11. The effect of the Ala16Val mutation on the secondary structure of the manganese superoxide dismutase mitochondrial targeting sequenceMatic Broz, Veronika Furlan, Samo Lešnik, Marko Jukič, Urban Bren, 2022, original scientific article Abstract: Manganese Superoxide Dismutase (MnSOD) represents a mitochondrial protein that scavenges reactive oxygen species (ROS) responsible for oxidative stress. A known single nucleotide polymorphism (SNP) rs4880 on the SOD2 gene, causing a mutation from alanine to valine (Ala16Val) in the primary structure of immature MnSOD, has been associated with several types of cancer and other autoimmune diseases. However, no conclusive correlation has been established yet. This study aims to determine the effect of the alanine to valine mutation on the secondary structure of the MnSOD mitochondrial targeting sequence (MTS). A model for each variant of the MTS was prepared and extensively simulated with molecular dynamics simulations using the CHARMM36m force field. The results indicate that the alanine variant of the MTS preserves a uniform α-helical secondary structure favorable for the protein transport into mitochondria, whereas the valine variant quickly breaks down its α-helix. Thus, the alanine MTS represents the more active MnSOD variant, the benefits of which have yet to be determined experimentally.
Keywords: manganese superoxide dismutase, polymorphism rs4880, mutation Ala16Val, molecular dynamics simulations, oxidative stress
Published in DKUM: 21.08.2023; Views: 370; Downloads: 16
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12. Development, fabrication and mechanical characterisation of auxetic bicycle handlebar gripNejc Novak, Vasja Plesec, Gregor Harih, Andrej Cupar, Jasmin Kaljun, Matej Vesenjak, 2023, original scientific article Abstract: The auxetic cellular structures are one of the most promising metamaterials for vibration damping and crash absorption applications. Therefore, their use in the bicycle handlebar grip was studied in this work. A preliminary computational design study was performed using various auxetic and non-auxetic geometries under four load cases, which can typically appear. The most representative geometries were then selected and fabricated using additive manufacturing. These geometries were then experimentally tested to validate the discrete and homogenised computational models. The homogenised computational model was then used to analyse the biomechanical behaviour of the handlebar grip. It was observed that handle grip made from auxetic cellular metamaterials reduce the high contact pressures, provide similar stability and hereby improve the handlebar ergonomics.
Keywords: auxetic cellular structures, computational simulations, experimental testing
Published in DKUM: 23.05.2023; Views: 413; Downloads: 48
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13. Analysis and implementation of different modulation strategies for one-phase inverter based on TMS320F28335 microcontroller : magistrsko deloTomislav Sinković, 2019, master's thesis Abstract: This master’s thesis is about researching different modulation strategies used on one-phase inverters. Given results and quality of the particular modulation strategy will be measured on output terminals of the whole system or load, which will be, for this purpose, a classical pure resistive load. Signal response will be measured with oscilloscope and the obtained signal will be saved in CSV form for further computer analysis using MATLAB/Simulink. Stored results will be passed through Fast Fourier Transformation method, which can estimate the magnitude of higher harmonics component in the output signal and thus quality of the signal. Whole algorithm and low-level signal generation is performed with TMS320F28335 microcontroller which supports MATLAB/Simulink to be compiled in C language. Real »Power board« is done with the milling machine with prior designing in Altium Designer PCB software package.
Keywords: one-phase inverter, different modulation strategies, TMS320F28335, power board, simulations
Published in DKUM: 22.11.2019; Views: 1000; Downloads: 140
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14. Simulation of automotive air-conditioning system in 1D simulation software : diplomsko deloMarko Copot, 2019, undergraduate thesis Abstract: The development of state-of-the-art vehicles requires advanced simulations tools in heating, ventilation and air-conditioning (HVAC). The focus of this thesis is the construction of an automotive HVAC model, its calibration and the simulation of the behaviour of the HVAC model in various ambient conditions. The theoretical background of refrigeration system as part of the HVAC system is presented. The model is constructed with following components: compressor, condenser, throttling device, evaporator and battery chiller, which is a heat exchanger between coolant and refrigerant. The description and role of each component in the HVAC model is presented. All heat exchangers are calibrated, which is done with multiple simulations that have defined input data. The results are compared to experimental data. With addition of vehicle cabin with air recirculation, HVAC control logic is implemented. The behaviour of the system is simulated in defined environmental conditions. The results of the simulations are presented in graphs and tables.
Keywords: 1D simulations, air-conditioning, HVAC, calibration, thermodynamics, cooling
Published in DKUM: 23.09.2019; Views: 1453; Downloads: 109
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15. INJECTION MOULDING PROCESS OPTIMIZATION OF CITRUS FIBER BIOCOMPOSITES BY SIMULATIONS AND TAGUCHI EXPERIMENTAL DESIGN : magistrsko deloPeter Fajs, 2019, master's thesis Abstract: The objective of the master thesis is to determine the filling properties of injection moulding process for newly created material, and to understand how the variation of processing parameters affects the flow possibilities. In thesis two materials were analysed, i.e. neat PLA material, which was used as a benchmark material and newly created composite CitrusPLA that is based on biodegradable PLA matrix and reinforced with citrus fibres. To fulfil the aim, the virtual and experimental design of experiment with the Taguchi methodology was conducted with use of spiral flow test, where the flow length of material through mould cavity was observed. The experimental results were the basis for the accuracy validation of numerical results and also to determine the optimum process parameters for injection moulding products with best flow conditions through statistical evaluation.
It has been concluded that the newly created composite has lower viscosity compared to benchmark virgin PLA which results in better flow conditions in spiral flow test analysis. Both materials have the same optimal conditions in terms of flow conditions. The contribution of mould temperature is in both cases negligible. However, other two variated parameters i.e. melt temperature and injection speed have higher influence on filling characteristics for both materials.
Keywords: injection moulding optimization, material characterization, Moldflow, injection moulding simulations, Taguchi DOE, bio-composites, citrus waste fibres, PLA
Published in DKUM: 07.06.2019; Views: 1665; Downloads: 37
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16. Perspectives on the introduction of computer-supported real laboratory exercises into biology teaching in secondary schools : teachers as part of the problemAndreja Špernjak, Andrej Šorgo, 2009, original scientific article Abstract: Computer supported virtual and real laboratories are recognized as tools that can help in raising the quality of biology instruction, and raising development competences in students. Yet biology teachers have been treating the computer as typewriter, as a source of information and as a tool for communication, all of which usages are common to all subjects. The uses of ICT that can significantly help in developing scientific literacy and that are primary tools in science teaching - such as the use of data loggers - are only rarely on the syllabus. The lack of equipment is not the most important reason for failure to use such applications; instead, this is probably due to teachers' attitudes, opinions and knowledge. Students cannot be recognized as an obstacle in working with ICT. Lawer secondary school students aged between 10 and 14 performed three laboratory exercises (Activity of yeast, Gas exchange in breathing, Heart rate) using three different methods: classic, computer-supported and virtual laboratory. As a result of testing, we know that all three methods are suitable even for younger students. When students were asked which method they liked the most, their first choice was computer-supported laboratory, followed by classic laboratory, with virtual laboratory in the third place.
Keywords: education, biology, secondary education, computer-supported laboratory, laboratory work, ICT, simulations
Published in DKUM: 15.12.2017; Views: 1774; Downloads: 123
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17. How close to reality is the „as-is” business process simulation model?Bartlomiej Gawin, Bartosz Marcinkowski, 2015, original scientific article Abstract: Background and Purpose: Business process simulation (BPS) model is based on real-life data form sources like databases, observations and interviews. It acts as “as-is” business scenario can used for reengineering. The main challenge is to gather relevant data and to develop simulation model. Research aims to elaborate BPS model and to systematically assess how close to reality it is.
Design/Methodology/Approach: The research has been performed in Polish telecommunications company. Authors investigate technical process of expanding cellular network. After elaborating “as-is” model, authors use ADONIS simulation tool to run a series simulations and confront simulation results with actual historical events. After this, assessment whether computer simulation model can precisely map real-life business process - and consequently act as credible basis for process improvement - is made.
Results: The simulation model has been constructed with data from the WfMS database, observations, staff knowledge and their experience. Fully equipped simulation model is found to allow reconstructing the historical execution of business activity with low margin for error. Some limitation were identified and discussed.
Conclusion: BPS is not a popular approach for process reengineering and improvement yet. Data collection issues for BPS that require adopting process mining techniques and additional information sources are among the reasons for that. In our study, computer simulation outputs are compatible with historical events. Hence the model reflects the business reality and can be taken as a reference model while redesigning the process.
Keywords: business process, business process simulations, data acquisition, workflow systems
Published in DKUM: 30.11.2017; Views: 1317; Downloads: 441
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18. Numerical analysis of temperature field during hardfacing process and comparison with experimental resultsVukić Lazić, Ivana Ivanović, Aleksandar Sedmak, Rebeka Rudolf, Mirjana Lazić, Zoran Radaković, 2014, original scientific article Abstract: The three-dimensional transient nonlinear thermal analysis of the hard facing process is performed by using the finite element method. The simulations were executed on the open source Salome platform using the open source finite element solver Code Aster. The Gaussian double ellipsoid was selected in order to enable greater possibilities for the calculation of the moving heat source. The numerical results were compared with available experimental results.
Keywords: welding simulations, numerical analysis, thermal analysis, simulations, transient heat conduction, moving heat source
Published in DKUM: 07.07.2017; Views: 1489; Downloads: 396
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19. Premature seizure of traffic flow due to the introduction of evolutionary gamesMatjaž Perc, 2007, original scientific article Abstract: We study the impact of evolutionary games on the flow of traffic. Since traffic participants do not always conform to the imposed rules, the introduction of games, i.e. set of strategies defining the behavioural pattern of agents on the road, appears justified. With this motivation, and the fact that individuals can change their strategy in the course of time, the evolutionary prisoner's dilemma game is introduced between neighbouring agents, enabling them to choose between cooperation and defection. Mutual cooperation enables forwarding to both agents for one step, while the defector is able to advance two steps when facing a cooperator, whereby the latter is forced to go one step backwards. Two defectors end up in a halt until the next iteration. Irrespective of their strategy, however, agents can move only if the road ahead is free. Jumps are never allowed. We show that this simple and plausible supplementation of the discrete cellular automaton Biham-Middleton-Levine (BML) model induces a traffic flow seizure by a substantially lower initial density of cars as in the absence of evolutionary games. The phenomenon is explained by studying the one-dimensional variant of the BML model with different advancement steps on the circular ring. In view of the proposed explanation, findings are generalized also to other types of games, such is the snowdrift game, and some statistical properties of gridlock formation in the presence of evolutionary rules are outlined. Our findings suggest that 'bending the law' results in a premature occurrence of traffic jams and thus unnecessarily burdens the transportation system.
Keywords: dynamic systems, traffic flow, theory of games, evolutionary rules, flow simulations, prisoner's dilemma
Published in DKUM: 03.07.2017; Views: 1136; Downloads: 406
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20. Pacemaker-driven stochastic resonance on diffusive and complex networks of bistable oscillatorsMatjaž Perc, Marko Gosak, 2008, original scientific article Abstract: We study the phenomenon of stochastic resonance on diffusive, small-world and scale-free networks consisting of bistable overdamped oscillators. Important thereby is the fact that the external subthreshold periodic forcing is introduced only to a single oscillator of the network. Hence, the forcing acts as a pacemaker trying to impose its rhythm on the whole network through the unit to which it is introduced. Without the addition of additive spatiotemporal noise, however, the whole network, including the unit that is directly exposed to the pacemaker, remains trapped forever in one of the two stable steady states of the local dynamics. We show that the correlation between the frequency of subthreshold pacemaker activity and the response of the network is resonantly dependent on the intensity of additive noise. The reported pacemaker-driven stochastic resonance depends most significantly on the coupling strength and the underlying network structure. Namely, the outreach of the pacemaker obeys the classic diffusion law in the case of nearest-neighbor interactions, thus being proportional to the square root of the coupling strength, whereas it becomes superdiffusive by an appropriate small-world or scale-free topology of the interaction network. In particular, the scale-free topology is identified as being optimal for the dissemination of localized rhythmic activity across the whole network. Also, we show that the ratio between the clustering coefficient and the characteristic path length is the crucial quantity defining the ability of a small-world network to facilitate the outreach of the pacemaker-emitted subthreshold rhythm. We additionally confirm these findings by using the FitzHugh-Nagumo excitable system as an alternative to the bistable overdamped oscillator.
Keywords: noise, bistable dynamics, stochastic simulations, complex networks
Published in DKUM: 03.07.2017; Views: 1498; Downloads: 471
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