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- lignin (4)
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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.
Background: To protect renewable packaging materials against autoxidation and decomposition when substituting harmful synthetic stabilizers with bioactive and bio-based compounds, extracts from Aesculus hippocastanum L. seeds were evaluated. The study objectives were to determine the antioxidant efficacy of bioactive compounds in horse chestnut seeds with regard to different seed fractions, improve their extraction, and to evaluate waste reuse. Methods: Different extraction techniques for field samples were evaluated and compared with extracts of industrial waste samples based on total phenolic content and total antioxidant capacity (2,2’-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS)). The molecular weight distribution and absorbance in ultraviolet range (UV) of seed coat extracts were determined, and the possibility of extracts containing proanthocyanidins was examined. Results: Seed coat extracts show a remarkable antioxidant activity and a high UV absorbance. Passive extractions are efficient and much less laborious. Applying waste product seed coats leads to a reduced antioxidant activity, total phenolic content, and UV absorbance compared to the field sample counterparts. In contrast to peeled seed extracts, all seed coat extracts contain proanthocyanidins. Discussion: Seed coats are a potential source of bioactive compounds, particularly regarding sustainable production and waste reuse. With minimum effort, highly bioactive extracts with high potential as additives can be prepared.
This work addresses the issue of finding an optimal flight zone for a side-by-side tracking and following Unmanned Aerial Vehicle(UAV) adhering to space-restricting factors brought upon by a dynamic Vector Field Extraction (VFE) algorithm. The VFE algorithm demands a relatively perpendicular field of view of the UAV to the tracked vehicle, thereby enforcing the space-restricting factors which are distance, angle and altitude. The objective of the UAV is to perform side-by-side tracking and following of a lightweight ground vehicle while acquiring high quality video of tufts attached to the side of the tracked vehicle. The recorded video is supplied to the VFE algorithm that produces the positions and deformations of the tufts over time as they interact with the surrounding air, resulting in an airflow model of the tracked vehicle. The present limitations of wind tunnel tests and computational fluid dynamics simulation suggest the use of a UAV for real world evaluation of the aerodynamic properties of the vehicle’s exterior. The novelty of the proposed approach is alluded to defining the specific flight zone restricting factors while adhering to the VFE algorithm, where as a result we were capable of formalizing a locally-static and a globally-dynamic geofence attached to the tracked vehicle and enclosing the UAV.
Due to global ecological and economic challenges that have been correlated to the transition from fossil-based to renewable resources, fundamental studies are being performed worldwide to replace fossil fuel raw materials in plastic production. One aspect of current research is the development of lignin-derived polyols to substitute expensive fossil-based polyol components for polyurethane and polyester production. This article describes the synthesis of bioactive lignin-based polyurethane coatings using unmodified and demethylated Kraft lignins. Demethylation was performed to enhance the reaction selectivity toward polyurethane formation. The antimicrobial activity was tested according to a slightly modified standard test (JIS Z 2801:2010). Besides effects caused by the lignins themselves, triphenylmethane derivatives (brilliant green and crystal violet) were used as additional antimicrobial substances. Results showed increased antimicrobial capacity against Staphylococcus aureus. Furthermore, the coating color could be varied from dark brown to green and blue, respectively.
Lignocellulose feedstock (LCF) provides a sustainable source of components to produce bioenergy, biofuel, and novel biomaterials. Besides hard and soft wood, so-called low-input plants such as Miscanthus are interesting crops to be investigated as potential feedstock for the second generation biorefinery. The status quo regarding the availability and composition of different plants, including grasses and fast-growing trees (i.e., Miscanthus, Paulownia), is reviewed here. The second focus of this review is the potential of multivariate data processing to be used for biomass analysis and quality control. Experimental data obtained by spectroscopic methods, such as nuclear magnetic resonance (NMR) and Fourier-transform infrared spectroscopy (FTIR), can be processed using computational techniques to characterize the 3D structure and energetic properties of the feedstock building blocks, including complex linkages. Here, we provide a brief summary of recently reported experimental data for structural analysis of LCF biomasses, and give our perspectives on the role of chemometrics in understanding and elucidating on LCF composition and lignin 3D structure.
The antiradical and antimicrobial activity of lignin and lignin-based films are both of great interest for applications such as food packaging additives. The polyphenolic structure of lignin in addition to the presence of O-containing functional groups is potentially responsible for these activities. This study used DPPH assays to discuss the antiradical activity of HPMC/lignin and HPMC/lignin/chitosan films. The scavenging activity (SA) of both binary (HPMC/lignin) and ternary (HPMC/lignin/chitosan) systems was affected by the percentage of the added lignin: the 5% addition showed the highest activity and the 30% addition had the lowest. Both scavenging activity and antimicrobial activity are dependent on the biomass source showing the following trend: organosolv of softwood > kraft of softwood > organosolv of grass. Testing the antimicrobial activities of lignins and lignin-containing films showed high antimicrobial activities against Gram-positive and Gram-negative bacteria at 35 °C and at low temperatures (0-7 °C). Purification of kraft lignin has a negative effect on the antimicrobial activity while storage has positive effect. The lignin release in the produced films affected the activity positively and the chitosan addition enhances the activity even more for both Gram-positive and Gram-negative bacteria. Testing the films against spoilage bacteria that grow at low temperatures revealed the activity of the 30% addition on HPMC/L1 film against both B. thermosphacta and P. fluorescens while L5 was active only against B. thermosphacta. In HPMC/lignin/chitosan films, the 5% addition exhibited activity against both B. thermosphacta and P. fluorescens.
The need for innovation around the control functions of inverters is great. PV inverters were initially expected to be passive followers of the grid and to disconnect as soon as abnormal conditions happened. Since future power systems will be dominated by generation and storage resources interfaced through inverters these converters must move from following to forming and sustaining the grid. As “digital natives” PV inverters can also play an important role in the digitalisation of distribution networks. In this short review we identified a large potential to make the PV inverter the smart local hub in a distributed energy system. At the micro level, costs and coordination can be improved with bidirectional inverters between the AC grid and PV production, stationary storage, car chargers and DC loads. At the macro level the distributed nature of PV generation means that the same devices will support both to the local distribution network and to the global stability of the grid. Much success has been obtained in the former. The later remains a challenge, in particular in terms of scaling. Yet there is some urgency in researching and demonstrating such solutions. And while digitalisation offers promise in all control aspects it also raises significant cybersecurity concerns.
The Potential of Sustainable Antimicrobial Additives for Food Packaging from Native Plants in Benin
(2019)
Pseudopotential (PP)-basierte Lattice-Boltzmann-Methoden werden zunehmend für die Simulation von Mehrphasenströmungen eingesetzt. Da sie auf einem phänomenologischen Ansatz basieren, ist ihr Einsatz mit einem hohen Modellierungsaufwand verbunden. Zudem entstehen an den Phasengrenzen sogenannte Scheingeschwindigkeiten, welche Genauigkeit und numerische Stabilität beeinträchtigen. Daher werden PP-Modelle in dieser Arbeit um drei neue Aspekte erweitert. Erstens wird gezeigt, dass bei der Modellierung unterschiedlicher Kontaktwinkel mit gängigen Methoden in Kombination mit verbesserten Kräfteschemata Scheintröpfchen entstehen. Diese werden durch einen neuartigen Ansatz eliminiert, der auf zusätzlichen Randbedingungen für alle Wechselwirkungskräfte basiert. Diese Technik verhindert nicht nur das Auftreten der Scheintröpfchen, sondern erhöht auch die Stabilität in wandgebundenen Strömungen. Zweitens wird ein neuartiges Verfahren zur Reduktion von Scheingeschwindigkeiten eingeführt. Dabei wird die Diskretisierung der Interaktionskräfte erweitert und die zusätzlichen, freien Koeffizienten in Simulationen statischer Tropfen numerisch optimiert. Die resultierende Diskretisierung wurde in Simulationen stationärer und dynamischer Testfälle validiert, wobei Scheingeschwindigkeiten deutlich reduziert werden konnten. Drittens und letztens wurden die Diffusionseigenschaften in Mehrstoffsystemen detailliert untersucht, wobei eine kritische Abhängigkeit zwischen den makroskopischen Diffusionskoeffizienten und dem Kräfteschema aufgezeigt wird. Diese Analyse bildet die Grundlage für den Vergleich und die zukünftige Entwicklung neuer Potentialfunktionen (für Mehrstoffsysteme) und reduziert den Modellierungsaufwand.
Bone tissue engineering is an ever-changing, rapidly evolving, and highly interdisciplinary field of study, where scientists try to mimic natural bone structure as closely as possible in order to facilitate bone healing. New insights from cell biology, specifically from mesenchymal stem cell differentiation and signaling, lead to new approaches in bone regeneration. Novel scaffold and drug release materials based on polysaccharides gain increasing attention due to their wide availability and good biocompatibility to be used as hydrogels and/or hybrid components for drug release and tissue engineering. This article reviews the current state of the art, recent developments, and future perspectives in polysaccharide-based systems used for bone regeneration.
Synthesis of Substituted Hydroxyapatite for Application in Bone Tissue Engineering and Drug Delivery
(2019)
Bioinspired stem cell-based hard tissue engineering includes numerous aspects: The synthesis and fabrication of appropriate scaffold materials, their analytical characterization, and guided osteogenesis using the sustained release of osteoinducing and/or osteoconducting drugs for mesenchymal stem cell differentiation, growth, and proliferation. Here, the effect of silicon- and silicate-containing materials on osteogenesis at the molecular level has been a particular focus within the last decade. This review summarizes recently published scientific results, including material developments and analysis, with a special focus on silicon hybrid bone composites. First, the sources, bioavailability, and functions of silicon on various tissues are discussed. The second focus is on the effects of calcium-silicate biomineralization and corresponding analytical methods in investigating osteogenesis and bone formation. Finally, recent developments in the manufacturing of Si-containing scaffolds are discussed, including in vitro and in vivo studies, as well as recently filed patents that focus on the influence of silicon on hard tissue formation.
Miscanthus x giganteus Stem Versus Leaf-Derived Lignins Differing in Monolignol Ratio and Linkage
(2019)
As a renewable, Miscanthus offers numerous advantages such as high photosynthesis activity (as a C4 plant) and an exceptional CO2 fixation rate. These properties make Miscanthus very attractive for industrial exploitation, such as lignin generation. In this paper, we present a systematic study analyzing the correlation of the lignin structure with the Miscanthus genotype and plant portion (stem versus leaf). Specifically, the ratio of the three monolignols and corresponding building blocks as well as the linkages formed between the units have been studied. The lignin amount has been determined for M. x giganteus (Gig17, Gig34, Gig35), M. nagara (NagG10), M. sinensis (Sin2), and M. robustus (Rob4) harvested at different time points (September, December, and April). The influence of the Miscanthus genotype and plant component (leaf vs. stem) has been studied to develop corresponding structure-property relationships (i.e., correlations in molecular weight, polydispersity, and decomposition temperature). Lignin isolation was performed using non-catalyzed organosolv pulping and the structure analysis includes compositional analysis, Fourier transform infradred (FTIR), ultraviolet/visible (UV-Vis), hetero-nuclear single quantum correlation nuclear magnetic resonsnce (HSQC-NMR), thermogravimetric analysis (TGA), and pyrolysis gaschromatography/mass spectrometry (GC/MS). Structural differences were found for stem and leaf-derived lignins. Compared to beech wood lignins, Miscanthus lignins possess lower molecular weight and narrow polydispersities (<1.5 Miscanthus vs. >2.5 beech) corresponding to improved homogeneity. In addition to conventional univariate analysis of FTIR spectra, multivariate chemometrics revealed distinct differences for aromatic in-plane deformations of stem versus leaf-derived lignins. These results emphasize the potential of Miscanthus as a low-input resource and a Miscanthus-derived lignin as promising agricultural feedstock.
Scratch assays enable the study of the migration process of an injured adherent cell layer in vitro. An apparatus for the reproducible performance of scratch assays and cell harvesting has been developed that meets the requirements for reproducibility in tests as well as easy handling. The entirely autoclavable setup is divided into a sample translation and a scratching system. The translational system is compatible with standard culture dishes and can be modified to adapt to different cell culture systems, while the scratching system can be adjusted according to angle, normal force, shape, and material to adapt to specific questions and demanding substrates. As a result, a fully functional prototype can be presented. This system enables the creation of reproducible and clear scratch edges with a low scratch border roughness within a monolayer of cells. Moreover, the apparatus allows the collection of the migrated cells after scratching for further molecular biological investigations without the need for a second processing step. For comparison, the mechanical properties of manually performed scratch assays are evaluated.
Healing of large bone defects requires implants or scaffolds that provide structural guidance for cell growth, differentiation, and vascularization. In the present work, an agarose-hydroxyapatite composite scaffold was developed that acts not only as a 3D matrix, but also as a release system. Hydroxyapatite (HA) was incorporated into the agarose gels in situ in various ratios by a simple procedure consisting of precipitation, cooling, washing, and drying. The resulting gels were characterized regarding composition, porosity, mechanical properties, and biocompatibility. A pure phase of carbonated HA was identified in the scaffolds, which had pore sizes of up to several hundred micrometers. Mechanical testing revealed elastic moduli of up to 2.8 MPa for lyophilized composites. MTT testing on Lw35human mesenchymal stem cells (hMSCs) and osteosarcoma MG-63 cells proved the biocompatibility of the scaffolds. Furthermore, scaffolds were loaded with model drug compounds for guided hMSC differentiation. Different release kinetic models were evaluated for adenosine 5′-triphosphate (ATP) and suramin, and data showed a sustained release behavior over four days.