methacrylate were polymerized in oil-in-water microemulsions that were stabilized by sodium dodecyl sulphate (SDS). A poly(N-acetylethylenimine) (PNAEI) macromer was also included in the recipe, as a cosurfactant and a comonomer. Polymerizations were initiated by UV-irradiation. The average diameters of latex particles, obtained by STM, were in the range of 17200 nm. The experimental data evidenced that the particle size was mainly dependent on the SDS/PNAEI ratio. Polymerization yields were around 7585%. The synthesized copolymers have viscosity average molecular weights in the range of 2.12.4×106 and glass transition temperatures of 38.043.5°C, lower than those obtained without using PNAEI. The investigation by means of FTIR and 1H-NMR techniques revealed that PNAEI was incorporated into the nanoparticles.
Veiseh, M, Zareie, HM & Zhang, M 2002, 'Highly Selective Protein Patterning on Gold-Silicon Substrates for Biosensor Applications', Langmuir, vol. 18, no. 17, pp. 6671-6678.View/Download from: Publisher's site
Proteins were precisely patterned on 2D sensor surfaces using photolithography and chemical selectivity. Microarrays of gold squares were fabricated on silicon substrates. The gold regions were modified with mixed COOH-terminated self-assembled monolayers (SAMs) to have a high affinity for the desired proteins or peptides. The silicon regions were modified with polyethylene glycol (PEG) by silanization to provide a high resistivity to protein adsorption. Protein surface coverage was visualized by fluorescence microscopy and atomic force microscopy (AFM). AFM was also used for studying protein morphology to understand the interaction of proteins with SAMs at the molecular level. Proteins and peptides immobilized on SAMs were examined by Fourier transform infrared (FTIR) spectroscopy. Contact angle measurements for surface wettability were conducted to confirm the success of the surface modification reactions. Protein resistance by the PEGs immobilized on bare silicon substrates and on the silicon regions of gold-patterned silicon substrates was compared, and it was found that the latter has a higher resistivity to protein adsorption. Both fluorescence and high-resolution AFM images indicated that bovine serum albumin (BSA) and fibronectin molecules formed a densely packed layer on the gold regions of the patterned substrates, while the immunoglobulin's (IgG) coverage was low. Specific antigen-antibody binding (BSA-anti-BSA) was studied using the surface plasmon resonance (SPR) technique for characterizing the bioactivity of the antigen attached to the gold substrates. The SPR results showed that the BSA proteins bound covalently to the gold surfaces have a much better bioactivity than those bound physically. This study suggests that protein or peptide, molecular structures, and the immobilization technique influence the coverage, morphology, and bioactivity of the attached proteins on the substrates which is crucial to the operational behavior of biosensors.
Zareie, HM, Dincer, S & Piskin, E 2002, 'Observation of phase transition of thermo-responsive poly(NIPA)-PEI block copolymers by STM', Journal of Colloid and Interface Science, vol. 251, no. 2, pp. 424-428.View/Download from: Publisher's site
N-isopropylacrylamide (NIPA) homopolymers having carboxylic acid-end groups were synthesized by using mercaptoacetic acid (MAA) as the chain transfer agent. Polymerization was achieved in ethanol using azobisisobutyronitrile (AIBN) as the initiator. Average molecular weight of the homopolymer estimated by titration was 1958. This carboxylic acid-ended poly(NIPA) was then copolymerized with polyethylenimine (PEI, MW-2000) using a water soluble carbodiimide (EDAC). With respect to carboxyl-ended poly(NIPA), the block copolymers exhibited a pH dependent-temperature sensitivity and higher LCST values in acidic pH. Scanning tunneling microscopy (STM) images of both the homopolymer and the copolymer were obtained at 25 and 45°C with tip-sample bias voltages of up to 800 mV and tunneling currents not, vert, similar1 nA. These images showed that STM can be used to visualize both the formation of copolymer chains and their structure, and also their stimuli-responsive behavior.
Zareie, HM, Khachan, J & Lukins, PB 2001, 'Atomic resolution structure of growth and etching patterns at the surface of microwave plasma chemical vapor deposited diamond films', Applied Physics Letters, vol. 78, no. 11, pp. 1520-1522.View/Download from: Publisher's site
Zareie, HM, Korbahti, BK & Tanyolac, A 2001, 'Non-passivating polymeric structures in electrochemical conversion of phenol in the presence of NaCl', Journal of Hazardous Materials, vol. 87, no. 1-3, pp. 199-212.View/Download from: Publisher's site
Zareie, HM, Ozer, F, Beskardes, MO & Piskin, E 2001, 'Nanoparticles carrying hydroxyl groups produced by microemulsion', Journal of Applied Polymer Science, vol. 82, no. 1, pp. 237-242.View/Download from: Publisher's site
Kocum, C, Zareie, HM, Ozer, F & Piskin, E 2000, 'Observation Of Nanoparticles And Film Formation By Scanning Tunneling Microscopy: Methyl Methacrylateperbutyl Methacrylate Nanoparticles Prepared By Microemulsion Polymerization', Colloid And Polymer Science, vol. 278, no. 6, pp. 587-590.View/Download from: Publisher's site
Latexes as dispersions of poly(methyl methacrylate-co-butyl methacrylate) copolymeric nanoparticles within water were produced by microemulsion polymerization of the respective comonomers. Polymer yield, number-average and weieht-average molecular weight
Zareie, HM, Bulmus, EV, Gunning, AP, Hoffman, AS, Piskin, E & Morris, VJ 2000, 'Investigation of a stimuli-responsive copolymer by atomic force microscopy', POLYMER, vol. 41, no. 18, pp. 6723-6727.View/Download from: Publisher's site
Mozafari, M, Zareie, HM, Piskin, E & Hasirci, V 1998, 'Formation Of Supramolecular Structures By Negatively Charged Liposomes In The Presence Of Nucleic Acids And Divalent Cations', Drug Delivery, vol. 5, no. 2, pp. 135-141.View/Download from: Publisher's site
Cationic liposomes are being increasingly studied as delivery vehicles for bioactive agents such as DNA and other polynucleotides, The mechanism of interaction of DNA with liposomes and the organization of these interacting structures during and after th
Tas, C, Kozluca, A, Onur, M, Tumer, A, Vahapoglu, H, Zareie, HM, Gunning, P & Piskin, E 1998, 'In Vivo Degradation And Release Kinetics Of Chloramphenicol-loaded Poly(d,l)-lactide Sponges', Tissue Engineering, vol. 4, no. 4, pp. 353-363.View/Download from: Publisher's site
Poly(D,L)-lactide (PDLLA) homopolymer, with an average molecular weight of 20,000 daltons, was produced by the ring-opening polymerization of D,L-lactide in the presence of SnCl2.2H(2)O as the catalyst. The PDLLA sponges loaded with chloramphenicol were
Zareie, HM, Sahin, F, Ergun, M, Kocum, C, Menevse, S, Menevse, A & Piskin, E 1998, 'Interactions Of Dna With Fluorescent Dyes: By Scanning Tunneling Microscopy', International Journal Of Biological Macromolecules, vol. 23, no. 1, pp. 7-10.View/Download from: Publisher's site
Genomic DNA was obtained from peripheral blood samples of healthy volunteers and interacted with two fluorescent dyes (i.e. Hoechst 33258 and ethidium bromide) in aqueous media. These media containing DNA-dye complexes deposited on the gold coated mica s
Zareie, HM, Zencir, Y, Unaleroglu, C, Zumreoglu-karan, B & Piskin, E 1998, 'Ph-independent Decomposition Reactions Of L-ascorbic Acid In Aqueous Metal Solutions. 2. Imaging By Scanning Tunneling Microscopy', Polyhedron, vol. 17, no. 16, pp. 2633-2638.View/Download from: Publisher's site
STM images of aqueous solutions of L-ascorbic acid containing Gd3+ ions at pH values of 2, 6 and 12 have been recorded periodically after drying the samples on gold coated mice. The results have revealed that the organisations of the AA molecules and met
Zareie, HM, Kavakli, C, Salih, B & Piskin, E 1997, 'Scanning Tunnelling Microscopy For Characterization Of Metathesis Catalysts Based On Photogenerated W(co)(6)perccl4', Journal Of Molecular Catalysis A-chemical, vol. 118, no. 2, pp. 195-203.View/Download from: Publisher's site
We attempted to form a W(CO)(6)perCCl4 catalyst from the gas phase reaction of W(CO)(6) and CCl4 by UV-irradiation and used this catalyst in a model metathesis reaction of 1-heptene. We analyzed both the intermediate volatile compounds using an on-line m
Zareie, HM, Borucu, A, Ozden, M, Hasirci, V & Piskin, E 1996, 'Imaging Of Liposomes By Scanning Tunneling Microscopy', Artificial Cells Blood Substitutes And Immobilization Biotechnology, vol. 24, no. 5, pp. 525-531.View/Download from: Publisher's site
In this study, unilamellar and multilamellar liposomes consisting of dipalmitoylphosphatidylcholine, cholesterol and dicetylphosphate were prepared. Scanning tunneling microscopy images of these liposomes on highly oriented pyrolytic graphite surfaces we
Zareie, HM, Erdem, G, Oner, C, Oner, R, Ogus, A & Piskin, E 1996, 'Investigation Of Ascorbate-cu(ii) Induced Cleavage Of Dna By Scanning Tunneling Microscopy', International Journal Of Biological Macromolecules, vol. 19, no. 1, pp. 69-73.View/Download from: Publisher's site
Scanning Tunneling Microscopy (STM) was used for the investigation of oxidative DNA damage. A PCR amplified fragment of human beta-globin gene was used as a model for time dependent cleavage reaction by ascorbate and copper. Cleavage reactions were carri
Zareie, HM, Kaitian, X & Piskin, E 1996, 'STM images of PDLLA-PEG copolymer micelles', COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS, vol. 112, no. 1, pp. 19-24.View/Download from: Publisher's site
Zareie, HM, Oztas, N, Gundogan, M, Piskin, E & Yurum, Y 1996, 'Images Of Demineralized Coal Surfaces By Scanning Tunnelling Microscopy', Fuel, vol. 75, no. 7, pp. 855-857.View/Download from: Publisher's site
Zonguldak bituminous coal was demineralized with HCl and HF. Mineral removal was followed by classical chemical analysis and FT-i.r. spectroscopy to determine the types of inorganics dissolved. Scanning tunnelling microscopy (STM) images of the surfaces
Edgar, JA, Zareie, HM, Blaber, MG, Dowd, AR & Cortie, MB 2008, 'Synthesis of hollow gold nanoparticles and rings using silver templates', International Conference on Nanoscience and Nanotechnology, ICONN 2008, IEEE International Conference on Nanoscience and Nanotechnology, IEEE, Melbourne, Australia, pp. 36-39.View/Download from: Publisher's site
Gold nanoshells have gained attention recently due to their versatile optical properties. In particular, their spectrally selective extinction has been exploited for experimental medical applications, functional coatings and contrast enhancement for analytical techniques. Here we discuss nanoshells and the formation of gold nanorings by the galvanic replacement of Ag nanosphere template particles. Hollow Au/Ag nanoshells can be converted to nanorings upon addition of excess HAuCl4. Nanorings present a distinct particle geometry, with optical properties exhibiting characteristics of both nanorods and nanoshells.
Ford, M, Kirkup, L, Gentle, AR, Zareie, HM & Cortie, MB 2005, 'How reliable are scanning tunneling microscopy measurements of electron transport in molecules? - art. no. 603604', Biomems And Nanotechnology Ii, Conference on BioMEMS and Nanotechnology II, Spie-Int Society Optical Engineering, Brisbane, AUSTRALIA, pp. 3604-3604.View/Download from: Publisher's site
Scanning tunneling microscopy measurements of tunneling through molecules adsorbed on a surface have been simulated using a standard empirical model based upon the Wentzel-Kramer-Brillouin method applied to tunneling through a barrier. The Gaussian noise
Zareie, HM, Sarikaya, M, McDonagh, AM, Barber, J, Cortie, MB & Phillips, M 2007, 'Self-organised materials: from organic molecules to genetically engineered gold-binding proteins', 2006 International Conference on Nanoscience and Nanotechnology, ICONN, IEEE, Brisbane, Australia, pp. 517-519.
We present examples of ordered assemblies of organic and biological molecules on gold(111) surfaces. The first example shows how control over mono or multilayer assemblies of 1,4-phenylenedimethanthiol can be achieved and monitored. The second example shows how monolayers on gold can be prepared using amine groups to anchor aromatic molecules to the surface. A third example whos how ordered assemblies of genetically-engineered inorganic-binding polypeptides can be formed on gold surfaces using a 3-repeat, 14 amino acid gold-binding protein (GBP1).
Cortie, MB, Xu, X, Chowdhury, HA, Zareie, HM & Smith, G 2004, 'Plasmonic heating of gold nanoparticles and its exploitation', Smart Structures, Devices, and Systems II: Proceedings Of The Society Of Photo-Optical Instrumentation Engineers (SPIE) Volume 5649, Conference on Smart Structures, Devices, and Systems II, SPIE, Sydney, Australia, pp. 565-573.View/Download from: Publisher's site
Nanoscale particles of metals such as gold can interact with light by means of a plasmon resonance, even. though they are much smaller than the wavelengths of visible light. The proportions of light that are absorbed and scattered vary with wavelength. A
Cortie, MB, Zareie, HM, Liu, J, Muller, KH & Ford, M 2004, 'Modelling and verification of the electrical properties of organic dielectric monolayers in capacitive configurations', Proceedings Of The Society Of Photo-Optical Instrumentation Engineers (SPIE) Vol 5649, Conference on Smart Structures, Devices, and Systems II, International Society for Optical Engineering (SPIE), Sydney, Australia, pp. 316-322.View/Download from: Publisher's site
The possible role of self-assembled monolayers (SAMs) as the dielectric component of nanoscale capacitors is considered. SAMs of two rather different molecules, á,á&PRIME;-p-xylyldithiol (&PRIME; XYL&PRIME;) and dodecanedithiol (&PRIME; C12&P