Browsing by Author "Demirkiran, Gokhan"

Now showing 1 - 10 of 10

Citation - WoS: 1
Citation - Scopus: 1
A 2-dimensional model of polynomial type for oscillatory ATM-Wipl dynamics in p53 network
(Institute of Electrical and Electronics Engineers Inc., 2017) Gökhan Demirkıran; Güleser Kalayci Demir; Cüneyt Güzeliş; Guzelis, Cuneyt; Demirkiran, Gokhan; Demir, Guleser Kalayc
Under gamma irradiation p53 gene regulatory network is able to exhibit three different modes namely low state oscillations and high state. There are experimental studies demonstrating that oscillatory behaviour of p53 is due to the interaction between upstream mediator of p53 i.e. ATM and a negative feedback loop formed by Wipl with that upstream. By proposing a canonical model based on ordinary differential equations made up of polynomial type birth and death terms we show mathematically that the simple interaction between ATM and Wipl is indeed able to exhibit three different behaviours relevant to DNA damage response of p53 network. We further carry out bifurcation analysis on the model with the aim of investigating the mutations such as Wip1 overexpression and ATM deficiency. Based on the proposed canonical model we show that Wipl is an important target for curing these types of mutations. © 2023 Elsevier B.V. All rights reserved.
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.
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
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.
Citation - WoS: 1
Citation - Scopus: 3
Design of an interactive fashion recommendation platform with intelligent systems, Proiectarea unei platforme interactive de recomandare a articolelor de modă cu sisteme inteligente
(Inst. Nat. Cercetare-Dezvoltare Text. Pielarie, 2024) Arzu Vuruşkan; Gökhan Demirkıran; Ender Yazgan Bulgun; Türker Ince; Cüneyt Güzeliş; Vuruskan, Arzu; Demirkiran, Gokhan; Ince, Turker; Bulgun, Ender; Guzelis, Cuneyt
With the increase in customer expectations in online fashion sales greater integration of fashion recommender systems (RSs) allows more personalization. Design decisions rely on personal taste as well as many other external influences such as trends and social media making it challenging to adapt intelligent systems for the fashion industry. Different methods for recommending personalized fashion items have been proposed however the literature still lacks an approach for recommending expert-suggested and personalized items. In this research an interactive web-based platform is developed to support personalized fashion styling focusing on users with diverse body shapes. To merge the user’s taste and the expert’s suggestion the proposed methodology in this research combines genetic algorithms and machine learning techniques allowing the system to access expert knowledge (including external influences) and incremental learning capability by adapting to the user preferences that unfold during interaction with the system. © 2024 Elsevier B.V. All rights reserved.
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.
Imaging the Cell Fate based on the Concept of Apoptogram
(IEEE, 2019) Gokhan Demirkiran; Demirkiran, Gokhan
This study investigates cell fate selection in a single cell by carrying out theoretical analysis on a parametric 2 Dimensional model. The investigated model involves eight fixed parameters and two tuneable parameters r and m where the tuneable parameters are the determinants of cell fate decision. Using these tuneable parameters as the axes the concept of apoptogram where the exact values of r and m pairs that lead to a certain cell fate decision are portrayed as regions is introduced. The boundaries that depicts the regions are theoretically determined in a parametric fashion so that one can construct an apoptogram image given the values of fixed parameters of the model. The regions that correspond to a cell fate decision in the apoptogram provide valuable insights to investigate and manipulate cell fate decisions. Further studies may utilize such concept as a new tool to explore the complexity of cancer and cancer therapy.
Investigation of Chaotic Mixing Performance on Characteristic Properties of Cake Batter
(IEEE, 2019) Ruhan Askin Uzel; Tolga Tugay Izmir; Gokhan Demirkiran; Savas Sahin; Cuneyt Guzelis; Uzel, Ruhan Askin; Izmir, Tolga Tugay; Demirkiran, Gokhan; Guzelis, Cuneyt; Tugay Izmir, Tolga; Sahin, Savas
Chaotification is the process of making an originally non chaotic system being chaotic by applying a suitable control input. The aim of the study was to create a chaotic mixing mechanism using a kitchen type mixer and to test its performance on the quality characteristics of cake batter material. A prototype mixer that works originally with conventional method has been realized with hardware and software changes on a commercial kitchen type mixer. The results obtained at the end of the study showed that the kitchen type mixer was able to successfully switch from the classical mixing mode to the chaotic mixing mode and this mixing mode positively affected the structural and sensory characteristics of the cake batter samples.
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.
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.