Related papers: The spatial structure of cell signaling systems
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…
Neural computation is associated with the emergence, reconfiguration and dissolution of cell assemblies in the context of varying oscillatory states. Here, we describe the complex spatio-temporal dynamics of cell assemblies through temporal…
Cells and microorganisms employ dynamic shape changes to enable steering and avoidance for efficient spatial exploration and collective organization. In contrast, active colloids, their synthetic counterparts, currently lack similar…
Many natural and engineered complex networks have intricate mesoscopic organization, e.g., the clustering of the constituent nodes into several communities or modules. Often, such modularity is manifested at several different hierarchical…
Understanding how biomechanical reorganization governs key biological processes, such as morphogenesis and development, requires predictive insights into stress distributions and cellular behavior. While traditional approaches focused on…
Coordinated responses to environmental stimuli are critical for multicellular organisms. To overcome the obstacles of cell-to-cell heterogeneity and noisy signaling dynamics within individual cells, cells must effectively exchange…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…
Living tissue is able to withstand large stresses in everyday life, yet it also actively adapts to dynamic loads. This remarkable mechanical behaviour emerges from the interplay between living cells and their non-living extracellular…
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells are largely based on transcriptomic single-cell…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
The performance of cellular system significantly depends on its network topology, where the spatial deployment of base stations (BSs) plays a key role in the downlink scenario. Moreover, cellular networks are undergoing a heterogeneous…
A mutualism is an interaction where the involved species benefit from each other. We study a two-dimensional hexagonal three-state cellular automaton model of a two-species mutualistic system. The simple model is characterized by four…
In vivo and in vitro cells rely on the support of an underlying biocompatible substrate, such as the extracellular matrix or a culture substrate, to spread and proliferate. The mechanical and chemical properties of such structures play a…
Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…
The emergence of spatial patterns and organized growth is a hallmark of developing tissues. While symmetry-breaking and scaling laws govern these processes, how cells coordinate spatial patterning with size regulation remains unclear. Here,…
We analyze the structure of two dimensional disordered cellular systems generated by extensive computer simulations. These cellular structures are studied as topological trees rooted on a central cell or as closed shells arranged…
The neural networks of the human brain act as very efficient parallel processing computers co-ordinating memory related responses to a multitude of input signals from sensory organs. Information storage, update and appropriate retrieval are…
We present a fiber-distributed model of the reinforcing collagen of the human cornea. The model describes the basic connections between the components of the tissue by defining an elementary block (cell) and upscaling it to the physical…