Related papers: Modeling Translation in Protein Synthesis with TAS…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
We simulate the evolution of model protein sequences subject to mutations. A mutation is considered neutral if it conserves 1) the structure of the ground state, 2) its thermodynamic stability and 3) its kinetic accessibility. All other…
We investigate a rich new class of exactly solvable particle systems generalizing the Totally Asymmetric Simple Exclusion Process (TASEP). Our particle systems can be thought of as new exactly solvable examples of tandem queues, directed…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
We examine the behavior of a single impurity particle embedded within a Totally Asymmetric Simple Exclusion Process (TASEP). By analyzing the impurity's dynamics, characterized by two arbitrary hopping parameters $ \alpha $ and $\beta$, we…
We describe the translation invariant stationary states of the one dimensional discrete-time facilitated totally asymmetric simple exclusion process (F-TASEP). In this system a particle at site $j$ in $Z$ jumps, at integer times, to site…
The Totally Asymmetric Simple Exclusion Process (TASEP) is an important example of a particle system driven by an irreversible Markov chain. In this paper we give a simple yet rigorous derivation of the chain stationary measure in the case…
In the asymmetric simple exclusion process on the integers each particle waits exponential time, then with probability p it moves one step to the right if the site is unoccupied, otherwise it stays put; and with probability q=1-p it moves…
Over the last decade, proteomic analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate quantification of thousands of proteins.…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
A new mechanism leading to a random version of Burgers' equation is introduced: it is shown that the Totally Asymmetric Exclusion Process in discrete time (TASEP) can be understood as an intrinsically stochastic, non-entropic weak solution…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The asymmetric simple exclusion process (ASEP) with periodic boundary conditions is investigated for shuffled dynamics. In this type of update, in each discrete timestep the particles are updated in a random sequence. Such an update is…
We consider an interacting particle system, which generalizes the classical totally asymmetric simple exclusion process (TASEP), in that each site can contain up to a fixed finite number of particles, and the particle movement is governed…
We study correlation functions of the totally asymmetric simple exclusion process (TASEP) in discrete time with backward sequential update. We prove a determinantal formula for the generalized Green function which describes transitions…
The Symmetric Exclusion Process (SEP), in which particles hop symmetrically on a discrete line with hard-core constraints, is a paradigmatic model of subdiffusion in confined systems. This anomalous behavior is a direct consequence of…
We consider a totally asymmetric exclusion process on the positive half-line. When particles enter in the system according to a Poisson source, Liggett has computed all the limit distributions when the initial distribution has an asymptotic…
We obtain the large deviation function for entropy production of the medium and its distribution function for two-site totally asymmetric simple exclusion process(TASEP) and three-state unicyclic network. Since such systems are described…
When it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling…