Dynein-Inspired Multilane Exclusion Process with Open Boundary Conditions.

Riya Nandi,Uwe C Täuber,Priyanka Priyanka

doi:10.3390/e23101343

Abstract

Motivated by the sidewise motions of dynein motors shown in experiments, we use a variant of the exclusion process to model the multistep dynamics of dyneins on a cylinder with open ends. Due to the varied step sizes of the particles in a quasi-two-dimensional topology, we observe the emergence of a novel phase diagram depending on the various load conditions. Under high-load conditions, our numerical findings yield results similar to the TASEP model with the presence of all three standard TASEP phases, namely the low-density (LD), high-density (HD), and maximal-current (MC) phases. However, for medium- to low-load conditions, for all chosen influx and outflux rates, we only observe the LD and HD phases, and the maximal-current phase disappears. Further, we also measure the dynamics for a single dynein particle which is logarithmically slower than a TASEP particle with a shorter waiting time. Our results also confirm experimental observations of the dwell time distribution: The dwell time distribution for dyneins is exponential in less crowded conditions, whereas a double exponential emerges under overcrowded conditions.

Highlights

Molecular motors are enzymatic protein molecules that use chemical energy released from the hydrolysis of an adenosine triphosphate (ATP) molecule to drive cellular transport along cytoskeletal filaments [1]
We describe a variation of the asymmetric exclusion process with shortand long-distance jumps to model the dynamics of dynein motors, and explored the ensuing collective dynamics in one dimension as well as in a quasi-two-dimensional topology with open boundary conditions
Our work highlights the non-trivial effects of geometry in out-of-equilibrium driven diffusive systems that may modify the phase diagram and change the nature of the accompanying phase transitions

Summary

Introduction

Molecular motors are enzymatic protein molecules that use chemical energy released from the hydrolysis of an adenosine triphosphate (ATP) molecule to drive cellular transport along cytoskeletal filaments [1]. Among the wide variety of molecular motors, linear ATP-driven motors include myosins, kinesins, and dyneins that are responsible for various cellular functions, including intracellular vesicle transport [1,2]. Incorporating stochastic features into theoretical modeling of molecular motor transport becomes essential to gain adequate statistical understanding of the ensuing fluctuations and their effects. Modeling such biological transport phenomena with the help of driven diffusive systems has been fruitful in capturing many essential properties of real systems [4,5,6,7]. Theoretical studies of dynein motors remain mostly unexplored to date, whence this constitutes the present work’s central theme

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Conclusion