Related papers: Quantifying different modeling frameworks using to…
A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
Von Neuman's work on universal machines and the hardware development have allowed the simulation of dynamical systems through a large set of interacting agents. This is a bottom-up approach which tries to derive global properties of a…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
One of the most important problems in contemporary science, and especially in biology, is to reveal mechanisms of pattern formation. On the level of biological tissues, patterns form due to interactions between cells. These interactions can…
We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Adhesion between cells plays an important role in many biological processes such as tissue morphogenesis and homeostasis, wound healing and cancer cell metastasis. From a mathematical perspective, adhesion between multiple cell types has…
A formal but intuitive framework is introduced to bridge the gap between data obtained from empirical studies and that generated by agent-based models. This is based on three key tenets. Firstly, a simulation can be given multiple formal…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
Complex biological processes involve collective behavior of entities (bacteria, cells, animals) over many length and time scales and can be described by discrete models that track individuals or by continuum models involving densities and…
To celebrate Hans Frauenfelder's achievements, we examine energy(-like) "landscapes" for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some…