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

Yılmaz, Ergin | Özer, Mahmut

Article | 2015 | Physica A: Statistical Mechanics and its Applications421 , pp.455 - 462

We study the effect of the delayed feedback loop on the weak periodic signal detection performance of a stochastic Hodgkin-Huxley neuron. We consider an electrical autapse characterized by its coupling strength and delay time. The stochastic Hodgkin-Huxley neuron exhibits subthreshold oscillations, and thus has an intrinsic time scale with the subthreshold oscillations. Therefore, we investigate the interplay of the subthreshold oscillations, coupling strength and delay time on the weak periodic signal detection. Results indicate that the delayed feedback either enhances or suppresses the weak signal detection depending on its param . . .eters, when compared to that without the feedback. The delayed feedback augments the weak periodic signal detection for the optimal values of the intrinsic noise and the coupling strength when the delay time is close to the integer multiples of the period of the intrinsic oscillations, due to the multiple resonance among the weak signal, the intrinsic oscillations, and the delayed feedback. We analyze the interspike interval histograms and show that the delayed feedback enhances or suppresses the weak periodic signal detection by increasing or decreasing the phase locking (synchronization) between the spiking and the weak periodic signal. We also show that an optimal phase locking is obtained when the delay time is close to the period of the intrinsic oscillations, leading a single dominant time scale in the spike trains. © 2014 Elsevier B.V. All rights reserved Daha fazlası Daha az

Narin, Ali | İşler, Yalçın | Özer, Mahmut | Perc, Matjaž

Article | 2018 | Physica A: Statistical Mechanics and its Applications509 , pp.56 - 65

Atrial fibrillation (AF) is the most common arrhythmia type and its early stage is paroxysmal atrial fibrillation (PAF). PAF affects negatively the quality of life by causing dyspnea, chest pain, feeling of excessive fatigue, and dizziness. In this study, our aim is to predict the onset of paroxysmal atrial fibrillation (PAF) events so that patients can take precautions to prevent PAF events. We use an open data from Physionet, Atrial Fibrillation Prediction Database. We construct our approach based on the heart rate variability (HRV) analysis. Short-term HRV analysis requires 5-minute data so that each dataset was divided into 5-mi . . .nute data segments. HRV features for each segment are calculated from time-domain measures and frequency-domain measures using power spectral density estimations of fast Fourier transform, Lomb–Scargle, and wavelet transform methods. Different combinations of these HRV features are selected by Genetic Algorithm and then applied to k-nearest neighbors classification algorithm. We compute the classifier performances by the 10-fold cross-validation method. The proposed approach results in 92% sensitivity, 88% specificity and 90% accuracy in the 2.5–7.5 min time interval priors to PAF event. The proposed method results in better classification performance than the similar studies in literature. Comparing the existing studies, we propose that our approach provide better tool to predict PAF events. © 2018 Elsevier B.V Daha fazlası Daha az

Baysal, Veli | Yılmaz, Ergin

Article | 2020 | Physica A: Statistical Mechanics and its Applications537 , pp.56 - 65

In this paper, Vibrational Resonance (VR), in which the response of some dynamical systems to a weak, low frequency signal can be enhanced by the optimal amplitude of high frequency signal, is investigated under the effects of electromagnetic induction in both single neurons and small-world networks. We find that the occurrence of VR in single neurons requires less energy in the presence of electromagnetic induction, although the resonant peak of the response reduces. Besides, VR can be obtained in small-world networks both with and without electromagnetic induction. In small-world neuronal networks, the highest resonance peak of VR . . . enhances with an increase in the probability of adding link in case of without electromagnetic induction. On the other hand, with the increasing of the probability of adding link, VR disappears in the presence of relatively strong electromagnetic induction, while it enhances in the presence of relatively weak electromagnetic induction. © 2019 Elsevier B.V Daha fazlası Daha az

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

Yılmaz, Ergin | Uzuntarla, Muhammet | Özer, Mahmut | Perc, Matjaž

Article | 2013 | Physica A: Statistical Mechanics and its Applications392 ( 22 ) , pp.5735 - 5741

We study the phenomenon of stochastic resonance in a system of coupled neurons that are globally excited by a weak periodic input signal. We make the realistic assumption that the chemical and electrical synapses interact in the same neuronal network, hence constituting a hybrid network. By considering a hybrid coupling scheme embedded in the scale-free topology, we show that the electrical synapses are more efficient than chemical synapses in promoting the best correlation between the weak input signal and the response of the system. We also demonstrate that the average degree of neurons within the hybrid scale-free network signifi . . .cantly influences the optimal amount of noise for the occurrence of stochastic resonance, indicating that there also exists an optimal topology for the amplification of the response to the weak input signal. Lastly, we verify that the presented results are robust to variations of the system size. © 2013 Elsevier B.V. All rights reserved Daha fazlası Daha az

Yılmaz, Ergin | Baysal, Veli | Özer, Mahmut | Perc, Matjaž

Article | 2016 | Physica A: Statistical Mechanics and its Applications444 , pp.538 - 546

We study the effects of an autapse, which is mathematically described as a self-feedback loop, on the propagation of weak, localized pacemaker activity across a Newman-Watts small-world network consisting of stochastic Hodgkin-Huxley neurons. We consider that only the pacemaker neuron, which is stimulated by a subthreshold periodic signal, has an electrical autapse that is characterized by a coupling strength and a delay time. We focus on the impact of the coupling strength, the network structure, the properties of the weak periodic stimulus, and the properties of the autapse on the transmission of localized pacemaker activity. Obta . . .ined results indicate the existence of optimal channel noise intensity for the propagation of the localized rhythm. Under optimal conditions, the autapse can significantly improve the propagation of pacemaker activity, but only for a specific range of the autaptic coupling strength. Moreover, the autaptic delay time has to be equal to the intrinsic oscillation period of the Hodgkin-Huxley neuron or its integer multiples. We analyze the inter-spike interval histogram and show that the autapse enhances or suppresses the propagation of the localized rhythm by increasing or decreasing the phase locking between the spiking of the pacemaker neuron and the weak periodic signal. In particular, when the autaptic delay time is equal to the intrinsic period of oscillations an optimal phase locking takes place, resulting in a dominant time scale of the spiking activity. We also investigate the effects of the network structure and the coupling strength on the propagation of pacemaker activity. We find that there exist an optimal coupling strength and an optimal network structure that together warrant an optimal propagation of the localized rhythm. © 2015 Elsevier B.V. All rights reserved Daha fazlası Daha az

Uzun, Rukiye | Yılmaz, Ergin | Özer, Mahmut

Article | 2017 | Physica A: Statistical Mechanics and its Applications486 , pp.386 - 396

An autapse is a special kind of synapse established between the axon and dendrites of the same neuron. In the present study, we have investigated the cooperative effects of autapse and ion channel block on the collective firing regularity of Newman–Watts small-world networks of stochastic Hodgkin–Huxley neurons. We obtain autaptic time delay induced multi-coherence resonance (MCR) phenomenon in the absence of ion channel block. When the ion channel block is considered, we find that this autaptic delay induced MCR phenomenon enhances with the increasing of potassium channel block, whereas it weakens with the increasing of sodium chan . . .nel block at weak and intermediate autaptic conductance regimes. However, at strong autaptic conductance regime neither sodium nor potassium channel block have a significant effect on the collective firing regularity of the network. Besides, we investigate the effects of the coupling strength, the network randomness and the cell size on the regularity. We obtain an optimal coupling strength value and an optimal cell size leading to a more prominent MCR effect. We also show that the MCR phenomenon increases with the increasing of network randomness in potassium channel block, but it needs to a minimum network randomness for its appearing in case of sodium channel block. © 2017 Elsevier B.V Daha fazlası Daha az

Özer, Mahmut

Article | 2005 | Physica A: Statistical Mechanics and its Applications357 ( 03.Apr ) , pp.397 - 414

In this study, we propose a theoretical framework for the determination of rate kinetics in the ion channels. In this framework, we firstly formulate the kinetic equation for the time-dependent open-state probability of the gate and forward and backward rate kinetics based on the path probability method with three parameters, explicitly. Then, we construct a tool to determine if fitted rate kinetics satisfy the experimental data by deriving kinetic coefficients of activation and inactivation gates based on the Onsager reciprocity theorem. The proposed framework is based on the principles of statistical physics and conceptually quite . . . different from those of conventional models. We also illustrate its applicability based on the empirical inactivation kinetics of T-type calcium channel from thalamic relay neurons, and then compare it with the linear and nonlinear thermodynamic models for the same calcium channel. The results of the present study indicate that our methodology suggests a general framework for the determination of rate kinetics in ion channels. © 2005 Elsevier B.V. All rights reserved Daha fazlası Daha az

Eryürek M. | Güven M.H.

Article | 2007 | Physica A: Statistical Mechanics and its Applications377 ( 2 ) , pp.514 - 522

The solid-liquid phase transitions of Ar55 cluster was simulated by the microcanonical molecular dynamics and microcanonical parallel tempering methods using Lennard-Jones potential, and thermodynamic quantities were calculated. The caloric curve of cluster has S-bend. To understand this behaviour, configurational and total entropies were evaluated, and the dents on the entropy curves were noticed as the sign of negative heat capacity. The heat capacities were evaluated by using configurational entropy data. The potential energy distributions have bimodal behaviour in the given range at the melting temperature. At the same time by u . . .sing configurational entropy canonical caloric curve and canonical heat capacity were calculated. To obtain entropy change upon melting, total entropy were calculated from the caloric curve. The microcanonical results melting temperature, latent heat and entropy change upon melting values were reported and compared with the values reported in the literature and the values calculated from the thermodynamic relations offered for bulk matter, consistent values were found. © 2006 Elsevier B.V. All rights reserved Daha fazlası Daha az