scholarly journals Unbounded solutions of models for glycolysis

2021 ◽  
Vol 82 (1-2) ◽  
Author(s):  
Pia Brechmann ◽  
Alan D. Rendall
Keyword(s):  
Periodic Solutions ◽  
Biological System ◽  
Mass Action ◽  
Hopf Bifurcations ◽  
Poincaré Compactification ◽  
Simple Description ◽  
Mass Action Kinetics ◽  
Unbounded Solutions ◽  
Shooting Argument ◽  
Cast Doubt

AbstractThe Selkov oscillator, a simple description of glycolysis, is a system of two ordinary differential equations with mass action kinetics. In previous work the authors established several properties of the solutions of this system. In the present paper we extend this to prove that this system has solutions which diverge to infinity in an oscillatory manner at late times. This is done with the help of a Poincaré compactification of the system and a shooting argument. This system was originally derived from another system with Michaelis–Menten kinetics. A Poincaré compactification of the latter system is carried out and this is used to show that the Michaelis–Menten system, like that with mass action, has solutions which diverge to infinity in a monotone manner. It is also shown to admit subcritical Hopf bifurcations and thus unstable periodic solutions. We discuss to what extent the unbounded solutions cast doubt on the biological relevance of the Selkov oscillator and compare it with other models for the same biological system in the literature.

scholarly journals Training an asymmetric signal perceptron through reinforcement in an artificial chemistry

2014 ◽  
Vol 11 (93) ◽  
pp. 20131100 ◽  
Author(s):  
Peter Banda ◽  
Christof Teuscher ◽  
Darko Stefanovic
Keyword(s):  
State Of The Art ◽  
Chemical Species ◽  
Mass Action ◽  
Mass Action Kinetics ◽  
Dna Strand Displacement ◽  
Autonomous Adaptation ◽  
Biochemical Systems ◽  
Dna Strand ◽  
Logic Functions ◽  
Application Specific

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis–Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible.

scholarly journals How is the effectiveness of immune surveillance impacted by the spatial distribution of spreading infections?

2015 ◽  
Vol 370 (1675) ◽  
pp. 20140289 ◽  
Author(s):  
Ulrich D. Kadolsky ◽  
Andrew J. Yates
Keyword(s):  
Spatial Distribution ◽  
Immune Surveillance ◽  
Critical Density ◽  
Search Time ◽  
Handling Time ◽  
Mass Action ◽  
Mass Action Kinetics ◽  
Expected Time ◽  
Target Ratio ◽  
Infected Cells

What effect does the spatial distribution of infected cells have on the efficiency of their removal by immune cells, such as cytotoxic T lymphocytes (CTL)? If infected cells spread in clusters, CTL may initially be slow to locate them but subsequently kill more rapidly than in diffuse infections. We address this question using stochastic, spatially explicit models of CTL interacting with different patterns of infection. Rather than the effector : target ratio, we show that the relevant quantity is the ratio of a CTL's expected time to locate its next target (search time) to the average time it spends conjugated with a target that it is killing (handling time). For inefficient (slow) CTL, when the search time is always limiting, the critical density of CTL (that required to control 50% of infections, C * ) is independent of the spatial distribution and derives from simple mass-action kinetics. For more efficient CTL such that handling time becomes limiting, mass-action underestimates C * , and the more clustered an infection the greater is C * . If CTL migrate chemotactically towards targets the converse holds— C * falls, and clustered infections are controlled most efficiently. Real infections are likely to spread patchily; this combined with even weak chemotaxis means that sterilizing immunity may be achieved with substantially lower numbers of CTL than standard models predict.

scholarly journals Toric ideals and graph theory to analyze Hopf bifurcations in mass action systems

2005 ◽  
Vol 40 (6) ◽  
pp. 1361-1382 ◽  
Author(s):  
Karin Gatermann ◽  
Markus Eiswirth ◽  
Anke Sensse
Keyword(s):  
Graph Theory ◽  
Mass Action ◽  
Hopf Bifurcations ◽  
Toric Ideals ◽  
Action Systems
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