Information Surfaces in Systems Biology and Applications to Engineering Sustainable Agriculture [PDF]
, 2011 Systems biology of plants offers myriad opportunities and many challenges in modeling. A number of technical challenges stem from paucity of computational methods for discovery of the most fundamental properties of complex dynamical systems.
Assadi, Amir +3 more
core +2 more sources
Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks
iScience, 2019 Summary: As we begin to design increasingly complex synthetic biomolecular systems, it is essential to develop rational design methodologies that yield predictable circuit performance.
Noah Olsman +2 more
doaj +1 more source
A trajectory-based loss function to learn missing terms in bifurcating dynamical systems
Scientific Reports, 2021 Missing terms in dynamical systems are a challenging problem for modeling. Recent developments in the combination of machine learning and dynamical system theory open possibilities for a solution.
Rahel Vortmeyer-Kley +2 more
doaj +1 more source
A Mathematical Framework for Agent Based Models of Complex Biological Networks [PDF]
, 2010 Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use ...
A. S. Jarrah +17 more
core +1 more source
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
iScience, 2019 Summary: We introduce and develop a method that demonstrates that the algorithmic information content of a system can be used as a steering handle in the dynamical phase space, thus affording an avenue for controlling and reprogramming systems.
Hector Zenil +7 more
doaj +1 more source
Introduction to Focus Issue: Dynamics in Systems Biology [PDF]
Chaos: An Interdisciplinary Journal of Nonlinear Science, 2010 The methods of nonlinear systems form an extensive toolbox for the study of biology, and systems biology provides a rich source of motivation for the development of new mathematical techniques and the furthering of understanding of dynamical systems. This Focus Issue collects together a large variety of work which highlights the complementary nature of
Brackley, Chris A. +6 more
openaire +2 more sources
Tractable nonlinear memory functions as a tool to capture and explain dynamical behaviors
Physical Review Research, 2020 Mathematical approaches from dynamical systems theory are used in a range of fields. This includes biology where they are used to describe processes such as protein-protein interaction and gene regulatory networks.
Edgar Herrera-Delgado +2 more
doaj +1 more source
Amplification without instability: applying fluid dynamical insights in chemistry and biology
New Journal of Physics, 2013 While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems.
Jonathan H McCoy
doaj +1 more source
Boolean Models of Bistable Biological Systems
, 2009 This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model.
A. Novick +16 more
core +1 more source
Global convergence of quorum-sensing networks [PDF]
, 2010 In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in the ...
Russo, Giovanni +1 more
core +1 more source