Related papers: Modeling Translation in Protein Synthesis with TAS…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…
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…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
We consider the totally asymmetric simple exclusion process (TASEP) on a finite lattice with open boundaries. We show, using the recursive structure of the Markov matrix that encodes the dynamics, that there exist two transfer matrices…
We study the transition probabilities for the totally asymmetric simple exclusion process (TASEP) on the infinite integer lattice with a finite, but arbitrary number of first and second class particles. Using the Bethe ansatz we present an…
The oriented swap process is a natural directed random walk on the symmetric group that can be interpreted as a multi-species version of the Totally Asymmetric Simple Exclusion Process (TASEP) on a finite interval. An open problem from a…
One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to…
We apply the Matrix Product Ansatz to study the Totally Asymmetric Simple Exclusion Process on a ring with a generalized discrete-time dynamics depending on two hopping probabilities, $p$ and $\tilde{p}$. The model contains as special cases…
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…
We study a minimal lattice model which describes bidirectional transport of "particles" driven along a one dimensional track, as is observed in microtubule based, motor protein driven bidirectional transport of cargo vesicles, lipid bodies…
In this paper the totally asymmetric exclusion process (TASEP) with parallel update on an open lattice of size $L$ is considered in the maximum-current region. A formal expression for the generating function for the weight of configurations…
We consider totally asymmetric simple exclusion processes with n types of particle and holes ($n$-TASEPs) on $\mathbb {Z}$ and on the cycle $\mathbb {Z}_N$. Angel recently gave an elegant construction of the stationary measures for the…
The totally asymmetric simple exclusion process (TASEP) on Z with the Bernoulli-rho measure as initial conditions, 0<rho<1, is stationary. It is known that along the characteristic line, the current fluctuates as of order t^{1/3}. The…
We find the formulas of the transition probabilities of the $N$-particle multi-species asymmetric simple exclusion processes (ASEP), and show that the transition probabilities are written as a determinant when the order of particles in the…
We obtain a new relation between the distributions $\mu_t$ at different times $t\ge 0$ of the continuous-time TASEP (Totally Asymmetric Simple Exclusion Process) started from the step initial configuration. Namely, we present a…
In this article we present a comprehensive study of the totally asymmetric simple exclusion process with pausing particles (pTASEP), a model initially introduced to describe RNAP dynamics during transcription. We extend previous mean-field…
We explore the stationary densities in totally asymmetric exclusion processes (TASEP) with open boundary conditions and spatially inhomogeneous hopping rates. We calculate the steady state density profiles that characterise the associated…
We identify the algorithm for constructing steady states of the $n$-species totally asymmetric simple exclusion process (TASEP) on $L$ site periodic chain by Ferrari and Martin with a composition of combinatorial $R$ for the quantum affine…
We present a new lattice model for proteins that incorporates a tube-like anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.
We give a combinatorial description of the stationary measure for a totally asymmetric exclusion process (TASEP) with second class particles, on either Z or on the cycle Z_N. The measure is the image by a simple operation of the uniform…