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TREE Jahresbericht 2018
(2019)
Herein we report an update to ACPYPE, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants. Prior to this work, ACPYPE only converted AMBER topologies that used uniform, default 1–4 scaling factors and positive dihedral force constants. We demonstrate that the updated ACPYPE accurately transfers the GLYCAM06 force field from AMBER to GROMACS topology files, which employs non-uniform 1–4 scaling factors as well as negative dihedral force constants. Validation was performed using β-d-GlcNAc through gas-phase analysis of dihedral energy curves and probability density functions. The updated ACPYPE retains all of its original functionality, but now allows the simulation of complex glycomolecular systems in GROMACS using AMBER-originated force fields. ACPYPE is available for download at https://github.com/alanwilter/acpype.
This paper proposes an approach to an ANN-based temperature controller design for a plastic injection moulding system. This design approach is applied to the development of a controller based on a combination of a classical ANN and integrator. The controller provides a fast temperature response and zero steady-state error for three typical heaters (bar, nozzle, and cartridge) for a plastic moulding system. The simulation results in Matlab Simulink software and in comparison to an industrial PID regulator have shown the advantages of the controller, such as significantly less overshoot and faster transient (compared to PID with autotuning) for all examined heaters. In order to verify the proposed approach, the designed ANN controller was implemented and tested using an experimental setup based on an STM32 board.
The paper presents the topological reduction method applied to gas transport networks, using contraction of series, parallel and tree-like subgraphs. The contraction operations are implemented for pipe elements, described by quadratic friction law. This allows significant reduction of the graphs and acceleration of solution procedure for stationary network problems. The algorithm has been tested on several realistic network examples. The possible extensions of the method to different friction laws and other elements are discussed.
In mathematical modeling by means of performance models, the Fitness-Fatigue Model (FF-Model) is a common approach in sport and exercise science to study the training performance relationship. The FF-Model uses an initial basic level of performance and two antagonistic terms (for fitness and fatigue). By model calibration, parameters are adapted to the subject’s individual physical response to training load. Although the simulation of the recorded training data in most cases shows useful results when the model is calibrated and all parameters are adjusted, this method has two major difficulties. First, a fitted value as basic performance will usually be too high. Second, without modification, the model cannot be simply used for prediction. By rewriting the FF-Model such that effects of former training history can be analyzed separately – we call those terms preload – it is possible to close the gap between a more realistic initial performance level and an athlete's actual performance level without distorting other model parameters and increase model accuracy substantially. Fitting error of the preload-extended FF-Model is less than 32% compared to the error of the FF-Model without preloads. Prediction error of the preload-extended FF-Model is around 54% of the error of the FF-Model without preloads.
Atmospheric aerosols affect the power production of solar energy systems. Their impact depends on both the atmospheric conditions and the solar technology employed. By being a region with a lack in power production and prone to high solar insolation, West Africa shows high potential for the application of solar power systems. However, dust outbreaks, containing high aerosol loads, occur especially in the Sahel, located between the Saharan desert in the north and the Sudanian Savanna in the south. They might affect the whole region for several days with significant effects on power generation. This study investigates the impact of atmospheric aerosols on solar energy production for the example year 2006 making use of six well instrumented sites in West Africa. Two different solar power technologies, a photovoltaic (PV) and a parabolic through (PT) power plant, are considered. The daily reduction of solar power due to aerosols is determined over mostly clear-sky days in 2006 with a model chain combining radiative transfer and technology specific power generation. For mostly clear days the local daily reduction of PV power (at alternating current) (PVAC) and PT power (PTP) due to the presence of aerosols lies between 13 % and 22 % and between 22 % and 37 %, respectively. In March 2006 a major dust outbreak occurred, which serves as an example to investigate the impact of an aerosol extreme event on solar power. During the dust outbreak, daily reduction of PVAC and PTP of up to 79 % and 100 % occur with a mean reduction of 20 % to 40 % for PVAC and of 32 % to 71 % for PTP during the 12 days of the event.
This study presents a microindentation system which allows spatially resolved local as well as bulk viscoelastic material information to be obtained within one instrument. The microindentation method was merged with dynamic mechanical analysis (DMA) for a tungsten cone indenter. Three tungsten cone indenters were investigated: tungsten electrode, tungsten electrode + 2% lanthanum, and tungsten electrode + rare earth elements. Only the tungsten electrode + 2% lanthanum indenter showed the sinusoidal response, and its geometry remained unaffected by the repeated indentations. Complex moduli obtained from dynamic microindentation for high-density polyethylene, polybutylene terephthalate, polycarbonate, and thermoplastic polyurethane are in agreement with the literature. Additionally, by implementing a specially developed x-y-stage, this study showed that dynamic microindentation with a tungsten cone indenter was an adequate method to determine spatially resolved local viscoelastic surface properties.
Process-dependent thermo-mechanical viscoelastic properties and the corresponding morphology of HDPE extrusion blow molded (EBM) parts were investigated. Evaluation of bulk data showed that flow direction, draw ratio, and mold temperature influence the viscoelastic behavior significantly in certain temperature ranges. Flow induced orientations due to higher draw ratio and higher mold temperature lead to higher crystallinities. To determine the local viscoelastic properties, a new microindentation system was developed by merging indentation with dynamic mechanical analysis. The local process-structure-property relationship of EBM parts showed that the cross-sectional temperature distribution is clearly reflected by local crystallinities and local complex moduli. Additionally, a model to calculate three-dimensional anisotropic coefficients of thermal expansion as a function of the process dependent crystallinity was developed based on an elementary volume unit cell with stacked layers of amorphous phase and crystalline lamellae. Good agreement of the predicted thermal expansion coefficients with measured ones was found up to a temperature of 70 °C.
It is shown that the electrochemical kinetics of alkaline methanol oxidation can be reduced by setting certain fast reactions contained in it to a steady state. As a result, the underlying system of Ordinary Differential Equations (ODE) is transformed to a system of Differential-Algebraic Equations (DAE). We measure the precision characteristics of such transformation and discuss the consequences of the obtained model reduction.
Energy Profiles of the Ring Puckering of Cyclopentane, Methylcyclopentane and Ethylcyclopentane
(2019)
Surrogate models are used to reduce the burden of expensive-to-evaluate objective functions in optimization. By creating models which map genomes to objective values, these models can estimate the performance of unknown inputs, and so be used in place of expensive objective functions. Evolutionary techniques such as genetic programming or neuroevolution commonly alter the structure of the genome itself. A lack of consistency in the genotype is a fatal blow to data-driven modeling techniques: interpolation between points is impossible without a common input space. However, while the dimensionality of genotypes may differ across individuals, in many domains, such as controllers or classifiers, the dimensionality of the input and output remains constant. In this work we leverage this insight to embed differing neural networks into the same input space. To judge the difference between the behavior of two neural networks, we give them both the same input sequence, and examine the difference in output. This difference, the phenotypic distance, can then be used to situate these networks into a common input space, allowing us to produce surrogate models which can predict the performance of neural networks regardless of topology. In a robotic navigation task, we show that models trained using this phenotypic embedding perform as well or better as those trained on the weight values of a fixed topology neural network. We establish such phenotypic surrogate models as a promising and flexible approach which enables surrogate modeling even for representations that undergo structural changes.
Are quality diversity algorithms better at generating stepping stones than objective-based search?
(2019)
The route to the solution of complex design problems often lies through intermediate "stepping stones" which bear little resemblance to the final solution. By greedily following the path of greatest fitness improvement, objective-based search overlooks and discards stepping stones which might be critical to solving the problem. Here, we hypothesize that Quality Diversity (QD) algorithms are a better way to generate stepping stones than objective-based search: by maintaining a large set of solutions which are of high-quality, but phenotypically different, these algorithms collect promising stepping stones while protecting them in their own "ecological niche". To demonstrate the capabilities of QD we revisit the challenge of recreating images produced by user-driven evolution, a classic challenge which spurred work in novelty search and illustrated the limits of objective-based search. We show that QD far outperforms objective-based search in matching user-evolved images. Further, our results suggest some intriguing possibilities for leveraging the diversity of solutions created by QD.
The initial phase in real world engineering optimization and design is a process of discovery in which not all requirements can be made in advance, or are hard to formalize. Quality diversity algorithms, which produce a variety of high performing solutions, provide a unique chance to support engineers and designers in the search for what is possible and high performing. In this work we begin to answer the question how a user can interact with quality diversity and turn it into an interactive innovation aid. By modeling a user's selection it can be determined whether the optimization is drifting away from the user's preferences. The optimization is then constrained by adding a penalty to the objective function. We present an interactive quality diversity algorithm that can take into account the user's selection. The approach is evaluated in a new multimodal optimization benchmark that allows various optimization tasks to be performed. The user selection drift of the approach is compared to a state of the art alternative on both a planning and a neuroevolution control task, thereby showing its limits and possibilities.
Background & Objective: Due to the policy goals for sustainable energy production, renewable energy plants such as photovoltaics are increasingly in use. The energy production from solar radiation depends strongly on atmospheric conditions. As the weather mostly changes, electrical power generation fluctuates, making technical planning and control of power grids to a complex problem. Due to used materials (semiconductors e.g. silicon, gallium arsenide, cadmium telluride) the photovoltaic cells are spectrally selective. It means that only radiation of certain wavelengths converts into electrical energy. A material property called spectral response characterizes a certain degree of conversion of solar radiation into the electric current for each wavelength of solar light.