This paper designs a multi-compartment soma-dendrite-spine model having nonlinear dynamics of an asynchronous cellular automaton. The model can exhibit various propagations of action potentials observed in neurons and these propagations are analyzed in detailed. Then, using the analysis results, a novel systematic design method of the model is proposed. It is shown that the model designed by the proposed method can realize robust conditioning based on spike-timing dependent plasticity (STDP). Also, the designed model is implemented by a field programmable gate array (FPGA) and experiments validate its STDP-based conditioning function. It is then shown that the designed model consumes fewer hardware resources and lower power compared to an ODE-based multi-compartment model.

As a strategy to address the difficulties encountered when modeling and controlling a musculoskeletal system, we present a straightforward implementation of an autonomous decentralized motion control system in this paper; the system is inspired by the spinal reflex system of animals. We developed an artificial receptor, a muscle, and a neuron to mechanically implement the reflex mechanisms of animals. Among the reflex mechanisms, this paper presents a reflex system with reciprocal innervation for a musculoskeletal quasi-quadruped robot, including antagonist muscles. In the experiments, the robot autonomously generated a leg trajectory and a gait pattern with smooth alternating motions of the antagonist muscles through the interaction between the body, the ground, and the artificial reflex systems. To evaluate the reciprocal innervation, we compared the developed robot with one that does not include antagonist muscles. The reciprocal innervation allows for twice as many muscle implementations as those offered by the robot without antagonist muscles. Moreover, it improves the running speed by 5% on average and the flexion and extension velocities of all joints by 28% on average at around touchdowns and liftoffs of the foot. This successful result lead to implement more advanced nervous systems by solely mechanical devices.

The bodies of quadrupeds have very complex muscle-tendon structure. In particular, it is known that in the horse hindlimb, multiple joints in the leg are remarkably interlocked due to the muscle-tendon structure. Although the function of these interlocking mechanisms during standing has been investigated in the field of anatomy, the function related to the emergence of limb trajectory during dynamic walking has not been revealed. To investigate the role of the interlocking mechanism, we developed a robot model imitating the muscle-tendon arrangement and the dynamics of a horse hindlimb. In the walking experiment, the robot autonomously generated a limb trajectory with a smooth transition between the swing phase and the stance phase by simply swinging the hip joint with sinusoidal input. Moreover, we compared the joint angles between successful and failed walking. The compared results indicate that the extension of the fetlock joint after hoof touchdown plays the crucial role in emergence of a function of supporting body.

In this paper, we propose a new kind of tripedal locomotion-namely, robotic walking with three legs. We develop a prototype robot, which we call Martian III, having three stretchable legs fixed to each other at the center of the body. Therefore the coxa (the hip joint) is completely fixed in this robot, and the only control we have are the linear actuators to stretch the three legs in the radial directions. The robot is developed as a minimal model to examine our basic idea, to make the robot swing by actuating the legs and then generate locomotion utilizing geometric effect of rigid body rolling on a flat floor. The experiments with robot succeeds in forwarding and rotary locomotion with appropriate choices of oscillatory along each leg. Further analysis of the movement of Martian III indicates that the direction of the swing leg depends on the deformation of each leg. Moreover, due to the result of the measurement experiment and movement analysis of rotation locomotion, we found out two typical type of gaits.

Cylinders exhibits characteristic dynamic behavior such as rolling with lateral-side or edges. In this paper, we propose a new type of rolling mobile robot with cylindrical aspect, which performs two contrastive modes of motion due to the geometry of its shape. In the first mode called lateral-side rolling, the robot is statically stable except few degree of freedom, whereas the robot is only dynamically stable in the other mode (called edge-rolling) and has potential of high mobility. In this work, we attempt to control this robot using an eccentric rotor without gyroscope and applying linear or nonlinear control theory.

This paper is concerned with realization of a new kind of three-legged walking machine. The proposed robot has neither coxa joint nor knee joint, so the three legs are just rigidly fixed to each other. Instead of pursuing elaborated joint mechanism for the coxa, we equipped it with two actuators and a pair of weights, so that it can generate torque about the yaw and the pitch axes. Thus it only rocks as a reaction of the mass driving unit. We show that, by appropriate choices of oscillatory controls (i.e., amplitudes, frequencies and phases of the pitch and the yaw actuators), it is indeed possible to achieve rotation and forwarding locomotion of the tripedal robot. In particular, combination of the frequencies selects the rotation/forwarding, while combination of the phases affects the direction of forwarding. We also remark that the realized motion naturally reflects the symmetry of the body structure.

Much attention has been paid to passive dynamic walking as an approach to investigate the walking of human beings and animals. As for quadrupedal passive dynamic walking, it is confirmed that walking resembles that of animals, and that the gait of the robot changes depending on the structure of robot or the environment. Based on these facts, it is conceivable that quadrupedal passive dynamic walking is related to walking of animals, and the walking principle is inherent in passive dynamic walking. In this research, we approach the walking principle through realization of a walking on the level ground by rational-energy input and investigation how gait changes depending on the input. In this paper, a quadrupedal quasi-passive dynamic walking robot named Duke has been developed by applying passive dynamic walking. This robot has only two rolling actuators, which simply provide with rocking motion and not drive the knee or hip joint directly. We conduct walking experiments by Duke with various inputs, and observe its gaits. As a result of walking experiments, it was verified that walking speed was related to the frequency and the phase difference of rocking motion. In addition, through analysis of a shape of soles, we revealed Duke has a nonholonomic constraint that is comparable to that of “two-wheeled robot” on its sole. As a result of analyses based on the nonlinear control theory, we conclude that the sole shape contributes to the transition of walking speed accompanying with change of a phase difference.

Human is capable of adaptive and supple locomotion in the real world characterized by rapid changes, high uncertainly, and limited availability of information. In order to understand the human walking, this work was motivated by the concept of passive dynamic walking robots, which have no actuation or control system except for gravity are capable of stable, human-looking walking. On the other hand, human can produce a stepping motion not only depend on the legs, but also the rotation of the Center of Mass, arm-swing, the motion of the torso and so on. In this paper, a three dimensional quasi-passive dynamic walking provoked by rocking motion in lateral plane has been investigated. The behavioral analyses with the robot experiments show that this robot can walk on a flat ground and a gait speed is related to the period of lateral rocking.

In this paper, we propose a new approach to the locomotion control of the trident snake robot, focusing on its ¿double-linked¿ case where the robot is composed of a triangular body and three branches of double-linked snakelike legs. Originally, this robot was proposed by the authors as a novel example of nonholonomic mobile robot. This robot is quite interesting from a theoretical point of view; the well-known LARC (Lie Algebra Rank Condition) for its nonlinear controllability has a unique structure that it contains two `generator' vector-fields and higher order Lie brackets, which makes its control problem extremely challenging. In this paper, for this difficult control problem, we first propose a design algorithm which partially achieves the desired locomotion. Then we discover that the resulting motion may or may not be a stable limit cycle, depending on the eigenvalues of the corresponding discrete-time dynamics on its Poincare¿ map. Finally, we propose a full controller design by combining the stable limit cycles. The validity of the proposed idea is examined by numerical simulations.

In this paper, we propose a new example of non-holonomic mobile robot, which we call the surface walker. This robot is composed of a hemisphere-shaped shell and a 2-d.o.f. mass-control device (pendulum) inside it, and undergoes the rolling contact constraint between the hemispherical surface of the robot and the ground. Unlike a lot of non-holonomic robots which have ever been researched, the drift term exists in the system of the hemisphere robot. First, we show basic concepts which the hemisphere robot has, and construct the kinetic model of this robot. Then we realize the locomotion control of the robot by periodically oscillating the internal pendulum and show its effectiveness by control experiments.

In this paper, we propose a new dynamical model of a spherical multi-degree-of-freedom (DOF) ultrasonic motor (USM) and its fundamental control method based on nonholonomic mechanics. This system is analogous to the so-called rolling sphere manipulation system as far as the kinematics is concerned, but there is also an indispensable influence of the momentum dynamics. We propose multi-cycle phase switching (MCPS) method to keep this influence under control, using only two pieces of piezoelectric oscillators for bending vibrations rather than three including a longitudinal vibration as required in the conventional methods.

This paper deals with the ball-plate manipulation problem considered as a typical but complicated model of a driftless nonholonomic system. Due to a strong nonlinearity of the ball-plate system, a state equation of the kinematic model cannot be transformed into a chained form, which is known to be effective in constructing a feedback control law for some driftless nonholonomic systems. To address this problem, we utilize a time-state control form, a kind of canonical form which covers a broader class of systems than the chained form. This form is first applied to two separate subproblems, position control, in which the planar position of the ball is controlled but not the orientation, and orientation control, in which the orientation is controlled without changing the positional relation between the ball and the plates. It turns out that there exists a linearly uncontrollable subspace in the transformed subsystem, which turns into controllable by a change of coordinates. This implies that the system has the structure of a system with two generators. We propose a control strategy using iterative changes of coordinates, ensuring convergence in the neighborhood of the origin. Finally, we unify the subproblems into simultaneous control of position and orientation, i.e., the whole configuration of the system. The important idea in the simultaneous control is the coordinate transformation, which enables us to avoid a singular point. Results of simulations show that the proposed method achieve robustness to a measurement noise and perturbation of radius of the ball.

Proposes a classification of nonholonomic systems from a viewpoint of classical mechanics as well as nonlinear control theory. We clarify this connection by recalling our previous results (1998) that the asymptotic stabilizability of the target equilibrium holds only if the dimension of the equilibria set is equal to the number of control inputs. We summarize a lot of nonholonomic control problems by relating their equilibria set and the numbers of control inputs, their mechanical properties (nonintegrability of constraints) and the existing control strategies proposed in recent years.

MOTIVATION: Automatic extraction of motifs that occur frequently on a set of unaligned DNA sequences is useful for predicting the binding sites of unknown transcription factors. Several programs for this purpose have been released. However, in our opinion, they are not practical enough to be applied to a large number of upstream sequences. RESULTS: We propose a new program called YEBIS (Yet another Environment for the analysis of BIopolymer Sequences) which is capable of extracting a set of motifs, without any a priori knowledge, from a number of functionally related DNA sequences. Using the hidden Markov model, these motifs are represented in a more general form than other conventional methods, such as the weight matrix method. When applied to several sets of benchmark data, it was found that YEBIS had comparable capability to the existing methods, but was much faster. Moreover, it could extract all known motifs from the LTR sequences (long terminal repeat sequences) in a single run. Finally, it could be successfully applied to approximately 400 human promoter sequences and some of the extracted motifs turned out to be known cis-elements. Therefore, YEBIS could be a practical tool for exploring the upstream sequences of genomic ORFs, some of which are regulated in a similar fashion. AVAILABILITY: YEBIS will be distributed to academic users free of charge. All requests should be sent to the address below. CONTACT: E-MAIL: [email protected]

MOTIVATION: Since the protein structure database has been growing very rapidly in recent years, the development of efficient methods for searching for similar structures is very important. RESULTS: This paper presents a novel method for searching for similar fragments of proteins. In this method, a hash vector (a vector of real numbers) is associated with each fixed-length fragment of three-dimensional protein structure. Each vector consists of low-frequency components of the Fourier-like spectrum for the distances between C alpha atoms and the centroid. Then, we can analyze the similarity between fragments by evaluating the difference between hash vectors. The novel aspect of the method is that the following property is proved theoretically: if the root mean square distance between two fragments is small, then the distance between the hash vectors is small. Several variants of this method were compared with a naive method and a previous method using PDB data. The results show that the fastest one among the variants is 18-80 times faster than the naive method, and 3-10 times faster than the previous method.

This paper investigates the position estimation of wheeled mobile robots governed by nonholonomic constraints. Using time-scale transformation and a proper choice of state variables, the problem is formulated as state estimation of nonlinear SISO systems. To deal with this problem, we construct the nonlinear observers via Lyapunov's direct method. Simulation results are also provided.

Multiple sequence alignment is an important problem in the biosciences. To date, most multiple alignment systems have employed a tree-based algorithm, which combines the results of two-way dynamic programming in a tree-like order of sequence similarity. The alignment quality is not, however, high enough when the sequence similarity is low. Once an error occurs in the alignment process, that error can never be corrected. Recently, an effective new class of algorithms has been developed. These algorithms iteratively apply dynamic programming to partially aligned sequences to improve their alignment quality. The iteration corrects any errors that may have occurred in the alignment process. Such an iterative strategy requires heuristic search methods to solve practical alignment problems. Incorporating such methods yields various iterative algorithms. This paper reports our comprehensive comparison of iterative algorithms. We proved that performance improves remarkably when using a tree-based iterative method, which iteratively refines an alignment whenever two subalignments are merged in a tree-based way. We propose a tree-dependent, restricted partitioning technique to efficiently reduce the execution time of iterative algorithms.

A multiple alignment methodology that can produce high-quality alignment is extremely important for predicting the structure of unknown proteins. Nearly all the methodologies developed so far have employed two-way alignment only. Although these methods are fast, the alignments they produce lose reliability as the similarity of sequences reduces. We developed the MASCOT multiple alignment system. MASCOT can sustain the reliability of alignment even when the similarity of sequences is low. MASCOT achieves high-quality alignment by employing three-way alignment in addition to two-way alignment. The resultant alignments are refined by simulated annealing to higher quality. We also use a cluster analysis of sequences to produce highly reliable alignments.

We have developed simulated annealing algorithms to solve the problem of multiple sequence alignment. The algorithm was shown to give the optimal solution as confirmed by the rigorous dynamic programming algorithm for three-sequence alignment. To overcome long execution times for simulated annealing, we utilized a parallel computer. A sequential algorithm, a simple parallel algorithm and the temperature parallel algorithm were tested on a problem. The results were compared with the result obtained by a conventional tree-based algorithm where alignments were merged by two-way dynamic programming. Every annealing algorithm produced a better energy value than the conventional algorithm. The best energy value, which probably represents the optimal solution, was reached within a reasonable time by both of the parallel annealing algorithms. We consider the temperature parallel algorithm of simulated annealing to be the most suitable for finding the optimal multiple sequence alignment because the algorithm does not require any scheduling for optimization. The algorithm is also useful for refining multiple alignments obtained by other heuristic methods.