Özer, Mahmut | İşler, Yalçın | Özer, Halil

Article | 2004 | Computer Methods and Programs in Biomedicine75 ( 1 ) , pp.51 - 57

In this paper, a new computer software package, Yalzer, is introduced for simulating single-compartmental model of neurons. Passive or excitable membranes with voltage-gated ion channels can be modeled, and current clamp and voltage clamp experiments can be simulated. In the Yalzer, first-order differential equations used to define the dynamics of the gate variables and the membrane potential are solved by two separate integration methods with variable time steps: forward Euler and exponential Euler methods. Outputs of the simulation are shown on a spreadsheet template for allowing flexible data manipulation and can be graphically d . . .isplayed. The user can define the model in detail, and examine the excitability of the model and the dynamics of voltage-gated ion channels. The software package addresses to ones who want to run simple simulations of neurons without need to any programming language skills or expensive software. It can also be used for educational purposes. © 2003 Elsevier Ireland Ltd. All rights reserved Daha fazlası Daha az

Özer, Mahmut | Ekmekçi, N. Hakan

Article | 2005 | Physics Letters, Section A: General, Atomic and Solid State Physics338 ( 2 ) , pp.150 - 154

Ion channel noise that stems from the stochastic nature of the channel has important effects on neuronal dynamics. In this context, we examine the effect of the channel noise on the time-course of recovery from inactivation of sodium channels by using a stochastic extension of the Hodgkin-Huxley model. We show that the channel noise provides both some amount of the non-inactivated channels and a smaller time-course for recovering from inactivation leading to an increased maximal sodium conductance compared to deterministic one. © 2005 Elsevier B.V. All rights reserved.

Özer, Mahmut

Article | 2007 | Physica A: Statistical Mechanics and its Applications379 ( 2 ) , pp.579 - 586

The linear, nonlinear and improved nonlinear thermodynamic models of the voltage-dependent ion channels were proposed to deduce the exact functional form of the rate constants. In this context, we present a comparative analysis of the linear, nonlinear and improved nonlinear thermodynamic models of voltage-dependent channel kinetics based on the sodium activation experimental data of Cav3.1 channel. We also provide some insight on the assumptions used to derive the thermodynamic models of the channels and show that the improved nonlinear thermodynamic model provides a simple and physically plausible approach to describe the behavior . . . of the voltage-dependent ion channels. © 2007 Elsevier B.V. All rights reserved Daha fazlası Daha az

Özer, Mahmut

Article | 2006 | Physics Letters, Section A: General, Atomic and Solid State Physics354 ( 4 ) , pp.258 - 263

The channel noise that stems from the stochastic nature of the ion channel has important effects on neuronal dynamics. In this context, we investigate the effect of the sub-threshold periodic current forcing on the regularity and synchronization of neuronal spiking activity by using a stochastic extension of the Hodgkin-Huxley model. We demonstrate that the intrinsic coherence resonance is independent of the forcing frequency for very small patch size while it is dependent on the frequency for larger sizes. We also show that the observed phase locking behavior occurs on the positive phase of the periodic current forcing for a small . . .frequency range while the spikes fire most frequently at negative phase as the frequency is increased. © 2006 Elsevier B.V. All rights reserved Daha fazlası Daha az