arXiv subjects

Ryo Kanada

Publications and source records attributed to Ryo Kanada.

3 recordsLinked to original sources

arXiv2018

Diffusion Enhancement of Brownian Motors Revealed by a Solvable Model

A solvable model is proposed and analyzed to reveal the mechanism underlying the diffusion enhancement recently reported for a model of molecular motors and predicted to be observed in the biological rotary motor $\rm F_1$-ATPase. It turns out that the diffusion enhancement for the present model can approximately described by a random walk in which the waiting time for a step to occur is exponentially distributed and it takes nonzero time to proceed forward by the step. It is shown that the diffusion coefficient of such a random walk can significantly be increased when the average waiting time is comparable to the average stepping time.

cond-mat.stat-mech↗

arXiv2008

Structural Fluctuations of Microtubule Binding Site of KIF1A in Different Nucleotide States

How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different nucleotide states that are realized in the ATP hydrolysis process by molecular dynamics simulations of Go-like model. We found that "alpha4 helix", which is a part of the microtubule (MT) binding site, changes its fluctuation systematically according to the nucleotide states. In particular, the frequency of large fluctuations of alpha4 strongly correlates with the affinity of KIF1A for microtubule. We also show how the strength of the thermal fluctuation and the interaction with the nucleotide affect the dynamics of microtubule binding site. These results suggest that KIF1A regulates the affinity to MT by changing the flexibility of alpha4 helix according to the nucleotide states.

q-bio.BM↗

arXiv2006

Efficiency of Energy Transduction in a Molecular Chemical Engine

A simple model of the two-state ratchet type is proposed for molecular chemical engines that convert chemical free energy into mechanical work and vice versa. The engine works by catalyzing a chemical reaction and turning a rotor. Analytical expressions are obtained for the dependences of rotation and reaction rates on the concentrations of reactant and product molecules, from which the performance of the engine is analyzed. In particular, the efficiency of energy transduction is discussed in some detail.

cond-mat.stat-mech↗