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Department: search.filters.department.Department of PhysicsSubject: search.filters.subject.Biophysics

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Now showing 1 - 10 of 22
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    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; 179997
    We 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.
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    Application of the nonlinear methods in pneumocardiogram signals
    (Springer, 2020) Akilli, Mahmut; Ozbek, Mustafa; Zeren, Tamer; Akdeniz, K. Gediz; Department of Physics; Yılmaz, Nazmi; Teaching Faculty; Department of Physics; College of Sciences; 178427
    In this work, the pneumocardiogram signals of nine rats were analysed by scale index, Boltzmann Gibbs entropy and maximum Lyapunov exponents. The scale index method, based on wavelet transform, was proposed for determining the degree of aperiodicity and chaos. It means that the scale index parameter is close to zero when the signal is periodic and has a value between zero and one when the signal is aperiodic. A new entropy calculation method by normalized inner scalogram was suggested very recently. In this work, we also used this method for the first time in an empirical data. We compared the both methods with maximum Lyapunov exponents and observed that using together the scale index and the entropy calculation method by normalized inner scalogram increases the reliability of the pneumocardiogram signal analysis. Thus, the analysis of the pneumocardiogram signals by those methods enables to compare periodical and/or nonlinear aspects for further understanding of dynamics of cardiorespiratory system.
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    Cation transport properties of Amphotericin-B membrane channel
    (Biophysical Society, 1999) Baginski, Maciej; Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of Sciences; N/A
    N/A
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    Coherent organization in gene regulation: a study on six networks
    (Iop Publishing Ltd, 2016) 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; 49854
    Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. Here we analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation in three organisms or cell types each, and show that they follow a version of Hebb's rule which we have termed coherence. More precisely, we find that simultaneously expressed genes with a common target are less likely to act antagonistically at the attractors of the regulatory dynamics. We then investigate the dependence of coherence on structural parameters, such as the mean number of inputs per node and the activatory/repressory interaction ratio, as well as on dynamically determined quantities, such as the basin size and the number of expressed genes.
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    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; 49854
    We 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.
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    Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels
    (Elsevier, 2002) Baginski, Maciej; Borowski, Edward; Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of Sciences; N/A
    Amphotericin B (AmB) is a very effective anti-fungal polyene macrolide antibiotic whose usage is limited by its toxicity. Lack of a complete understanding of AmB's molecular mechanism has impeded attempts to design less toxic AmB derivatives. The antibiotic is known to interact with sterols present in the cell membrane to form ion channels that disrupt membrane function. The slightly higher affinity of AmB toward ergosterol (dominant sterol in fungal cells) than cholesterol (mammalian sterol) is regarded as the most essential factor on which antifungal chemotherapy is based. To study these differences at the molecular level, two realistic model membrane channels containing molecules of AmB, sterol (cholesterol or ergosterol), phospholipid, and water were studied by molecular dynamics (MID) simulations. Comparative analysis of the simulation data revealed that the sterol type has noticeable effect on the properties of AmB membrane channels. In addition to having a larger size, the AmB channel in the ergosterol-containing membrane has a more pronounced pattern of intermolecular hydrogen bonds. The interaction between the antibiotic and ergosterol is more specific than between the antibiotic and cholesterol. These observed differences suggest that the channel in the ergosterol-containing membrane is more stable and, due to its larger size, would have a higher ion conductance. These observations are in agreement with experiments. (C) 2002 Elsevier Science B.V. All rights reserved.
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    Conformational properties of amphotericin b amide derivatives - impact on selective toxicity
    (Springer, 2000) Sungur, F. Aylin; Baginski, Maciej; Borowski, Edward; Aviyente, Viktorya; Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of Sciences; N/A
    Even though it is highly toxic, Amphotericin B (AmB), an amphipathic polyene macrolide antibiotic, is used in the treatment of severe systemic fungal infections as a life-saving drug. To examine the influence of conformational factors on selective toxicity of these compounds, we have investigated the conformational properties of five AmB amide derivatives. It was found that the extended conformation with torsional angles (phi,psi)=(290 degrees,180 degrees ) is a common minimum of the potential energy surfaces (PES) of unsubstituted AmB and its amide derivatives. The extended conformation of the studied compounds allows for the formation of an intermolecular hydrogen bond network between adjacent antibiotic molecules in the open channel configuration. Therefore, the extended conformation is expected to be the dominant conformer in an open AmB (or its amide derivatives) membrane channel. The derivative compounds for calculations were chosen according to their selective toxicity compared to AmB and they had a wide range of selective toxicity. Except for two AmB derivatives, the PES maps of the derivatives reveal that the molecules can coexist in more than one conformer. Taking into account the cumulative conclusions drawn from the earlier MD simulation studies of AmB membrane channel, the results of the potential energy surface maps, and the physical considerations of the molecular structures, we hypothesize a new model of structure-selective toxicity of AmB derivatives. In this proposed model the presence of the extended conformation as the only well defined global conformer for AmB derivatives is taken as the indicator of their higher selective toxicity. This model successfully explains our results. To further test our model, we also investigated an AmB derivative whose selective toxicity has not been experimentally measured before. Our prediction for the selective toxicity of this compound can be tested in experiments to validate or invalidate the proposed model.
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    Conformational properties of amphotericin B amide derivatives - impact on selective toxicity
    (Springer, 2000) Sungur, Fethiye Aylin; Beginski, Maciej; Borowski, Edward; Aviyente, Viktorya; Department of Physics; Reşat, Haluk; Faculty Member; Department of Physics; College of Sciences; N/A
    Even though it is highly toxic, Amphotericin B (AmB), an amphipathic polyene macrolide antibiotic, is used in the treatment of severe systemic fungal infections as a life-saving drug. To examine the influence of conformational factors on selective toxicity of these compounds, we have investigated the conformational properties of five AmB amide derivatives. It was found that the extended conformation with torsional angles (ΦΨ)=(290°, 180°) is a common minimum of the potential energy surfaces (PES) of unsubstituted AmB and its amide derivatives. The extended conformation of the studied compounds allows for the formation of an intermolecular hydrogen bond network between adjacent antibiotic molecules in the open channel configuration. Therefore, the extended conformation is expected to be the dominant conformer in an open AmB (or its amide derivatives) membrane channel. The derivative compounds for calculations were chosen according to their selective toxicity compared to AmB and they had a wide range of selective toxicity. Except for two AmB derivatives, the PES maps of the derivatives reveal that the molecules can coexist in more than one conformer. Taking into account the cumulative conclusions drawn from the earlier MD simulation studies of AmB membrane channel, the results of the potential energy surface maps, and the physical considerations of the molecular structures, we hypothesize a new model of structure-selective toxicity of AmB derivatives. In this proposed model the presence of the extended conformation as the only well defined global conformer for AmB derivatives is taken as the indicator of their higher selective toxicity. This model successfully explains our results. To further test our model, we also investigated an AmB derivative whose selective toxicity has not been experimentally measured before. Our prediction for the selective toxicity of this compound can be tested in experiments to validate or invalidate the proposed model.
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    Cyto/hemocompatible magnetic hybrid nanoparticles (ag2s-fe3o4) with luminescence in the near-infrared region as promising theranostic materials
    (Elsevier, 2015) Grandfils, Christian; Ojea-Jimenez, Isaac; Rossi, Francois; Dogan, Nurcan; Department of Physics; N/A; Department of Chemistry; Department of Chemistry; N/A; Kiraz, Alper; Hocaoğlu, İbrahim; Aşık, Didar; Acar, Havva Funda Yağcı; Ulusoy, Gülen; Faculty Member; PhD Student; Master Student; Faculty Member; N/A; Department of Physics; Department of Chemistry; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; 22542; N/A; N/A; 178902; N/A
    Small hybrid nanoparticles composed of highly biocompatible Ag2S quantum dots (QD) emitting in the near-infrared region and superparamagnetic iron oxide (SPION) are produced in a simple extraction method utilizing ligand exchange mechanism. Hybrid nanoparticles luminesce at the same wavelength as the parent QD, therefore an array of hybrid nanoparticles with emission between 840 and 912 nm were easily produced. Such hybrid structures have (1) strong luminescence in the medical imaging window eliminating the autofluoresence of cells as effective optical probes, (2) strong magnetic response for magnetic targeting and (3) good cyto/hemocompatibility. An interesting size dependent cytotoxicity behavior was observed in HeLa and NIH/3T3 cell lines: smallest particles are internalized significantly more by both of the cell lines, yet showed almost no significant cytotoxicity in HeLa between 10 and 25 mu g/mL Ag concentration but were most toxic in NIH/3T3 cells. Cell internalization and hence the cytotoxicity enhanced when cells were incubated with the hybrid nanoparticles under magnetic field, especially with the hybrid nanoparticles containing larger amounts of SPION in the hybrid composition. These results prove them as effective optical imaging agents and magnetic delivery vehicles. Combined with the known advantages of SPIONs as a contrast agent in MRI, these particles are a step forward for new theranostics for multimode imaging and magnetic targeting.
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    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/A
    Platelets 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.