Mikel Diez

A Kinematic Approach to Calculate Protein Motion Paths

Proteins play an essential role in biochemical processes. Recently, a new viewpoint has arisen within protein researches, based on the parallelisms between proteins and mechanism. In this paper the authors present a new approach to obtain protein motion paths based in computational kinematic considerations. Finally, simulation results for an specific protein are presented.

Protein Kinematic Motion Simulation Including Potential Energy Feedback

In this article a methodology for simulating proteins function movement is presented. The procedure uses a potential energy feedback algorithm that without minizing the energy obtains succesive positions of the protein. before the simulation process, structures are normalized reducing the experimental methods produced errors. The procedure presents a low computational cost in relation to the accuracy obtained. Finally, results of the simulation for a specific protein are shown.

Kinematic Analysis of a Flexible Tensegrity Robot

In the field of parallel kinematics few designs use highly deformable elements to obtain the end effector movement. Most compliant mechanisms rely on notches or shape changes to simulate a standard kinematic joint. In this work a kinematic model of a simple parallel continuum mechanism that combines a deformable element and cable is presented. The kinematic model is used to study the workspace of the manipulator and is validated by experimental measurements of a prototype.

Protein Secondary Structure Detection Using Dihedral Angle Parameters Evaluation

The detection of proteins secondary structures constitutes an essential task in the protein motion simulation. Secondary structures constitute rigid parts of the protein structure, hence, their detection is crucial so as to properly define the movement of the protein. During the simulation process, these rigid structures can be identified and, accordingly, their associated degrees of freedom are neglected. As a consequence, the computational cost is reduced. Current methods existing in the literature are based on the analysis of geometrical parameters distribution, such as \( C\alpha \) atoms distribution, and hydrogen bonds detection. These methods require specific procedures, independent of the simulation process, to determine these geometrical parameters, thereby increasing the computational cost. In this paper, a novel method for protein secondary structure detection is presented. This new method relies only on the evaluation of dihedral angles so as to detect the existence of secondary structures. The use of dihedral angles, which have been already evaluated during the simulation process, does not increase the computational cost of the simulation process.

Kinematic Analysis of Planar Mechanisms by Means of Examples

The aim of this work is to approach the difficulties students usually encounter when facing up to kinematic analysis of mechanisms. A deep understanding of the kinematic analysis is necessary to go a step further into design and synthesis of mechanisms. We can conclude from experience that supporting and complementing the theoretical lectures with specific software is really helpful. In this sense, software is used during the practical exercises, serving as an educational complementary tool reinforcing the knowledge acquired by the students. Several questions are outlined to the students, so that they are encouraged to justify the validity of their results. GIM software performs kinematic analysis and motion simulation of planar mechanisms. The main capacities of the software are: solving the position problem, computing velocities and accelerations, singular analysis, and visualization of instantaneous center of rotation, acceleration pole, curvature center and circle, fixed and moving centrodes and main circles. The graphical representation of all results favors the learning of the theoretical concepts explained in the subject and also, stimulates the critical reasoning the students must acquire.

Insights into mechanism kinematics for protein motion simulation

BackgroundThe high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein’s movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost.ResultsIn this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion.ConclusionsThe procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

Kinematic Analysis of a Continuum Parallel Robot

Continuum Parallel Robots are mechanical devices with closed loops where kinematic pairs have been eliminated and motion is obtained by large deformations of certain elements. Most compliant mechanisms use notches in thick elements to produce the effect of kinematic pairs. A few are designed so that slender elements can deform and produce the desired motion. Some microelectromechanical systems have used this principle to create bistable planar mechanisms. The purpose of this work is to extend such principle in the field of macro mechanisms for manipulation. The aim is to design the counterparts to some classical parallel manipulators solving the corresponding kinematic problems. In doing this, the authors will have to work out the most efficient way to solve a position problem where geometry and forces are involved. Such compliant mechanisms could be combined in the future with tensegrity systems to enhance the available workspace. In this first report we will focus on the simplest planar parallel mechanism of two degrees of freedom.

Side Chain Kinematics Simulation on Protein Conformational Changes

Protein simulation remains as one of the most difficult task for biologists, physicists or engineers. The huge computational requirements of the protein models makes it difficult to obtain simulations of big conformational changes on protein structure. Side chain modelization is a critical step when obtaining the protein structure model. The time scale at which side chain movement occur can greatly increase the computational cost of the process. In this paper, we propose a side chain orientation procedure with a very low computational cost. This procedure has been implemented in combination with other procedures to obtain a computationally efficient simulation tool for protein simulation. This simulation tool has been used to simulate several protein conformational changes with success.

Educational and Research Kinematic Capabilities of GIM Software

In this paper an educational and research software named GIM is presented. This software has been developed with the aim of approaching the difficulties students usually encounter when facing up to kinematic analysis of mechanisms. A deep understanding of the kinematic analysis is necessary to go a step further into design and synthesis of mechanisms. In order to support and complement the theoretical lectures, GIM software is used during the practical exercises, serving as an educational complementary tool reinforcing the knowledge acquired by the students.

Protein Motion Simulation Algorithm for Dihedral Angle Rotation Implementing Variable Speed

Most methodologies used for protein motion simulation either require a high computational cost, or the produced results do not fulfill kinematics requirements. For instance, molecular dynamics, which obtains the most accurate results, is hardly used to simulate proteins’ big conformational changes because of its huge computational requirements. Faster simulation methods, like interpolation procedures, do not produce realistic intermediate positions, mostly because of impossible kinematics between consecutive positions of the motion. In this paper, a new procedure is presented which simulates protein motion with affordable computational requirements. The procedure uses dihedral angle increments to produce the protein motion avoiding any energy minimization process. The kinematic model used for the protein structure is based on the ball and rods approach and is further refined by a normalization method to reduce experimental methods induced errors.