Applied Mathematics to Mechanisms and Machines

This book brings together all 16 articles published in the Special Issue "Applied Mathematics to Mechanisms and Machines" of the MDPI Mathematics journal, in the section “Engineering Mathematics”. The subject matter covered by these works is varied, but they all have mechanisms as the object of study and mathematics as the basis of the methodology used. In fact, the synthesis, design and optimization of mechanisms, robotics, automotives, maintenance 4.0, machine vibrations, control, biomechanics and medical devices are among the topics covered in this book. This volume may be of interest to all who work in the field of mechanism and machine science and we hope that it will contribute to the development of both mechanical engineering and applied mathematics

Cooperative Perception for Social Driving in Connected Vehicle Traffic

The development of autonomous vehicle technology has moved to the center of automotive research in recent decades. In the foreseeable future, road vehicles at all levels of automation and connectivity will be required to operate safely in a hybrid traffic where human operated vehicles (HOVs) and fully and semi-autonomous vehicles (AVs) coexist. Having an accurate and reliable perception of the road is an important requirement for achieving this objective. This dissertation addresses some of the associated challenges via developing a human-like social driver model and devising a decentralized cooperative perception framework. A human-like driver model can aid the development of AVs by building an understanding of interactions among human drivers and AVs in a hybrid traffic, therefore facilitating an efficient and safe integration. The presented social driver model categorizes and defines the driver\u27s psychological decision factors in mathematical representations (target force, object force, and lane force). A model predictive control (MPC) is then employed for the motion planning by evaluating the prevailing social forces and considering the kinematics of the controlled vehicle as well as other operating constraints to ensure a safe maneuver in a way that mimics the predictive nature of the human driver\u27s decision making process. A hierarchical model predictive control structure is also proposed, where an additional upper level controller aggregates the social forces over a longer prediction horizon upon the availability of an extended perception of the upcoming traffic via vehicular networking. Based on the prediction of the upper level controller, a sequence of reference lanes is passed to a lower level controller to track while avoiding local obstacles. This hierarchical scheme helps reduce unnecessary lane changes resulting in smoother maneuvers. The dynamic vehicular communication environment requires a robust framework that must consistently evaluate and exploit the set of communicated information for the purpose of improving the perception of a participating vehicle beyond the limitations. This dissertation presents a decentralized cooperative perception framework that considers uncertainties in traffic measurements and allows scalability (for various settings of traffic density, participation rate, etc.). The framework utilizes a Bhattacharyya distance filter (BDF) for data association and a fast covariance intersection fusion scheme (FCI) for the data fusion processes. The conservatism of the covariance intersection fusion scheme is investigated in comparison to the traditional Kalman filter (KF), and two different fusion architectures: sensor-to-sensor and sensor-to-system track fusion are evaluated. The performance of the overall proposed framework is demonstrated via Monte Carlo simulations with a set of empirical communications models and traffic microsimulations where each connected vehicle asynchronously broadcasts its local perception consisting of estimates of the motion states of self and neighboring vehicles along with the corresponding uncertainty measures of the estimates. The evaluated framework includes a vehicle-to-vehicle (V2V) communication model that considers intermittent communications as well as a model that takes into account dynamic changes in an individual vehicle’s sensors’ FoV in accordance with the prevailing traffic conditions. The results show the presence of optimality in participation rate, where increasing participation rate beyond a certain level adversely affects the delay in packet delivery and the computational complexity in data association and fusion processes increase without a significant improvement in the achieved accuracy via the cooperative perception. In a highly dense traffic environment, the vehicular network can often be congested leading to limited bandwidth availability at high participation rates of the connected vehicles in the cooperative perception scheme. To alleviate the bandwidth utilization issues, an information-value discriminating networking scheme is proposed, where each sender broadcasts selectively chosen perception data based on the novelty-value of information. The potential benefits of these approaches include, but are not limited to, the reduction of bandwidth bottle-necking and the minimization of the computational cost of data association and fusion post processing of the shared perception data at receiving nodes. It is argued that the proposed information-value discriminating communication scheme can alleviate these adverse effects without sacrificing the fidelity of the perception

Bioinformatic analysis and deep learning on large-scale human transcriptomic data: studies on aging, Alzheimer’s neurodegeneration and cancer

[ES] El objetivo general del proyecto ha sido el análisis bioinformático integrativo de datos múltiples de proteómica y genómica combinados con datos clínicos asociados para la búsqueda de biomarcadores y módulos poligénicos causales aplicado a enfermedades complejas; principalmente, cáncer de origen primario desconocido, en sus distintos tipos y subtipos y enfermedades neurodegenerativas (ND) mayormente Alzheimer, además de neurodegeneración debida a la edad. Además, se ha hecho un uso intensivo de técnicas de inteligencia artificial, más en concreto de técnicas de redes neuronales de aprendizaje profundo para el análisis y pronóstico de dichas enfermedades

Vibration, Control and Stability of Dynamical Systems

From Preface: This is the fourteenth time when the conference “Dynamical Systems: Theory and Applications” gathers a numerous group of outstanding scientists and engineers, who deal with widely understood problems of theoretical and applied dynamics. Organization of the conference would not have been possible without a great effort of the staff of the Department of Automation, Biomechanics and Mechatronics. The patronage over the conference has been taken by the Committee of Mechanics of the Polish Academy of Sciences and Ministry of Science and Higher Education of Poland. It is a great pleasure that our invitation has been accepted by recording in the history of our conference number of people, including good colleagues and friends as well as a large group of researchers and scientists, who decided to participate in the conference for the first time. With proud and satisfaction we welcomed over 180 persons from 31 countries all over the world. They decided to share the results of their research and many years experiences in a discipline of dynamical systems by submitting many very interesting papers. This year, the DSTA Conference Proceedings were split into three volumes entitled “Dynamical Systems” with respective subtitles: Vibration, Control and Stability of Dynamical Systems; Mathematical and Numerical Aspects of Dynamical System Analysis and Engineering Dynamics and Life Sciences. Additionally, there will be also published two volumes of Springer Proceedings in Mathematics and Statistics entitled “Dynamical Systems in Theoretical Perspective” and “Dynamical Systems in Applications”

How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study Using N-Myristoyltransferases as a Model System

Under embargo until: 2020-08-19A model system of two related enzymes with conserved binding sites, namely N-myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. Using a combination of computational and experimental tools, two different selectivity-determining features were identified. For some ligands, a change in side-chain flexibility appears to be responsible for selective inhibition. Remarkably, this was observed for residues orienting their side chains away from the ligands. For other ligands, selectivity is caused by interfering with a water molecule that binds more strongly to the off-target than to the target. On the basis of this finding, a virtual screen for selective compounds was conducted, resulting in three hit compounds with the desired selectivity profile. This study delivers a guideline on how to assess selectivity-determining features in proteins with conserved binding sites and to translate this knowledge into the design of selective inhibitors.acceptedVersio

Mechatronic Systems

Mechatronics, the synergistic blend of mechanics, electronics, and computer science, has evolved over the past twenty five years, leading to a novel stage of engineering design. By integrating the best design practices with the most advanced technologies, mechatronics aims at realizing high-quality products, guaranteeing at the same time a substantial reduction of time and costs of manufacturing. Mechatronic systems are manifold and range from machine components, motion generators, and power producing machines to more complex devices, such as robotic systems and transportation vehicles. With its twenty chapters, which collect contributions from many researchers worldwide, this book provides an excellent survey of recent work in the field of mechatronics with applications in various fields, like robotics, medical and assistive technology, human-machine interaction, unmanned vehicles, manufacturing, and education. We would like to thank all the authors who have invested a great deal of time to write such interesting chapters, which we are sure will be valuable to the readers. Chapters 1 to 6 deal with applications of mechatronics for the development of robotic systems. Medical and assistive technologies and human-machine interaction systems are the topic of chapters 7 to 13.Chapters 14 and 15 concern mechatronic systems for autonomous vehicles. Chapters 16-19 deal with mechatronics in manufacturing contexts. Chapter 20 concludes the book, describing a method for the installation of mechatronics education in schools

Development of an active vision system for robot inspection of complex objects

Dissertação de mestrado integrado em Engenharia Mecânica (área de especialização em Sistemas Mecatrónicos)The dissertation presented here is in the scope of the IntVis4Insp project between University of Minho and the company Neadvance. It focuses on the development of a 3D hand tracking system that must be capable of extracting the hand position and orientation to prepare a manipulator for automatic inspection of leather pieces. This work starts with a literature review about the two main methods for collecting the necessary data to perform 3D hand tracking. These divide into glove-based methods and vision-based methods. The first ones work with some kind of support mounted on the hand that holds all the necessary sensors to measure the desired parameters. While the second ones recur to one or more cameras to capture the hands and through computer vision algorithms track their position and configuration. The selected method for this work was the vision-based method Openpose. For each recorded image, this application can locate 21 hand keypoints on each hand that together form a skeleton of the hands. This application is used in the tracking system developed throughout this dissertation. Its information is used in a more complete pipeline where the location of those hand keypoints is crucial to track the hands in videos of the demonstrated movements. These videos were recorded with an RGB-D camera, the Microsoft Kinect, which provides a depth value for every RGB pixel recorded. With the depth information and the 2D location of the hand keypoints in the images, it was possible to obtain the 3D world coordinates of these points considering the pinhole camera model. To define the hand, position a point is selected among the 21 for each hand, but for the hand orientation, it was necessary to develop an auxiliary method called “Iterative Pose Estimation Method” (ITP), which estimates the complete 3D pose of the hands. This method recurs only to the 2D locations of every hand keypoint, and the complete 3D world coordinates of the wrists to estimate the right 3D world coordinates of all the remaining points on the hand. This solution solves the problems related to hand occlusions that a prone to happen due to the use of only one camera to record the inspection videos. Once the world location of all the points in the hands is accurately estimated, their orientation can be defined by selecting three points forming a plane.A dissertação aqui apresentada insere-se no âmbito do projeto IntVis4Insp entre a Universidade do Minho e a empresa Neadavance, e foca-se no desenvolvimento de um sistema para extração da posição e orientação das mãos no espaço para posterior auxílio na manipulação automática de peças de couro, com recurso a manipuladores robóticos. O trabalho inicia-se com uma revisão literária sobre os dois principais métodos existentes para efetuar a recolha de dados necessária à monitorização da posição e orientação das mãos ao longo do tempo. Estes dividem-se em métodos baseados em luvas ou visão. No caso dos primeiros, estes recorrem normalmente a algum tipo de suporte montado na mão (ex.: luva em tecido), onde estão instalados todos os sensores necessários para a medição dos parâmetros desejados. Relativamente a sistemas de visão estes recorrem a uma câmara ou conjunto delas para capturar as mãos e por via de algoritmos de visão por computador determinam a sua posição e configuração. Foi selecionado para este trabalho um algoritmo de visão por computador denominado por Openpose. Este é capaz de, em cada imagem gravada e para cada mão, localizar 21 pontos pertencentes ao seu esqueleto. Esta aplicação é inserida no sistema de monitorização desenvolvido, sendo utilizada a sua informação numa arquitetura mais completa onde é efetuada a extração da localização dos pontos chave de cada mão nos vídeos de demonstração dos movimentos de inspeção. A gravação destes vídeos é efetuada com uma câmara RGB-D, a Microsoft Kinect, que fornece um valor de profundidade para cada pixel RGB gravado. Com os dados de profundidade e a localização dos pontos chave nas imagens foi possível obter as coordenadas 3D no mundo destes pontos considerando o modelo pinhole para a câmara. No caso da posição da mão é selecionado um ponto de entre os 21 para a definir ao longo do tempo, no entanto, para o cálculo da orientação foi desenvolvido um método auxiliar para estimação da pose tridimensional da mão denominado por “Iterative Pose Estimation Method” (ITP). Este método recorre aos dados 2D do Openpose e às coordenadas 3D do pulso de cada mão para efetuar a correta estimação das coordenadas 3D dos restantes pontos da mão. Isto permite essencialmente resolver problemas com oclusões da mão, muito frequentes com o uso de uma só câmara na gravação dos vídeos. Uma vez estimada corretamente a posição 3D no mundo dos vários pontos da mão, a sua orientação pode ser definida com recurso a quaisquer três pontos que definam um plano

Differential Models, Numerical Simulations and Applications

This Special Issue includes 12 high-quality articles containing original research findings in the fields of differential and integro-differential models, numerical methods and efficient algorithms for parameter estimation in inverse problems, with applications to biology, biomedicine, land degradation, traffic flows problems, and manufacturing systems

Multicellular Systems Biology of Development

Embryonic development depends on the precise coordination of cell fate specification, patterning and morphogenesis. Although great strides have been made in the molecular understanding of each of these processes, how their interplay governs the formation of complex tissues remains poorly understood. New techniques for experimental manipulation and image quantification enable the study of development in unprecedented detail, resulting in new hypotheses on the interactions between known components. By expressing these hypotheses in terms of rules and equations, computational modeling and simulation allows one to test their consistency against experimental data. However, new computational methods are required to represent and integrate the network of interactions between gene regulation, signaling and biomechanics that extend over the molecular, cellular and tissue scales. In this thesis, I present a framework that facilitates computational modeling of multiscale multicellular systems and apply it to investigate pancreatic development and the formation of vascular networks. This framework is based on the integration of discrete cell-based models with continuous models for intracellular regulation and intercellular signaling. Specifically, gene regulatory networks are represented by differential equations to analyze cell fate regulation; interactions and distributions of signaling molecules are modeled by reaction-diffusion systems to study pattern formation; and cell-cell interactions are represented in cell-based models to investigate morphogenetic processes. A cell-centered approach is adopted that facilitates the integration of processes across the scales and simultaneously constrains model complexity. The computational methods that are required for this modeling framework have been implemented in the software platform Morpheus. This modeling and simulation environment enables the development, execution and analysis of multi-scale models of multicellular systems. These models are represented in a new domain-specific markup language that separates the biological model from the computational methods and facilitates model storage and exchange. Together with a user-friendly graphical interface, Morpheus enables computational modeling of complex developmental processes without programming and thereby widens its accessibility for biologists. To demonstrate the applicability of the framework to problems in developmental biology, two case studies are presented that address different aspects of the interplay between cell fate specification, patterning and morphogenesis. In the first, I focus on the interplay between cell fate stability and intercellular signaling. Specifically, two studies are presented that investigate how mechanisms of cell-cell communication affect cell fate regulation and spatial patterning in the pancreatic epithelium. Using bifurcation analysis and simulations of spatially coupled differential equations, it is shown that intercellular communication results in a multistability of gene expression states that can explain the scattered spatial distribution and low cell type ratio of nascent islet cells. Moreover, model analysis shows that disruption of intercellular communication induces a transition between gene expression states that can explain observations of in vitro transdifferentiation from adult acinar cells into new islet cells. These results emphasize the role of the multicellular context in cell fate regulation during development and may be used to optimize protocols for cellular reprogramming. The second case study focuses on the feedback between patterning and morphogenesis in the context of the formation of vascular networks. Integrating a cell-based model of endothelial chemotaxis with a reaction-diffusion model representing signaling molecules and extracellular matrix, it is shown that vascular network patterns with realistic morphometry can arise when signaling factors are retained by cell-modified matrix molecules. Through the validation of this model using in vitro assays, quantitative estimates are obtained for kinetic parameters that, when used in quantitative model simulations, confirm the formation of vascular networks under measured biophysical conditions. These results demonstrate the key role of the extracellular matrix in providing spatial guidance cues, a fact that may be exploited to enhance vascularization of engineered tissues. Together, the modeling framework, software platform and case studies presented in this thesis demonstrate how cell-centered computational modeling of multi-scale and multicellular systems provide powerful tools to help disentangle the complex interplay between cell fate specification, patterning and morphogenesis during embryonic development