Related papers: Dynamical-systems theory of cellular reprogramming
Consider first a memoryless population model described by the usual branching process with a given mean reproduction matrix on a finite space of types. Motivated by the consequences of atavism in Evolutionary Biology, we are interested in a…
We propose a new theory for aging based on dynamical systems and provide a data-driven computational method to quantify the changes at the cellular level. We use ergodic theory to decompose the dynamics of changes during aging and show that…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological…
Based on extensive study of a dynamical systems model of the development of a cell society, a novel theory for stem cell differentiation and its regulation is proposed as the ``chaos hypothesis''. Two fundamental features of stem cell…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
This chapter is an overview of foundational results in the mathematical theory of replicator systems. Its primary aim is to provide a unified framework for the mathematical formalisation of evolutionary processes in the spirit of…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
In the first half of the paper, some recent advances in coupled dynamical systems, in particular, a globally coupled map are surveyed. First, dominance of Milnor attractors in partially ordered phase is demonstrated. Second, chaotic…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
Any algorithm (in the sense of Gurevich's abstract-state-machine axiomatization of classical algorithms) operating over any arbitrary unordered domain can be simulated by a dynamic cellular automaton, that is, by a pattern-directed cellular…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
We investigate the predictive power of recurrent neural networks for oscillatory systems not only on the attractor, but in its vicinity as well. For this we consider systems perturbed by an external force. This allows us to not merely…
Hundreds of Evolutionary Computation approaches have been reported. From an evolutionary perspective they focus on two fundamental mechanisms: cultural inheritance in Swarm Intelligence and genetic inheritance in Evolutionary Algorithms.…
Reverse engineering the brain is proving difficult, perhaps impossible. While many believe that this is just a matter of time and effort, a different approach might help. Here, we describe a very simple idea which explains the power of the…
In the mammalian brain, newly acquired memories depend on the hippocampus for maintenance and recall, but over time the neocortex takes over these functions, rendering memories hippocampus-independent. The process responsible for this…