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Classification of Motor Imagery in Electroencephalogram Signal Based on Spatio-temporal Feature selection Using Elastic Net
, M.Sc. Thesis Sharif University of Technology ; Jahed, Mehran (Supervisor)
Abstract
Motor imagery causes Event related Synchronization/Desynchronization (ERS/ERD) in Electroencephalogram (EEG) signal. These potentials can be used as an input for a Brain Computer Interface (BCI) system. To do so, it is necessary for these inputs to be correctly classified. The quality of classification is severely affected by the features extracted. Common Spatial Patterns (CSP) algorithm is often used for this task. Some of this method disadvantages are neglecting non-stationary properties of EEG signal and its proneness to overfitting. Additionally, its success is highly dependent on the frequency band that the algorithm is performed in. The most suitable sub band is interchangeable...
Vibration Modes of Membrane Proteins by Application of Elastic Network Model
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Mobasheri, Hamid (Supervisor) ; Naghdabadi, Reza (Co-Advisor)
Abstract
Outer membrane proteins play the role of molecular machines in the outer membrane of bacteria to regulate their basic functions. These macromolecules have nano-scale dimensions and they are involved in the classifications of nano-machines and nano-pores. Protein structure is constructed of chain of amino acids. Coarse grained elastic network model of the protein introduces a network of selected point masses, which is located on α-carbon of each amino acid, linked together with harmonic springs that represent the interactions between residues, both the chemical (protein backbone) and physical bonds. Using the harmonic network potential and theory of mechanical vibration, normal modes of...
Membrane interactions control residue fluctuations of outer membrane porins
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 81, Issue 5 , May , 2010 ; 15393755 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2010
Abstract
Bacterial outer membrane porins (Omp) that have robust β -barrel structures, show potential applications for nanomedicine devices in synthetic membranes and single molecule detection biosensors. Here, we explore the conformational dynamics of a set of 22 outer membrane porins, classified into five major groups: general porins, specific porins, transport Omps, poreless Omps and composed pores. Normal mode analysis, based on mechanical vibration theory and elastic network model, is performed to study the fluctuations of residues of aforementioned porins around their equilibrium positions. We find that a simple modification in this model considering weak interaction between protein and...
Gating and conduction of nano-channel forming proteins: A computational approach
, Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2013
Abstract
Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used...