Related papers: New insights on the Dynamic Cellular Metabolism
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
The motility of eukaryotic cells is strongly influenced by their environment, with confined cells often developing qualitatively different motility patterns from those migrating on simple two-dimensional substrates. Recent experiments,…
We develop numerical and analytical approaches to calculate mutual information between complete paths of two molecular components embedded into a larger reaction network. In particular, we focus on a continuous-time Markov chain formalism,…
In Hopfield-type associative memory models, memories are stored in the connectivity matrix and can be retrieved subsequently thanks to the collective dynamics of the network. In these models, the retrieval of a particular memory can be…
Our work combines aspects of three promising paradigms in machine learning, namely, attention mechanism, energy-based models, and associative memory. Attention is the power-house driving modern deep learning successes, but it lacks clear…
A large number of neural network models of associative memory have been proposed in the literature. These include the classical Hopfield networks (HNs), sparse distributed memories (SDMs), and more recently the modern continuous Hopfield…
We study a fully connected Hopfield-type associative memory network with online activity-dependent synaptic plasticity, where neural states and synaptic couplings coevolve during retrieval. Using the generating-functional formalism, we…
Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Growing experimental evidence shows that cell monolayers can induce long-lived perturbations to their environment, akin to footprints, which in turn influence the global dynamics of the system. Inspired by these observations, we propose a…
Memory systems can store vastly different amounts of information despite similar hardware constraints. Here, we show that superior spatial memory emerges from a discrete stiffening of hippocampal population geometry-a transition from…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
The purpose of this study is to investigate how homophily, memory constraints, and adversarial disruptions collectively shape the resilience and adaptability of complex networks. To achieve this, we develop a new framework that integrates…
We propose and analyze a new variation of the so-called {\em exponential Hopfield model}, a recently introduced family of associative neural networks with unprecedented storage capacity. Our construction is based on a cost function defined…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control…
Cancer cells have the plasticity to adjust their metabolic phenotypes for survival and metastasis. During metastasis, a developmental program known as the epithelial-mesenchymal transition (EMT) plays a critical role. There is extensive…
Conducting Polymer Dendrites (CPD) can engrave sophisticated patterns of electrical interconnects in their morphology with low-voltage spikes and few resources: they may unlock in operando manufacturing functionalities for electronics using…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…