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Safak Ozhan Kocakaya 대한화학회 2014 Bulletin of the Korean Chemical Society Vol.35 No.6
Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/ Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.
Safak Ozhan Kocakaya,Gökçe Alt parmak,Zulbiye Önal,Yahya Güzel,Hayriye Y lmaz 대한화학회 2011 Bulletin of the Korean Chemical Society Vol.32 No.12
A four dimensional quantitative structure activity relationship analysis was applied to a series of 50 flavonoid inhibitors of p56^lck protein tyrosine kinase by the molecular comparative electron topological method. It was found that the -log (IC50) values of the compounds were highly dependent on the topology, size and electrostatic character of the substituents at seven positions of the flavonoid scaffold in this study. Depending on the negative or positive charge of the groups correctly embedded in these substituents, three-dimensional bio-structure to increase or decrease -log (IC50) values in the training set of 39 compounds was predicted. The test set of 11 compounds was used to evaluate the predictivity of the model. To generate 4D-QSAR model, the defined function groups and pharmacophore used as topological descriptors in the calculation of activity were of sufficient statistical quality (R^2 = 0.72 and Q^2 = 0.69). Ligand docking approach by using Dock 6.0. These compounds include many flavonoid analogs, They were docked onto human families of p56lck PTKs retrieved from the Protein Data Bank, 1lkl.pdb.
Altun, Ali Ozhan,Jeong, Jun-Ho,Rha, Jong-Joo,Kim, Ki-Don,Lee, Eung-Sug IOP Pub 2007 Nanotechnology Vol.18 No.46
<P>Cubic boron nitride (c-BN) is one of the hardest known materials (second after diamond). It has a high level of chemical resistance and high UV transmittance. In this study, a stamp for ultra-violet nanoimprint lithography (UV-NIL) was fabricated using a bi-layered BN film deposited on a quartz substrate. Deposition of the BN was done using RF magnetron sputtering. A hexagonal boron nitride (h-BN) layer was deposited for 30 min before c-BN was deposited for 30 min. The thickness of the film was measured as 160 nm. The phase of the c-BN layer was investigated using Fourier transform infrared (FTIR) spectrometry, and it was found that the c-BN layer has a 40% cubic phase. The deposited film was patterned using focused ion beam (FIB) lithography for use as a UV-NIL stamp. Line patterns were fabricated with the line width and line distance set at 150 and 150 nm, respectively. The patterning process was performed by applying different currents to observe the effect of the current value on the pattern profile. The fabricated patterns were investigated using AFM, and it was found that the pattern fabricated by applying a current value of 50 picoamperes (pA) has a better profile with a 65 nm line depth. The UV transmittance of the 160 nm thick film was measured to be 70–86%. The hardness and modulus of the BN was measured to be 12 and 150 GPa, respectively. The water contact angle of the stamp surface was measured at 75°. The stamp was applied to UV-NIL without coating with an anti-adhesion layer. Successful imprinting was proved via scanning electron microscope (SEM) images of the imprinted resin.</P>
Stamping-Based Planarization of Flexible Substrate for Low-Pressure UV Nanoimprint Lithography
Altun, Ali Ozhan,Jeong, Jun-Ho,Jung, Sung-Un,Kim, Ki-Don,Choi, Dae-Geun,Choi, Jun-Hyuk,Shim, Jong-Youp,Lee, Dong-II,Lee, Eung-Sug American Scientific Publishers 2008 Journal of Nanoscience and Nanotechnology Vol.8 No.11
<P>Patterning flexible substrates in nano scale is an important and challenging issue in the fabrication of next-generation devices based on a non-silicon substrate. Step and Flash imprint lithography (S-FIL<SUP>®</SUP>) which is a room temperature and low pressure process offers several important advantages, such as the use of a smaller and therefore cheaper stamp or the possibility of the overlay imprinting, as a transparent stamp is utilized. However, it is very difficult to perform S-FIL on a flexible substrate successfully due to the high waviness. The waviness of a flexible substrate is not a constant value in contrast to a rigid substrate. It depends on the imprint pressure applied onto the substrate. In this paper, in section two, the effect of the imprint pressure on the waviness of the surface of the flexible substrate is examined. It is proved that the waviness of the surface of the flexible substrate could not be reduced sufficiently to assure a successful imprint at low imprint pressures. In the third section, a method of patterning polymer substrates using ultra-violet nanoimprint lithography (UV-NIL) is presented. The method consists of two stages, stamping-based planarization and S-FIL. In stamping-based planarization, a planarization layer of transparent polymer is formed onto the flexible substrate. Waviness of the blank stamp (in this study, glass wafer) is transferred to the planarization layer. S-FIL is performed with the nanoimprint tool IMPRIO100 directly onto the planarization layer employing a 1 × 1 in.<SUP>2</SUP> quartz stamp. Optical microscope and SEM images of the successfully imprinted patterns were also presented.</P>
Kocakaya, Safak Ozhan Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.6
Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.
UV 나노임프린트 리소그래피를 위한 불화 함유 다이아몬드 상 탄소 스탬프의 제작
알툰 알리(Altun Ali Ozhan),정준호(Jun-ho Jeong),나종주(Jong-joo Rha),최대근(Dae-geun Choi),김기돈(Ki-don Kim),이응숙(Eung-sug Lee) 한국정밀공학회 2006 한국정밀공학회 학술발표대회 논문집 Vol.2006 No.5월
A fluorine-doped diamond-like carbon (F-DLC) stamp which has high contact angle, high UV-transmittance and sufficient hardness, was fabricated using the following direct etching method: F-DLC is deposited on a quartz substrate using DC and RF magnetron sputtering, PMMA is spin coated and patterned using e-beam lithography and finally, O2 plasma etching is performed to transfer the line patterns having 100 ㎚ line width, 100 ㎚ line space and 70 ㎚ line depth on F-DLC. The optimum fluorine concentration was determined after performing several pre-experiments. The stamp was applied successfully to UV-NIL without being coated with an anti-adhesion layer.
Multilevel Noncontiguous Spinal Fractures: Surgical Approach towards Clinical Characteristics
Mehmet Seçer,Fatih Alagöz,Ozhan Uçkun,Oğuz Durmuş Karakoyun,Murat Ömer Ulutaş,Ömer Polat,Ergün Dağlıoğlu,Ali Dalgıç,Deniz Belen 대한척추외과학회 2015 Asian Spine Journal Vol.9 No.6
Study Design: The study retrospectively investigated 15 cases with multilevel noncontiguous spinal fractures (MNSF). Purpose: To clarify the evaluation of true diagnosis and to plane the surgical treatment. Overview of Literature: MNSF are defined as fractures of the vertebral column at more than one level. High-energy injuries caused MNSF, with an incidence ranging from 1.6% to 16.7%. MNSF may be misdiagnosed due to lack of detailed neurological and radiological examinations. Methods: Patients with metabolic, rheumatologic diseases and neoplasms were excluded. Despite the presence of a spinal fracture associated clearly with the clinical picture, all patients were scanned within spinal column by direct X-rays, computed tomography and magnetic resonance imaging. When there were ≥5 intact vertebrae between two fractured vertebral segments, each fracture region was managed with a separated stabilization. In cases with ≤4 intact segments between two fractured levels, both fractures were fixed with the same rod and screw system. Results: There were 32 vertebra fractures in 15 patients. Eleven (73.3%) patients were male and age ranged from 20 to 64 years (35.9±13.7 years). Eleven cases were the American Spinal Injury Association (ASIA) E, 3 were ASIA A, and one was ASIA D. Ten of the 15 (66.7%) patients returned to previous social status without additional deficit or morbidity. The remaining 5 (33.3%) patients had mild or moderate improvement after surgery. Conclusions: The spinal column should always be scanned to rule out a secondary or tertiary vertebra fracture in vertebral fractures associated with high-energy trauma. In MNSF, each fracture should be separately evaluated for decision of surgery and planned approach needs particular care. In MNSF with ≤4 intact vertebra in between, stabilization of one segment should prompt the involvement of the secondary fracture into the system.
Lee, Jihye,Choi, Dae-Geun,Altun, Ali Ozhan,Kim, Ki-Don,Choi, Jun-Hyuk,Lee, Eung-Sug,Jeong, Jun-Ho American Scientific Publishers 2010 Journal of nanoscience and nanotechnology Vol.10 No.9
<P>This study reports the pattern definable and low cost fabrication of nanopatterned conducting polymer film on flexible substrates. Noble nanopatterned polymer hard template was fabricated by using nanoimprint lithography (NIL) and used for electropolymerization of conducting polymer. Conducting polymer was electrochemically deposited on the template and transferred over to flexible substrates. Eventually conducting polymer films with various nanopatterns were fabricated on flexible substrates. High pattern definability was achieved by nanoimprinted polymer template, which was molded from lithographically fabricated stamp. Low cost fabrication was accomplished due to low cost NIL, reusable polymer templates, and low material consumption of electrodeposition. The electrodeposited films were transferred using double sided tape. Because the templates are made of flexible polymer, the transfer bonding method applied in this study is adaptable to both wafers and flexible polymer substrates. The fabricated nanopatterned conducting polymer film can be applied to gas sensors, super capacitors, super wetting films, and neuron interfaces due to its characteristic of high surface to volume. For an illustrative application, the gas sensing properties of films were tested. The result showed enhanced sensing characteristic with nanopatterned film, which are attributed to the high surface to volume ratio of nanopatterned films.</P>