arXiv subjects

Fumiko Takagi

Publications and source records attributed to Fumiko Takagi.

5 recordsLinked to original sources

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

Structural Change of Myosin Motor Domain and Nucleotide Dissociation

We investigated the structural relaxation of myosin motor domain from the pre-power stroke state to the near-rigor state using molecular dynamics simulation of a coarse-grained protein model. To describe the structural change, we propose a "dual Go-model," a variant of the Go-like model that has two reference structures. The nucleotide dissociation process is also studied by introducing a coarse-grained nucleotide in the simulation. We found that the myosin structural relaxation toward the near-rigor conformation cannot be completed before the nucleotide dissociation. Moreover, the relaxation and the dissociation occurred cooperatively when the nucleotide was tightly bound to the myosin head. The result suggested that the primary role of the nucleotide is to suppress the structural relaxation.

q-bio.BM↗

arXiv2000

The Carnot Cycle for Small Systems: Irreversibility and the Cost of Operations

We employ the recently developed framework of the energetics of stochastic processes (called `stochastic energetics'), to re-analyze the Carnot cycle in detail, taking account of fluctuations, without taking the thermodynamic limit. We find that both processes of connection to and disconnection from heat baths and adiabatic processes that cause distortion of the energy distribution are sources of inevitable irreversibility within the cycle. Also, the so-called null-recurrence property of the cumulative efficiency of energy conversion over many cycles and the irreversible property of isolated, purely mechanical processes under external `macroscopic' operations are discussed in relation to the impossibility of a perpetual machine, or Maxwell's demon.

cond-mat.stat-mech↗

arXiv1999

Thermal Noise Can Facilitate Energy Conversion by Ratchet System?

Molecular motors in biological systems are expected to use ambient fluctuation. In a recent Letter [Phys. Rev. Lett. {\bf 80}, 5251 (1998)], it was showed that the following question was unsolved, ``Can thermal noise facilitate energy conversion by ratchet system?'' We consider it using stochastic energetics, and show that there exist systems where thermal noise helps the energy conversion.

cond-mat.stat-mech↗

arXiv1998

Energetics of Forced Thermal Ratchet

Molecular motors are known to have the high efficiency of energy transformation in the presence of thermal fluctuation. Motivated by the surprising fact, recent studies of thermal ratchet models are showing how and when work should be extracted from non-equilibrium fluctuations. One of the important finding was brought by Magnasco where he studied the temperature dependence on the fluctuation-induced current in a ratchet (multistable) system and showed that the current can generically be maximized in a finite temperature. The interesting finding has been interpreted that thermal fluctuation is not harmful for the fluctuation-induced work and even facilitates its efficiency. We show, however, this interpretation turns out to be incorrect as soon as we go into the realm of the energetics [Sekimoto,J.Phys.Soc.Jpn.66,1234-1237(1997)]: the efficiency of energy transformation is not maximized at finite temperature, even in the same system that Magnasco considered. The maximum efficiency is realized in the absence of thermal fluctuation. The result presents an open problem whether thermal fluctuation could facilitate the efficiency of energetic transformation from force-fluctuation into work.

cond-mat.soft↗