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Gdańsk University of Technology

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Publications from the year 2020

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  • Molywood: streamlining the design and rendering of molecular movies
    • Miłosz Wieczór
    • Adam Hospital
    • Genis Bayarri
    • Jacek Czub
    • Modesto Orozco
    2020 Full text BIOINFORMATICS

    Motivation High-quality dynamic visuals are needed at all levels of science communication, from the conference hall to the classroom. As scientific journals embrace new article formats, many key concepts – particularly in structural biology – are also more easily conveyed as videos than still frames. Notwithstanding, the design and rendering of a complex molecular movie remain an arduous task. Here, we introduce Molywood, a robust and intuitive tool that builds on the capabilities of VMD to automate all stages of movie rendering. Results Molywood is a Python-based script that uses an integrated workflow to give maximal flexibility in movie design. It implements the basic concepts of actions, layers, grids and concurrency and requires no programming experience to run. Availability The script is freely available on GitLab (gitlab.com/KomBioMol/molywood) and PyPI (through pip), and features an extended documentation, tutorial and gallery hosted on mmb.irbbarcelona.org/molywood.

  • Moments of Hermite-Gaussian functionals
    • Marek Beśka
    • Mateusz Gałka
    2020 Full text Applicationes Mathematicae

    Moments of finite products of Hermite-Gaussian functionals are expressed by covariances of Gaussian sequence.

  • Monetary values estimates of solvents emissions
    • Marek Tobiszewski
    • Marta Bystrzanowska
    2020 Full text GREEN CHEMISTRY

    The impact values for environmental emissions of 52 solvents are estimated and expressed in monetary units. The impact values of solvents present in the air are calculated on the basis of 13 impact indicators and for solvents present in water on additional 2 impact indicators. These impact values are weighted with the results obtained with multi-compartment distribution model, allowing to calculate the fraction of solvent emitted to the environment present in each of the compartments. The results show that the impact values of solvents emissions are in range 0.7 – 1179.06 $ L-1, with mean value 20.69 $ L-1, expressed in USD2019. These impacts are considerably lower for short chain aliphatic hydrocarbons, alcohols, ethers, aldehydes, ketones and esters. High impact values are obtained for long chain aliphatic hydrocarbons, aromatic hydrocarbons, terpenes and extremely high value for carbon tetrachloride. Monetary values calculated to assess the solvents emissions impact have the advantage that they are quantitative, and easily applicable.

  • Monitoring the BTEX Volatiles during 3D Printing with Acrylonitrile Butadiene Styrene (ABS) Using Electronic Nose and Proton Transfer Reaction Mass Spectrometry
    • Wojciech Wojnowski
    • Kaja Kalinowska
    • Jacek Gębicki
    • Bożena Zabiegała
    2020 Full text SENSORS

    We describe a concept study in which the changes of concentration of benzene, toluene, ethylbenzene, and xylene (BTEX) compounds and styrene within a 3D printer enclosure during printing with different acrylonitrile butadiene styrene (ABS) filaments were monitored in real-time using a proton transfer reaction mass spectrometer and an electronic nose. The quantitative data on the concentration of the BTEX compounds, in particular the concentration of carcinogenic benzene, were then used as reference values for assessing the applicability of an array of low-cost electrochemical sensors in monitoring the exposure of the users of consumer-grade fused deposition modelling 3D printers to potentially harmful volatiles. Using multivariate statistical analysis and machine learning, it was possible to determine whether a set threshold limit value for the concentration of BTEX was exceeded with a 0.96 classification accuracy and within a timeframe of 5 min based on the responses of the chemical sensors.

  • Mono- and bimetallic (Pt/Cu) titanium(IV) oxide photocatalysts. Physicochemical and photocatalytic data of magnetic nanocomposites’ shell
    • Zuzanna Bielan
    • Kowalska Ewa
    • Szymon Dudziak
    • Kunlei Wang
    • Bunsho Ohtani
    • Anna Zielińska-Jurek
    2020 Full text Data in Brief

    Surface modification of titania with noble and semi-noble metals resulted in significant enhancement of photocatalytic activity. Presented data, showing the photocatalytic properties of TiO2-M (where M is Pt and/or Cu) photocatalysts were further used as Fe3O4@SiO2/TiO2-M magnetic nanocomposites shells in "Mono- and bimetallic (Pt/Cu) titanium(IV) oxide core-shell photocatalysts with Vis light activity and magnetic separability" [1]. Platinum and copper were photodeposited on four different titania matrices (commercial and self-obtained ones). The prepared photocatalysts were characterized by X-ray diffraction (XRD) analysis, specific surface area measurements using the Brunauer-Emmet-Teller (BET) isotherm, diffuse reflectance spectroscopy (DR-UV/Vis) analysis as well as scanning transmission electron microscopy (STEM) analysis. Photocatalytic properties were investigated in three different reactions: H2 generation, acetic acid oxidation to CO2, and phenol degradation.

  • Morze możliwości
    • Karol Moszyk
    • Łukasz Rogatka
    2020 Kaizen

    Z Karolem Moszykiem, Kierownikiem ds. Rozwoju Operacyjnego/ Lean Six Sigma Black Belt, DCT Gdańsk SA i prelegentem pierwszego Gdańskiego Manager Clubu - o ciągłbym doskonaleniu w głębokowodnym terminalu kontenerowym - rozmawiał Łukasz Rogatka

  • Mountain pass solutions to Euler-Lagrange equations with general anisotropic operator
    • Magdalena Chmara
    • Jakub Maksymiuk
    2020 Full text JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS

    Using the Mountain Pass Theorem we show that the problem \begin{equation*} \begin{cases} \frac{d}{dt}\Lcal_v(t,u(t),\dot u(t))=\Lcal_x(t,u(t),\dot u(t))\quad \text{ for a.e. }t\in[a,b]\\ u(a)=u(b)=0 \end{cases} \end{equation*} has a solution in anisotropic Orlicz-Sobolev space. We consider Lagrangian $\Lcal=F(t,x,v)+V(t,x)+\langle f(t), x\rangle$ with growth conditions determined by anisotropic G-function and some geometric conditions of Ambrosetti-Rabinowitz type.

  • Możliwości wykorzystania spektroskopii fotoelektronów w analizie jakości środowiska wodnego
    • Jacek Ryl
    • Tadeusz Ossowski
    • Maria Elektorowicz
    • Elżbieta Niemirycz
    2020 Technologia Wody

    Spektroskopia fotoelektronów w zakresie promieniowania X, (XPS, z ang. X-ray photoelectron spectroscopy) jest nowoczesną metodą analityczną wykorzystywaną w wielu wiodących ośrodkach naukowych na świecie. Jest ona stale ulepszana, jak też poznawane są nowe obszary jej zastosowania. W niniejszym artykule przedstawione zostały możliwości wykorzystania metody XPS w ramach obszarów badawczych powiązanych z gospodarką wodną, takich jak analiza jakościowa i ilościowa wód oraz osadów dennych, ocena stanu technicznego obiektów i instalacji wodnych oraz badania technik membranowych i bioreaktorów wykorzystywanych w ochronie środowiska wodnego.

  • MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
    • Sanket Rajan Gupte
    • Dharm Skandh Jain
    • Ashwin Srinivasan
    • Raviprasad Aduri
    2020

    —Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence learning tasks. We use transfer learning to generate the MP3vecs by training a deep neural network on the source problem of protein secondary structure prediction, and then extracting representations learned by the trained network for use in related downstream prediction tasks. ML methods using MP3vecs perform as well as the state-of-the-art (or better) on the target problems, while being orders of magnitude faster in terms of training time. We suggest that MP3vec can act as a strong baseline for comparative work on the use of ML in protein-prediction tasks; and for future extensions with domainspecific features.

  • Multi-agent graph searching and exploration algorithms
    • Dorota Osula
    2020 Full text

    A team of mobile entities, which we refer to as agents or searchers interchangeably, starting from homebases needs to complete a given task in a graph.The goal is to build a strategy, which allows agents to accomplish their task. We analyze strategies for their effectiveness (e.g., the number of used agents, the total number of performed moves by the agents or the completion time).Currently, the fields of on-line (i.e., agents have no a priori knowledge about the graph topology) multi-agent graph searching and exploration are rapidly expanding. Recent studies have presented new approaches and models to better describe real-life problems like clearing danger areas by a group of robots or constructing a map of an unknown terrain. A centralized searching and exploration in the off-line setting (i.e., when the topology of a graph is known in advance) are well studied, due to their wide applications in robotic and network fields, and many profound results have been established. In this thesis we are focusing on the issues of the monotone connected decontamination problem, the on-line collaborative exploration and the partial exploration of digraphs. Firstly, we provide two comprehensive surveys on the topics of graph searching and exploration. Then in the four subsequent chapters, we present the following results: - We give a distributed algorithm for the searchers that allows them to compute a connected and monotone strategy that guarantees searching any unknown partial grid of order n with the use of O(\sqrt{n}) searchers. Moreover, we give a lower bound of Ω(\sqrt{n}/log n) in terms of achievable competitive ratio of any distributed algorithm. - Checking if the connected pathwidth of any graph is at most some fixed integer k can be done in polynomial time. - Let the cost of a strategy be the total distance traversed by agents coupled with the price of invoking them. We construct two cost-optimal off-line algorithms for rings and trees, respectively. For unknown rings, we give a 2-competitive algorithm. We prove a lower bound of competitive ratio of 3/2 (for rings) and 2 (for trees) for any on-line algorithm. - The problem of establishing if there exists a subgraph, which connects a chosen vertices and can be explored by a given number of agents is NP-hard and FPT.

  • Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
    • Paweł Wojtkiewicz
    • Daria Biernacka
    • Patrycja Gorzelak
    • Anna Stupak
    • Gracjana Klein-Raina
    • Satish Raina
    2020 Full text INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

    Consistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S), transcriptional factors (DksA and SrrA), replication proteins Hda/DiaA, asparatokinase MetL, Cmk and acid resistance regulator (AriR) overcome some defects of Δ6ppi strains. Interestingly, viability of Δ6ppi bacteria requires the presence of transcriptional factors DksA, SrrA, Cmk or Hda. DksA, MetL and Cmk are for the first time shown to exhibit PPIase activity in chymotrypsin-coupled and RNase T1 refolding assays and their overexpression also restores growth of a Δ(dnaK/J/tig) strain, revealing their mechanism of suppression. Mutagenesis of DksA identified that D74, F82 and L84 amino acid residues are critical for its PPIase activity and their replacement abrogated multicopy suppression ability. Mutational studies revealed that DksA-mediated suppression of either Δ6ppi or ΔdnaK/J is abolished if GroL/S and RpoE are limiting, or in the absence of either major porin regulatory sensory kinase EnvZ or RNase H, transporter TatC or LepA GTPase or Pi-signaling regulator PhoU.

  • MULTI-CRITERIA COMPARATIVE ANALYSIS OF THE USE OF SUBTRACTIVE AND ADDITIVE TECHNOLOGIES IN THE MANUFACTURING OF OFFSHORE MACHINERY COMPONENTS
    • Mariusz Deja
    • Mieczysław Siemiątkowski
    • Dawid Zieliński
    2020 Full text Polish Maritime Research

    The dynamic development of additive manufacturing technologies, especially over the last few years, has increased the range of possible industrial applications of 3D printed elements. This is a consequence of the distinct advantages of additive techniques, which include the possibility of improving the mechanical strength of products and shortening lead times. Offshore industry is one of these promising areas for the application of additive manufacturing. This paper presents a decision support method for the manufacturing of offshore equipment components, and compares a standard subtractive method with an additive manufacturing approach. An analytic hierarchy process was applied to select the most effective and efficient production method, considering CNC milling and direct metal laser sintering. A final set of decision criteria that take into account the specifics of the offshore industry sector are provided.

  • Multi-criteria Differential Evolution for Optimization of Virtual Machine Resources in Smart City Cloud
    • Jerzy Balicki
    • Honorata Balicka
    • Piotr Dryja
    • Maciej Tyszka
    2020

    In a smart city, artificial intelligence tools support citizens and urban services. From the user point of view, smart applications should bring computing to the edge of the cloud, closer to citizens with short latency. However, from the cloud designer point of view, the trade-off between cost, energy and time criteria requires the Pareto solutions. Therefore, the proposed multi-criteria differential evolution can optimize virtual machine resources in smart city clouds to find compromises between preferences of citizens and designers. In this class of distributed computer systems, smart mobile devices share computing workload with the set of virtual machines that can be migrated among the nodes of the cloud. Finally, some numerical results are studied for the laboratory cloud GUT-WUT.

  • Multifactor consciousness level assessment of participants with acquired brain injuries employing human–computer interfaces
    • Andrzej Czyżewski
    • Adam Kurowski
    • Piotr Odya
    • Piotr Szczuko
    2020 Full text Biomedical Engineering Online

    Background A lack of communication with people suffering from acquired brain injuries may lead to drawing erroneous conclusions regarding the diagnosis or therapy of patients. Information technology and neuroscience make it possible to enhance the diagnostic and rehabilitation process of patients with traumatic brain injury or post-hypoxia. In this paper, we present a new method for evaluation possibility of communication and the assessment of such patients’ state employing future generation computers extended with advanced human–machine interfaces. Methods First, the hearing abilities of 33 participants in the state of coma were evaluated using auditory brainstem response measurements (ABR). Next, a series of interactive computer-based exercise sessions were performed with the therapist’s assistance. Participants’ actions were monitored with an eye-gaze tracking (EGT) device and with an electroencephalogram EEG monitoring headset. The data gathered were processed with the use of data clustering techniques. Results Analysis showed that the data gathered and the computer-based methods developed for their processing are suitable for evaluating the participants’ responses to stimuli. Parameters obtained from EEG signals and eye-tracker data were correlated with Glasgow Coma Scale (GCS) scores and enabled separation between GCS-related classes. The results show that in the EEG and eye-tracker signals, there are specific consciousness-related states discoverable. We observe them as outliers in diagrams on the decision space generated by the autoencoder. For this reason, the numerical variable that separates particular groups of people with the same GCS is the variance of the distance of points from the cluster center that the autoencoder generates. The higher the GCS score, the greater the variance in most cases. The results proved to be statistically significant in this context. Conclusions The results indicate that the method proposed may help to assess the consciousness state of participants in an objective manner.

  • Multimedia Communications, Services and Security MCSS. 10th International Conference, MCSS 2020, Preface
    • Andrzej Dziech
    • Wim Mees
    • Andrzej Czyżewski
    2020

    Multimedia surrounds us everywhere. It is estimated that only a part of the recorded resources are processed and analyzed. These resources offer enormous opportunities to improve the quality of life of citizens. As a result, of the introduction of a new type of algorithms to improve security by maintaining a high level of privacy protection. Among the many articles, there are examples of solutions for improving the operation of monitoring systems or preventing threats in the industrial environment. The important group of issues is the creation of solutions and functionalities into ready-to-use systems. The practical use of research results was discussed during the conference. Connecting them with modern architectures is a natural necessity in the case of future implementation

  • Multimodal Genetic Algorithm with Phase Analysis to Solve Complex Equations of Electromagnetic Analysis
    • Damian Trofimowicz
    • Tomasz Stefanski
    2020 Full text

    In this contribution, a new genetic-algorithm-based method of finding roots and poles of a complex function of a complex variable is presented. The algorithm employs the phase analysis of the function to explore the complex plane with the use of the genetic algorithm. Hence, the candidate regions of root and pole occurrences are selected and verified with the use of discrete Cauchy's argument principle. The algorithm is evaluated in an electromagnetic benchmark that successfully solves the eigenvalue problem determining the propagation of surface waves along a spatially dispersive graphene sheet. The numerical results show that the possibility to find all roots and poles of the function may be limited by the initial population size, especially when the search region is large and roots and poles are located close to each other.

  • Multimodal Particle Swarm Optimization with Phase Analysis to Solve Complex Equations of Electromagnetic Analysis
    • Damian Trofimowicz
    • Tomasz Stefanski
    2020 Full text

    In this paper, a new meta-heuristic method of finding roots and poles of a complex function of a complex variable is presented. The algorithm combines an efficient space exploration provided by the particle swarm optimization (PSO) and the classification of root and pole occurrences based on the phase analysis of the complex function. The method initially generates two uniformly distributed populations of particles on the complex plane and extracts the function phase in a position of each particle. By collecting phase samples, the candidate regions of root and pole occurrences are selected. Then, the second population, by iteratively converging towards candidate regions, thoroughly explores an area outside candidate regions and reduces the possibility of root or pole omission. The subsequent swarms are generated locally to explore candidate regions and decrease their size. The algorithm is verified in electromagnetic benchmark that solves the equation determining surface waves on a microstrip antenna. The numerical results show that the algorithm is able to solve multimodal problems quickly even with a small initial population and a small number of generated swarms.

  • Multiparameter sensitivity analysis of a GFRP composite footbridge of a sandwich structure and U-shaped cross-section
    • Tomasz Ferenc
    2020 Full text COMPOSITE STRUCTURES

    The paper deals with multiparameter sensitivity analysis of a composite footbridge. A shell‐like structure is 14.5 m long shows U‐shaped cross‐section and inner service dimensions 1.3 × 2.5 m. Glass fiber reinforced polymer GFRP laminate constitutes faces of a sandwich structure while PET foam received from recycled bottle builts a core. The structure was divided into 285 independent areas where the thickness of laminates and stiffness modulus of PET foam were established as design variables. The impact of their variation on variation of state variables was investigated, vertical displacement of structure, longitudinal strain in handrail and transverse strain in deck were addressed here. Sensitivity vector was computed by a semi‐analytical method and, subsequently, expressed in a matrix form and next presented graphically in the form of sensitivity areas. The conducted sensitivity analysis exhibits areas that can be strengthened in order to minimize vertical displacement, longitudinal strain in handrail and transverse strain deck, determining the areas where parameters can be reduced without increasing the value of state variables. The obtained results are bound to support the structural design process or to improve the performance of existing structures.

  • Multiple reference frame theory in the synchronous generator model considering harmonic distortions caused by nonuniform pole shoe saturation
    • Filip Kutt
    • Michał Michna
    • Grzegorz Kostro
    2020 IEEE TRANSACTIONS ON ENERGY CONVERSION

    The paper describes a synchronous generator model developed based on the multiple reference frame theory. The main physical phenomena included in the model are the machine armature non-sinusoidal voltage waveform and the influence of armature current in load conditions on the armature voltage waveform higher harmonic components. The modified multiple reference frame theory model is proposed. In this modified theory model the field and armature currents are the cause of the non-sinusoidal airgap spatial field distribution. The influence of this airgap spatial field distribution is also investigated. The resulting nonuniform saturation of the pole shoe affects the machine voltage waveform in load conditions. Simulation and measurements of the machine performance in steady and transient states are conducted in order to validate the model.

  • Multisine impedimetric probing of biocatalytic reactions for label-free detection of DEFB1 gene: How to verify that your dog is not human?
    • Paweł Niedziałkowski
    • Paweł Ślepski
    • Joanna Wysocka
    • Joanna Chamier-Ciemińska
    • Łukasz Burczyk
    • Michał Sobaszek
    • Anna Wcisło
    • Tadeusz Ossowski
    • Robert Bogdanowicz
    • Jacek Ryl
    2020 Full text SENSORS AND ACTUATORS B-CHEMICAL

    Albert is a dog (Canis familiaris), but he does not realize this. Albert loves human food (and beer), watching movies on the internet, sleeping in bed, and more. But he should not do all these things. To convince him that, we have desinged a test procedure. The DEFB1 gene is unique to human species. Detecting its presence from saliva and in short periods may offer an advantage in the field of forensic medicine, and influence Albert’s bad habits. This study reveals novel utilization of the multisine impedance spectroscopy carried out during potentiodynamic polarization (pDEIS) of the electrode. We have utilized pDEIS to detect DEFB1 gene in collected saliva samples. The detection process was conducted at the boron-doped diamond surfaces functionalized with DEFB1-complimentary oligonucleotide sequence, anchored at the electrode surface. Next, a short-term electrode incubation in presence of target DNA sample allows for achieving DNA hybridization when exposed to human DNA material. The dsDNA orientation vs electrode surface is affected by polarization, and tracked by changes in the electrode kinetics preceded by subtle capacitance dispersion effects. The optimized measurement conditions range between +0.5 and +0.9 V vs Ag|AgCl due to nonspecific DNA adsorption, affecting heterogeneous charge transfer. The DNA hybridization is not achieved in the case of non-complimentary ssDNA originated from any other species subjected to this test. The discussed differences obtained during electrode incubation are supported by the XPS analyses.