Related papers: A mechanistic model for +1 frameshifts in eubacter…
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding…
Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been…
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…
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…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally…
We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Respiration in bacteria involves a sequence of energetically-coupled electron and proton transfers creating an electrochemical gradient of protons (a proton-motive force) across the inner bacterial membrane. With a simple kinetic model we…
The deformation of cellular membranes regulates trafficking processes, such as exocytosis and endocytosis. Classically, the Helfrich continuum model is used to characterize the forces and mechanical parameters that cells tune to accomplish…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
Knowledge about grain boundary migration is a prerequisite for understanding and ultimately modulating the properties of polycrystalline materials. Evidence from experiments and molecular dynamics (MD) simulations suggests that the…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
We study a model for the translocation of proteins across membranes through a nanopore using a ratcheting mechanism. When the protein enters the nanopore it diffuses in and out of the pore according to a Brownian motion. Moreover, it is…
A theory for qualitative models of gene regulatory networks has been developed over several decades, generally considering transcription factors to regulate directly the expression of other transcription factors, without any intermediate…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…