Structural Fluctuations of Microtubule Binding Site of KIF1A in Different Nucleotide States (2008)
Kanada, Ryo, Takagi, Fumiko, Kikuchi, Macoto
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...
Kei Tokita, Macoto Kikuchi, Yukito Iba
A new approach to protein design is proposed. Our dynamical equation approach is based on the criterion by Kurosky and Deutsch 1), 2), with which the probability of a target structure in a...
Free-Energy Landscape of Kinesin by a Realistic Lattice Model (2007)
Kenzaki, Hiroo, Kikuchi, Macoto
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte...
Structural Change of Myosin Motor Domain and Nucleotide Dissociation (2006)
Takagi, Fumiko, Kikuchi, Macoto
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...
Thermodynamics of aggregation of two proteins (2006)
Nakanishi, Kazuki, Kikuchi, Macoto
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model....
Diversity in Free Energy Landscape of Proteins with the Same Native Topology (2005)
Kenzaki, Hiroo, Kikuchi, Macoto
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two...
Emergence of a Barchan Belt in a Unidirectional Flow: Experiment and Numerical Simulation (2004)
Katsuki, Atsunari, Kikuchi, Macoto, Endo, Noritaka
We observed time evolution of dune fields in a water tank experiment and simulated it by using a simple model without taking complex fluid dynamics into account. The initial sand bed changed its form...
Cluster Analysis of the Ising Model and Universal Finite-Size Scaling (2000)
Okabe, Yutaka, Kaneda, Kazuhisa, Tomita, Yusuke, Kikuchi, Macoto, Hu, Chin-Kun
The recent progress in the study of finite-size scaling (FSS) properties of the Ising model is briefly reviewed. We calculate the universal FSS functions for the Binder parameter $g$ and the...
Dynamical Equation Approach to Protein Design (2000)
Kei Tokita, Macoto Kikuchi, Yukito Iba
Introduction After the decades of the primary and phenomenological approaches to protein design 4) - 12) , general techniques have been developed 1) - 3), 13) - 23) for rational and e#cient design of...
Shape Effects of Finite-Size Scaling Functions for Anisotropic Three-Dimensional Ising Models (1999)
Kaneda, Kazuhisa, Okabe, Yutaka, Kikuchi, Macoto
The finite-size scaling functions for anisotropic three-dimensional Ising models of size $L_1 \times L_1 \times aL_1$ ($a$: anisotropy parameter) are studied by Monte Carlo simulations. We study the...
Multi-Self-Overlap Ensemble for protein folding: ground state search and thermodynamics (1999)
Chikenji, George, Kikuchi, Macoto, Iba, Yukito
Long chains of the HP lattice protein model are studied by the Multi-Self-Overlap Ensemble(MSOE) Monte Carlo method, which was developed recently by the authors. MSOE successfully finds the lowest...
Design Equation: A Novel Approach to Heteropolymer Design (1998)
Iba, Yukito, Kikuchi, Macoto, Tokita, Kei
A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at...
Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble (1998)
Iba, Yukito, Chikenji, George, Kikuchi, Macoto
A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically...
Dissipation Enhanced Asymmetric Transport in Quantum Ratchets (1997)
Tatara, Gen, Kikuchi, Macoto, Yukawa, Satoshi, Matsukawa, Hiroshi
Quantum mechanical motion of a particle in a periodic asymmetric potential is studied theoretically at zero temperature. It is shown based on semi-classical approximation that the tunneling...
Yukawa, Satoshi, Kikuchi, Macoto, Tatara, Gen, Matsukawa, Hiroshi
The concept of thermal ratchets is extended to the system governed by quantum mechanics. We study a tight-binding model with an asymmetric periodic potential contacting with a heat bath under an...
Coupled Map Traffic Flow Simulator Based on Optimal Velocity Functions (1997)
Shin-ichi Tadaki, Macoto Kikuchi, Yuki Sugiyama, Satoshi Yukawa
. A coupled map tra#c flow model is introduced based on optimal velocity functions. The model can be simulated under open boundary conditions. It is able to bear a variety of noises as well. Noises...
Kikuchi, Macoto, Okabe, Yutaka
The multi-spin coding of the Monte Carlo simulation of the three-state Potts model on the simple cubic lattice is presented. The ferromagnetic (F) model, the antiferromagnetic (AF) model, and the...
Universal Finite-Size-Scaling Functions (1996)
Okabe, Yutaka, Kikuchi, Macoto
The idea of universal finite-size-scaling functions of the Ising model is tested by Monte Carlo simulations for various lattices. Not only regular lattices such as the square lattice but...
Statistical Dependence Analysis (1996)
Kikuchi, Macoto, Ito, Nobuyasu, Okabe, Yutaka
We review our recent studies on the dynamical correlations in MC simulations from the view point of the statistical dependence. Attentions are paid to the reduction of the statistical degrees of...
Coupled-Map Modeling of One-Dimensional Traffic Flow (1994)
Yukawa, Satoshi, Kikuchi, Macoto
We propose a new model of one-dimensional traffic flow using a coupled map lattice. In the model, each vehicle is assigned a map and changes its velocity according to it. A single map is designed so...
Jam phases in two-dimensional cellular automata model of traffic flow (1994)
Tadaki, Shin-ichi, Kikuchi, Macoto
The jam phases in a two-dimensional cellular automata model of traffic flow are investigated by computer simulations. Two different types of the jam phases are found. The spatially diagonal...
Statistical Dependence and Related Topics (1994)
Kikuchi, Macoto, Ito, Nobuyasu, Okabe, Yutaka
On the basis of the dynamical interpretation of Monte Carlo simulations, we discuss the relation of the equilibrium relaxation time, the susceptibility and the statistical error. We introduce a new...
Recycle of random sequences (1993)
Ito, Nobuyasu, Kikuchi, Macoto, Okabe, Yutaka
The correlation between a random sequence and its transformed sequences is studied. In the case of a permutation operation or, in other word, the shuffling operation, it is shown that the correlation...
What is the role of non-native intermediates of β-lactoglobulin in protein folding?
Chikenji, George, Kikuchi, Macoto
The mechanism of α→β transition in folding of β-lactoglobulin is discussed based on free energy landscape analysis of a long lattice model. It is found that helical propensity of...
What is the role of non-native intermediates of β-lactoglobulin in protein folding?
Chikenji, George, Kikuchi, Macoto
The mechanism of α→β transition in folding of β-lactoglobulin is discussed based on free energy landscape analysis of a long lattice model. It is found that helical propensity of...
Structural Change and Nucleotide Dissociation of Myosin Motor Domain: Dual Gō Model Simulation
Takagi, Fumiko, Kikuchi, Macoto
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...