Related papers: Biomolecular resource utilization in elementary ce…
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory…
It is now well established that the cell is a highly crowded environment. Yet, the effects of crowding on the dynamics of signaling pathways, gene regulation networks and metabolic networks are still largely unknown. Crowding can alter both…
We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
The dynamics of active matter driven by interacting molecular motors has a non-potential structure at the local scale. However, we show that there exists a quasi-potential effectively describing the collective self-organization of the…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…
A ubiquitous way that cells share information is by exchanging molecules. Yet, the fundamental ways that this information exchange is influenced by intracellular dynamics remain unclear. Here we use information theory to investigate a…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…
The living cell expends energetic and material resources to reliably process information from its environment. To do so, it utilises unreliable molecular circuitry that is subject to thermal and other fluctuations. Here, we argue that…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
Cell is the structural and functional unit of life. This Resource Letter serves as a guide to the literature on nano-machines which drive not only intracellular movements, but also motility of the cell. These machines are usually proteins…
Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems…
Recently, several theoretical and experimental studies have been undertaken to probe the effect of stochasticity on gene expression (GE). In experiments, the GE response to an inducing signal in a cell, measured by the amount of…
We investigate the percolation properties of a two-state (occupied - empty) cellular automaton, where at each time step a cluster of occupied sites is removed and the same number of randomly chosen empty sites are occupied again. We find a…
Myosin II molecular motors slide actin filaments relatively to each other and are essential for force generation, motility and mechanosensing in animal cells. For non-muscle cells, evolution has resulted in three different isoforms, which…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
Numerical investigation of the interaction of electromagnetic fields with eukaryotic cells requires specifically adapted computer models. Virtual microdosimetry, used to investigate exposure, requires volumetric cell models, which are…