Özer, Mahmut | Bal, Abdullah

Article | 2004 | Istanbul University Journal of Electrical and Electronics Engineering4 ( 1 ) , pp.1091 - 1104

In this paper, we investigate dynamics of voltage-gated ionic channels which are of great importance in integrating the information received by neurons. Understanding of dynamical behavior of voltage-gated ionic channels plays a major role for determining underlying mechanism of spike activity and predicting the neuronal behavior. Investigation is carried out based on Hodgkin-Huxley (H-H) mathematical formalism. Ionic channel gate model is discussed briefly. Relaxation phenomenon is studied in the gate variables. Then effects of temperature on dynamics of gate variables are examined. Finally voltage-clamped simulations are carried o . . .ut to determine their dynamic behaviors based on squid giant axon. In this paper, we investigate dynamics of voltage-gated ionic channels which are of great importance in integrating the information received by neurons. Understanding of dynamical behavior of voltage-gated ionic channels plays a major role for determining underlying mechanism of spike activity and predicting the neuronal behavior. Investigation is carried out based on Hodgkin-Huxley (H-H) mathematical formalism. Ionic channel gate model is discussed briefly. Relaxation phenomenon is studied in the gate variables. Then effects of temperature on dynamics of gate variables are examined. Finally voltage-clamped simulations are carried out to determine their dynamic behaviors based on squid giant axon Daha fazlası Daha az

Özer, Mahmut

Article | 2004 | NeuroReport15 ( 9 ) , pp.1451 - 1455

We previously formulated dynamics of ion channel gates by the path probability method. In this study, we apply that theoretical approach to derive the activation rate kinetics of T-type calcium channel in thalamic relay neurons. We derive explicit expressions of the forward and backward rate constants and show that the proposed rate constants accurately capture form of the empirical time constant, and that they also provide its saturation to a constant value at depolarized membrane potentials. We also compare our derivations with linear and nonlinear thermodynamic models of rate kinetics obtained from the same calcium channel, and s . . .how that it is possible to capture saturation of the time constant for the depolarized membrane potentials by the only proposed rate constants. © 2004 Lippincott Williams & Wilkins Daha fazlası Daha az

Genç, Ayten | Tosun, İsmail

Article | 2004 | Chemical Engineering Communications191 ( 1 ) , pp.125 - 136

A mathematical model based on multiphase filtration theory is developed to describe the electrofiltration process. The model takes both electrophoretic and electroosmotic effects into account. The electrophoretic migration velocity of solid particles is predicted from the model using the filtrate volume time data obtained from electrofiltration experiments.

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 | Erdem, Rıza

Article | 2004 | Physica A: Statistical Mechanics and its Applications331 ( 01.Feb ) , pp.51 - 60

Dynamics of voltage-gated ion channels in the excitable cell membranes is formulated by the path probability method of nonequilibrium statistical physics and approaches of the system toward the steady or equilibrium states are presented. For a single-particle noninteractive two-state model, a first-order rate equation or dynamic equation is derived by introducing the path probability rate coefficients which satisfy the detailed balancing relation. Using known parameters for the batrachotoxin (BTX)-modified sodium channels in giand squid axon as an example, the rate equation is solved and voltage dependence of the time constant (?) a . . .nd its temperature effect are investigated. An increase in voltage caused a shift in ? towards shorter durations while increasing temperature caused a shift in time distribution towards longer durations. Results are compared with the kinetic model for the squid axon BTX-modified sodium channels by the cut-open axon technique and a very good agreement is found. © 2003 Elsevier B.V. All rights reserved Daha fazlası Daha az

Özer, Mahmut

Article | 2004 | NeuroReport15 ( 12 ) , pp.1953 - 1957

Thermodynamic models of ionic currents are used to deduce exact functional form of rate constant. It is first assumed that free energy depends linearly on voltage. A major criticism of this approach is that time constant can reach arbitrarily small values resulting in an aberrant behavior. Recently, non-linear effects of electric field on the free energy were considered to solve this problem based on T-type calcium channel. In this study, we show that the current model approximately captures the voltage-dependence of the time constant only in a specific range of voltage and does not provide saturation of the time constant outside th . . .is range. Then, we propose an improved non-linear thermodynamic model and illustrate its applicability based on T-type calcium channel. © 2004 Lippincott Williams & Wilkins Daha fazlası Daha az

Özer, Mahmut | Erdem, Rıza | Provaznik, Ivo

Article | 2004 | NeuroReport15 ( 2 ) , pp.335 - 338

Voltage-gated ion channels are of great importance in the generation and propagation of electrical signals in the excitable cell membranes. How these channels respond to changes in the potential across the membrane has been a challenging problem, and different approaches have been proposed to address the mechanism of voltage sensing and gating in these channels. In this study, we attempt a new approach by considering a simple two-state gate system and applying the path probability method to construct a nonequilibrium statistical mechanical model of the system. The model which is based on the principles of statistical physics provide . . .s a firm physical basis for ion channel gating. © 2004 Lippincott Williams & Wilkins Daha fazlası Daha az

Tecer, Lokman Hakan | Yılmaz, Ali | Yıldırım, Yılmaz

Proceedings | 2004 | AIR POLLUTION MODELING AND ITS APPLICATION XVI16 , pp.637 - 638

In this study air pollution level in the city center of Sivas for a 10 years' period was analyzed. Winter season' and annual averages of sulfur dioxide and particulate matter measurements have been carried out in central area of Sivas by City Health Management. Specifically the winter seasons' concentrations are presented and their causes and their change with respect to meteorological parameters are discussed. The statistical relations between pollutants and meteorological parameters have been found to be significant.

Yıldırım, Yılmaz | Bayramoğlu, Mahmut | Tecer, Lokman Hakan | Yalçın, Gültekin

Proceedings | 2004 | AIR POLLUTION MODELING AND ITS APPLICATION XVI16 , pp.559 - 567

Air pollution continues to be a major problem in many countries. Mathematical models are useful in relating emissions to air quality under a variety of meteorological conditions and source emission concentrations over an urban area. Meanwhile, the forecasting capability of sophisticated models is limited to very large and complex terrains. In this study, adaptive neuro-fuzzy logic method has been proposed to estimate the impact of meteorological factors on SO2 pollution levels. The model forecasts satisfactorily the trends in SO2 concentration levels, with performance between 78-90%.

Kobya, Mehmet | Demirbaş, Erhan | Demircioğlu, Nesli | Yıldırım, Yılmaz | Yıldız, Şevki Yalçın

Article | 2004 | Desalination160 ( 3 ) , pp.253 - 262

Coupled transport of thiocyanate ions through a liquid membrane containing quaternary ammonium chloride salts in chloroform was examined. The influences of the carrier type in the membrane phase on the coupled transport of thiocyanate ions were investigated. The kinetics of the coupled transport were analyzed in the formalism of two consecutive irreversible first-order reactions and the kinetic parameters (k1d, k2m, k2a, Rmmax, tmax, Jdmax, Jamax,) were also calculated. For the coupled transport of thiocyanate ions, quaternary ammonium chloride salts having different carbon atom numbers (Cn) used as carriers were found to increase t . . .hiocyanate ions transport efficiency with increasing carbon atom numbers. Tetradecyl trimethylammonium chloride (TDTMACl), hexadecyl trimethylammonium chloride (HDTMACl), and tetraoctyl ammonium chloride (TOACl) were found to be the most effective carrier types for transport of thiocyanate ions when Cn is greater than 16. The activation energies for maximum membrane entrance and exit fluxes were calculated as 32.45 kJ/mol and 34.75 kJ/mol, respectively. The values of the activation energy indicate that the process is controlled by species diffusion Daha fazlası Daha az

Özer, Mahmut

Article | 2004 | Iranian Journal of Science and Technology, Transaction B: Engineering28 ( 3 B ) , pp.351 - 358

In this study, the time-course of the recovery from inactivation of molluscan ionic currents is examined. Molluscan voltage-gated ionic currents are described in Hodgkin-Huxley-like equations. The peak value function of the recovering conductance is derived from the mathematical equivalent of an experimental procedure of the recovery process in a general form by including the number of inactivation gates. Then the curves of the recovery and its approximation for the molluscan ionic currents are obtained. It is shown that recovering conductance of molluscan ionic currents is asymptotically exponential. © Shiraz University.

Çakmaklı, Birten | Hazer, Baki | Tekin, İshak Özel | Kızgut, Sait | Köksal, Murat | Menceloğlu, Yusuf

Article | 2004 | Macromolecular Bioscience4 ( 7 ) , pp.649 - 655

Syntheses of wholly natural polymeric linseed oil (PLO) containing peroxide groups have been reported. Peroxidation, epoxidation and/or perepoxidation reactions of linseed oil, either under air or under oxygen flow at room temperature, resulted in polymeric peroxides, PLO-air and PLO-ofl, containing 1.3 and 3.5 wt.-% of peroxide, with molecular weights of 2 100 and 3 780 Da, respectively. PLO-air contained cross-linked film up to 46.1 wt.-% after a reaction time of 60 d, associated with a waxy, soluble part (PLO-air-s) that was isolated with chloroform extraction. PLO-ofl was obtained as a waxy, viscous liquid without any cross-link . . .ed part at the end of 24 d under visible irradiation and oxygen flow. Polymeric peroxides, PLO-air-s and PLO-ofl initiated the free radical polymerization of both methyl methacrylate (MMA) and styrene (S) to give PMMA-graft-PLO and PS-graft-PLO graft copolymers in high yields with Mw varying from 37 to 470 kDa. The polymers obtained were characterized by FT-IR, 1H NMR, TGA, DSC and GPC techniques. Cross-linked polymers were also studied by means of swelling measurements. PMMA-graft-PLO graft copolymer film samples were also used in cell-culture studies. Fibroblast cells were well adhered and proliferated on the copolymer film surfaces, which is important in tissue engineering Daha fazlası Daha az