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Publication Metadata only A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons(Springer, 2014) Sutay, Berkay; Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129In this work, we present a theoretical study of the interaction between a diatomic iodine molecule with planar naphthalene and several other small polyaromatic hydrocarbons (PAHs). Our aim was to understand the general characteristics of the potential energy surface (PES) of this system; that is locating various local minima, finding the variation of PES around these optimum points by means of first principle calculations at MP2, SCS-MP2 and CCSD(T) levels of theory. Two basic orientations of the iodine molecule, i.e., parallel or perpendicular with respect to the naphthalene plane, are discussed. The PES of the former was investigated in detail, including the translation and rotation of I-2 (as a rigid rotor) along the naphtalene surface. It was concluded that, although the perpendicular conformations are usually 1 kcal mol(-1) more stable than the parallel conformation, this small difference does not exclude the presence of both conformations in the gas phase. Both structures were stable enough to hold more than 20 vibrational states. NBO analysis showed that the mutual polarization effects were greater for the perpendicular conformation. It was also observed that the I-2+naphtalene dimer interaction is almost twice of that of I-2+naphtalene, showing the long range character of the interaction.Publication Metadata only Anharmonicity, mode-coupling and entropy in a fluctuating native protein(Iop Publishing Ltd, 2010) N/A; Department of Physics; Department of Computer Engineering; N/A; Department of Chemical and Biological Engineering; Kabakçıoğlu, Alkan; Yüret, Deniz; Gür, Mert; Erman, Burak; Faculty Member; Faculty Member; PhD Student; Faculty Member; Department of Physics; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 49854; 179996; 216930; 179997We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. the effect of anharmonicity and mode-coupling on the fluctuational entropy is in the order of a few percent.Publication Metadata only Binding stability of peptides on major histocompatibility complex class I proteins: role of entropy and dynamics(Institute of Physics (IOP) Publishing, 2018) Gul, Ahmet; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies. The computation of the entropies is based on a simple model that requires short molecular dynamics trajectories and allows for approximate but rapid determination. The paper draws attention to the long neglected dynamic aspects of peptide binding, and provides a fast computation scheme that allows for rapid scanning of large numbers of peptides on selected HLA antigens, which may be useful in defining the right peptides for personal immunotherapy.Publication Metadata only Characterization of neonatal aortic cannula jet flow regimes for improved cardiopulmonary bypass(Elsevier Sci Ltd, 2013) Menon, Prahlad G.; Teslovich, Nikola; Chen, Chia-Yuan; Undar, Akif; Department of Mechanical Engineering; Pekkan, Kerem; Faculty Member; Department of Mechanical Engineering; College of Engineering; 161845During pediatric and neonatal cardiopulmonary bypass (CPB), tiny aortic outflow cannulae (2-3 mm inner diameter), with micro-scale blood-wetting features transport relatively large blood volumes (0.3 to 1.0 L/min) resulting in high blood flow velocities (2 to 5 m/s). These severe flow conditions are likely to complement platelet activation, release pro-inflammatory cytokines, and further result in vascular and blood damage. Hemodynamically efficient aortic outflow cannulae are required to provide high blood volume flow rates at low exit force. In addition, optimal aortic insertion strategies are necessary in order to alleviate hemolytic risk, post-surgical neurological complications and developmental defects, by improving cerebral perfusion in the young patient. The methodology and results presented in this study serve as a baseline for design of superior aortic outflow cannulae. In this study, direct numerical simulation (DNS) computational fluid dynamics (CFD) was employed to delineate baseline hemodynamic performance of jet wakes emanating from microCT scanned state-of-the-art pediatric cannula tips in a cuboidal test rig operating at physiologically relevant laminar and turbulent Reynolds numbers (Re: 650-2150, steady inflow). Qualitative and quantitative validation of CFD simulated device-specific jet wakes was established using time-resolved flow visualization and particle image velocimetry (PIV). For the standard end-hole cannula tip design, blood damage indices were further numerically assessed in a subject-specific cross-clamped neonatal aorta model for different cannula insertion configurations. Based on these results, a novel diffuser type cannula tip is proposed for improved jet flow-control, decreased blood damage and exit force and increased permissible flow rates. This study also suggests that surgically relevant cannula orientation parameters such as outflow angle and insertion depth may be important for improved hemodynamic performance. The jet flow design paradigm demonstrated in this study represents a philosophical shift towards cannula flow control enabling favorable pressure-drop versus outflow rate characteristics.Publication Metadata only Coherent regulation in yeast's cell-cycle network(Iop Publishing Ltd, 2015) N/A; Department of Physics; Aral, Neşe; Kabakçıoğlu, Alkan; PhD Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 49854We define a measure of coherent activity for gene regulatory networks, A property that reflects the unity of purpose between the regulatory agents with a common target. We propose that such harmonious regulatory action is desirable under a demand for energy efficiency and may be selected for under evolutionary pressures. We consider two recent models of the cell-cycle regulatory network of the yeast, Saccharomyces cerevisiae as a case study and calculate their degree of coherence. a comparison with random networks of similar size and composition reveals that the yeast's cell-cycle regulation is wired to yield an exceptionally high level of coherent regulatory activity. We also investigate the mean degree of coherence as a function of the network size, connectivity and the fraction of repressory/activatory interactions.Publication Metadata only Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs(Wiley-Blackwell, 2013) Marusic, Maja; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Azizoğlu, Selimcan; Kızılel, Rıza; Kavaklı, İbrahim Halil; Erman, Burak; Kızılel, Seda; Master Student; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 114475; 40319; 179997; 28376This paper reports the previously unknown interactions between eight low molecular weight commercially available drugs (130800Da) and DNA repair protein photolyase using computational docking simulations and surface plasmon resonance (SPR) experiments. Theoretical dissociation constants, Kd, obtained from molecular docking simulations were compared with the values found from SPR experiments. Among the eight drugs analyzed, computational and experimental values showed similar binding affinities between selected drug and protein pairs. We found no significant differences in binding interactions between pure and commercial forms of the drug lornoxicam and DNA photolyase. Among the eight drugs studied, prednisone, desloratadine, and azelastine exhibited the highest binding affinity (Kd=1.65, 2.05, and 8.47M, respectively) toward DNA photolyase. Results obtained in this study are promising for use in the prediction of unknown interactions of common drugs with specific proteins such as human clock protein cryptochrome. Copyright (c) 2013 John Wiley & Sons, Ltd.Publication Metadata only Computational modeling of vascular growth in patient-specific pulmonary arterial patch reconstructions(Elsevier Sci Ltd, 2021) Coban, Gursan; Kose, Banu; Salihoglu, Ece; Department of Mechanical Engineering; Department of Mechanical Engineering; Lashkarinia, Seyedeh Samaneh; Pekkan, Kerem; Researcher; Faculty Member; Department of Mechanical Engineering; College of Engineering; College of EngineeringRecent progress in vascular growth mechanics has involved the use of computational algorithms to address clinical problems with the use of three-dimensional patient specific geometries. The objective of this study is to establish a predictive computational model for the volumetric growth of pulmonary arterial (PA) tissue following complex cardiovascular patch reconstructive surgeries for congenital heart disease patients. For the first time in the literature, the growth mechanics and performance of artificial cardiovascular patches in contact with the growing PA tissue domain is established. An elastic growing material model was developed in the open source FEBio software suite to first examine the surgical patch reconstruction process for an idealized main PA anatomy as a benchmark model and then for the patient-specific PA of a newborn. Following patch reconstruction, high levels of stress and strain are compensated by growth on the arterial tissue. As this growth progresses, the arterial tissue is predicted to stiffen to limit elastic deformations. We simulated this arterial growth up to the age of 18 years, when somatic growth plateaus. Our research findings show that the non-growing patch material remains in a low strain state throughout the simulation timeline, while experiencing high stress hot-spots. Arterial tissue growth along the surgical stitch lines is triggered mainly due to PA geometry and blood pressure, rather than due to material property differences in the artificial and native tissue. Thus, nonuniform growth patterns are observed along the arterial tissue proximal to the sutured boundaries. This computational approach is effective for the pre-surgical planning of complex patch surgeries to quantify the unbalanced growth of native arteries and artificial non-growing materials to develop optimal patch biomechanics for improved postoperative outcomes.Publication Metadata only Does the magnetic field of a magnetic stirrer in an optical aggregometer affect concurrent platelet aggregation?(2013) Sağdilek, Engin; Çelebi, Gürbüz; Department of Physics; Sebik, Oğuz; Researcher; Department of Physics; College of Sciences; N/APlatelets are subjected to extremely low frequency electromagnetic fields during standard aggregometry measurements owing to the use of a magnetic stir bar in the instrument. This study evaluates the effects of this magnetic field exposure on platelet aggregation by comparing the results obtained in a modified aggregometer. Blood samples from healthy volunteers were anticoagulated using citrate or heparin. Platelet-rich plasma (PRP) samples were prepared. A mechanical stirring device was attached to the aggregometer instead of the magnetic stir bar system. The PRP samples were stirred using a stirring rod tip that did not produce any magnetic fields in one channel of the aggregometer; in the other channel, a stirring rod carrying a small magnet at its tip was used. As a result, a magnetic field in the extremely low frequency range and in the amplitude range of 1.9–65 mT was applied to the platelets assigned to the channel where the magnetic stirring rod tip was used. Aggregation was induced using adenosine diphosphate (ADP), collagen, or epinephrine. The slopes, maximum aggregation values, and areas under the aggregation curves were compared between the magnetic and neutral stirring rod tip groups. For samples stirred with the magnetic stirring rod tip, a significant decrease was observed in 12 of the 14 parameters evaluated for aggregations induced with ADP or collagen compared to the neutral stirring rod tip, regardless of the method used for anticoagulation. This observation indicates that the magnetic stir bars used in standard aggregometry may significantly alter aggregation parameters and platelets may be possible targets of electromagnetic fields.Publication Metadata only Embryonic aortic arch material properties obtained by optical coherence tomography-guided micropipette aspiration(Elsevier Ltd, 2023) Çoban, Gürşan; Yap, Choon Hwai; Department of Mechanical Engineering; N/A; Department of Mechanical Engineering; Lashkarinia, Seyedeh Samaneh; Siddiqui, Hummaira Banu; Pekkan, Kerem; Researcher; PhD Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 161845It is challenging to determine the in vivo material properties of a very soft, mesoscale arterial vesselsof size ∼ 80 to 120 μm diameter. This information is essential to understand the early embryonic cardiovascular development featuring rapidly evolving dynamic microstructure. Previous research efforts to describe the properties of the embryonic great vessels are very limited. Our objective is to measure the local material properties of pharyngeal aortic arch tissue of the chick-embryo during the early Hamburger-Hamilton (HH) stages, HH18 and HH24. Integrating the micropipette aspiration technique with optical coherence tomography (OCT) imaging, a clear vision of the aspirated arch geometry is achieved for an inner pipette radius of Rp = 25 μm. The aspiration of this region is performed through a calibrated negatively pressurized micro-pipette. A computational finite element model is developed to model the nonlinear behaviour of the arch structure by considering the geometry-dependent constraints. Numerical estimations of the nonlinear material parameters for aortic arch samples are presented. The exponential material nonlinearity parameter (a) of aortic arch tissue increases statistically significantly from a = 0.068 ± 0.013 at HH18 to a = 0.260 ± 0.014 at HH24 (p = 0.0286). As such, the aspirated tissue length decreases from 53 μm at HH18 to 34 μm at HH24. The calculated NeoHookean shear modulus increases from 51 Pa at HH18 to 93 Pa at HH24 which indicates a statistically significant stiffness increase. These changes are due to the dynamic changes of collagen and elastin content in the media layer of the vessel during development.Publication Metadata only Extracellular glucose level regulates dependence on 78 for cell surface localization of multipass transmembrane proteins in HeLa cells(Wiley, 2018) Toyoda, Yusuke; Sarov, Mihail; Saitoh, Shigeaki; Department of Molecular Biology and Genetics; Akarlar, Büşra; Other; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; N/A; 105301
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