Related papers: Sensitivity of mRNA Translation
The generalized totally asymmetric exclusion process (TASEP) [J. Stat. Mech. P05014 (2012)] is an integrable generalization of the TASEP equipped with an interaction, which enhances the clustering of particles. The process interpolates…
For a given inhomogeneous exclusion processes on $N$ sites between two reservoirs, the trajectories probabilities allow to identify the relevant local empirical observables and to obtain the corresponding rate function at Level 2.5. In…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
The totally asymmetric simple exclusion process (TASEP) is a paradigmatic lattice model for one-dimensional particle transport subject to excluded-volume interactions. Solving the inhomogeneous TASEP in which particles' hopping rates vary…
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developing attenuated virus strains that can be used for…
The ribosome flow model on a ring (RFMR) is a deterministic model for translation of a circularized mRNA. We derive a new spectral representation for the optimal steady-state production rate and the corresponding optimal steady-state…
In [AAV] Amir, Angel and Valk{\'o} studied a multi-type version of the totally asymmetric simple exclusion process (TASEP) and introduced the TASEP speed process, which allowed them to answer delicate questions about the joint distribution…
We study a continuous-space version of the totally asymmetric simple exclusion process (TASEP), consisting of interacting Brownian particles subject to a driving force in a periodic external potential. Particles are inserted at the leftmost…
The TASEP (totally asymmetric simple exclusion process) is a basic model for an one-dimensional interacting particle system with non-reversible dynamics. Despite the simplicity of the model it shows a very rich and interesting behaviour. In…
We study the totally asymmetric simple exclusion process (TASEP) on $\mathbb{Z}$ with a general initial condition and a deterministically moving wall in front of the particles. Using colour-position symmetry, we express the one-point…
Gene expression estimation from pathology images has the potential to reduce the RNA sequencing cost. Point-wise loss functions have been widely used to minimize the discrepancy between predicted and absolute gene expression values.…
The dynamics of an asymmetric tracer in the symmetric simple exclusion process (SEP) is mapped, in the continuous scaling limit, to the local current through the origin in the zero-range process (ZRP) with a biased bond. This allows us to…
We report here results on the study of the totally asymmetric simple exclusion processes (TASEP), defined on an open network, consisting of head and tail simple chain segments with a double-chain section inserted in-between. Results of…
We introduce a mean-field theoretical framework to describe multiple totally asymmetric simple exclusion processes (TASEPs) with different lattice lengths, entry and exit rates, competing for a finite reservoir of particles. We present…
We extend one dimensional asymmetric simple exclusion process (ASEP) to a surface and show that the effect of transverse diffusion is to induce a continuous phase transition from a constant density phase to a maximal current phase as the…
Many ribosomes simultaneously move on the same messenger RNA (mRNA), each separately synthesizing the protein coded by the mRNA. Earlier models of ribosome traffic represent each ribosome by a ``self-propelled particle'' and capture the…
Consider the stationary measure of open asymmetric simple exclusion process (ASEP) on the lattice $\{1,\dots,n\}$. Taking $n$ to infinity while fixing the jump rates, this measure converges to a measure on the semi-infinite lattice. In the…
We study an open-chain totally asymmetric exclusion process (TASEP) with stochastic gates present at the two boundaries. The gating dynamics has been modeled keeping the physical system of ion-channel gating in mind. These gates can…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
Recent work has shown that expression level is the main predictor of a gene’s evolutionary rate, and that more highly expressed genes evolve slower. A possible explanation for this observation is selection for proteins which fold…