Related papers: New insights on the Dynamic Cellular Metabolism
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Neural population activity in cortical and hippocampal circuits can be flexibly reorganized by context, suggesting that cognition relies on dynamic manifolds rather than static representations. However, how such dynamic organization can be…
The mitogen-activated protein kinase (MAPK) signaling cascade, an evolutionarily conserved motif present in all eukaryotic cells, is involved in coordinating critical cell-fate decisions, regulating protein synthesis, and mediating learning…
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…
Network systems can exhibit memory effects in which the interactions between different pairs of nodes adapt in time, leading to the emergence of preferred connections, patterns, and sub-networks. To a first approximation, this memory can be…
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Attractor networks are an influential theory for memory storage in brain systems. This theory has recently been challenged by the observation of strong temporal variability in neuronal recordings during memory tasks. In this work, we study…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
Commonly studied cellular automata are memoryless and have fixed topology of connections between cells. However by allowing updates of links and short-term memory in cells we may potentially discover novel complex regimes of spatio-temporal…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
Hopfield models, originally developed to study memory retrieval in neural networks, have become versatile tools for modeling diverse biological systems in which function emerges from collective dynamics. In this review, we provide a…
The Hopfield associative memory model stores random patterns in synaptic couplings according to Hebb's rule and retrieves them through gradient descent on an energy function. This conventional setting, where neurons are assumed to have…
Dense Associative Memories are high storage capacity variants of the Hopfield networks that are capable of storing a large number of memory patterns in the weights of the network of a given size. Their common formulations typically require…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…