Demirkiran, Gökhan

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https://gcris.yasar.edu.tr/handle/123456789/12654
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Doç.Dr.
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Main Affiliation
01.01.09.02. Elektrik- Elektronik Mühendisliği
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Current Staff
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ORCID ID
0000-0002-0076-6036
Scopus Author ID
57200319546
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Google Scholar ID
t07qKwoAAAAJ
WoS Researcher ID
JAC-5273-2023
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gokhan.demirkiran.jpg (8.31 KB)

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NO POVERTY1
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ZERO HUNGER2
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GOOD HEALTH AND WELL-BEING3
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QUALITY EDUCATION4
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GENDER EQUALITY5
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CLEAN WATER AND SANITATION6
CLEAN WATER AND SANITATION
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AFFORDABLE AND CLEAN ENERGY7
AFFORDABLE AND CLEAN ENERGY
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DECENT WORK AND ECONOMIC GROWTH8
DECENT WORK AND ECONOMIC GROWTH
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INDUSTRY, INNOVATION AND INFRASTRUCTURE9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
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REDUCED INEQUALITIES10
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SUSTAINABLE CITIES AND COMMUNITIES11
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RESPONSIBLE CONSUMPTION AND PRODUCTION12
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CLIMATE ACTION13
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LIFE BELOW WATER14
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LIFE ON LAND15
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PEACE, JUSTICE AND STRONG INSTITUTIONS16
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Documents

15

Citations

34

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Documents

13

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Scholarly Output

17

Articles

9

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WoS Citation Count

22

Scopus Citation Count

34

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WoS Citations per Publication

1.29

Scopus Citations per Publication

2.00

Open Access Source

7

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JournalCount
IET Systems Biology3
11th International Conference on Electrical and Electronics Engineering (ELECO)2
10th International Conference on Electrical and Electronics Engineering ELECO 20172
Chaos, Solitons & Fractals1
Communications in Nonlinear Science and Numerical Simulation1
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Now showing 1 - 10 of 17
  • Thumbnail Image
    Article
    Citation - WoS: 5
    Citation - Scopus: 6
    Two-dimensional polynomial type canonical relaxation oscillator model for p53 dynamics
    (Institution of Engineering and Technology journals@theiet.org, 2018) Gökhan Demirkıran; Güleser Kalayci Demir; Cüneyt Güzeliş; Güzelis, Cüneyt; Demirkiran, Gökhan; Demir, Güleser Kalayci
    p53 network which is responsible for DNA damage response of cells exhibits three distinct qualitative behaviours, low state oscillation and high state which are associated with normal cell cycle progression cell cycle arrest and apoptosis respectively. The experimental studies demonstrate that these dynamics of p53 are due to the ATM and Wip1 interaction. This paper proposes a simple two-dimensional canonical relaxation oscillator model based on the identified topological structure of ATM and Wip1 interaction underlying these qualitative behaviours of p53 network. The model includes only polynomial terms that have the interpretability of known ATM and Wip1 interaction. The introduced model is useful for understanding relaxation oscillations in gene regulatory networks. Through mathematical analysis we investigate the roles of ATM and Wip1 in forming of these three essential behaviours and show that ATM and Wip1 constitute the core mechanism of p53 dynamics. In agreement with biological findings we show that Wip1 degradation term is a highly sensitive parameter possibly related to mutations. By perturbing the corresponding parameters our model characterizes some mutations such as ATM deficiency and Wip1 overexpression. Finally we provide intervention strategies considering our observation that Wip1 seems to be an important target to conduct therapies for these mutations. © 2018 Elsevier B.V. All rights reserved.
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    Conference Object
    Citation - WoS: 1
    Citation - Scopus: 1
    A 2-dimensional reduced oscillator model with rational nonlinearities for p53 dynamics
    (Institute of Electrical and Electronics Engineers Inc., 2017) Gökhan Demirkıran; Güleser Kalayci Demir; Cüneyt Güzeliş; Guzelis, Cuneyt; Demirkiran, Gokhan; Demir, Guleser Kalayc
    p53 tumour suppressor network plays the key role in DNA damage response of the cell. We present a comprehensive 2-dimensional oscillator model for p53 network dynamics. The model is reduced from the known 17-dimensional two-phase model of p53 network which shows temporary oscillatory behaviour under DNA damage type of Double Strand Breaks. The introduced oscillator model shows the same qualitative dynamics of two-phase model of p53 network such as bistability and oscillations when the parameters are adjusted accordingly. With the help of the identified oscillator in p53 network we introduce a new oscillator perspective: p53 network has an oscillator in the centre which other systems in the cell manipulate this oscillator to contribute to cell fate. The introduction of such low dimensional oscillator model will make it possible to study p53 network and the effects of other biological systems in the context of oscillations. © 2023 Elsevier B.V. All rights reserved.
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    Article
    Citation - WoS: 5
    Citation - Scopus: 5
    Revealing determinants of two-phase dynamics of P53 network under gamma irradiation based on a reduced 2D relaxation oscillator model
    (Institution of Engineering and Technology journals@theiet.org, 2018) Gökhan Demirkıran; Güleser Kalayci Demir; Cüneyt Güzeliş; Guzelis, Cuneyt; Demirkiran, Gokhan; Demir, Guleser Kalayci
    This study proposes a two-dimensional (2D) oscillator model of p53 network which is derived via reducing the multidimensional two-phase dynamics model into a model of ataxia telangiectasia mutated (ATM) and Wip1 variables and studies the impact of p53-regulators on cell fate decision. First the authors identify a 6D core oscillator module then reduce this module into a 2D oscillator model while preserving the qualitative behaviours. The introduced 2D model is shown to be an excitable relaxation oscillator. This oscillator provides a mechanism that leads diverse modes underpinning cell fate each corresponding to a cell state. To investigate the effects of p53 inhibitors and the intrinsic time delay of Wip1 on the characteristics of oscillations they introduce also a delay differential equation version of the 2D oscillator. They observe that the suppression of p53 inhibitors decreases the amplitudes of p53 oscillation though the suppression increases the sustained level of p53. They identify Wip1 and P53DINP1 as possible targets for cancer therapies considering their impact on the oscillator supported by biological findings. They model some mutations as critical changes of the phase space characteristics. Possible cancer therapeutic strategies are then proposed for preventing these mutations' effects using the phase space approach. © 2018 Elsevier B.V. All rights reserved.
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    Conference Object
    Citation - Scopus: 8
    Control of an Inverted Pendulum by Reinforcement Learning Method in PLC Environment
    (Institute of Electrical and Electronics Engineers Inc., 2020) Gökhan Demirkıran; Ozcan Erdener; Onay Akpinar; Pelin Demirtas; M. Yagiz Arik; Emre Guler; Akpinar, Onay; Guler, Emre; Demirkiran, Gokhan; Demirtas, Pelin; Erdener, Ozcan; Arik, M. Yagiz
    The aim of this study is to implement Q-learning algorithm to move an inverted pendulum from the downright position to upright position in a PLC environment. Instead of using classical control algorithms that need a linear model of the system to be controlled we used model-free control algorithm i.e. Q-learning and relaxed the linearity assumption. We demonstrate that reinforcement learning can be successfully used in industrial machine learning applications to learn complex control policies without having a detailed model of the controlled system. An experimental set up is designed using PLC controlled mechanical parts and the code is written in PLC. After about three hours of learning stage the Q learning algorithm successfully moved inverted pendulum from downright position to upright position and keep it in balanced upright position. © 2020 Elsevier B.V. All rights reserved.
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    Article
    Construction of a Waddington-like landscape model that can guide clinical exploration of p53-dynamics-activating parameters in the face of divergent p53 dynamics
    (ELSEVIER, 2024) Gokhan Demirkiran; Demirkıran, Gökhan
    The primary strategy of radiotherapies is to manipulate cell fate decision a process mainly regulated by a spectrum of p53 dynamics. Based on their biological relevance we analytically categorize the range of p53 levels into seven distinct level -forms leading to the identification of eleven non -chaotic phenomena of p53 level -form dynamics. The superimposing of cell fate attractors on the co -dimension two bifurcation diagram of eleven p53 level -form dynamics under quasi -steady state assumption provides a mechanistic tool that can be posted as a Waddingtonlike landscape model for cell fate regulation by p53 dynamics. In the proposed model the (location of) cell is represented as a control point in the bifurcation diagram representing a flattened landscape composed of 11 distinct behavioral regions and the effort that moves the cell on the landscape is exerted by accumulating death factors upon DNA damage. Further analysis reveals that intrinsically -resistant cancer attractors inevitably exist on the landscape and cells might have evolved to use a safe operational area whose cusp bifurcation shape is contributing to robustness via hysteresis. We further reveal specific mechanisms through which tumors acquire resistance under therapy. The proposed landscape model can be put to productive use via a reverse control methodology. The reconstruction of cancer -specific landscape can inform the design of personalized p53 -dynamics -based drug combination strategies suffering from the combinatorial explosion of target parameters and the divergent p53 dynamics. We conclude that the reverse control of the proposed landscape model has the potential to bridge the gap between theoretical and clinical studies of p53 dynamics for p53 -dynamics -based cancer therapies.
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    Article
    A Novel Clustering-based Forecast Framework: The Clusters with Competing Configurations Approach
    (2023) Gökhan Demirkıran; Miray Alp; Alp, Miray; Demirkıran, Gökhan
    Accurate aggregate (total) short-term load forecasting of Smart Homes (SHs) is essential in planning and management of power utilities. The baseline approach consists of simply designing and training predictors for the aggregated consumption data. Nevertheless better performance can be achieved by using a clustering-based forecasting strategy. In such strategy the SHs are grouped according to some metric and the forecast of each group's total consumption are summed to reach the forecast of aggregate consumption of all SHs. Although the idea is simple its implementation requires fine-detailed steps. This paper proposes a novel clustering-based aggregate-level forecast framework so called Clusters with Competing Configurations (CwCC) approach and then compares its performance to the baseline strategy namely Clusters with the Same Configurations (CwSC) approach. The Configurations in the name refers to the configurations of ARIMA Multi-Layer Perceptron (MLP) and Long Short-Term Memory (LSTM) forecasting methods which the CwCC approach uses. We test the CwCC approach on Smart Grid Smart City Dataset. The results show that better performance can be achieved using the CwCC approach for each of the three forecast methods and LSTM outperforms other methods in each scenario.
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    Conference Object
    Citation - Scopus: 1
    Effect of Chaotic Mixing on the Rheological Characterization of Mayonnaise
    (IEEE, 2017) Seda Genc; Tolga Tugay Izmir; Ruhan Askin Uzel; Gokhan Demirkiran; Savas Sahin; Cuneyt Guzelis; Uzel, Ruhan Askin; Izmir, Tolga Tugay; Demirkiran, Gokhan; Guzelis, Cuneyt; Genc, Seda; Sahin, Savas
    In this study a new mixing method for mayonnaise was developed. A chaotic hand mixer was designed. The speed of the mixer rotor was chaotically changed with the proposed method. Performance of the mixed mayonnaise was evaluated by a rheological characterization method. The results showed that the proposed chaotic mixing for mayonnaise has a better performance in terms of energy efficiency than conventional mixed ones indicating potential use in industry or as home appliance.
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    Article
    Citation - WoS: 4
    Citation - Scopus: 4
    A Canonical 3-D P53 Network Model that Determines Cell Fate by Counting Pulses
    (ISTANBUL UNIV FAC ENGINEERING, 2018) Gokhan Demirkiran; Guleser Kalayci Demir; Cuneyt Guzelis; Güzeliş, Cüneyt; Demirkıran, Gökhan; Demir, Güleser Kalaycı
    From a system theory perspective p53 network dynamics is interesting since it can exhibit three dynamical modes of p53 namely low-level equilibrium oscillation and high-level equilibrium. Each of these modes are associated with different cell fate outcomes: cell survival cell cycle arrest and apoptosis. The literature reveals that a high level (apoptosis) is seen only after ending the oscillation phase so called two-phase dynamics which provides the decision of apoptosis depending on the oscillation duration. This paper proposes that a negative feedback can keep time by counting the pulses of oscillation to take the decision of apoptosis or cell survival. P53DINP1 which is the mediator of this feedback is added as a variable to a 2-D oscillator model of the p53 network. The resulting canonical 3-D model successfully replicates the two-phase dynamics. That is it possesses temporary oscillatory behavior in which first oscillations (first phase) and then high level state (second phase) are observed. By introducing a new variable to the core oscillator in the p53 network this study demonstrates that p53 network can be considered a modular structure which consists of an oscillator and other variables that control this oscillator to contribute to cell fate determination.
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    Conference Object
    Stochastic Microgrid Control Problems: Effects of Load Distribution and Planning Horizon
    (IEEE, 2019) Aysegul Kahraman; Onder Bulut; Emrah Biyik; Cuneyt Guzelis; Gokhan Demirkiran; Demirkiran, Gokhan; Guzelis, Cuneyt; Kahraman, Aysegul; Bulut, Onder; Biyik, Emrah
    Microgrids enable the integration of distributed energy resources with high renewable penetration into the main power grid. In this study a microgrid problem that takes into account the stochastic nature of the net load defined as the difference between actual demand and renewable generation is studied. The problem is formulated as a Mixed Integer Linear Stochastic Optimization Programming and is solved under different net load distributions and planning horizons. Numerical results show that increasing variance causes a rise in total system cost for the approach that solves the stochastic problem by ignoring randomness (as in most real-life applications) as well as for the one that solves the problem with the true distribution. It is observed that enlarging the planning horizon also has similar effects.
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    Conference Object
    Comparative Forecasting of Energy Generation Using ARIMA and BiLSTM Models with Hyperparameter Optimization
    (Springer Science and Business Media Deutschland GmbH, 2025) Ozcan, Huseyin Gunhan; Emaminia, Sara; Demirkiran, Gokhan