Genetic sequences are being collected at an ever increasing rate due to rapid cost reductions; however, experimental approaches to determine the structure and function of the protein(s) each gene codes are not keeping pace. Therefore, computational methods to augment experimental structures with comparative (i.e. homology) models using physics-based methods for building residues, loops and domains are needed to thread new sequences onto homologous structures. In addition, even experimental structure determination relies on analogous first principles structure refinement and prediction algorithms to place structural elements that are not defined by the data alone. Computational methods developed to find the global free energy minimum of an amino acid sequence (i.e. the protein folding problem) are increasingly successful, but limitations in accuracy and efficiency remain. Optimization efforts have focused on subsets of systems and environments by utilizing potential energy functions ranging from fixed charged force fields (Fiser, Do, & Sali, 2000; Jacobson et al., 2004), statistical or knowledge based potentials (Das & Baker, 2008) and/or potentials incorporating experimental data (Brunger, 2007; Trabuco, Villa, Mitra, Frank, & Schulten, 2008). Although these methods are widely used, limitations include 1) a target function global minimum that does not correspond to the actual free energy minimum and/or 2) search protocols that are inefficient or not deterministic due to rough energy landscapes characterized by large energy barriers between multiple minima. Our Global Optimization Using Metadynamics and a Polarizable Force Field (GONDOLA) approach tackles the first limitation by incorporating experimental data (i.e. from X-ray crystallography, CryoEM or NMR experiments) into a hybrid target function that also includes information from a polarizable molecular mechanics force field (Lopes, Roux, & MacKerell, 2009; Ponder & Case, 2003). The second limitation is overcome by driving the sampling of conformational space by adding a time-dependent bias to the objective function, which pushes the search toward unexplored regions (Alessandro Barducci, Bonomi, & Parrinello, 2011; Zheng, Chen, & Yang, 2008). The GONDOLA approach incorporates additional efficiency constructs for search space exploration that include Monte Carlo moves and fine grained minimization. Furthermore, the dimensionality of the search is reduced by fixing atomic coordinates of known structural regions while atoms of interest explore new coordinate positions. The overall approach can be used for optimization of side-chains (i.e. set side-chain atoms active while constraining backbone atoms), residues (i.e. side-chain atoms and backbone atoms active), ligand binding pose (i.e. set atoms along binding interface active), protein loops (i.e. set atoms connecting two terminating residues active) or even entire protein domains or complexes. Here we focus on using the GONDOLA general free energy driven optimization strategy to elucidate the structural details of missing protein loops, which are often missing from experimental structures due to conformational heterogeneity and/or limitations in the resolution of the data. We first show that the correlation between experimental data and AMOEBA (i.e. a polarizable force field) structural minima is stronger than that for OPLS-AA (i.e. a fixed charge force field). This suggests that the higher order multipoles and polarization of the AMOEBA force field more accurately represented the true crystalline environment than the simpler OPLS-AA model. Thus, scoring and optimization of loops with AMOEBA is more accurate than with OPLS-AA, albeit at a slightly increased computational cost. Next, missing PDZ domain protein loops and protein loops from a loop decoy data set were optimized for 5 ns using the GONDOLA approach (i.e. under the AMOEBA polarizable force field) as well as a commonly used global optimization procedure (i.e. simulated annealing under the OPLS-AA fixed charge force field). The GONDOLA procedure was shown to provide more accurate structures in terms of both experimental metrics (i.e. lower Rfree values) and structural metrics (i.e. using the MolProbity structure validation tool). In terms of Rfree, only one out of seven simulated annealing results was better than the Gondola global optimization. Similarly, one simulated anneal loop had a better MolProbity score, but none of the simulated annealing loops were better in both categories. On average, GONDOLA achieved an Rfree value 19.48 and simulated annealing saw an average Rfree value of 19.63, and the average MolProbity scores were 1.56 for GONDOLA and 1.75 for simulated annealing. In addition to providing more accurate predictions, GONDOLA was shown to converge much faster than the simulated annealing protocol. Ten separate 5 ns optimizations of the 4 residue loop missing from one of the PDZ domains were conducted. Five were done using GONDOLA and five with the simulated annealing protocol. The fastest four converging results belonged to the GONDOLA approach. Thus, this work demonstrates that GONDOLA is well-suited to refine or predict the coordinates of missing residues and loops because it is both more accurate and converges more rapidly.

Current clinical practice regarding upper body prosthesis prescription and training is lacking a standarized, quantitative method to evaluate the impact of the prosthetic device. The amputee care team typically uses prior experiences to provide prescription and training customized for each individual. As a result, it is quite challenging to determine the right type and fit of a prosthesis and provide appropriate training to properly utilize it early in the process. It is also very difficult to anticipate expected and undesired compensatory motions due to reduced degrees of freedom of a prosthesis user. In an effort to address this, a tool was developed to predict and visualize the expected upper limb movements from a prescribed prosthesis and its suitability to the needs of the amputee. It is expected to help clinicians make decisions such as choosing between a body-powered or a myoelectric prosthesis, and whether to include a wrist joint. To generate the motions, a robotics-based model of the upper limbs and torso was created and a weighted least-norm (WLN) inverse kinematics algorithm was used. The WLN assigns a penalty (i.e. the weight) on each joint to create a priority between redundant joints. As a result, certain joints will contribute more to the total motion. Two main criteria were hypothesized to dictate the human motion. The first one was a joint prioritization criterion using a static weighting matrix. Since different joints can be used to move the hand in the same direction, joint priority will select between equivalent joints. The second criterion was to select a range of motion (ROM) for each joint specifically for a task. The assumption was that if the joints' ROM is limited, then all the unnatural postures that still satisfy the task will be excluded from the available solutions solutions. Three sets of static joint prioritization weights were investigated: a set of optimized weights specifically for each task, a general set of static weights optimized for all tasks, and a set of joint absolute average velocity-based weights. Additionally, task joint limits were applied both independently and in conjunction with the static weights to assess the simulated motions they can produce. Using a generalized weighted inverse control scheme to resolve for redundancy, a human-like posture for each specific individual was created. Motion capture (MoCap) data were utilized to generate the weighting matrices required to resolve the kinematic redundancy of the upper limbs. Fourteen able-bodied individuals and eight prosthesis users with a transradial amputation on the left side participated in MoCap sessions. They performed ROM and activities of daily living (ADL) tasks. The methods proposed here incorporate patient's anthropometrics, such as height, limb lengths, and degree of amputation, to create an upper body kinematic model. The model has 23 degrees-of-freedom (DoFs) to reflect a human upper body and it can be adjusted to reflect levels of amputation. The weighting factors resulted from this process showed how joints are prioritized during each task. The physical meaning of the weighting factors is to demonstrate which joints contribute more to the task. Since the motion is distributed differently between able-bodied individuals and prosthesis users, the weighting factors will shift accordingly. This shift highlights the compensatory motion that exist on prosthesis users. The results show that using a set of optimized joint prioritization weights for each specific task gave the least RMS error compared to common optimized weights. The velocity-based weights had a slightly higher RMS error than the task optimized weights but it was not statistically significant. The biggest benefit of that weight set is their simplicity to implement compared to the optimized weights. Another benefit of the velocity based weights is that they can explicitly show how mobile each joint is during a task and they can be used alongside the ROM to identify compensatory motion. The inclusion of task joint limits gave lower RMS error when the joint movements were similar across subjects and therefore the ROM of each joint for the task could be established more accurately. When the joint movements were too different among participants, the inclusion of task limits was detrimental to the simulation. Therefore, the static set of task specific optimized weights was found to be the most accurate and robust method. However, the velocity-based weights method was simpler with similar accuracy. The methods presented here were integrated in a previously developed graphical user interface (GUI) to allow the clinician to input the data of the prospective prosthesis users. The simulated motions can be presented as an animation that performs the requested task. Ultimately, the final animation can be used as a proposed kinematic strategy that a prosthesis user and a clinician can refer to, during the rehabilitation process as a guideline. This work has the potential to impact current prosthesis prescription and training by providing personalized proposed motions for a task.

<p>Atlas Copco Surface Drilling Equipment is one of the leading manufacturers of surface drill rigs. To stay in the top segment it is of great importance to have a well functioning development strategy as well as rig functions that makes the work as easy as possible for the operator. In this master thesis one development strategy has been evaluated and a dub tip control has been developed from idea to test on rig.</p><p> </p><p>Today the conventional method to position the drill is to use two joysticks with three axes each where each axis corresponds to one hydraulic actuator on the boom and feeder structure. The dub tip control system enables the operator to position the drill in Cartesian coordinates with only one 3-axes joystick. After the definition of the desired drill angle is done, the control system makes sure that this angle is obtained throughout the positioning motion. This system makes it considerably easier for an inexperienced operator to position the drill.</p><p> </p><p>For development, simulation and verification of the control algorithms and regulators <em>Matlab/Simulink</em> has been used. To test the control system on rig, a configuration with <em>LabVIEW</em> together with a <em>compactDAQ</em> has been evaluated. <em>LabVIEW </em>is chosen because it provides the opportunity to create a user friendly graphical user interface. To use this configuration is however not recommended for persons with little or none experience from using <em>LabVIEW</em>.</p><p> </p><p>This development strategy can be used for tests and verifications of control algorithms, but since neither <em>Windows </em>nor the <em>compactDAQ </em>are real time systems, there are solutions that are better but of course to a higher price.</p><p> </p><p>The master thesis work has shown that it is possible to implement a dub tip control on a rig of this dimension. It has also concluded that compensated valves are necessary to achieve optimal performance of a velocity controlled dub tip positioning.</p>

In this thesis, an actuation system is developed for a Two-Axis Gyroscopic (TAG) adapter. This adapter is a fixture with two auxiliary axes which is used for the Single Point Incremental Forming (SPIF) technique to enhance a three-axis mill to have five-axis capabilities. With five-axis mill capabilities, variable angles between line segments of the toolpath and the tool can be obtained. To achieve specialized angles between a line segment and the SPIF tool, the sheet is rotated. Inverse kinematic equations for the TAG adapter are derived to calculate the required rotations for the TAG adapter’s auxiliary axes for a line segment of a toolpath. If the next line segment requires a different orientation of the sheet, the sheet is rotated while the tool follows the rotation of the sheet to maintain its position at the connecting point of the line segments of the toolpath. Five equations of motions are derived to calculate the three translations of the mill and two rotations of the TAG adapter’s frames, during forming. A toolpath execution algorithm is implemented in MATLAB which uses the five equations of motion to execute a toolpath. The algorithm generates an array of data points that can be used by a Computer Numerically Controlled (CNC) machine to follow a desired path. A visual representation for the execution of the toolapth is implemented in MATLAB and is used to illustrate the successful completion of a toolpath. A computer controlled motor system is selected and tested in this thesis which will ultimately be integrated with a worm gear system and a CNC machine to develop a full CNC actuation system. / UOIT

Modular and Reconfigurable Robots (MRRs) are those designed to address the increasing demand for flexible and versatile manipulators in manufacturing facilities. The term, modularity, indicates that they are constructed by using a limited number of interchangeable standardized modules which can be assembled in different kinematic configurations. Thereby, a wide variety of specialized robots can be built from a set of standard components. The term, reconfigurability, implies that the robots can be disassembled and rearranged to accommodate different products or tasks rather than being replaced. A set of MRR modules may consist of joints, links, and end-effectors. Different kinematic configurations are achieved by using different joint, link, and end-effector modules and by changing their relative orientation. The number of distinct kinematic configurations, attainable by a set of modules, varies with respect to the size of the module set from several tens to several thousands. Although determining the most suitable configuration for a specific task from a predefined set of modules is a highly nonlinear optimization problem in a hybrid continuous and discrete search space, a solution to this problem is crucial to effectively utilize MRRs in manufacturing facilities. The objective of this thesis is to develop novel optimization methods that can effectively search the Kinematic Configuration (KC) space to identify the most suitable manipulator for any given task. In specific terms, the goal is to develop and synthesize fast and efficient algorithms for a Task-Based Configuration Optimization (TBCO) from a given set of constraints and optimization criteria. To achieve such efficiency, a TBCO solver, based on Memetic Algorithms (MA), is proposed. MAs are hybrids of Genetic Algorithms (GAs) and local search algorithms. MAs benefit from the exploration abilities of GAs and the exploitation abilities of local search methods simultaneously. Consequently, MAs can significantly enhance the search efficiency of a wide range of optimization problems, including the TBCO. To achieve more optimal solutions, the proposed TBCO utilizes all the solutions of the Inverse Kinematics(IK) problem. Another objective is to develop a method for incorporating the multiple solutions of the IK problem in a trajectory optimization framework. The output of the proposed trajectory optimization method consists of a sequence of desired tasks and a single IK solution to reach each task point. Moreover, the total cost of the optimized trajectory is utilized in the TBCO as a performance measure, providing a means to identify kinematic configurations with more efficient optimized trajectories. The final objective is to develop novel IK solvers which are both general and complete. Generality means that the solvers are applicable to all the kinematic configurations which can be assembled from the available module inventory. Completeness entails the algorithm can obtain all the possible IK solutions.

Atlas Copco Surface Drilling Equipment is one of the leading manufacturers of surface drill rigs. To stay in the top segment it is of great importance to have a well functioning development strategy as well as rig functions that makes the work as easy as possible for the operator. In this master thesis one development strategy has been evaluated and a dub tip control has been developed from idea to test on rig.   Today the conventional method to position the drill is to use two joysticks with three axes each where each axis corresponds to one hydraulic actuator on the boom and feeder structure. The dub tip control system enables the operator to position the drill in Cartesian coordinates with only one 3-axes joystick. After the definition of the desired drill angle is done, the control system makes sure that this angle is obtained throughout the positioning motion. This system makes it considerably easier for an inexperienced operator to position the drill.   For development, simulation and verification of the control algorithms and regulators Matlab/Simulink has been used. To test the control system on rig, a configuration with LabVIEW together with a compactDAQ has been evaluated. LabVIEW is chosen because it provides the opportunity to create a user friendly graphical user interface. To use this configuration is however not recommended for persons with little or none experience from using LabVIEW.   This development strategy can be used for tests and verifications of control algorithms, but since neither Windows nor the compactDAQ are real time systems, there are solutions that are better but of course to a higher price.   The master thesis work has shown that it is possible to implement a dub tip control on a rig of this dimension. It has also concluded that compensated valves are necessary to achieve optimal performance of a velocity controlled dub tip positioning.

Modular and Reconfigurable Robots (MRRs) are those designed to address the increasing demand for flexible and versatile manipulators in manufacturing facilities. The term, modularity, indicates that they are constructed by using a limited number of interchangeable standardized modules which can be assembled in different kinematic configurations. Thereby, a wide variety of specialized robots can be built from a set of standard components. The term, reconfigurability, implies that the robots can be disassembled and rearranged to accommodate different products or tasks rather than being replaced. A set of MRR modules may consist of joints, links, and end-effectors. Different kinematic configurations are achieved by using different joint, link, and end-effector modules and by changing their relative orientation. The number of distinct kinematic configurations, attainable by a set of modules, varies with respect to the size of the module set from several tens to several thousands. Although determining the most suitable configuration for a specific task from a predefined set of modules is a highly nonlinear optimization problem in a hybrid continuous and discrete search space, a solution to this problem is crucial to effectively utilize MRRs in manufacturing facilities. The objective of this thesis is to develop novel optimization methods that can effectively search the Kinematic Configuration (KC) space to identify the most suitable manipulator for any given task. In specific terms, the goal is to develop and synthesize fast and efficient algorithms for a Task-Based Configuration Optimization (TBCO) from a given set of constraints and optimization criteria. To achieve such efficiency, a TBCO solver, based on Memetic Algorithms (MA), is proposed. MAs are hybrids of Genetic Algorithms (GAs) and local search algorithms. MAs benefit from the exploration abilities of GAs and the exploitation abilities of local search methods simultaneously. Consequently, MAs can significantly enhance the search efficiency of a wide range of optimization problems, including the TBCO. To achieve more optimal solutions, the proposed TBCO utilizes all the solutions of the Inverse Kinematics(IK) problem. Another objective is to develop a method for incorporating the multiple solutions of the IK problem in a trajectory optimization framework. The output of the proposed trajectory optimization method consists of a sequence of desired tasks and a single IK solution to reach each task point. Moreover, the total cost of the optimized trajectory is utilized in the TBCO as a performance measure, providing a means to identify kinematic configurations with more efficient optimized trajectories. The final objective is to develop novel IK solvers which are both general and complete. Generality means that the solvers are applicable to all the kinematic configurations which can be assembled from the available module inventory. Completeness entails the algorithm can obtain all the possible IK solutions.

Advances in graphics and robotics have increased the importance of tools for synthesizing humanoid movements to control animated characters and physical robots. There is also an increasing need for analyzing human movements for clinical diagnosis and rehabilitation. Existing tools can be expensive, inefficient, or difficult to use. Using simulated physics and motion capture to develop an interactive virtual reality environment, we capture natural human movements in response to controlled stimuli. This research then applies insights into the mathematics underlying physics simulation to adapt the physics solver to support many important tasks involved in analyzing and synthesizing humanoid movement. These tasks include fitting an articulated physical model to motion capture data, modifying the model pose to achieve a desired configuration (inverse kinematics), inferring internal torques consistent with changing pose data (inverse dynamics), and transferring a movement from one model to another model (retargeting). The result is a powerful and intuitive process for analyzing and synthesizing movement in a single unified framework. / text

Este trabalho consiste na elaboração de uma estratégia para a geração de trajetórias otimizadas para um robô cilíndrico de cinco graus de liberdade acionado pneumaticamente. Como resultado da aplicação do método desenvolvido obtêm-se as trajetórias no espaço das juntas que resultam no movimento adequado do efetuador do robô, de acordo com algum critério de otimização. Para a obtenção das trajetórias das juntas do robô a partir de uma dada trajetória desejada para o efetuador, resolveu-se o problema de cinemática inversa por meio de uma abordagem algébrica. Para a geração de trajetórias entre os pontos no espaço de trabalho do robô propõe-se a utilização de um algoritmo de aproximação de pontos através de splines compostas por polinômios de sétimo grau. Essa escolha garante a continuidade da função de posição, bem como de suas três primeiras derivadas, sendo essa uma condição necessária para a implantação de importantes leis e estratégias de controle (como, por exemplo, a estratégia em cascata, utilizada com sucesso no controle de sistemas servopneumáticos). O método proposto para a geração de splines possibilita, através do ajuste de parâmetros em função da exigência de cada aplicação, a obtenção de curvas no espaço das juntas com valores otimizados de jerk, aceleração ou velocidade. Para aplicação na geração de trajetórias para o robô, a interpolação dos pontos é realizada no espaço dos atuadores a fim de fornecer ao controlador as curvas de referência para posição, velocidade, aceleração e jerk. Para a demonstração da aplicação do método no seguimento de trajetórias, são utilizadas como referência curvas tridimensionais cujos valores numéricos são comparados com os resultados fornecidos a partir da metodologia proposta. Assim, uma vez calculadas as trajetórias em cada uma das juntas através da cinemática inversa, utiliza-se as transformações homogêneas da cinemática direta do robô, obtidas a partir do método de Denavit-Hartenberg, para obter a trajetória do efetuador e verificar a funcionalidade do modelo resultante. / This work consists of developing a strategy to generate optimized trajectories for a cylindrical robot with five degrees of freedom which is actuated pneumatically. As a result of the application of the developed method, trajectories in joint space are obtained and result in the proper motion of the robot’s end-effector according to a given optimizing criteria. In order to obtain the trajectories of the robot’s joints from a given desired trajectory for the end-effector, the problem of inverse kinematics was solved by an algebraic approach. To generate trajectories between points in the robot’s workspace it was proposed the use of an algorithm for approximation of points through splines composed by seventh degrees polynomials. This choice ensures the continuity of the position function as well as its first three derivatives. It is a necessary condition for the implementation of important laws and control strategies (for example, the cascade strategy which is successfully used in servo-pneumatic control systems). The proposed method to generate splines allows, through the adjustment of parameters taking into account the requirements of each application, the obtainment of curves in the joint space with optimized values of jerk, acceleration and speed. In order to apply the method in the generation of trajectories for the robot, the interpolation of the points is performed in the space of the actuators with the purpose of providing the controller reference curves for position, speed, acceleration and jerk. To demonstrate the application of the method in trajectory tracking, three-dimensional curves are used and their numerical values are compared with the results provided by the proposed methodology. Therefore, once the calculated trajectory in each joint through inverse kinematics is obtained, homogeneous transformations of the direct kinematics of the robot, obtained by Denavit-Hartenberg’s method, are employed to find out the trajectory of the end-effector and verify the functionality of the resulting model.

Este trabalho consiste na elaboração de uma estratégia para a geração de trajetórias otimizadas para um robô cilíndrico de cinco graus de liberdade acionado pneumaticamente. Como resultado da aplicação do método desenvolvido obtêm-se as trajetórias no espaço das juntas que resultam no movimento adequado do efetuador do robô, de acordo com algum critério de otimização. Para a obtenção das trajetórias das juntas do robô a partir de uma dada trajetória desejada para o efetuador, resolveu-se o problema de cinemática inversa por meio de uma abordagem algébrica. Para a geração de trajetórias entre os pontos no espaço de trabalho do robô propõe-se a utilização de um algoritmo de aproximação de pontos através de splines compostas por polinômios de sétimo grau. Essa escolha garante a continuidade da função de posição, bem como de suas três primeiras derivadas, sendo essa uma condição necessária para a implantação de importantes leis e estratégias de controle (como, por exemplo, a estratégia em cascata, utilizada com sucesso no controle de sistemas servopneumáticos). O método proposto para a geração de splines possibilita, através do ajuste de parâmetros em função da exigência de cada aplicação, a obtenção de curvas no espaço das juntas com valores otimizados de jerk, aceleração ou velocidade. Para aplicação na geração de trajetórias para o robô, a interpolação dos pontos é realizada no espaço dos atuadores a fim de fornecer ao controlador as curvas de referência para posição, velocidade, aceleração e jerk. Para a demonstração da aplicação do método no seguimento de trajetórias, são utilizadas como referência curvas tridimensionais cujos valores numéricos são comparados com os resultados fornecidos a partir da metodologia proposta. Assim, uma vez calculadas as trajetórias em cada uma das juntas através da cinemática inversa, utiliza-se as transformações homogêneas da cinemática direta do robô, obtidas a partir do método de Denavit-Hartenberg, para obter a trajetória do efetuador e verificar a funcionalidade do modelo resultante. / This work consists of developing a strategy to generate optimized trajectories for a cylindrical robot with five degrees of freedom which is actuated pneumatically. As a result of the application of the developed method, trajectories in joint space are obtained and result in the proper motion of the robot’s end-effector according to a given optimizing criteria. In order to obtain the trajectories of the robot’s joints from a given desired trajectory for the end-effector, the problem of inverse kinematics was solved by an algebraic approach. To generate trajectories between points in the robot’s workspace it was proposed the use of an algorithm for approximation of points through splines composed by seventh degrees polynomials. This choice ensures the continuity of the position function as well as its first three derivatives. It is a necessary condition for the implementation of important laws and control strategies (for example, the cascade strategy which is successfully used in servo-pneumatic control systems). The proposed method to generate splines allows, through the adjustment of parameters taking into account the requirements of each application, the obtainment of curves in the joint space with optimized values of jerk, acceleration and speed. In order to apply the method in the generation of trajectories for the robot, the interpolation of the points is performed in the space of the actuators with the purpose of providing the controller reference curves for position, speed, acceleration and jerk. To demonstrate the application of the method in trajectory tracking, three-dimensional curves are used and their numerical values are compared with the results provided by the proposed methodology. Therefore, once the calculated trajectory in each joint through inverse kinematics is obtained, homogeneous transformations of the direct kinematics of the robot, obtained by Denavit-Hartenberg’s method, are employed to find out the trajectory of the end-effector and verify the functionality of the resulting model.