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Izmir, Turkey

İzmir Institute of Technology is a public research university in İzmir, Turkey. İYTE maintains a strong emphasis on the natural science and engineering. It is the only Turkish institute of technology. İzmir Institute of Technology is often cited as among Turkey's top universities. The medium of instruction in all the departments of İYTE is English. Wikipedia.

Kaya A.,Izmir Institute of Technology
Computer Methods in Applied Mechanics and Engineering | Year: 2014

In this paper a finite difference scheme is proposed for multidimensional convection-diffusion-reaction equations, particularly designed to treat the most interesting case of small diffusion. It is based closely on the work S¸endur and Neslitu¨rk (2011). Application of the method to multidimensional convection-diffusion-reaction equation is based on a simple splitting of the convection-diffusion-reaction equation and then joining their approximations obtained with S¸endur and Neslitu¨rk (2011). The method adapts very well to all regimes with continuous transitions from one regime to another. Numerical tests show good performance of the method and superiority with respect to well known stabilized finite element methods. © 2014 Elsevier B.V. Source

Sacar M.D.,Izmir Institute of Technology
Journal of integrative bioinformatics | Year: 2013

Experimental detection and validation of miRNAs is a tedious, time-consuming, and expensive process. Computational methods for miRNA gene detection are being developed so that the number of candidates that need experimental validation can be reduced to a manageable amount. Computational methods involve homology-based and ab inito algorithms. Both approaches are dependent on positive and negative training examples. Positive examples are usually derived from miRBase, the main resource for experimentally validated miRNAs. We encountered some problems with miRBase which we would like to report here. Some problems, among others, we encountered are that folds presented in miRBase are not always the fold with the minimum free energy; some entries do not seem to conform to expectations of miRNAs, and some external accession numbers are not valid. In addition, we compared the prediction accuracy for the same negative dataset when the positive data came from miRBase or miRTarBase and found that the latter led to more precise prediction models. We suggest that miRBase should introduce some automated facilities for ensuring data quality to overcome these problems. Source

Demir D.A.,Izmir Institute of Technology
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

We study gravitational properties of vacuum energy by erecting a geometry on the stress-energy tensor of vacuum, matter and radiation. Postulating that the gravitational effects of matter and radiation can be formulated by an appropriate modification of the spacetime connection, we obtain varied geometrodynamical equations which properly comprise the usual gravitational field equations with, however, Planck-suppressed, non-local, higher-dimensional additional terms. The prime novelty brought about by the formalism is that, the vacuum energy does act not as the cosmological constant but as the source of the gravitational constant. The formalism thus deafens the cosmological constant problem by channeling vacuum energy to gravitational constant. Nevertheless, quantum gravitational effects, if any, restore the problem via the graviton and graviton-matter loops, and the mechanism proposed here falls short of taming such contributions to cosmological constant. © 2011 Elsevier B.V. Source

Kanbar B.,Izmir Institute of Technology
Biotechnology progress | Year: 2010

Thermal stability of carbonic anhydrase (CA) immobilized within polyurethane (PU) foam was investigated. The catalytic activity of the enzyme was estimated by using p-nitrophenyl acetate (p-NPA) as the substrate in tris buffer containing 10% acetonitrile. The immobilized CA was stable during the repeatable washings and stability tests over 45 days stored in tris buffer at ambient conditions indicating that the CA was covalently attached to the polyurethane (PU) foam by crosslinking. The immobilized CA was found to be 98% stable below 50°C, whereas a drastic decrease was seen at temperatures between 50 and 60°C. The optimum temperature for the immobilized CA was found to be 45°C and it lost its activity completely at 60°C. Thermal deactivation energies for the free and immobilized CA were estimated to be 29 and 86 kcal/mol, respectively. The association of unfolded CA with the polymeric backbone chains of the PU foam was also addressed. It was concluded that the immobilized CA was highly stable at temperatures less than 50°C and could be used in biomimetic CO sequestration processes. © 2010 American Institute of Chemical Engineers Source

Allmer J.,Izmir Institute of Technology
Expert Review of Proteomics | Year: 2011

Proteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Database search methods are typically employed to identify proteins from complex mixtures. However, databases are not often available or, despite their availability, some sequences are not readily found therein. To overcome this problem, de novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them are detailed in this article. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and, finally, examples are used to construct possible future perspectives of the field. © 2011 Expert Reviews Ltd. Source

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