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1.
Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors
Marko Jukič, Dušanka Janežič, Urban Bren, 2020, original scientific article

Abstract: SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CLpro or Mpro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CLpro active site. These compounds will facilitate further 3CLpro inhibitor design.
Keywords: COVID-19, SARS-CoV-2, Mpro, 3CLpro, 3C-like protease, virtual screening, inhibitors, in silico drug design, free-energy calculations
Published: 10.12.2020; Views: 166; Downloads: 38
.pdf Full text (2,99 MB)

2.
The direct and indirect relationships between design orientation and market orientation
Sanja Rocco, 2019, doctoral dissertation

Abstract: The main purpose of this doctoral thesis is to investigate the relationship between design orientation and market orientation and propose a new conceptual model. Existing models were investigated. The initial conceptual model was proposed as the starting point. The research combined qualitative and quantitative methods. Quantitative research was conducted among managers and CEOs from Croatian companies in different industries. According to the final PLS-SEM model, design orientation has a direct and significant impact on market orientation and an indirect but significant impact on business success. Managerial approach has a direct and significant impact on design orientation, as well as on market orientation of a company. The new design orientation-market orientation model contributes to both marketing and design scholars, as well as implications for marketers, designers, and managers in practice. Our findings demonstrate that companies with higher level of market orientation and supported with design orientation also have the potential for achieving better results in the market and, consequently, better financial performance. It also provides the basis for future research on the topic.
Keywords: market orientation, design orientation, relationships, conceptual model, implications
Published: 22.07.2020; Views: 217; Downloads: 19
.pdf Full text (6,06 MB)

3.
FORMULATION, PREPARATION AND CHARACTERIZATION OF NANOEMULSIONS FOR PARENTERAL NUTRITION
Dušica Mirković, 2019, doctoral dissertation

Abstract: The aim of this doctoral research was to develop and optimize parenteral nanoemulsions as well as the total parenteral nutrition (TPN) admixture containing a nanoemulsion obtained in the course of the optimization process (hereinafter referred to as optimal nanoemulsion), and to examine their physicochemical and biological quality as well. In addition, the quality of the prepared nanoemulsions was compared with the quality of the industrial nanoemulsion (Lipofundin® MCT/LCT 20%), and, in the end, the TPN admixture initially prepared was also compared with the admixture into which the industrial emulsion was incorporated. Parenteral nanoemulsions that were considered in this dissertation were prepared by the high-pressure homogenization method. This method is the most widely applied method for the production of nanoemulsions due to the shortest length of homogenization time, the best-obtained homogeneity of the product and the smallest droplet diameter. For the nanoemulsion formulation, preparation and optimization purposes, by using, firstly, the concept of the computer-generated fractional design, and, after that, the full experimental design, the assessment of both direct effects of different formulation and process parameters (the oil phase type, the emulsifier type and concentration, a number of homogenization cycles and the pressure under which homogenization was carried out) as well as the effects of their interactions on the characteristics of prepared nanoemulsions was performed. Monitoring the nanoemulsion physical and chemical stability parameters was carried out immediately after their preparation, and then after 10, 30 and 60 days. It included the visual inspection, the measurement of the droplet diameter (the mean and volume droplet diameter), the polydispersity index, the ζ-potential, the pH value, the electrical conductivity, and the peroxide number. After the preparation and after 60 days, the biological evaluation (the sterility test and the endotoxic test) of the prepared nanoemulsions was carried out. As far as the characterization of the TPN admixture is concerned, it included practically the same parameters. The dynamics of monitoring the characteristics of the TPN admixture was determined on the basis of practical needs of hospitalized patients (0h, 24h and 72h). The scope and comprehensiveness of this issue indicated the need to divide the doctoral dissertation into three basic stages. The first stage was preliminary. Using the 24-1 fractional factorial design, nanoemulsions for the parenteral nutrition were prepared. They contained either a combination of soybean and fish oil, or a combination of medium chain triglycerides and fish oil. In addition, the type and the amount of an emulsifier used, a number of high-pressure homogenization cycles, and the homogenization pressure, were also varied. The measurement of the above-mentioned parameters for the industrial nanoemulsion was parallely carried out (Lipofundin® MCT/LCT 20%). The objective of this part of the research was to identify critical numerical factors having the most significant effect on the characteristics that define the prepared parenteral nanoemulsions. Parameters that were singled out as the result of this stage of the research (the emulsifier concentration and a number of homogenization cycles) were used as independent variables in the second stage of the research.
Keywords: nanoemulsions, total parenteral nutrition admixtures, high pressure homogenization, design of experiments, optimization, analysis of variance, artificial neural networks
Published: 07.06.2019; Views: 10734; Downloads: 0
.pdf Full text (2,82 MB)

4.
Models of social housing in post-war Syria
Stasha Jovanovikj, 2018, master's thesis

Abstract: abstract Civil war in Syria could be acknowledged as one of the greatest catastrophes of the 21st century, as it had a massive impact, even on a global scale. An abundant number of victims, large cities turned into ruins, 11 million people left without a home, and 5.6 million people who fled the country are just one piece of the Syria problem puzzle. The main issue that we are inquiring into is the housing problem of the people of Syria, especially those with lower social standing, without a home or a safe haven. Culture, tradition, and climate are crucial factors in designing models for residential architecture. These housing models have to be flexible and, with an optimal scale, offer an exceptional value for adjusting according to individual needs. In this thesis we propose a modular system for family houses and residential apartment buildings. In order to meet different needs and to respond to different site conditions in chosen locations, we present different housing models in various shapes, sizes, and functions. These can be implemented in any neighborhood design, which is presented through an example of building and rebuilding in the old city center.
Keywords: post-war architecture, modular architecture, urban design, urban regeneration, Syria
Published: 25.10.2018; Views: 497; Downloads: 180
.pdf Full text (107,10 MB)

5.
Design of geometry and numerical simulation of the operating characteristic of the rotor of the wind turbine
aljaž Janič, 2018, undergraduate thesis

Abstract: The diploma thesis consists of design and numerical simulation of the wind turbine. Geometries are designed according to two theories, the Betz theory and the Schmitz theory. I used Solidworks for 3D modeling of the both rotors. Using Ansys software package, we performed numerical simulations of a rigid body for two different wind speed regimes. We were interested in the angular velocity of the spinning blades, which in combination with moment give us power.
Keywords: Renewable energy, wind energy, numerical simulation, wind turbine, blade design, Betz and Schmitz theory
Published: 09.08.2018; Views: 620; Downloads: 142
.pdf Full text (2,19 MB)

6.
An unsaturated-soils approach to the bearing capacity of foundation structures
Taha Taskiran, 2017, original scientific article

Abstract: Unsaturated soils are maintaining their importance for researchers and there is still much need to investigate the many engineering aspects of these soils. A new technique is proposed here to predict the variation of the bearing capacity of unsaturated soils with matric suction. The proposed method is an extension of conventional bearing-capacity theories and conceptually based on the logarithmic model of the shear strength of unsaturated soils, which only include one unknown, unsaturated parameter (the airentry value, AEV). The possibility of predicting the unsaturated bearing capacity of soils is shown by the saturated effective shear-strength parameters c' and Ø' and the AEV from the soil-water retention curve (SWRC). Considering the necessity of validating new methods with other researchers’ data, the proposed equation is tested using the published unsaturated experimental study by the author, in addition to some reported experimental studies on the shear strength for unsaturated soils and also a model footing loading on unsaturated sand under controlled suction conditions. The results of the study indicate that there is a good comparison between the “unsaturated bearing capacities” obtained via predicted and measured unsaturated strength parameters (ctotal , Ø) and also between the measured/ calculated bearing values of a model footing loading. Consequently, it is shown that, without needing complex unsaturated testing facilities, the proposed equation is capable of predicting the unsaturated bearing capacity for both fine-grained and sandy soils, requiring only one unsaturated parameter, which can be obtained from the SWRC or predicted using the basic soil-index properties.
Keywords: unsaturated soils, unsaturated bearing capacity, suction strength, foundation design
Published: 18.06.2018; Views: 406; Downloads: 38
.pdf Full text (347,24 KB)
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7.
3D response of an excavation adjacent to buildings supported by inclined struts
Zahra Sabzi, Ali Fakher, 2017, original scientific article

Abstract: The presented study focuses on field observations and a 3D numerical analysis of open-cut excavations adjacent to a building supported by inclined struts. The performance of the struts in carrying the building loads and decreasing the deflections is investigated. Struts reduce the amount of deformations and also create a corner effect similar to the diaphragm walls corner. The influence of the distance between the struts is studied and the optimum struts interval is proposed. The most effective configuration of struts installation in reducing the deflections and building damage is proposed. A displacement-based design guideline is also presented based on the results of numerical studies.
Keywords: measurement, 3D finite-element analysis, displacement-based design
Published: 18.06.2018; Views: 309; Downloads: 35
.pdf Full text (2,85 MB)
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8.
A practical method for the optimal design of continuous footing using ant-colony optimization
Boonchai Ukritchon, Suraparb Keawsawasvong, 2016, original scientific article

Abstract: The objective of this paper is to present a practical method for the optimal design of a continuous footing subjected to vertical and horizontal loads. The design problem of finding the optimal size of footing as well as the minimum steel reinforcement is formulated in a nonlinear minimization form. The continuous footing is subjected to the vertical and horizontal loads acting on the top of the column. There are four design variables in the design problem, i.e., the width of the footing, the thickness of the footing, the soil-embedment depth, and the amount of steel reinforcement. The required geotechnical constraints include the bearing capacity, overturning, as well as global sliding and local sliding at the footing corners. Short-term stability and long-term stability are considered simultaneously in the same formulation. The structural constraints are enforced to control the shear force and bending moment within the section resistance. The formulation of the problem’s constraints leads to the nonlinear programming, whose objective function is to minimize the total cost of the footing material, including the concrete and steel reinforcement. The optimal solution is solved using the ant-colony optimization algorithm MIDACO. The proposed optimization method is demonstrated through the actual design of the footing for supporting a large machine moving on rails.
Keywords: optimal design, footing, stability, nonlinear programming, ant-colony optimization
Published: 18.06.2018; Views: 420; Downloads: 36
.pdf Full text (446,51 KB)
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9.
New Architecture of The Berane Airport
Ivan Pićurić, 2018, master's thesis

Abstract: This Master's Thesis explores the concept of the New Berane Airport that will serve as a turning point for improving the winter tourism offer of Montenegro and the region, thereby attracting a greater number of tourists to the country. The new facility must follow the guidelines of modern architecture, modern design, and the surrounding mountain landscapes, which represents an additional challenge in terms of construction and design. The main aim is to create an efficient structure, a new regional aviation centre, with well-designed transport links that will meet the needs of a large number of passengers and visitors from the region and the rest of the world. The visual aspects of the structure must be in line with the dominant type of architecture in the municipality of Berane, which is why the use of local materials and traditional elements has been foreseen. The new urban plan will follow the existing plan, although its capacity and content will be expanded in accordance with the former plans for the airport. In the planning phase, appropriate use of airport and traffic manuals is essential.
Keywords: airport, architecture, concrete, shell roof, glass facade, tourism, transport, parametric design, regional centre, Berane
Published: 15.06.2018; Views: 560; Downloads: 199
.pdf Full text (38,54 MB)

10.
A simplified approach to the settlement estimation of piled rafts
Volkan Kalpakci, Mehmet Yener Özkan, 2012, original scientific article

Abstract: In this study, a simplified approach to the settlement estimation of piled rafts resting on over-consolidated clay deposits is presented. For this purpose, a series of plane-strain and three-dimensional analyses were performed and their results are compared with the available data in the literature. It was found that the percentage decrease in the total settlements with the addition of piles with respect to the unpiled case is very closely estimated by both the plane-strain and the three-dimensional, simplified, numerical analyses. Using this phenomenon, a simple method of analysis is suggested for the total settlement estimation of the piled raft foundations and design charts are provided for the cases studied (for the specific soil conditions only) throughout this study.
Keywords: piled rafts, settlement, over-consolidated clay, foundation design
Published: 13.06.2018; Views: 342; Downloads: 39
.pdf Full text (481,96 KB)
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