Related papers: New insights on the Dynamic Cellular Metabolism

Associative Memories like the famous Hopfield Networks are elegant models for describing fully recurrent neural networks whose fundamental job is to store and retrieve information. In the past few years they experienced a surge of interest…

We solve the dynamics of Hopfield-type neural networks which store sequences of patterns, close to saturation. The asymmetry of the interaction matrix in such models leads to violation of detailed balance, ruling out an equilibrium…

Learning and memory are acquired through long-lasting changes in synapses. In the simplest models, such synaptic potentiation typically leads to runaway excitation, but in reality there must exist processes that robustly preserve overall…

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and…

The primate heteromodal cortex presents an evident functional modularity at a mesoscopic level, with physiological and anatomical evidence pointing to it as likely substrate of long-term memory. In order to investigate some of its…

Cells store information in DNA and in stable programs of gene expression, which thereby implement forms of long-term cellular memory. Cells must also possess short-term forms of information storage, implemented post-translationally, to…

Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…

Understanding how biomechanical reorganization governs key biological processes, such as morphogenesis and development, requires predictive insights into stress distributions and cellular behavior. While traditional approaches focused on…

We study the dynamics of two two-level atoms embedded near to the interface of paired meta-material slabs, one of negative permeability and the other of negative permittivity. The interface behaves as a plasmonic waveguide composed of…

We present a dynamical model of lipoprotein metabolism derived by combining a cascading process in the blood stream and cellular level regulatory dynamics. We analyse the existence and stability of equilibria and show that this…

The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…

Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…

Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains"…

Traditional joint source-channel coding employs static learned semantic representations that cannot dynamically adapt to evolving source distributions. Shared semantic memories between transmitter and receiver can potentially enable…

Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…

Complementary Learning Systems theory holds that intelligent agents need two learning systems. Semantic memory is encoded in the neocortex with dense, overlapping representations and acquires structured knowledge. Episodic memory is encoded…

Attractor dynamics are a fundamental computational motif in neural circuits, supporting diverse cognitive functions through stable, self-sustaining patterns of neural activity. In these lecture notes, we review four key examples that…

The analysis of network dynamics is oftentimes restricted to networks with one-dimensional internal dynamics. Here, we show how symmetry explains the relation between behavior of systems with one-dimensional internal dynamics and with…

Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…

We introduce the Dreaming $L$-directional Associative Memory (DLAM), a multi-layer Hebbian architecture in which off-line dreaming and supervised heteroassociative coupling coexist within a single energy function, placing our approach…