Codebase release 1.1 for TASEPy

Luca Ciandrini; Richmond L. Crisostomo; Juraj Szavits-Nossan

doi:10.21468/SciPostPhysCodeb.22-r1.1

Codebase release 1.1 for TASEPy

Luca Ciandrini, Richmond L. Crisostomo, Juraj Szavits-Nossan

School of Biological Sciences

Research output: Non-textual form › Software

Abstract

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 rate vary across the lattice is a long-standing problem. In recent years, a power series approximation (PSA) has been developed to tackle this problem, however no computer algorithm currently exists that implements this approximation. This paper addresses this issue by providing a Python-based package TASEPy that finds the steady state solution of the inhomogeneous TASEP for any set of hopping rates using the PSA truncated at a user-defined order.

Original language	English
Publisher	SciPost Foundation
Media of output	Code
DOIs	https://doi.org/10.21468/SciPostPhysCodeb.22-r1.1
Publication status	Published - 13 Dec 2023

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10.21468/SciPostPhysCodeb.22-r1.1

https://scipost.org/10.21468/SciPostPhysCodeb.22-r1.1

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Modelling the fits and starts of how genes burst into expression
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1/04/21 → 31/03/24
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1 Article

TASEPy: A Python-based package to iteratively solve the inhomogeneous exclusion process
Ciandrini, L., Crisostomo, R. L. & Szavits-Nossan, J., 13 Dec 2023, In: SciPost Physics Codebases. 22, 23 p.
Research output: Contribution to journal › Article › peer-review

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Cite this

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abstract = "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 rate vary across the lattice is a long-standing problem. In recent years, a power series approximation (PSA) has been developed to tackle this problem, however no computer algorithm currently exists that implements this approximation. This paper addresses this issue by providing a Python-based package TASEPy that finds the steady state solution of the inhomogeneous TASEP for any set of hopping rates using the PSA truncated at a user-defined order.",

author = "Luca Ciandrini and Crisostomo, {Richmond L.} and Juraj Szavits-Nossan",

year = "2023",

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AU - Ciandrini, Luca

AU - Crisostomo, Richmond L.

AU - Szavits-Nossan, Juraj

PY - 2023/12/13

Y1 - 2023/12/13

N2 - 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 rate vary across the lattice is a long-standing problem. In recent years, a power series approximation (PSA) has been developed to tackle this problem, however no computer algorithm currently exists that implements this approximation. This paper addresses this issue by providing a Python-based package TASEPy that finds the steady state solution of the inhomogeneous TASEP for any set of hopping rates using the PSA truncated at a user-defined order.

AB - 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 rate vary across the lattice is a long-standing problem. In recent years, a power series approximation (PSA) has been developed to tackle this problem, however no computer algorithm currently exists that implements this approximation. This paper addresses this issue by providing a Python-based package TASEPy that finds the steady state solution of the inhomogeneous TASEP for any set of hopping rates using the PSA truncated at a user-defined order.

U2 - 10.21468/SciPostPhysCodeb.22-r1.1

DO - 10.21468/SciPostPhysCodeb.22-r1.1

M3 - Software

PB - SciPost Foundation

ER -

Codebase release 1.1 for TASEPy

Abstract

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Modelling the fits and starts of how genes burst into expression

Research output

TASEPy: A Python-based package to iteratively solve the inhomogeneous exclusion process

Cite this