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Gdańsk University of Technology

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Publications from the year 2021

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  • Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
    • Maryam Zarghami Dehaghani
    • Farrokh Yousefi
    • Farzad Seidi
    • Babak Bagheri
    • Amin Hamed Mashhadzadeh
    • Ghasem Naderi
    • Amin Esmaeili
    • Otman Abida
    • Sajjad Habibzadeh
    • Mohammad Saeb
    • Maksym Rybachuk
    2021 Full text Scientific Reports

    The use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The encapsulation process was modelled, considering an aqueous solution, by a molecular dynamics (MD) simulation under a canonical NVT ensemble. The interactions between the atoms of Isatin were obtained from the DREIDING force filed. The storage capacity of the capped SWCNT host was evaluated to quantify its capacity to host multiple Isatin molecules. Our results show that the Isatin can be readily trapped inside the volume cavity of the capped SWCNT and it remained stable, as featured by a reduction in the van der Waals forces between Isatin guest and the SWCNT host (at approximately − 30 kcal mol−1) at the end of the MD simulation (15 ns). Moreover, the free energy of encapsulation was found to be − 34 kcal mol−1 suggesting that the Isatin insertion procedure into the SWCNT occurred spontaneously. As calculated, a capped SWCNT (10,10) with a length of 30 Å, was able to host eleven (11) molecules of Isatin, that all remained steadily encapsulated inside the SWCNT volume cavity, showing a potential for the use of carbon nanotubes as drug delivery cargo systems.

  • Endothelial Dysfunction Driven by Hypoxia—The Influence of Oxygen Deficiency on NO Bioavailability
    • Anna Janaszak-Jasiecka
    • Anna Siekierzycka
    • Agata Płoska
    • Iwona T. Dobrucki
    • Leszek Kalinowski
    2021 Full text Biomolecules

    Cardiovascular diseases (CVDs) are the leading cause of death worldwide. The initial stage of CVDs is characterized by endothelial dysfunction, defined as the limited bioavailability of nitric oxide (NO). Thus, any factors that interfere with the synthesis or metabolism of NO in endothelial cells are involved in CVD pathogenesis. It is well established that hypoxia is both the triggering factor as well as the accompanying factor in cardiovascular disease, and diminished tissue oxygen levels have been reported to influence endothelial NO bioavailability. In endothelial cells, NO is produced by endothelial nitric oxide synthase (eNOS) from L-Arg, with tetrahydrobiopterin (BH4) as an essential cofactor. Here, we discuss the mechanisms by which hypoxia affects NO bioavailability, including regulation of eNOS expression and activity. What is particularly important is the fact that hypoxia contributes to the depletion of cofactor BH4 and deficiency of substrate L-Arg, and thus elicits eNOS uncoupling—a state in which the enzyme produces superoxide instead of NO. eNOS uncoupling and the resulting oxidative stress is the major driver of endothelial dysfunction and atherogenesis. Moreover, hypoxia induces impairment in mitochondrial respiration and endothelial cell activation; thus, oxidative stress and inflammation, along with the hypoxic response, contribute to the development of endothelial dysfunction.

  • ENERGIEEFFIZIENZ DER ZAHLUNGSOPERATIONEN
    • Tetiana Osadcha
    • Oleksandr Melnychenko
    2021 Full text

    Heute kannman nach verschiedenen Schätzungen mehr als zehn Möglichkeiten nutzen, um Einzelhandelswaren, Dienstleistungen oder geleistete Arbeit zu bezahlen. Die beliebtesten, bedeutendsten und sensibelsten sind Bargeld-und bargeldlose Zahlungen. Als die modernste kann man Kryptowährungzahlungen schätzen. Jede Zahlungsart ist mit Zeit-und Energiekosten für ihre Wartung und dementsprechend mit finanziellen Kosten verbunden. Etwa die Hälfte von diesen Kosten wird von Einzelhandelsgeschäften und Banken getragen. Der Zeitaufwand des Kassierers für Zahlungsdienste verursacht erhebliche Energiekosten für Handelsunternehmen und insgesamt für die Gesellschaft aufgrund der Unvollkommenheit der Zahlungsmittel und der Zahlungsinfrastruktur,. In diesem Bericht konzentrieren wiruns auf die Energieeffizienz von Zahlungsinstrumenten, von denen das schnellste bargeldlose Zahlungsmittel durch die Einführung einer besseren Zahlungsinfrastruktur noch energieeffizienter sein kann. Auch zeigen wir, dass Kryptowährung am wenigsten energieeffiziente Zahlungsmittel ist

  • ENERGY ANALYSIS OF THE PROPULSION SHAFT FATIGUE PROCESS IN A ROTATING MECHANICAL SYSTEM PART III DIMENSIONAL ANALYSIS
    • Zbigniew Korczewski
    • Konrad Marszałkowski
    2021 Full text Polish Maritime Research

    This article presents the third and last part of the problem of diagnosing the fatigue of marine propulsion shafts in terms of energy with the use of the action function, undertaken by the authors. Even the most perfect physical models of real objects, observed under laboratory conditions and developed based on the results of their research, cannot be useful in diagnostics without properly transferring the obtained results to the scale of the real object. This paper presents the method of using dimensional analyses and the Buckingham theorem (the so-called π theorem) to determine the dimensionless numbers of the dynamic similarity of the physical model of the propulsion shaft and its real ship counterpart, which enable the transfer of the results of the research on the energy processes accompanying the ship propulsion shaft fatigue from the physical model to the real object.

  • Energy Efficiency Study of Audio-video Content Consumption on Selected Android Mobile Terminals
    • Przemysław Falkowski-Gilski
    • Maciej Pańkowski
    2021

    Mobile devices are widely used by billions of users worldwide. Thanks to their main advantage, which is portability, they should be fully operational as long as possible, without the need to recharge or connect them to external power sources. This paper describes a study, carried out on four different mobile devices, with different hardware and software parameters, running the Android operating system. The research campaign involved several scenarios, including consumption of audio-visual content by different means of wireless communication (cellular and Wi-Fi), designed to best reflect the common daily use of a modern smartphone. Those scenarios were based on a user experience survey conducted at the beginning of the study. Obtained results illustrate user preferences as well as resource consumption of multimedia on different devices with varying distribution of the Android OS.

  • Energy Losses Due to Imperfect Payment Infrastructure and Payment Instruments
    • Oleksandr Melnychenko
    2021 Full text ENERGIES

    One of the strategic objectives of the European Union is a reduction in greenhouse gas emissions and improvement of energy efficiency by at least 32.5% in different areas of the economy by 2030. However, little is known about the impact of payment in retail on energy consumption. The purpose of this paper is to assess the chain of losses of time and energy, and therefore financial losses, that occur due to the imperfection of payment infrastructure and instruments using data of cashiers’ working time. The research is based on a regression analysis method, where the energy cost per payment transaction is considered in this study as a function of the number of customers per hour and the energy cost. The results of the panel models highlight that the number of customers per hour has a negative impact on the cost of energy per payment transaction. Furthermore, modern means and methods of payment, including cryptocurrencies, do not solve the problem of the excessive time that it takes to service payments, which entails a waste of energy and money. The empirical results give valuable insights into how to best organise payment in retail to achieve lower energy costs and improve energy efficiency in payment infrastructure.

  • Enhanced electrochemical kinetics of highly-oriented (111)-textured boron-doped diamond electrodes induced by deuterium plasma chemistry
    • Anna Dettlaff
    • Michał Sobaszek
    • Tomasz Klimczuk
    • Robert Bogdanowicz
    2021 Full text CARBON

    Novel highly-oriented (111)-textured boron-doped diamond electrodes (BDDD) featuring high electrochemical activity and electrode stability toward electrochemical analytics were fabricated by deuterium-rich microwave plasma CVD. The high flux deuterium plasma-induced preferential formation of (111)-faceted diamond as revealed by XRD. The highly-oriented diamond surface exhibited improved boron dopant incorporation and activation, whereas the crystals showed enhanced carrier electron acceptance and donation, which accelerated the electron transfer during electrochemical redox mediation. The standard rate constant and peak-to-peak separation E for the oxidation and reduction of the Fe(CN)63-/4- and Ru(NH3)62+/3+ redox probes reached E values of only 60.6 and 59.8 mV, respectively. The enriched electrochemical performance of the BDDD electrodes is an advantageous feature allowing them to be applied as ultrasensitive electrodes, demonstrated here by paracetamol determination. The differential pulse voltammetry results revealed an enhanced electrochemical oxidation effect for paracetamol at the deuterium-grown (111)-rich diamond electrode. A single linear range from 1 to 125 μM along with a low detection limit of 0.76 μM were achieved.

  • Enhanced photocatalytic activity of accordion-like layered Ti3C2 (MXene) coupled with Fe-modified decahedral anatase particles exposing {1 0 1} and {0 0 1} facets
    • Anna Grzegórska
    • Paweł Głuchowski
    • Jakub Karczewski
    • Jacek Ryl
    • Izabela Wysocka
    • Katarzyna Siuzdak
    • Grzegorz Trykowski
    • Katarzyna Grochowska
    • Anna Zielińska-Jurek
    2021 Full text CHEMICAL ENGINEERING JOURNAL

    New composites consisting of decahedral anatase particles exposing {001} and {101} facets coupled with accordion-like layered Ti3C2 with boosted photocatalytic activity towards phenol and carbamazepine degradation were investigated. The photocatalysts were characterized with X-ray diffraction (XRD), diffuse reflectance spectroscopy (DR/UV–Vis), Brunauer-Emmett-Teller (BET) specific surface area, Raman spectroscopy, scanning electron microscopy (SEM), electron paramagnetic resonance (EPR) spectroscopy, emission spectroscopy, luminescence decay analysis, electrochemical impedance spectroscopy (EIS), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and electrophoretic mobility measurements. The effect of hydrothermal reaction parameters on physicochemical, structural, and photocatalytic properties was studied. In all photodegradation processes, ortho-hydroxyphenol and para-hydroxyphenol were detected as the first intermediates of phenol decomposition. For the TiO2/Ti3C2(140,12) sample containing VTi, a higher concentration of para-hydroxyphenol than ortho-hydroxyphenol was observed, whereas for sample TiO2/Ti3C2(220,24) higher concentration of ortho-hydroxyphenol was noticed. The formation of surface heterojunction between {101} and {001} facets of decahedral anatase particles grown on Ti3C2 surface led to improved photoelectron transfer and enhanced photocatalytic activity towards degradation of carbamazepine - non-biodegradable and susceptible to bioaccumulation in living organisms commonly used pharmaceutical agent. Moreover, modification of TiO2/Ti3C2 surface with iron by magnetron sputtering deposition markedly improved photocatalytic activity in carbamazepine decomposition, with nearly 100% degradation in 60 min of irradiation under simulated solar light.

  • Enhancement of PUR/PIR foam thermal stability after addition of Zostera marina biomass component investigated via thermal analysis and isoconversional kinetics
    • Adrian Olejnik
    • Paulina Kosmela
    • Łukasz Piszczyk
    2021 JOURNAL OF POLYMER SCIENCE

    In the present work, a thorough thermogravimetric (TG) analysis of bio-based polyurethane–polyisocyanurate (PUR–PIR) foams in both nitrogen and oxygen atmosphere is performed. A sustainable element of the foam is a biopolyol obtained via acid-catalyzed liquefaction of Zostera marina and Enteromorpha Algae biomass. Based on isoconversional analysis and apparent activation energies, several conclusions are obtained. In contradiction to the common understanding, biopolyol based foams exhibit enhanced stability in both oxidative atmosphere and in nitrogen compared to purely petrochemical foams. Relationships between thermal stability and structure of the foams are established. Enhanced stability of bio-based foams in oxygen is attributed to two factors. First is an increased cross-linking density due to higher hydroxyl number of biopolyol compared to petrochemical one. Possibly the presence of more amount of aromatic compounds in the structure of polyols that come from lignin or aromatic ketones contribute to further enhancement of thermal stability. Those results suggest that the studied biobased foams are prospective alternatives to standard petrochemical PUR foams.

  • Enhancing Resilience of FSO Networks to Adverse Weather Conditions
    • Ilya Kalesnikau
    • Michał Pióro
    • Jacek Rak
    • Hristo Ivanov
    • Emma Fitzgerald
    • Erich Leitgeb
    2021 Full text IEEE Access

    Optical wireless networks realized by means of gigabit optical wireless communication (OWC) systems are becoming, in a variety of applications, an important alternative, or a complementary solution, to their fiber-based counterparts. However, performance of the OWC systems can be considerably degraded in periods of unfavorable weather conditions, such as heavy fog, which temporarily reduce the effective capacity of the network. In this paper, we focus on optical wireless mesh networks that use terrestrial links (called FSO – free-space optical – links) composed of several parallel full-duplex FSO systems, and present two complementary solutions that together provide a means to maximize network traffic performance in various weather conditions encountered during network operation. The first solution is a method for estimating the degradation of the effective FSO link capacity in adverse weather conditions such as fog, rain and snow (called the weather states in this paper). The second solution is an optimization model aiming at maximizing the network traffic throughput for a given list of weather states, derived from the conducted measurements. The model assumes the so-called affine flow thinning (AFT) traffic routing and protection mechanism capable of controlling the end-to-end traffic flows in response to fluctuations of capacity available on FSO links caused by changing weather conditions. The proposed link capacity modeling approach and the elaborated optimization model are verified through an exhaustive numerical study, illustrating the trade-off between the increase of traffic performance of the FSO networks and the corresponding cost of additional OWC systems.

  • Ensuring sustainable development of urban public transport: A case study of the trolleybus system in Gdynia and Sopot (Poland)
    • Marcin Wołek
    • Michał Wolański
    • Mikołaj Bartłomiejczyk
    • Olgierd Wyszomirski
    • Krzysztof Grzelec
    • Katarzyna Hebel
    2021 Full text JOURNAL OF CLEANER PRODUCTION

    Electromobility is a vital tool in reducing the environmental impact of transportation. A technologically mature means of public transport is the trolleybus. Based on a case study of the Polish cities of Gdynia and Sopot, this paper explores the factors that influence the development of the trolleybus system. Recent developments of in-motion charging (IMC) technology are analysed what provides a new analytical framework for the trolleybus development, bringing the original path for the expansion of the electromobility in urban areas without overhead lines. The use of an economic model has made it possible to assess the total lifecycle costs of trolleybuses and to specify a threshold that makes it more cost-effective than diesel buses. Operational data allows for a simulation that reveals the minimal rate of catenary coverage of a route in terms of speed and two charging power values. Results indicate that after including external costs into the economic calculation, trolleybus transport is economically efficient, although the energy mix is an important factor. In-motion charging trolleybus can be seen as a compromise solution between capital costs and battery capacity and is recommended for cities already operating this system.

  • Ensuring the QoE-Related Fairness to Reduce the User Abandonment Ratio
    • Izabela Mazur
    • Jacek Rak
    • Krzysztof Nowicki
    2021 Full text SENSORS

    These days, it is quite a challenge for app owners to keep users engaged with an app. Currently, the level of user abandonment is one of the key parameters that application owners are interested in. To meet these challenges, we are conducting an extended study of a previously proposed solution that significantly reduces the abandonment rate of a given application. The investigated solution is based on the methods of fairness using QoE and QoS approach. This paper shows that application abandonment ratios can be reduced by using an appropriate approach to fair bandwidth allocation. Adjusting the bandwidth allocation to users taking into account the quality of the user experience has a more effective effect on reducing app abandonment ratios than if quality of service is taken into account. This is because the users make the decision to abandon the application based on their feelings rather than technical parameters. In order to effectively reduce application abandonment ratios, a suitable bandwidth allocation algorithm must be used. This paper presents the impact of using different algorithms on the abandonment ratio and compares the popularly used algorithms and the previously proposed bandwidth allocation algorithm.

  • Entrepreneurial competencies and intentions among students of technical universities
    • Julita Wasilczuk
    • Nataliya Chukhray
    • Oleh Karyy
    • Liubov Halkiv
    2021 Full text Problems and Perspectives in Management

    The study investigates the entrepreneurial competencies and intentions of students. Their formation is a requirement of modern times. The question arises whether students of modern technical universities get entrepreneurial competencies and whether they transform these competencies into their entrepreneurial intentions. More than 3.6 thousand students from six technical universities from Poland, Ukraine, Latvia, Bulgaria, and Lithuania were surveyed. Methods of summarizing and grouping data, analysis of the structure of the population and distributions of its elements, evaluation of relationships were used to analyze the results of the survey. It was found that studying at technical universities is not an obstacle to the existence of entrepreneurial intentions among students. The respondents positively assessed their ability to recognize market opportunities for new business (the sum of the shares of positive answers exceeded the sum of the shares of negative answers by 12.4%). A positive generalized assessment was determined when assessing the ability to persuade others to invest in their business, while negative – their ability to write a formal business plan. It is proved that students who highly value their entrepreneurial abilities are much more likely to show the intention to start their own business (р < 0.001). Students’ focus on starting their own business is partly explained by the fact that they connect employment in corporations with a low guarantee of job retention. High positive integrated assessments received the following advantages of own entrepreneurship: prestige (0.302), chance to be realized (0.362), and the ability to create jobs (0.597).

  • Enviromental factors az the elements determingthe development of floating homes
    • Emilia Miszewska
    • Maciej Niedostatkiewicz
    • Radosław Wiśniewski
    2021 Full text Inżynieria Bezpieczeństwa Obiektów Antropogenicznych

    The popularity of Floating Homes in Western Europe and North America is noticeable. The interest in thesefacilities in Poland is also constantly growing. The popularity of Floating Homes is due to climate change, risingland prices and population density in city centers. However, environmental factors play a significant role in theirdevelopment. The publication presents the results of research on the impact of environmental factors on the de-velopment of Floating Homes in Poland. As part of the research, the most important environmental factors wereidentified and then, using the State of the Surroundings Scenarios (SSS) method, an initial scenario of their devel-opment was developed. The most probable scenario was developed, the purpose of which was to identify the mostfavorable factors - strengths and unfavorable factors - weaknesses responsible for the development opportunitiesof Floating Homes in Poland. Additionally, a surprise scenario was prepared, which indicated factors that mayunexpectedly accelerate the development of Floating Homes in Poland or slow it down.

  • Environmental problems and health risks with disposable baby diapers: Monitoring of toxic compounds by application of analytical techniques and need of education
    • Patrycja Makoś-Chełstowska
    • Aleksandra Kurowska-Susdorf
    • Justyna Płotka-Wasylka
    2021 Full text TRAC-TRENDS IN ANALYTICAL CHEMISTRY

    Due to the widespread use of disposable diapers in healthy babies as well as children prone to allergiesand premature babies with reduced immunity, disposable diapers should only be made of non-toxic andnatural ingredients. Unfortunately, disposable diaper manufacturers are reluctant to present their exactchemical composition, claiming that their trade secrets apply. However, several reports show thatdisposable diapers of well-known brands,“store”brands and“bio”brands may contain a number of toxiccompounds. There is very little study focused on the chemical composition of disposable baby diapers.Commonly, diapers may contain different pollutants including polychlorodibenzo-p-dioxins (PCDDs),organically active compounds of ethylene benzene, xylene and toluene, polyacrylates or phthalates.Some of them may be risky for children's health. Only few methodologies are reported for the deter-mination of some groups of compounds that could have a negative impact on the baby's skin condition.These procedures are mainly based on chromatographic separation. Another issue connected withdisposable baby diapers is its enormous impact on the environment, starting from the production step,finishing at disposal procedure. Thus, the aim of this review is to present problems connected withdisposable baby diapers and its impact on the baby's health and on the environment. One of theimportant issues in this range is the limited knowledge in society and this aspect is also described.Another topic discussed here is related to the occurrence of toxic compounds in disposable baby diapers.Moreover, the importance of analysis and monitoring of these xenobiotics is reviewed in the article.

  • Enzymatic and Chemical Cross-Linking of Bacterial Cellulose/Fish Collagen Composites—A Comparative Study
    • Agata Sommer
    • Paulina Dederko-Kantowicz
    • Hanna Staroszczyk
    • Sławomir Sommer
    • Marek Michalec
    2021 Full text INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

    This article compares the properties of bacterial cellulose/fish collagen composites (BC/Col) after enzymatic and chemical cross-linking. In our methodology, two transglutaminases are used for enzymatic cross-linking—one recommended for the meat and the other proposed for the fish industry—and pre-oxidated BC (oxBC) is used for chemical cross-linking. The structure of the obtained composites is characterized by scanning electron microscopy, thermogravimetric analysis, X-ray diffraction, and Fourier transform infrared spectroscopy, and their functional properties by mechanical and water barrier tests. While polymer chains in uncross-linked BC/Col are intertwined by H-bonds, new covalent bonds in enzymatically cross-linked ones are formed—resulting in increased thermal stability and crystallinity of the material. The C2–C3 bonds cleavage in D-glucose units, due to BC oxidation, cause secondary alcohol groups to vanish in favor of the carbonyl groups’ formation, thus reducing the number of H-bonded OHs. Thermal stability and crystallinity of oxBC/Col remain lower than those of BC/Col. The BC/Col formation did not affect tensile strength and water vapor permeability of BC, but enzymatic cross-linking with TGGS improved them significantly.

  • Epoxy/Ionic Liquid-Modified Mica Nanocomposites: Network Formation–Network Degradation Correlation
    • Maryam Jouyandeh
    • Vahideh Akbari
    • Seyed Mohammad Reza Paran
    • Sébastien Livi
    • Luanda Lins
    • Henri Vahabi
    • Mohammad Saeb
    2021 Full text Nanomaterials

    We synthesized pristine mica (Mica) and N-octadecyl-N’-octadecyl imidazolium iodide (IM) modified mica (Mica-IM), characterized it, and applied it at 0.1–5.0 wt.% loading to prepare epoxy nanocomposites. Dynamic differential scanning calorimetry (DSC) was carried out for the analysis of the cure potential and kinetics of epoxy/Mica and epoxy/Mica-IM curing reaction with amine curing agents at low loading of 0.1 wt.% to avoid particle aggregation. The dimensionless Cure Index (CI) was used for qualitative analysis of epoxy crosslinking in the presence of Mica and Mica-IM, while qualitative cure behavior and kinetics were studied by using isoconversional methods. The results indicated that both Mica and Mica-IM improved the curability of epoxy system from a Poor to Good state when varying the heating rate in the interval of 5–15 °C min−1. The isoconversional methods suggested a lower activation energy for epoxy nanocomposites with respect to the blank epoxy; thus, Mica and Mica-IM improved crosslinking of epoxy. The higher order of autocatalytic reaction for epoxy/Mica-IM was indicative of the role of liquid crystals in the epoxide ring opening. The glass transition temperature for nanocomposites containing Mica and Mica-IM was also lower than the neat epoxy. This means that nanoparticles participated the reaction because of being reactive, which decelerated segmental motion of the epoxy chains. The kinetics of the thermal decomposition were evaluated for the neat and mica incorporated epoxy nanocomposites epoxy with varying Mica and Mica-IM amounts in the system (0.5, 2.0 and 5.0 wt.%) and heating rates. The epoxy/Mica-IM at 2.0 wt.% of nanoparticle showed the highest thermal stability, featured by the maximum value of activation energy devoted to the assigned system. The kinetics of the network formation and network degradation were correlated to demonstrate how molecular-level transformations can be viewed semi-experimentally.

  • Equal Baseline Camera Array—Calibration, Testbed and Applications
    • Adam Kaczmarek
    • Bernhard Blaschitz
    2021 Full text Applied Sciences-Basel

    This paper presents research on 3D scanning by taking advantage of a camera array consisting of up to five adjacent cameras. Such an array makes it possible to make a disparity map with a higher precision than a stereo camera, however it preserves the advantages of a stereo camera such as a possibility to operate in wide range of distances and in highly illuminated areas. In an outdoor environment, the array is a competitive alternative to other 3D imaging equipment such as Structured-light 3D scanners or Light Detection and Ranging (LIDAR). The considered kinds of arrays are called Equal Baseline Camera Array (EBCA). This paper presents a novel approach to calibrating the array based on the use of self-calibration methods. This paper also introduces a testbed which makes it possible to develop new algorithms for obtaining 3D data from images taken by the array. The testbed was released under open-source. Moreover, this paper shows new results of using these arrays with different stereo matching algorithms including an algorithm based on a convolutional neural network and deep learning technology.

  • Equivalence of equicontinuity concepts for Markov operators derived from a Schur-like property for spaces of measures
    • Sander C. Hille
    • Tomasz Szarek
    • Daniel Worm
    • Maja Ziemlańska
    2021 Full text STATISTICS & PROBABILITY LETTERS

    Various equicontinuity properties for families of Markov operators have been – and still are – used in the study of existence and uniqueness of invariant probability for these operators, and of asymptotic stability. We prove a general result on equivalence of equicontinuity concepts. It allows comparing results in the literature and switching from one view on equicontinuity to another, which is technically convenient in proofs. More precisely, the characterisation is based on a ‘Schur-like property’ for measures: if a sequence of finite signed Borel measures on a Polish space is such that it is bounded in total variation norm and such that for each bounded Lipschitz function the sequence of integrals of this function with respect to these measures converges, then the sequence converges in dual bounded Lipschitz norm to a measure.

  • ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
    • Emilia Lubecka
    • Adam Liwo
    2021 Full text JOURNAL OF COMPUTATIONAL CHEMISTRY

    A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high-resolution non-homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR-determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton–proton distances of the NMR-determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all-atom-chain reconstruction algorithm and to the 0.12 Å standard deviation of the average-structure proton–proton distance of NMR-determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse-grained molecular dynamics.