Insights into mechanism kinematics for protein motion simulation

Background: The 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. Results: In 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. Conclusions: The 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.The authors wish to acknowledge the financial support received from the Spanish Government through the Ministerio de Economia y Competitividad (Project DPI2011-22955), the Regional Government of the Basque Country through the Departamento de Educacion, Universidades e Investigacion (Project IT445-10) and UPV/EHU under program UFI 11/29 and by Grants from the Department of Education, Universities and Research of the Basque Government (PI2010-17), from the Department of Industry of the Basque Government (ETORTEK Program IE05-147 and IE07-202), from the Bizkaia Country (Exp. 7/13/08/2006/11 and 7/13/08/2005/14), and from the Spanish Ministry of Economy and Innovation (BFU2010-17857 and SICI-CONSOLIDER Program CSD2008-00005) (all to L.A.M.-C.)

Improving Skills in Mechanism and Machine Science Using GIM Software

The field of education has evolved significantly in recent years as it has incorporated new pedagogical methodologies. Many of these methodologies are designed to encourage students’ participation in the learning process. The traditional role of the student as a passive receiver of content is no longer considered valid. Teaching in mechanical engineering is no stranger to these changes either, where new learning activities have been designed to complement theory-heavy lectures. These activities take place in both physical and virtual laboratories. In case of the latter, the use of the GIM software (developed at the Department of Mechanical Engineering of the University of the Basque Country UPV/EHU, Spain) is a promising option. In this paper, features of the GIM that are most frequently used to support and exemplify the theoretical concepts taught in lectures are described using a case study. In addition, GIM is integrated into different learning activities to show its potential as a tool for learning and self-evaluation.This research was funded by Ministerio de Economía y Competitividad, Spanish Government Project, MINECO/FEDER, UE (grant number DPI2015-67626-P), Departamento de Educación, Política Lingüística y Cultura, Regional Government of the Basque Country (grant number IT949-16) and University of the Basque Country UPV/EHU (grant number PIE2012/14)

Kinematic Analysis of a Tendon-Driven Hybrid Rigid–Flexible Four-Bar; Application to Optimum Dimensional Synthesis

In design matters, mechanisms with deformable elements are a step behind those with rigid bars, particularly if dimensional synthesis is considered a fundamental part of mechanism design. For the purposes of this work, a hybrid rigid–flexible four-bar mechanism has been chosen, the input bar being a continuum tendon of constant curvature. The coupler curves are noticeably more complex but offer more possibilities than the classical rigid four-bar counterpart. One of the objectives of this work is to completely characterize the coupler curves of this hybrid rigid–flexible mechanism, determining the number and type of circuits as well as constituent branches. Another important aim is to apply optimization techniques to the dimensional synthesis of path generation. Considerable progress in finding the best design solutions can be obtained if all the acquired knowledge about the coupler curves of this hybrid mechanism is integrated into the optimization algorithm.This research was funded by the Spanish government through the Ministerio de Ciencia e Innovación (Project PID2020-116176GB-I00), financed by MCIN/AEI/10.13039/501100011033, and funded by the Departamento de Educación from the Regional Basque Government through Project IT1480-22

Parallel manipulators: practical applications and kinematic design criteria. Towards the modular reconfigurable robots

Post-PrintModern robotic manipulators play an essential role in industry, developing several tasks in an easy way, enhancing the accuracy of the final product and reducing the executing time. Also they can be found in other fields as aerospace industry, several medical applications, gaming industry, and so on. In particular, the parallel manipulators have acquired a great relevance in the last years. Indeed, many research activities and projects deal with the study and develop-ment of this type of robots. Nevertheless, usually, a bilateral communication between industry and research does not exist, even among the different existing research areas. This causes a lack of knowledge regarding works that have been carried out, the ones that are under devel-opment and the possible future investigations. Hence, once a specific field of knowledge has acquired a certain level of maturity, it is convenient to reflect its current state of the art. In this sense, the authors of this paper present a review of the different fields in which parallel ma-nipulators have a significant participation, and also the most active research topics in the anal-ysis and design of these robots. Besides, several contributions of the authors to this field are cited.The authors wish to acknowledge the financial support received from the Spanish Government through the "Ministerio de Economía y Competitividad" (Project DPI2015-67626-P (MINECO/FEDER, UE)), the financial support from the Uni-versity of the Basque Country (UPV/EHU) under the program UFI 11/29 and the support to the research group, through the project with ref. IT949-16, given by the "Departamento de Educación, Política Lingüística y Cultura" of the Regional Government of the Basque Country

Hybrid Optimization Based Mathematical Procedure for Dimensional Synthesis of Slider-Crank Linkage

In this paper, an optimization procedure for path generation synthesis of the slider-crank mechanism will be presented. The proposed approach is based on a hybrid strategy, mixing local and global optimization techniques. Regarding the local optimization scheme, based on the null gradient condition, a novel methodology to solve the resulting non-linear equations is developed. The solving procedure consists of decoupling two subsystems of equations which can be solved separately and following an iterative process. In relation to the global technique, a multi-start method based on a genetic algorithm is implemented. The fitness function incorporated in the genetic algorithm will take as arguments the set of dimensional parameters of the slider-crank mechanism. Several illustrative examples will prove the validity of the proposed optimization methodology, in some cases achieving an even better result compared to mechanisms with a higher number of dimensional parameters, such as the four-bar mechanism or the Watt’s mechanism.The authors wish to acknowledge financial support received from the Spanish government through the Ministerio de Economía y Competitividad (Project DPI2015−67626-P (MINECO/FEDER, UE)), the support for the research group through Project Ref. IT949−16, provided by the Departamento de Educación, Política Lingüística y Cultura from the regional Basque Government, and the Program BIKAINTEK 2020 (Ref. 012-B2/2020) provided by the Departamento de Desarrollo Económico, Sostenibilidad y Medio Ambiente from the regional Basque Government

Translational parallel manipulator with Pa2 kinematic joints

The kinematic pair Pa2 is composed of two interlinked parallelograms. It has two degrees of freedom that generate a translational plane variable with position. It has a structure different from the PaPa pair, which is composed also by two parallelograms but generates a constant translational plane. Currently, the Pa2 pair is used at conceptual level but it is not used in al-most any practical application. There are advantages and drawbacks in using it. The main drawback is the high number of redundant constraints that this pair possesses. However, sub-stituting carefully the revolute joints by spherical joints can eliminate these redundant con-straints. Also, this pair constitutes a more rigid structure that replaces adequately the problem-atic passive prismatic joints. In this paper, will be presented a preliminary study of a translational parallel manipulator (PM) based on the use of the Pa2 pair: the 3-PPa2 that contains redundant constraints in its global structure. To study the potentiality of the PM presented in this paper, the following analyses will be done: position and velocity (direct and inverse kinematics), workspace and singularity analysis. Also the potentiality to be optimised will be studied.This work was supoorted by the Spanish Government through the Ministerio de Economía y Competitividad (Project DPI2015-67626-P (MINECO/FEDER, UE)), the financial support from the University of the Basque Country (UPV/EHU) under the program UFI 11/29 and the support to the research group, through the project with ref. IT949-16, given by the Departamento de Educación, Política Lingüística y Cultura of the Regional Government of the Basque Country

Multioperation capacity of parallel manipulators basing on generic kinematic chain approach

The idea of designing multioperation mechanisms capable of performing different tasks has gained prominence in the last years. These mechanisms, commonly called reconfig- urable mechanisms, have the ability to change their configuration. At present, this type of mechanisms is capturing the attention of design engineers because of their great po- tential in many industrial applications. In this paper, the basis for the development of a methodology intended for the analysis and design of multioperational parallel manipu- lators is presented. First, the structural synthesis of 6 degree-of-freedom (dof) kinematic chains that can form a 6 dof manipulator is established. Next, a general purpose approach for non-redundant parallel manipulators (PM) will be presented. This procedure enables obtaining the Jacobian matrices of any 6 dof or low-mobility PM whose kinematic chains belong to the library of chains derived from the structural synthesis. To demonstrate the versatility of the procedure, it will be applied to three PM: the first one, a 6 dof PM, the second one, a reconfigurable 6 dof PM, and finally, a low-mobility PM.This work was supoorted by the Spanish Government through the Ministerio de Economía y Competitividad (Project DPI2015-67626-P (MINECO/FEDER, UE)), the financial support from the University of the Basque Country (UPV/EHU) un- der the program UFI 11/29 and the support to the research group, through the project with ref. IT949-16 , given by the Departamento de Educación , Política Lingüística y Cultura of the Regional Government of the Basque Country

Developments and results in the context of the JEM-EUSO program obtained with the ESAF simulation and analysis framework

JEM-EUSO is an international program for the development of space-based Ultra-High Energy Cosmic Ray observatories. The program consists of a series of missions which are either under development or in the data analysis phase. All instruments are based on a wide-field-of-view telescope, which operates in the near-UV range, designed to detect the fluorescence light emitted by extensive air showers in the atmosphere. We describe the simulation software ESAF in the framework of the JEM-EUSO program and explain the physical assumptions used. We present here the implementation of the JEM-EUSO, POEMMA, K-EUSO, TUS, Mini-EUSO, EUSO-SPB1 and EUSO-TA configurations in ESAF. For the first time ESAF simulation outputs are compared with experimental data.Comunidad de Madri

Estudio de las proteínas desde una perspectiva biocinemática: estado del arte

Las proteínas son las macromoléculas encargadas de llevar a cabo la gran mayoría de las funciones vitales que los seres vivos requieren para su existencia. Estas macromoléculas, las cuales se asemejan a pequeños mecanismos o robots, fueron descubiertas hace 200 años y observadas en su forma funcional hace menos de 60, y suponen uno de los campos de estudio más prometedores del momento. El ámbito de estudio de las proteínas es increíblemente rico y multidisciplinar, no pudiéndose abordar completamente si no es desde una combinación de la biología y la ingeniería. La investigación actual presenta grandes retos: la complejidad de las fuerzas que gobiernan las uniones atómicas, las cuales todavía estamos comenzando a comprender, y las limitaciones tecnológicas actuales que presentan serios obstáculos a la hora de tratar de comprender mejor el funcionamiento de estos robots de la naturaleza. En este trabajo, se presenta un breve estado del arte de los métodos desarrollados para resolver problemas como el plegado de proteínas o la simulación del mecanismo molecular. El artículo se centra especialmente en aquellos que están más estrechamente relacionados con la ingeniería, pero sin olvidar los métodos clásicos para tratar de comprender un poco mejor el estado actual de la técnica.Los autores desean agradecer el soporte financiero recibido por parte del Gobierno a través del Ministerio de Economía y Competitividad (Proyectos DPI2015-67626-P y DPI2015-64450-R (MINECO/FEDER, UE)) y el apoyo al grupo de investigación, a través del proyecto con Ref. IT949-16, del Departamento de Educación, Política Lingüística y Cultura del Gobierno Vasco