Deterministic modelling of linear and nonlinear interactions in biological systems



Deterministic modeling and inference of biological systems
Seçilmiş, Deniz; Purutçuoğlu Gazi, Vilda; Department of Bioinformatics (2017)
The mathematical description of biological networks can be performed mainly by stochastic and deterministic models. The former gives more information about the system, whereas, it needs very detailed measurements. On the other hand, the latter is relatively less informative, but, the collection of their data is easier than the stochastic ones, rendering it a more preferable modeling approach. In this study, we implement the deterministic modeling of biological systems due to the underlying advantage. Among ...
Deterministic integrated tuning of multicavity resonances and phase for slow-light in coupled photonic crystal cavities
Gu, T.; Kocaman, Serdar; Yang, X.; McMillan, J.F.; Yu, M.B.; Lo, G.-Q.; Kwong, D.-L.; Wong, C.W. (AIP Publishing, 2011-03-21)
We present the integrated chip-scale tuning of multiple photonic crystal cavities. The optimized implementation allows effective and precise tuning of multiple cavity resonances (up to similar to 1.60 nm/mW) and intercavity phase (similar to 0.038 pi/mW) by direct local temperature tuning on suspended silicon nanomembranes. Through designing the serpentine metal electrodes and careful electron-beam alignment to avoid cavity mode overlap, the coupled photonic crystal L3 cavities preserve their high quality f...
Stochastic simulations of biological networks under impulses
Yazıcı, Müge; Purutçuoğlu Gazi, Vilda; Department of Statistics (2016)
The impulses are one of the sources of fluctuations which lead to the sharp changes in the biochemical systems such as the changes in epidemic and population models. In this study, as the novelty, we implement these effects in exact stochastic simulation algorithms, namely, the Gillespie method and the first reaction method, by changing the chemical master equations (CME) with impulses. Hereby in the extension of these approaches with impulses, we consider different scenarios such as the sudden decrease of ...
Probabilistic recognition of orthogonal and symplectic groups
Yalçınkaya, Şükrü; Berkman, Ayşe; Department of Mathematics (2001)
Stochastic modeling of biochemical systems with filtering and smoothing
Haksever, Merve; Uğur, Ömür; Department of Scientific Computing (2019)
Deterministic modeling approach is the traditional way of analyzing the dynamical behavior of a reaction network. However, this approach ignores the discrete and stochastic nature of biochemical processes. In this study, modeling approaches, stochastic simulation algorithms and their relationships to each other are investigated. Then, stochastic and deterministic modeling approaches are applied to biological systems, Lotka-Volterra prey-predator model, Michaelis-Menten enzyme kinetics and JACK-STAT signalin...
Citation Formats
M. Ağraz and V. Purutçuoğlu Gazi, “Deterministic modelling of linear and nonlinear interactions in biological systems,” 2016, Accessed: 00, 2021. [Online]. Available: