Related papers: Sensitivity of mRNA Translation
This work is devoted to investigating the evolution of concentration in a genetic regulation system, when the synthesis reaction rate is under additive and multiplicative asymmetric stable L\'evy fluctuations. By focusing on the impact of…
We theoretically discuss the preservation of squeezing and continuous variable entanglement of two mode squeezed light when the two modes are subjected to unequal transmission. One of the modes is transmitted through a slow light medium…
We study the traffic of two types of molecular motors using the two-species symmetric simple exclusion process (ASEP) with periodic boundary conditions and with attachment and detachment of particles. We determine characteristic properties…
Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…
The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered lattice of sites, but only if the next site is empty. ASEP has…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
The discrete-time version of totally asymmetric simple-exclusion process (TASEP) on a finite one-dimensional lattice is studied with the periodic boundary condition. Each particle at a site hops to the next site with probability $0 \leq p…
A multi-species generalization of the asymmetric simple exclusion process (ASEP) is studied in ordered sequential and sub-lattice parallel updating schemes. In this model particles hop with their own specific probabilities to their…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
The totally asymmetric simple exclusion process (TASEP) is a paradigmatic stochastic model for non-equilibrium physics, and has been successfully applied to describe active transport of molecular motors along cytoskeletal filaments.…
We study the steady state of the two-species Asymmetric Simple Exclusion Process (ASEP) with open boundary conditions. The matrix product method works for the determination of the stationary probability distribution. Several physical…
We consider the asymmetric simple exclusion process (TASEP) on open network consisting of three consecutively coupled macroscopic chain segments with a shortcut between the tail of the first segment and the head of the third one. The model…
We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication…
We present explicit formulas for total crossing events in the multi-species asymmetric exclusion process ($r$-ASEP) with underlying $U_q(\widehat{\mathfrak{sl}}_{r+1})$ symmetry. In the case of the two-species TASEP these can be derived…
To mimic the complex transport-like collective phenomena in a man-made or natural system, we study an open network junction model of totally asymmetric simple exclusion process with bulk particle attachment and detachment. The stationary…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Cell migration, which can be significantly affected by intracellular signaling pathways (ICSP) and extracellular matrix (ECM), plays a crucial role in many physiological and pathological processes. The efficiency of cell migration, which is…