The effect of side motion in the dynamics of interacting molecular motors

Midha, Tripti; Gupta, Arvind; Kolomeisky, Anatoly B.

doi:10.1088/1742-5468/aa75e1

Cited by 14 publications

(10 citation statements)

References 36 publications

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“…For complex dynamic processes that involve correlations simple mean-field methods, which assume that the occupation of neighboring sites are independent from each other, fail to properly describe the systems properties. In this case, more advanced cluster mean-field methods are required [39]. The main idea here is to consider dynamics inside of a cluster of several sites exactly, while the correlations between the clusters can be neglected.…”

Section: Cluster Mean-field Theorymentioning

confidence: 99%

Theoretical investigations of asymmetric simple exclusion processes for interacting oligomers

et al. 2018

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Motivated by biological transport phenomena that involve the motion of interacting molecular motors along linear filaments, we developed a theoretical framework to analyze the dynamics of interacting oligomers (extended size particles) on one-dimensional lattices. Our method extends the asymmetric simple exclusion processes for interacting monomers to particles of arbitrary size, and it utilizes cluster mean-field calculations supplemented by extensive Monte Carlo computer simulations. Interactions between particles are accounted for by a thermodynamically consistent method that views the formation and breaking bonds between particles as a chemical process. The dynamics of the system are analyzed for both periodic and open boundary conditions. It is found that the nature of the current-density relation depends on the strength of interactions, on the size of oligomers and on the way interactions influence particles transition rates. Stationary phase diagram is also fully evaluated, and it is shown how the dynamic properties depend on the interactions and on the sizes of the particles. To explain the dynamic behavior of the system particles density correlations are explicitly analyzed for dierent ranges of parameters. Theoretical calculations generally agree well with the results from the computer PAPER: Classical statistical mechanics, equilibrium and non-equilibrium

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Section: Cluster Mean-field Theorymentioning

confidence: 99%

Theoretical investigations of asymmetric simple exclusion processes for interacting oligomers

et al. 2018

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“…Besides LK, the presence of mutual interactions among particles also has a major impact on the steady-state properties of DDS. The driven exclusion processes with nearestneighbor interactions and without LK have been extensively studied for a single [1,16,[19][20][21][22][23][24][25][26][27][28][29] as well as multilane TASEP systems [30,31], using the thermodynamically consistent [27][28][29][30][31] and phenomenological approaches [1,16,[19][20][21][22][23][24][25]. The interactions in these systems are theoretically handled using the cluster mean-field and the modified cluster mean-field approaches.…”

Section: Introductionmentioning

confidence: 99%

Interactions in nonconserving driven diffusive systems

2018

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Motivated by biological transport phenomena and vehicular traffic flow we investigate the dynamics of interacting molecular motors or interacting vehicles that move along linear filaments (tracks) and can reversibly associate or dissociate from them. To analyze these processes, we introduced a model assimilating the interactions in a totally asymmetric simple exclusion process coupled with nonconserving Langmuir kinetics. The model is analyzed first using the continuum version of the simple mean-field approach that neglects the correlations between the particles. It is shown that even for weak interactions theoretical predictions deviate significantly from computer simulation results. To alleviate the problems, we developed a theoretical method that takes into account some correlations in the system. The effect of interactions on stationary phase diagrams, particle currents, and densities are explicitly evaluated. The analysis of two-point correlation function on the lattice indicates that the correlations are stronger at the locations of localized shocks. Our theoretical calculations are in excellent agreement with Monte Carlo computer simulations.

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“…1. This picture is inspired by the transport of kinesins along microtubule cytoskeleton filaments [21][22][23]. Each lattice site can be occupied or empty, and no more than one particle can be found at the same location -this is the exclusion part of the interactions.…”

Section: Modelmentioning

confidence: 99%

“…At the same time, the single-molecule imaging of in vitro dynamics and processivity of kinesin molecules concluded that kinesins most probably weakly repel during each encounter [13]. The importance of interactions for motor proteins stimulated multiple theoretical investigations that aimed to uncover the role of interactions in the collective dynamics [14][15][16][17][18][19][20][21][22][23]. Most of them utilized totally asymmetric simple exclusion processes (TASEPs), which are non-equilibrium multi-particle models that have been widely employed to analyze various dynamic processes in chemistry, physics and biology [24][25][26].…”

Section: Introductionmentioning

confidence: 99%

“…Most of these theoretical studies treated the effect of interactions in collective dynamics of molecular motors in a phenomenological way [14][15][16][17][18][19][20]. A more fundamental approach to describe interactions has utilized thermodynamic arguments to describe the formation and breaking contacts between neighboring motor proteins [21][22][23], providing a better microscopic connection between properties of molecular motors and their cooperative behavior.…”

Section: Introductionmentioning

confidence: 99%

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Dynamics of relaxation to a stationary state for interacting molecular motors

Gomes¹,

Kolomeisky²

2017

J. Phys. A: Math. Theor.

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Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular motors usually perform their cellular tasks by acting collectively, and there are interactions between individual motors that specify the overall collective behavior. One of the fundamental issues related to the collective dynamics of motor proteins is the question if they function at stationary-state conditions. To investigate this problem, we analyze a relaxation to the stationary state for the system of interacting molecular motors. Our approach utilizes a recently developed theoretical framework, which views the collective dynamics of motor proteins as a totally asymmetric simple exclusion process of interacting particles, where interactions are taken into account via a thermodynamically consistent approach. The dynamics of relaxation to the stationary state is analyzed using a domain-wall method that relies on a mean-field description, which takes into account some correlations. It is found that the system quickly relaxes for repulsive interactions, while attractive interactions always slow down reaching the stationary state. It is also predicted that for some range of parameters the fastest relaxation might be achieved for a weak repulsive interaction. Our theoretical predictions are tested with Monte Carlo computer simulations. The implications of our findings for biological systems are briefly discussed. PACS numbers:

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The effect of side motion in the dynamics of interacting molecular motors

Cited by 14 publications

References 36 publications

Theoretical investigations of asymmetric simple exclusion processes for interacting oligomers

Theoretical investigations of asymmetric simple exclusion processes for interacting oligomers

Interactions in nonconserving driven diffusive systems

Dynamics of relaxation to a stationary state for interacting molecular motors

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