Multi-Level Modeling and Simulation in Space
speaker: Adelinde Uhrmacher (University of Rostock)abstract: Proteins, individual cells, and cell populations denote di erent levels of an organizational hierarchy, each of which with its own dynamics. Multi-level modeling is concerned with describing a system at these di erent levels and relating their dynamics. Referring to space, multi-level modeling typically implies compartmental dynamics. We will present three di erent rule-based modeling approaches that support dynamic nesting and integrate compartmental dynamics with a) non-spatial stochastic simulation (Gillespie-type), b) grid-based stochastic reaction di usion simulation (Next Subvolume Method) and particle-based simulation in continuous space (pure Brownian Dynamics), and c) particle-based simulation that in addition uses potentials for particle-particle interactions. We will discuss how the di erent approaches aim at bridging molecular and cellular scales from the modeling point of view (and the role that the expressiveness of the modeling languages play in this), discuss implications for simulation, and illuminate features of the approaches and lessons learned based on a set of small cell biological models.
timetable:
Mon 1 Oct, 9:30 - 10:45, Aula Dini
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