TY  - GEN
A1  - Alonso, Sergio
A1  - Stange, Maike
A1  - Beta, Carsten
T1  - Modeling random crawling, membrane deformation and intracellular polarity of motile amoeboid cells
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - Amoeboid movement is one of the most widespread forms of cell motility that plays a key role in numerous biological contexts. While many aspects of this process are well investigated, the large cell-to-cell variability in the motile characteristics of an otherwise uniform population remains an open question that was largely ignored by previous models. In this article, we present a mathematical model of amoeboid motility that combines noisy bistable kinetics with a dynamic phase field for the cell shape. To capture cell-to-cell variability, we introduce a single parameter for tuning the balance between polarity formation and intracellular noise. We compare numerical simulations of our model to experiments with the social amoeba Dictyostelium discoideum. Despite the simple structure of our model, we found close agreement with the experimental results for the center-of-mass motion as well as for the evolution of the cell shape and the overall intracellular patterns. We thus conjecture that the building blocks of our model capture essential features of amoeboid motility and may serve as a starting point for more detailed descriptions of cell motion in chemical gradients and confined environments.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1014 
KW  - signaling system
KW  - eukaryotic chemotaxis
KW  - Dictyostelium cells
KW  - actin cytoskeleton
KW  - excitable networks
KW  - PIP3 waves
KW  - migration
KW  - dynamics
KW  - oscillations
KW  - transduction
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-459745
SN  - 1866-8372
IS  - 1014
ER  - 
TY  - GEN
A1  - Kaminski, Roland
A1  - Schaub, Torsten H.
A1  - Siegel, Anne
A1  - Videla, Santiago
T1  - Minimal intervention strategies in logical signaling networks with ASP
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 596 
KW  - systems biology
KW  - transduction
KW  - circuits
KW  - models
KW  - sets
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415704
SN  - 1866-8372
IS  - 4-5
SP  - 675
EP  - 690
ER  -