Related papers: Modeling HIF-ILK Interaction Using Continuous Petr…
Motivated by experiments on single-headed kinesin KIF1A, we develop a model of intra-cellular transport by interacting molecular motors. It captures explicitly not only the effects of ATP hydrolysis, but also the ratchet mechanism which…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
In this study, we provide a dynamical systems perspective to the modelling of pathological states induced by tumors or infection. A unified disease model is established using the innate immune system as the reference point. We propose a…
Sensing and reciprocating cellular systems (SARs) are important for the operation of many biological systems. Production in interferon (IFN) SARs is achieved through activation of the Jak-Stat pathway, and downstream upregulation of IFN…
Leaky integrate-and-fire (LIF) networks are standard reduced models for spike-based neural dynamics and a natural substrate for neuromorphic computation. We study time-driven Euler--Maruyama simulation of current-based LIF networks with…
Travelling waves of neural firing activity are observed in brain tissue as a part of various sensory, motor and cognitive processes. They represent an object of major interest in the study of excitable networks, with analysis conducted in…
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic…
The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
Observational studies of HII region-molecular cloud interactions constrain models of feedback and quantify its impact on the surrounding environment. A recent hypothesis proposes that a characteristic spectral signature in ground state…
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than…
We propose a new type of diffuse interface model describing the evolution of a tumor mass under the effects of a chemical substance (e.g., a nutrient or a drug). The process is described by utilizing the variables $\varphi$, an order…
It is a longstanding debate on the absence of threshold for susceptible-infected-susceptible (SIS) model on networks with finite second order moment of degree distribution. The eigenvector localization of the adjacency matrix for a network…
In the present work we investigate the chemotactically and proteolytically driven tissue invasion by cancer cells. The model employed is a system of advection-reaction-diffusion equations that features the role of the serine protease…
Recent experiments in epithelial wound healing have demonstrated the necessity of Mitogen-activated protein kinase (MAPK) for coordinated cell movement after damage. This MAPK activity is characterized by two wave-like phenomena. One MAPK…
Microscale oxygenation plays a prominent role in tumour progression. Spatiotemporal variability of oxygen distribution in the tumour microenvironment contributes to cellular heterogeneity and to the emergence of normoxic and hypoxic…
Hypoxia and acidity act as environmental stressors promoting selection for cancer cells with a more aggressive phenotype. As a result, a deeper theoretical understanding of the spatio-temporal processes that drive the adaptation of tumour…
Cancer progression arises from interactions across multiple biological layers, especially beyond morphological and across molecular layers that remain invisible to image-only models. To capture this broader biological landscape, we present…
Studies into the statistical properties of biological networks have led to important biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of…