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Cell-based models are mathematical models that represent biological cells as discrete entities. Within the field of computational biology they are often simply called agent-based models [1] of which they are a specific application and they are used for simulating the biomechanics of multicellular structures such as tissues. to study the influence of these behaviors on how tissues are organised ...
An embedded graph uniquely defines cyclic orders of edges incident to the same vertex. The set of all these cyclic orders is called a rotation system.Embeddings with the same rotation system are considered to be equivalent and the corresponding equivalence class of embeddings is called combinatorial embedding (as opposed to the term topological embedding, which refers to the previous ...
In graph theory, a branch of mathematics, a cycle basis of an undirected graph is a set of simple cycles that forms a basis of the cycle space of the graph. That is, it is a minimal set of cycles that allows every even-degree subgraph to be expressed as a symmetric difference of basis cycles.
The flow across the cells is determined based on μ(k) and λ(k), two monotonic functions that uniquely define the fundamental diagram as shown in Figure 1. The density of the cells is updated based on the conservation of inflows and outflows. Thus, the flow and density are derived as: Where: and represent density and flow in cell i at time t.
The eukaryotic cell cycle is very complex and is one of the most studied topics, since its misregulation leads to cancers. It is possibly a good example of a mathematical model as it deals with simple calculus but gives valid results. Two research groups [1] [2] have produced several models of the cell cycle simulating several organisms. They ...
A cellular automaton consists of a regular grid of cells, each in one of a finite number of states, such as on and off (in contrast to a coupled map lattice). The grid can be in any finite number of dimensions. For each cell, a set of cells called its neighborhood is defined relative to the specified cell.
Simulink is a MATLAB-based graphical programming environment for modeling, simulating and analyzing multidomain dynamical systems. Its primary interface is a graphical block diagramming tool and a customizable set of block libraries. It offers tight integration with the rest of the MATLAB environment and can either drive MATLAB or be scripted ...
The models can be simulated and analysed using Python libraries, but PySB models can also be exported into BNGL, [4] kappa, [1] and SBML. [34] Models involving multi-state and multi-component species can also be specified in Level 3 of the Systems Biology Markup Language (SBML) [34] using the multi package. A draft specification is available.