Methodological approaches from experimental to computational analysis in vibrational spectroscopy and microspectroscopy

Severcan, Feride
Akkaş, Sara Banu
Türker, Sevgi
Yücel, Recai


Yaman, Oğuz Ulaş; Çalık, Pınar; Department of Chemical Engineering (2022-8-31)
In this MSc thesis, the aim is to propose methodologies for predicting transcription factor binding sites in yeast cells. This aim is achieved, first, by modeling P. pastoris central carbon metabolism genes using phylogenetic footprinting; and next, by modelling S. cerevisiae transcription factors’ affinity towards 8-mers using the Machine Learning algorithmic models, i.e., Random Forest, XGBoost, and Deep Learning. In the first part of the thesis, a novel phylogenetic footprinting algorithm is introduced,...
Methodological issues in building, training, and testing artificial neural networks in ecological applications
Ozesmi, Stacy L.; Tan, Can O.; Ozesmi, Uygar (2006-05-15)
We evaluate the use of artificial neural networks, particularly the feedforward multilayer perceptron with back-propagation for training (MLP), in ecological modelling and make suggestions on its use. in MLP modelling, there are no assumptions about the underlying form of the data that must be met as in standard statistical techniques. Instead, researchers must clarify the process of modelling, as this is most critical to how the model performs and is interpreted. Overfitting on the data, a potential proble...
Method for Dynamic Material Property Characterization of Soft-Tissue-Mimicking Isotropic Viscoelastic Materials Using Fractional Damping Models
Martin, Bryn A.; Kutluay, Umit; Yazıcıoğlu, Yiğit (ASTM International, 2013-09-01)
Characterization of the mechanical properties of human-tissue-mimicking silicone elastomers is important for producing accurate tissue models for experimentation. However, the viscoelastic and frequency-dependent material properties of elastomers are difficult to quantify. We present a material characterization technique for a silicone elastomer used to mimic human soft tissue based on generalized-Maxwell-type material models with and without fractional dissipating mechanisms. The silicone specimens were pr...
Computational spectral imaging techniques using diffractive lenses and compressive sensing
Kar, Oğuzhan Fatih; Öktem, Sevinç Figen; Department of Electrical and Electronics Engineering (2019)
Spectral imaging is a fundamental diagnostic technique in physical sciences with application in diverse fields such as physics, chemistry, biology, medicine, astronomy, and remote sensing. In this thesis, we first present a modified version of a high-resolution computational spectral imaging modality and develop a fast sparse recovery method to solve the associated large-scale inverse problems. This technique uses a diffractive lens called photon sieve for dispersing the optical field. We then extend this t...
Quantitative analysis of nonlinear dynamics of quantum light transmission in strongly coupled quantum dot-cavity systems
Tugen, Alperen; Kocaman, Serdar (Elsevier BV, 2019-04-01)
We compared transmission spectra of coupled high-Q cavity with quantum dot (QD) systems in the strong coupling regime with Input-Output Formalism (IOF) and Incoherent Pumping Mechanism (IPM) based on Lindblad master equation approach. The peak transmission of Dipole Induced Transparency (DIT) together with its full-width-half-maximum (FWHM) are enquired for detailed analysis. Both methods exhibit the same vacuum Rabi splitting in on-resonant case, in contrast, the peak of DIT is estimated smaller between 50...
Citation Formats
F. Severcan, S. B. Akkaş, S. Türker, and R. Yücel, Methodological approaches from experimental to computational analysis in vibrational spectroscopy and microspectroscopy. 2012, p. 52.