相关论文: A deterministic model for non-monotone relationshi…
We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO). This model encapsulates many realistic features of translation including…
We develop a method for solving mathematical models of messenger RNA (mRNA) translation based on the totally asymmetric simple exclusion process (TASEP). Our main goal is to demonstrate that the method is versatile and applicable to…
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 propose and study a conceptual one-dimensional model to explore how the combined interplay between fixed resources and particle exchanges between different parts of an extended system can affect the stationary densities in a current…
mRNA translation is a crucial process that leads to protein synthesis in living cells. Therefore, it is a process that needs to work optimally for a cell to stay healthy and alive. With advancements in microscopy and novel experimental…
We study the nonequilibrium steady states of an asymmetric exclusion process (TASEP) coupled to a reservoir of unlimited capacity. We elucidate how the steady states are controlled by the interplay between the reservoir population that…
Pansharpening, a pivotal task in remote sensing for fusing high-resolution panchromatic and multispectral imagery, has garnered significant research interest. Recent advancements employing diffusion models based on stochastic differential…
We explore how the interplay of finite availability, carrying capacity of particles at different parts of a spatially extended system and particle diffusion between them control the steady state currents and density profiles in a…
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally,…
Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA…
We develop a power series method for the nonequilibrium steady state of the inhomogeneous one-dimensional totally asymmetric simple exclusion process (TASEP) in contact with two particle reservoirs and with site-dependent hopping rates in…
Asymmetric exclusion process (TASEP) along a one-dimensional (1D) open channel sets the paradigm for 1D driven models and nonequilibrium phase transitions in open 1D models. Inspired by the phenomenologies of an open TASEP with Langmuir…
The totally asymmetric simple exclusion process (TASEP) is a stochastic model for the unidirectional flow of interacting particles on a 1D-lattice that is much used in systems biology and statistical physics. Its master equation describes…
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of non-equilibrium statistical physics, the totally…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
Theoretical advances in the study of non-equilibrium phenomena are briefly reviewed with emphasis on steady state properties of one-dimensional driven lattice gases. The presentation is focused on the totally asymmetric simple-exclusion…
The steady-state currents and densities of a one-dimensional totally asymmetric exclusion process (TASEP) with particles that occlude an integer number ($d$) of lattice sites are computed using various mean field approximations and Monte…
Sampling from high-dimensional distributions is a fundamental problem in statistical research and practice. However, great challenges emerge when the target density function is unnormalized and contains isolated modes. We tackle this…
In transonic turbine stages, complex interactions between trailing edge shocks from nozzle guide vanes and rotor blades generate unsteady wall pressure fields, impacting rotor aerodynamic performance and structural integrity. While…
We theoretically study the Totally Asymmetric Exclusion Process (TASEP) with quenched jumping rates disorder and finite lifetime chain. TASEP is widely used to model the translation of messenger RNAs by Ribosomes in protein synthesis. Since…