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Geçiş elementi içeren organik moleküllerin elektronik yapısı
No full textThesis (Doctoral)--Izmir Institute of Technology, Physics, Izmir, 2019Includes bibliographical references (leaves: 184-191)Text in English; Abstract: Turkish and EnglishHemoglobin including iron atom, vitamin B12 containing cobalt atom and ruthenium-
based dye molecules are examples of organic molecules. We explore whether electron
correlations arising from transition-metal atoms have any special role in the functioning
of organic molecules using the effective multi-orbital Anderson model. We choose deoxy
and oxy-heme molecules which are examples of hemoglobin derivatives because
they have many experimental and theoretical studies. The experimental magnetic susceptibility
measurements find that deoxy and oxy-heme molecules exhibit a high-spin
to low-spin transition. We use four different computational methods: density functional
theory (DFT), DFT+U, DFT+mean-field approximation (DFT+MFA) and DFT+quantum
Monte Carlo (DFT+QMC) to study this transition. In this thesis, we compare the results
of these methods with each other and the experimental results. DFT and DFT+U methods
do not yield the high-spin state for deoxy-heme. DFT method correctly does not find the
location of impurity bound state (IBS) known as correlated new electronic states. These
methods obtain low-spin for oxy-heme, but they find that magnetic correlations are very
small. DFT+MFA works well for high-spin, but this technique does not obtain low-spin
because it does not find the location of IBS correctly. DFT+QMC gives the high(low)-
spin state for deoxy-heme (oxy-heme) and finds IBS and magnetic correlations. We obtain
that DFT+QMC works better among these methods for deoxy and oxy-heme molecules.
Moreover, we investigate whether we can observe the IBS and magnetic correlations for
vitamin B12, dye molecules and single-atom catalysts by using these computational approaches.Demir atomu içeren hemoglobin, kobalt atomu içeren vitamin B12 ve rutenyumbazlı boya molekülleri organik moleküllere örnektir. Geçiş-metali atomlarından kaynaklanan elektron korelasyonlarının, etkin çok-orbitalli Anderson modelini kullanarak organik moleküllerin işleyişinde özel bir rolü olup olmadığını araştırıyoruz. Hemoglobin türevlerinin örnekleri olan deoksi ve oksi-hem moleküllerini, birçok deneysel ve teorik çalışmaları olduğu için seçtik. Deneysel manyetik duyarlılık ölçümleri, deoksi ve oksihem
molekülleri yüksek-spinden düşük-spine geçiş sergilediğini tespit eder. Bu geçişi çalışmak için dört farklı hesapsal metot kullandık: yoğunluk fonksiyonel teorisi (YFT), YFT+U, YFT+ortalama-alan yaklaşımı (YFT+OAY) ve YFT+kuantum Monte Carlo (YFT+KMC). Bu tezde, bu yöntemlerin sonuçlarını birbirleri ile ve deneysel sonuçlarla karşılaşstırıyoruz. YFT ve YFT+U metotları deoksi için yüksek-spin durumunu vermiyor. YFT metodu, korelasyonlu yeni elektronik durum olarak bilinen safsızlık bağıl durumunun
(SBD) yerini doğru şekilde bulamaz. Bu metotlar oksi-hem için düşük-spini elde eder, fakat manyetik korelasyonların çok küçük olduğunu bulurlar. YFT+OAY, yüksek-spin için çok iyi çalışır, ancak SBD’nin yerini doğru şekilde bulamadığı için düşük-spin durumunu elde edemez. YFT+KMC, deoksi-hem (oksi-hem) için yüksek(düşük)-spin durumunu verir, ve SBD ve manyetik korelasyonları bulur. YFT+KMC’nin deoksi ve oksihem molekülleri için bu yöntemler arasında daha iyi çalıştığını elde ettik. Ayrıca, bu
hesapsal yaklaşımları kullanarak vitamin B12, boya molekülleri ve tek-atom katalizörleri için SBD ve manyetik korelasyonları gözlemleyip gözlemleyemeyeceğimizi araştırıyoruz.TUBITAK (110T387 and 113F242) and TUBITAK ULAKBI
In vitro antimicrobial activity screening of ethanol extract of Lavandula stoechas and investigation of its biochemical composition
No full textThe aim of this study was to test antimicrobial activity of ethanol extract of Lavandula stoechas against 22 bacteria and 1 yeast. Also, biochemical composition of the extract was investigated. A wide range of Gram-positive, Gram-negative microorganisms, and multidrug resistant bacteria were selected to test the antimicrobial activity. As a result, the extract is observed to contain fenchone (bicyclo[2.2.1]heptan-2-one, 1,3,3-trimethyl-, (1R)-) and camphor (+)-2-bornanone) as major components and showed antimicrobial activity against all studied microorganisms except Escherichia coli ATCC 25922 and Klebsiella pneumoniae. The results of the study present that L. stoechas is active against MDR strains too
Search for long-lived particles decaying into displaced jets in proton-proton collisions at √s=13 TeV
No full textA search for long-lived particles decaying into jets is presented. Data were collected with the CMS detector at the LHC from proton-proton collisions at a center-of-mass energy of 13 TeV in 2016, corresponding to an integrated luminosity of 35.9 fb(-1). The search examines the distinctive topology of displaced tracks and secondary vertices. The selected events are found to be consistent with standard model predictions. For a simplified model in which long-lived neutral particles are pair produced and decay to two jets, pair production cross sections larger than 0.2 fb are excluded at 95% confidence level for a long-lived particle mass larger than 1000 GeV and proper decay lengths between 3 and 130 mm. Several supersymmetry models with gauge-mediated supersymmetry breaking or R-parity violation, where pair-produced long-lived gluinos or top squarks decay to several final-state topologies containing displaced jets, are also tested. For these models, in the mass ranges above 200 GeV, gluino masses up to 2300-2400 GeV and top squark masses up to 1350-1600 GeV are excluded for proper decay lengths approximately between 10 and 100 mm. These are the most restrictive limits to date on these models
Measurement of differential cross sections for Z boson pair production in association with jets at √s=8 and 13 TeV
No full textThis Letter reports measurements of differential cross sections for the production of two Z bosons in association with jets in proton-proton collisions at root s = 8 and 13 TeV. The analysis is based on data samples collected at the LHC with the CMS detector, corresponding to integrated luminosities of 19.7 and 35.9 fb(-1) at 8 and 13 TeV, respectively. The measurements are performed in the leptonic decay modes ZZ -> l(+)l(-)l'(+)l'(-), where, l, l' = e, mu The differential cross sections as a function of the jet multiplicity, the transverse momentum p(T), and pseudorapidity of the P-T-leading and subleading jets are presented. In addition, the differential cross sections as a function of variables sensitive to the vector boson scattering, such as the invariant mass of the two P-T-leading jets and their pseudorapidity separation, are reported. The results are compared to theoretical predictions and found in good agreement within the theoretical and experimental uncertainties. (C) 2018 The Author(s). Published by Elsevier B.V
Effects of N-terminal and C-terminal polyhistidine tag on the stability and function of the thermophilic P450 CYP119
No full textPubMed: 31320891Biocatalysts are sought-after in synthesis of pharmaceuticals and agrochemicals due to their high regioselectivity and enantioselectivity. Among biocatalysts, heme-containing cytochrome P450 (P450) oxygenases are an attractive target since they catalyze oxidation of "unactivated" carbon-hydrogen bonds with high efficiency. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius, which has the potential to be widely used as a biocatalyst since it shows activity at high temperatures and low pH. Polyhistidine tags (His-tags) are widely used to simplify purification of proteins. However, His-tags can cause changes to protein structure and function. Here, we demonstrate the effects of His-tags on CYP119. To this end, the His-tags were cloned at the N-terminus or C-terminus of the CYP119, and His-tagged proteins were expressed and isolated. The thermostability and peroxidase activity of His-tagged CYP119s were tested and compared to wild type CYP119. Results indicated that while addition of His-tags increased the yield and simplified isolation of CYP119, they also influenced the electronic structure of active site and the activity of the protein. We show that N-terminal His-tagged CYP119 has desirable properties and potential to be used in industrial applications, but mechanistic studies using this protein need careful interpretation since the His-tag affects electronic properties of the active site heme iron
Kuasi bir boyutlu geçiş metali dikalkojenit yapıların elektronik, titreşimsel ve taşınım özellikleri
No full textThesis (Master)--Izmir Institute of Technology, Physics, Izmir, 2019Includes bibliographical references (leaves: 38-43)Text in English; Abstract: Turkish and EnglishThermoelectric materials have attracted great attention due to their ability to convert heat to electrical energy. As the application area of nanoscience expands, nanostructuring becomes a promising approach for enhancing thermoelectric properties. In this thesis, thermoelectric enhancement of the T-phase HfSe2 structures is studied via nanostructuring. Density functional theory (DFT) based electronic and vibrational spectra of two-dimensional (2D) and quasi-one dimensional T-phase HfSe2 structures are investigated and their ballistic thermoelectric transport properties are examined within the Landauer formalism. For the first time, it was reported that the nanoribbons of the Tphase HfSe2 are dynamically stable and semiconducting materials. They have promising thermoelectric properties. We reported the enhancement of the p-type ZT parameter of T-phase HfSe2 at both low and high temperatures. Moreover, the width dependency of the thermoelectric properties of the nanoribbons are studied.Termoelektrik malzemeler, ısı ve elektrik enerjisi arasında çevirim yapabildikleri için büyük ilgi çekmektedirler. Nanobilimdeki uygulama alanları genişledikçe, termoelektrik verimliliği artırmada, nanoyapılandırma umut vadeden bir yaklas¸ım olmuştur. Bu çalışmada, T-fazına sahip HfSe2 yapısının termoelektrik verimliliğinin nanoyapılandırma ile artırılması çalışılmıştır. Yoğunluk fonksiyoneli (DFT) teorisi kullanılarak, iki boyutlu ve kuasi-bir boyutlu malzemelerin elektronik ve titreşimsel bant yapıları incelenmiş ve balistik termal taşınım özellekleri Landauer formalizmi kullanılarak elde edilmiştir. İlk defa bu çalışmada, T-fazı HfSe2’nin kuasi-bir boyutlu nanoşeritleri incelenmiştir. Dinamik olarak kararlı bulunmuşlardır ve her bir malzeme yarı iletken karaktere sahiptir. Hem düşük, hem de yüksek sıcaklıklarda p-type ZT parametresinde artış hesaplanmıştır. Nanoşeritlerin kalınlıklarına bağlı termoelektrik özellikleri de incelenmiştir.TUBITAK (117F131 and 117F480
Modification of commercial boron carbide powder using Rapid Carbothermal Reduction
No full textNon-uniform morphology and existence of free carbon are two main problems for commercial boron carbide powders. This work proposes a method for eliminating free carbon and changing the morphology of commercial powders using Rapid Carbothermal Reduction (RCR) process. Free carbon is eliminated from commercial boron carbide powders and morphology is evolved to less angular shapes with limited particle size growth. Commercial and modified powders were densified by Spark Plasma Sintering at 1900 degrees C with 0, 5, and 20 minutes dwell. Despite the particle size growth, modified boron carbide powders reached >99% TD with shorter dwell times compared with commercial starting powders. Improved microhardness observed with dense modified samples as a result of enhanced morphology and increased twinning
Study of the underlying event in top quark pair production in pp collisions at 13 TeV
No full textPubMed: 30863200Measurements of normalized differential cross sections as functions of the multiplicity and kinematic variables of charged-particle tracks from the underlying event in top quark and antiquark pair production are presented. The measurements are performed in proton-proton collisions at a center-of-mass energy of 13<, and are based on data collected by the CMS experiment at the LHC in 2016 corresponding to an integrated luminosity of 35.9fb(-1). Events containing one electron, one muon, and two jets from the hadronization and fragmentation of b quarks are used. These measurements characterize, for the first time, properties of the underlying event in top quark pair production and show no deviation from the universality hypothesis at energy scales typically above twice the top quark mass
Performance evaluation of WebRTC-based online consultation platform
No full textInformation technologies give patients the opportunity to communicate with medical professionals remotely. Telemedicine uses these technologies to provide advanced healthcare and medical services. We present a medical online consultation application based on Web Real-Time Communications (WebRTC) technology enabling chat, audio, and video calls. Communication architecture and protocols of the application are explained in detail. Additionally, the user interface of the application is shown via performed calls. The application is tested and evaluated on different network connections (3G, 4G, local, and DSL) and different browsers and mobile operating systems (Android, Chrome, Firefox, Internet Explorer, iOS, Opera, Safari). During calls, communication quality parameters such as round-trip time (RTT) and packet loss, obtained via the WebRTC application programming interface, are analyzed. 3G, 4G, and local connections show low packet losses (1%) in Android, Chrome, iOS, Opera, and Safari for DSL connection, but RTT values are low (<100 ms) in all different conditions excluding iOS. In the presented application, RTT and packet loss remain lower than 100 ms and 1%, respectively, in various scenarios, indicating good communication quality. RTT and packet loss are related to total time and hang time parameters, which describe the necessary time to establish and to end a call. It is shown that communication quality of the application can simply be measured by analyzing the total time parameter. This enables predictable information for communication quality for WebRTC-based applications without continuously monitoring RTT and packet loss for the first time
Search for new particles decaying to a jet and an emerging jet
No full textA search is performed for events consistent with the pair production of a new heavy particle that acts as a mediator between a dark sector and normal matter, and that decays to a light quark and a new fermion called a dark quark. The search is based on data corresponding to an integrated luminosity of 16.1 fb(-1) from proton-proton collisions at =13 TeV collected by the CMS experiment at the LHC in 2016. The dark quark is charged only under a new quantum-chromodynamics-like force, and forms an emerging jet via a parton shower, containing long-lived dark hadrons that give rise to displaced vertices when decaying to standard model hadrons. The data are consistent with the expectation from standard model processes. Limits are set at 95% confidence level excluding dark pion decay lengths between 5 and 225 mm for dark mediators with masses between 400 and 1250 GeV. Decay lengths smaller than 5 and greater than 225 mm are also excluded in the lower part of this mass range. The dependence of the limit on the dark pion mass is weak for masses between 1 and 10 GeV. This analysis is the first dedicated search for the pair production of a new particle that decays to a jet and an emerging jet