11 papers
Simulating is not always understanding: When model complexity obscures biology
Lendert Gelens, Alejandro Fábregas-Tejeda, Grant Ramsey +2
In cell biology, computational models of biological systems range from minimal representations with a handful of parameters to whole-cell simulations tracking thousands of molecula…
The Belousov-Zhabotinsky reaction reveals two regimes of non-Arrhenius temperature scaling in relaxation oscillators
Simen Jacobs, Nikita Frolov, Panna Farkas +3
The period of biological and chemical oscillators scales with temperature in a characteristic way. Some oscillators are very well described by an Arrhenius law, while others show s…
Data-driven discovery of dynamical models in biology
Bartosz Prokop, Lendert Gelens
Dynamical systems theory provides a mathematical framework for describing how interacting biological components evolve over time and space, from molecular oscillators to large-scal…
Isolas of limit cycles and birhythmicity induced by cooperative feedback in a glycolysis model
Fangyuan Wang, Lendert Gelens, Yancong Xu +1
We investigate how cooperative feedback shapes global oscillatory dynamics in a glycolysis model with product recycling and allosteric phosphofructokinase regulation. Using bifurca…
Understanding the temperature response of biological systems: Part II -- Network-level mechanisms and emergent dynamics
Simen Jacobs, Julian B. Voits, Nikita Frolov +2
Building on the phenomenological and microscopic models reviewed in Part I, this second part focuses on network-level mechanisms that generate emergent temperature response curves.…
Understanding the temperature response of biological systems: Part I -- Phenomenological descriptions and microscopic models
Simen Jacobs, Julian Voits, Nikita Frolov +2
Virtually every biological rate depends on temperature, yet the resulting rate-temperature relationships often deviate strongly from simple Arrhenius behavior. In this first part o…