Related papers: Dynamical-systems theory of cellular reprogramming
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
Replay in neural networks involves training on sequential data with memorized samples, which counteracts forgetting of previous behavior caused by non-stationarity. We present a method where these auxiliary samples are generated on the fly,…
Regardless of the marked differences between biological and artificial neural systems, one fundamental similarity is that they are essentially dynamical systems that can learn to imitate other dynamical systems, without knowing their…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
Despite tremendous progress, machine learning and deep learning still suffer from incomprehensible predictions. Incomprehensibility, however, is not an option for the use of (deep) reinforcement learning in the real world, as unpredictable…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
Mechanical cues from the extracellular microenvironment play a central role in regulating the structure, function and fate of living cells. Nevertheless, the precise nature of the mechanisms and processes underlying this crucial cellular…
The paper introduces a biologically and evolutionarily plausible neural architecture that allows a single group of neurons, or an entire cortical pathway, to be dynamically reconfigured to perform multiple, potentially very different…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
We describe an approach to model genetic regulatory networks at the level of promotion-inhibition circuitry through a class of stochastic spin models that includes spatial and temporal density fluctuations in a natural way. The formalism…
We investigate recurrent neural networks with asymmetric interactions and demonstrate that the inclusion of self-couplings or sparse excitatory inter-module connections leads to the emergence of a densely connected manifold of dynamically…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape.…
This paper develops a quasispecies model where cells can adopt a two-cell survival strategy. Within this strategy, pairs of cells join together, at which point one of the cells sacrifices its own replicative ability for the sake of the…
A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the…
Many real-world systems studied are governed by complex, nonlinear dynamics. By modeling these dynamics, we can gain insight into how these systems work, make predictions about how they will behave, and develop strategies for controlling…