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Accurate predictions and representations of plant growth patterns in simulated and controlled environments are important for addressing various challenges in plant phenomics research. This review explores various works on state-of-the-art…
The growth of cities has traditionally been studied from a population perspective, while urban expansion-its spatial growth-has often been approached qualitatively. However, characterizing and modeling this spatial expansion is crucial,…
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…
Many processes in eukaryotic cells, including cell motility, rely on the growth of branched actin networks from surfaces. Despite its central role the mechano-chemical coupling mechanisms which guide the growth process are poorly…
The capability of cells to form surface extensions to non-locally probe the surrounding environment plays a key role in cell migration. The existing mathematical models for migration of cell populations driven by this non-local form of…
Blood coagulation is governed by tightly regulated reaction networks that unfold within a flowing, heterogeneous microvascular environment. Reduced kinetic models of the intrinsic and extrinsic pathways have seen limited in vitro…
Understanding of vascular organization is a long-standing problem in quantitative biology and biophysics and is essential for the growth of large cultured tissues. Approaches are needed that (1) make predictions of optimal arteriovenous…
We consider a nonlinear dynamical system on a signed graph, which can be interpreted as a mathematical model of social networks in which the links can have both positive and negative connotations. In accordance with a concept from social…
Simulation of population dynamics is a central research theme in computational biology, which contributes to understanding the interactions between predators and preys. Conventional mathematical tools of this theme, however, are incapable…
Like other social animals and biological systems, human groups constantly exchange information. Network models provide a way of quantifying this process by representing the pathways of information propagation between individuals. Existing…
The field of active matter explores the behaviors of self propelled agents out of equilibrium, with active suspensions, such as swimming bacteria in solutions, serving as impactful models. These systems exhibit spatio-temporal patterns akin…
Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a…
Cardiovascular networks span the body by branching across many generations of vessels. The resulting structure delivers blood over long distances to supply all cells with oxygen via the relatively short-range process of diffusion at the…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
We describe a simple spatial model of urban growth for systems of cities at the macroscopic scale, which combines direct interaction between cities and an indirect effect of physical network flows as population growth drivers. The model is…
The compartmental model is a basic tool for studying signal propagation in neurons, and, if the model parameters are adequately defined, it can also be of help in the study of electrical or fluid transport. Here we show that the input…
The structure of social relations is fundamental for the construction of plausible simulation scenarios. It shapes the way actors interact and create their identity within overlapping social contexts. Each actor interacts in multiple…
We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of…
Self-regulation of living tissue as an example of self-organization phenomena in hierarchical systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
In this paper, we develop a variational method to track and make predictions about a real-world system from continuous imperfect observations about this system, using an agent-based model that describes the system dynamics. By combining the…