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Gdańsk University of Technology

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Publications from the year 2017

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  • Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
    • Jacek Czub
    • Miłosz Wieczór
    • Bartosz Prokopowicz
    • Helmut Grubmüller
    2017 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

    F1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned energy conversion mechanism are not fully understood. Here, we use extensive molecular dynamics simulations to reconcile recent single-molecule experiments with structural data and provide a consistent thermodynamic, kinetic and mechanistic description of the main rotary substep in the synthetic cycle of mammalian ATP synthase. The calculated free energy profiles capture a discrete pattern in the rotation of the central γ-shaft, with a metastable intermediate located—consistently with recent experimental findings—at 70° relative to the X-ray position. We identify this rotary step as the ATP-dependent substep, and find that the associated free energy input supports the mechanism involving concurrent nucleotide binding and release. During the main substep, our simulations show no significant opening of the ATP-bound β subunit; instead, we observe that mechanical energy is transmitted to its nucleotide binding site, thus lowering the affinity for ATP. Simultaneously, the empty subunit assumes a conformation that enables the enzyme to harness the free energy of ADP binding to drive ATP release. Finally, we show that ligand exchange is regulated by a checkpoint mechanism, an apparent prerequisite for high efficiency in protein nanomotors.

  • Meeting Requirements Imposed by Secure Software Development Standards and Still Remaining Agile
    • Janusz Górski
    • Katarzyna Łukasiewicz
    2017

    The paper introduces the AgileSafe method of selecting agile practices for software development projects that are constrained by assurance requirements resulting from safety and/or security related standards. Such requirements are represented by argumentation templates which explain how the evidence collected during agile practices implementation will support the conformity with the requirements. Application of the method is demonstrated by referring to a case study of development of a medical domain related application that is supposed to meet the requirements imposed by the IEC 62443-4.1 standard.

  • MEMS Gyro in the Context of Inertial Positionning
    • Jerzy Demkowicz
    2017

    The article undertake some vital aspect in geodesy, namely an inertial positioning problem using MEMS. Although MEMS inertial sensors offer affordable, appropriately scaled units, and though their inherent measurement noise can be relatively easily mitigated, there are still parameters due to they are not currently capable of meeting all requirements for the accurate and precise inertial positioning. The article presents crucial gyro errors usually not taken into account and not mentioned or omitted for some reasons, but crucial for MEMS record processing and of serious impact on overall inertial system performance. The results of undertaken researches in that area, and pointing out the main difficulties behind the INS when using a few top MEMS technologies where presented as well.

  • MEMS Technology Evaluation for Submerged Vehicle Navigation
    • Jerzy Demkowicz
    2017 Full text HYDROACOUSTICS

    Analysis of some vital aspects of inertial navigation using MEMS. The paper presents a few aspects of MEMS gyro errors, and their estimation process in the context of INS processing flow. These errors have a serious impact on overall inertial system performance. The results of undertaken researches in that area, and pointing out the main difficulties behind the INS when using a few top MEMS technologies, including sophisticated software were presented as well.

  • Mercury contamination, a potential threat to the globally endangered aquatic warbler Acrocephalus paludicola
    • Aneta Pacyna-Kuchta
    • Carlos Zumalacárregui Martínez
    • David Miguélez
    • Frédéric Jiguet
    • Żaneta Polkowska
    • Katarzyna Wojczulanis-Jakubas
    2017 Full text ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

    Mercury (Hg) contamination is considered a global concern for humans and wildlife, and although the number of studies dealing with that issue continues to increase, some taxonomic groups such as small passerine birds are largely understudied. In this paper, concentration of mercury in the aquatic warbler (Acrocephalus paludicola) feathers, a globally threatened passerine species, was examined. The concentration differences between two ages and sexes were investigated. The comparison of feathers taken on autumn migrants of two age categories act as a comparison of the species’ exposure within the two different areas (European breeding or African wintering grounds). The average Hg concentration for all sampled individuals [2.32 μg/g dw (range 0.38–12.76)] is relatively high, compared with values found in other passerine species. An age difference was found, with first-year individuals displaying higher mercury concentrations than adults. This indicates that birds are exposed to mercury pollution during the breeding season, i.e., in the continental floodplains of eastern Europe. The average Hg concentration in feathers grown on the breeding grounds was 3.88 ± 2.59 μg/g dw, closer to the critical value of 5 μg/g dw, which is considered to impair the health of individuals. The findings suggest that mercury pollution may constitute a threat so far neglected for the endangered aquatic warbler.

  • MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
    • Paweł Czarnul
    • Jarosław Kuchta
    • Mariusz Matuszek
    • Jerzy Proficz
    • Paweł Rościszewski
    • Julian Szymański
    • Michał Wójcik
    2017 Full text SIMULATION MODELLING PRACTICE AND THEORY

    In this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects and easily allows various formulas to model execution and communication times of particular blocks of code. A simulator engine within the MERPSYS environment simulates execution of the application that consists of processes with various codes, to which distinct labels are assigned. The simulator runs one Java thread per label and scales computations and communication times adequately. This approach allows fast coarse-grained simulation of large applications on large-scale systems. We have performed tests and verification of results from the simulator for three real parallel applications implemented with C/MPI and run on real HPC clusters: a master-slave code computing similarity measures of points in a multidimensional space, a geometric single program multiple data parallel application with heat distribution and a divide-and-conquer application performing merge sort. In all cases the simulator gave results very similar to the real ones on configurations tested up to 1000 processes. Furthermore, it allowed us to make predictions of execution times on configurations beyond the hardware resources available to us.

  • Metabolic activity of tree saps of different origin towards cultured human cells in the light of grade correspondence analysis and multiple regression modeling
    • Artur Wnorowski
    • Maciej Bilek
    • Kinga Stawarczyk
    • Michał Gostkowski
    • Marcin Olszewski
    • Magdalena Wójciak-Kosior
    • Ireneusz Sowa
    2017 Full text ACTA SOCIETATIS BOTANICORUM POLONIAE

    Tree saps are nourishing biological media commonly used for beverage and syrup production. Although the nutritional aspect of tree saps is widely acknowledged, the exact relationship between the sap composition, origin, and effect on the metabolic rate of human cells is still elusive. Thus, we collected saps from seven different tree species and conducted composition-activity analysis. Saps from trees of Betulaceae, but not from Salicaceae, Sapindaceae, nor Juglandaceae families, were increasing the metabolic rate of HepG2 cells, as measured using tetrazolium-based assay. Content of glucose, fructose, sucrose, chlorides, nitrates, sulphates, fumarates, malates, and succinates in sap samples varied across different tree species. Grade correspondence analysis clustered trees based on the saps’ chemical footprint indicating its usability in chemotaxonomy. Multiple regression modeling showed that glucose and fumarate present in saps from silver birch (Betula pendula Roth.), black alder (Alnus glutinosa Gaertn.), and European hornbeam (Carpinus betulus L.) are positively affecting the metabolic activity of HepG2 cells.

  • Metaboliczny potencjał energetyczny miast
    • Tomasz Parteka
    2017

    Tekst przedstawia koncepcje przepływów energii w strukturach zurbanizowanych. Zaprezentowano kolejno: metabolizm jako próbę oznaczenia zmiany, cechy anaboliczne i kataboliczne w dynamice miasta, nowe zwiastuny metabolizmu, rozlewanie i kurczenie się miast oraz "chirurgów" metabolizmu polskich miast.

  • Metalowe przegrody i obudowy ścian i dachów. Cz. 3. Wyroby z metali nieżelaznych
    • Dariusz Kowalski
    2017 Full text Builder

    Wyroby okładzinowe wykonane z materiałów metalowych stanowią istotny asortyment możliwości stosowanych zewnętrznych okładzin ściennych jak i dachowych. W wielu przypadkach zapewniają funkcje nośne dla fasad ściennych, w tym szklano-metalowych, jak i przekryć dachowych. W budownictwie stosujemy nie tylko materiały metalowe oparte na stali, lecz równie powszechnie wykorzystujemy materiały nieżelazne w postaci miedzi, aluminium, cynku.

  • Metalowe przegrody i obudowy ścian oraz dachów. Cz. 2. Wyroby stalowe
    • Dariusz Kowalski
    2017 Full text Builder

    W artykule przedstawiono możliwości kształtowania przegród ściennych, dachowych i osłonowych wykorzystujących technologię lekkiej obudowy, w której głównym elementem są materiały metalowe i kształtowane z nich wyroby.

  • Metalowe przegrody i obudowy ścian oraz dachów. Cz.1
    • Dariusz Kowalski
    2017 Full text Builder

    Materiały metalowe znajdują zastosowanie w konstrukcjach lekkich przegród budowlanych prawie we wszystkich rodzajach przegród i z uwagi na swoje właściwości spełniają różne funkcje, nawet w tak zaskakującym dla nich parametrze, jakim jest przezierność...

  • Method for the determination of carboxylic acids in industrial effluents using dispersive liquid-liquid microextraction with injection port derivatization gas chromatography–mass spectrometry
    • Patrycja Makoś
    • Andre Fernandes
    • Grzegorz Boczkaj
    2017 Full text JOURNAL OF CHROMATOGRAPHY A

    The paper presents a new method for the determination of 15 carboxylic acids in samples of postoxidative effluents from the production of petroleum bitumens using ion-pair dispersive liquid-liquid microextraction and gas chromatography coupled to mass spectrometry with injection port derivatization. Several parameters related to the extraction and derivatization efficiency were optimized. Under optimized experimental conditions,the obtained limit of detection and quantification ranged from 0.0069 to 1.12 ug/mL and 0.014 to 2.24 ug/mL, respectively. The precision (RSD ranged 1.29–6.42%) and recovery (69.43–125.79%) were satisfactory. Nine carboxylic acids at concentrations ranging from 0.10 ug/mL to 15.06 ug/mL were determined in the raw wastewater and in samples of effluents treated by various oxidation methods. The studies revealed a substantial increase of concentration of benzoic acids, in samples of wastewater after treatment, which confirms the need of carboxylic acids monitoring during industrial effluent treatment processes.

  • Method of determining the residual fluxes in transformer core
    • Jacek Horiszny
    2017

    The article presents the method of calculating the residual induction in transformer columns. The method is based on measurement of the magnetic induction in selected points around the transformer core. The values of residual induction are calculated as linear combination of the results of measurement.

  • METHOD OF ROUTING SHIPS SAILING IN DEDICATED ENVIRONMENT
    • Marcin Życzkowski
    2017 Full text Annual of Navigation

    The method for determining the suboptimal route of sailing vessels operating in a restricted area of the sea are proposed in the paper. The dynamics of the environment including weather conditions and speed characteristics of ships sailing are considered. As optimiza-tion criterion, measure sailing time T, and the number of maneuvers performed ω, are taken into account. An heuristic algorithm, and the appropriate application routing for fixed starting points and targets is designed in the method. In addition author analyzed the behavior of the algorithm, depending on the number of direction changes of the course, and granularity of the description of the surface of area.

  • Methodology for assessing the lighting of pedestrian crossings based on light intensity parameters
    • Piotr Tomczuk
    • Marcin Chrzanowicz
    • Tomasz Mackun
    2017 Full text MATEC Web of Conferences

    One of the possible preventive measures that could improve safety at crossings is to assess the state of illumination of the lighting installation located in the transition area for pedestrians. The City of Warsaw has undertaken to comprehensively assess the pedestrian crossings to determine the level of road safety and the condition of lighting. The lighting conditions related to pedestrian crossings without traffic lights in three central districts of the city were investigated. The conducted field research and the work of the team of experts lead to the development of tools to assess the level of risk due to the lighting conditions measured at night. The newly developed and used method of assessment and the experience gained should provide a valuable contribution to the development of uniform risk assessment rules for pedestrian crossings in Poland. The authors of this paper have attempted to systematize the description of the method of evaluation of the lighting installed in the area of pedestrian crossings.

  • Methodology of estimating temperature measurement uncertainty in a system for endurance tests.
    • Anna Golijanek-Jędrzejczyk
    • Ariel Dzwonkowski
    • Leszek Rafiński
    2017 Full text Zeszyty Naukowe Wydziału Elektrotechniki i Automatyki Politechniki Gdańskiej

    The team consisting of the article authors developed a non-invasive method and a system for measuring temperature during an endurance test. A thermocouple which provided the required accuracy of changes in temperature dynamics measurements was used for the purpose of the required research. The paper presents the methodology for estimating uncertainty of temperature measurement done with the presented system, using a method based on the GUM guide and a comparison with results obtained using the Monte Carlo method.

  • Methods of estimating the cost of traffic safety equipment’s life cycle
    • Beata Grzyl
    • Adam Kristowski
    • Kazimierz Jamroz
    • Anna Gobis
    2017 Full text MATEC Web of Conferences

    n the article, the authors discuss the preliminary information necessary to determine the scope and direction of further research conducted within the project called “The influence of time and operating conditions on the durability and functionality of road safety elements”. The main objective of the project is to develop the concept of a method for optimizing the life cycle costs of road safety devices. The authors draw attention to the close connection between the decisions taken at the design stage and expenses incurred in the course of maintenance and the use of road safety devices, present the specificity of road infrastructure in terms of life cycle costs, discuss the components of the costs and give examples of the LCC analysis applied to the concrete barrier.

  • Methods of measurement signal acquisition from the rotational flow meter for frequency analysis
    • Dariusz Świsulski
    • Robert Hanus
    • Marcin Zych
    • Leszek Petryka
    2017 EPJ Web of Conferences

    One of the simplest and commonly used instruments for measuring the flow of homogeneous substances is the rotational flow meter. The main part of such a device is a rotor (vane or screw) rotating at a speed which is the function of the fluid or gas flow rate. A pulse signal with a frequency proportional to the speed of the rotor is obtained at the sensor output. For measurements in dynamic conditions, a variable interval between pulses prohibits the analysis of the measuring signal. Therefore, the authors of the article developed a method involving the determination of measured values on the basis of the last inter-pulse interval preceding the moment designated by the timing generator. For larger changes of the measured value at a predetermined time, the value can be determined by means of extrapolation of the two adjacent interpulse ranges, assuming a linear change in the flow. The proposed methods allow analysis which requires constant spacing between measurements, allowing for an analysis of the dynamics of changes in the test flow, eg. using a Fourier transform. To present the advantages of these methods simulations of flow measurement were carried out with a DRH-1140 rotor flow meter from the company Kobold.

  • Metoda analizy syntaktycznej przestrzeni (space syntax analysis) jako narzędzie planistyczne
    • Weronika Maria Mazurkiewicz
    2017

    Artykuł dotyczy zastosowania analizy syntaktycznej przestrzeni (space syntax analysies) w procesie analiz planistycznych i planowania przestrzeni. Jest to narzędzie pozwalające na planowanie miasta, którego konfiguracja przestrzenna będzie sprzyjać interakcjom społecznym wewnątrz niego. Metoda analizy syntaktycznej przestrzeni stojąca na styku dziedzin pozwala na kompleksową analizę składni przestrzeni. Metodologia przydatna jest na każdym etapie planowania. Za jej pomocą możliwe jest opisanie i wytłumaczenie relacji przestrzennych, jak również przewidywanie skutków decyzji projektowych. Metoda znajdująca wielu zwolenników wśród zagranicznych urbanistów, socjologów, planistów, projektantów wnętrz, informatyków itd. nie jest jeszcze dobrze znana i rozpowszechniana w Polsce. W referacie zostanie opisana geneza metody analizy syntaktycznej przestrzeni, zostaną zdefiniowane jej podstawowe pojęcia, jak również ukazane zostanie jej zastosowanie umożliwiające planowanie tkanki miejskiej przyjaznej dla jej użytkowników. Na podstawie przykładu zastosowania tego narzędzia w przestrzeni urbanistycznej Londynu zostaną ukazane jego zalety. W rozwinięciu referatu każda z poszczególnych miar syntaktycznych, formuły matematyczne, oraz przedstawienie ich zastosowań podczas planowania przestrzeni przyjaznym ludziom zostaną również szczegółowo wyjaśnione.

  • Metoda analizy związanych z czasem wymagań dotyczących bezpieczeństwa systemów komputerowych
    • Grzegorz Gołaszewski
    2017 Full text

    Bezpieczeństwo jest pożądaną cecha systemów przemysłowych, transportowych i innych typów. A ponieważ do sterowania tymi systemami powszechnie stosuje się systemy komputerowe, jest ono również ważną cechą oprogramowania. Analiza bezpieczeństwa oprogramowania jest jednak, ze względu na jego niematerialność, trudniejsza od typowej analizy. Ponadto, ze względu na skomplikowane reguły sterujące oraz naturę kontrolowanych systemów, bezpieczeństwo może się opierać na skomplikowanych regułach czasowych. Celem przedstawionej rozprawy było zaproponowanie metody identyfikowania uwarunkowanych czasem wymagań względem systemu komputerowego na podstawie analizy bezpieczeństwa środowiska, z którym system ten współpracuje. Celem było również opracowanie narzędzi wspomagających zastosowanie proponowanej metody w odniesieniu do rzeczywistych przypadków komputerowych systemów związanych z bezpieczeństwem. Cel został zrealizowany poprzez stworzenie metody TREM (Timing Requirements sElection Method). Metoda ta wykorzystuje: - analizę drzew niezdatności rozszerzoną o zależności czasowe, - klasyfikację zdarzeń prostych w drzewie, - algorytm wywodzenia kandydujących wymagań czasowych. W ramach metody TREM zaproponowano cztery algorytmy określania zależności czasowych w Minimalnych Zbiorach Przyczyn (nazywanych również scenariuszami hazardu). Opracowano również dwa algorytmy redukcji nadmiarowości w zidentyfikowanych zależnościach czasowych. W celu określenia czasowych wymagań wobec systemu zaproponowano sposób klasyfikacji zdarzeń występujących w opisach scenariuszy hazardu oraz algorytm, który na podstawie tych danych przeszukuje scenariusze hazardu celem identyfikacji zależności czasowych, które uniemożliwiłyby wystąpienie danego scenariusza hazardu. W doborze tych zależności uwzględniane są ograniczenia dziedzinowe oraz możliwość wywarcia wpływu na opisywane w takiej zależności zdarzenia poprzez decyzje projektowe. Wszystkie wymienione algorytmy zostały zaimplementowane w ramach PolymorphFT2 – narzędzia wspierającego zaproponowaną metodę. Osiągnięte wyniki zostały ocenione w dwóch studiach przypadków, w których ocenione zostały zarówno złożoność obliczeniowa zaproponowanych algorytmów, względna pracochłonność użycia otrzymanych wyników w procesie zapewniania bezpieczeństwa analizowanego systemu oraz potencjał poprawy bezpieczeństwa systemu rozumiany jako odsetek scenariuszy hazardu, dla których udało zidentyfikować wymagania czasowe blokujące ich wystąpienie.