NOVEL TRENDS IN CHEMISTRY, RESEARCH AND EDUCATION at the Faculty of Science of Pavol Jozef Šafárik University in Košice 2022

E-book

Erik Bruoth - Juraj Šebej - Ľubomír Antoni

In these university-level textbooks, we present the fundamental concepts of networks and graph theory. We explore breadth-first and depth-first graph searching. We present static and dynamic network models. We describe the issue of detecting overlapping and non-overlapping communities in directed and undirected networks. Various approaches to anomaly detection in networks also form an important part of this textbook. The final chapter is dedicated to spectral clustering, which plays a significant role in data mining in network graphs for various application domains.

These textbooks are suitable for first and second-year university students in computer science programs. The study materials are also suitable for students in non-computer science fields, with the aim of improving their knowledge and practical experience in computer science-related areas, and provide an opportunity for students to find employment in IT companies to solve practical tasks.

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E-book

Vladislav Kolarčik

Flow cytometry is a diagnostic and research technique that enables rapid analysis of cells, nuclei and organelles of plants and other organisms. In plant biology, it is most often used for DNA content analysis in a wide range of applications. It is the method of first choice and its importance is even increasing compared to competing technologies. It is unrivaled in speed, accuracy, repeatability and low cost. Flow cytometry has become a standard tool in laboratories focused on biological-ecological plant research.

This textbook provides information on the historical development of flow cytometry and its establishment in the analysis of the plant genome. It describes the procedure of sample analysis to determine the nuclear DNA content and presents the basic applications, such as determination of genome size, ploidy level and reproduction modes of plants and determination of endopolyploidy level in plant tissues. These college textbooks are intended for students, teachers and anyone interested in the use of flow cytometry in scientific work with plant cells.

Download e-book for free (pdf)

E-book

Karel Saksl

Solving crystal structures is the royal discipline of X-ray crystallography. Its primary task, with the exception of defects, is to describe the atomic structure of the motif that, by its repetition, fills the volume of the entire crystal or crystalline phase. This task is nowadays more or less routine for single-crystal X-ray diffraction, which can locate hundreds to thousands of non-hydrogen atoms in large unit cells. However, in real practice, we often have material available only in powder form instead of single crystals. Solving the atomic structure from its X-ray diffraction data is non-trivial, mainly because the three-dimensional diffraction space of a single crystal is reduced to one dimension by measuring a large number of randomly oriented microcrystals (crystallites). Therefore, the solution itself requires, in addition to proper measurement methodology, the selection of suitable tools, procedures, and strategies that, through optimization, will lead to the solution and refinement of the given crystalline phase. The current limit of this method is approximately 100 non-hydrogen atoms in the asymmetric part of the unit cell, which, however, is sufficient for most inorganic materials.

The goal of these educational texts is to provide students in the second and third levels of university studies with specific guidance on solving crystal structures from powder X-ray diffraction data. These scripts build upon my first monograph and require practical knowledge of its content. Similar to my previous monograph, I offer solved examples without a deep theoretical introduction, demonstrating procedures and strategies leading to the correct solution of crystalline phases using the freely available GSAS-II program. The examples are arranged from simpler to more complex, and the reader will find many useful pieces of information in the literature references as well as in the comments below the line. Part of these scripts are data intended for your individual practice of the described procedures. 

Karel Sakls

Download the e-book for free  (pdf)

 Andrej Oriňak - Renáta Oriňaková - Andrea Fedorková

Nanotechnology represent the fastest developing science in the present. They are based on the technologies that enable the matter manipulation at atomic level. Nanotechnology offer prepartion of the new materials with unknown and very specific properties and functions.Recent nanotechnology still stay in formative phase of their development. But more and more they are visible with nano-specific phenomenons in the fundamental control of the properties as well mater behaviour. This is quite possible that without nanotechnology will not work any science to the future, moreover that science will not exist anymore. Nanotechnolgy will give a chance and force to transform world to more environmental and comfortable. Expected is expansion of the nanotechnolgy to molecular nanosystems – heterogenous nets, in which molecules and supramolecules work as the nanodevices. The computers and robots will be reduced to the small and ultrasmall dimensions. In medicine will foremost the application of nanotechnology in genetic therapy and elimination of ageing. Nanosurgery will work at molecular level, cancer cells will be identified early and filtered , then substituted with healthy and unchanged. It is necessary to inform university or high school students  about principles of nanotechnolgy, preparation of the nanostructures, functionality of them and to offer full representation about molecular systems and nanodevices; the methods of nanostructures characterization and about application in miniaturized systems. 

Authors

E-book

Katarína Cechlárová - Eva Pitoňáková (eds.)

Proceedings of Abstracts from Contributions by Participants of the Student Scientific Conference at the Faculty of Science, UPJŠ in Košice, Held on April 26, 2017

This is the fifth edition of the proceedings from the Student Scientific Conference (ŠVK) at the Faculty of Science, Pavol Jozef Šafárik University in Košice. We are pleased that ŠVK has become an integral part of faculty life and a showcase for the quality of education provided. In 2017, ŠVK took place as part of the traditional Science Days on April 26, 2017. 105 students from the Faculty of Science presented their work. Contributions were organized into 15 sections, supplemented by an open programming competition involving 17 students and the final round of the IHRA competition, which included 27 teams from across Slovakia.

The abstracts in this proceedings demonstrate that students at the Faculty of Science, UPJŠ, acquire knowledge and skills in their field not only through theoretical study of disciplines but also through active engagement in solving partial scientific problems aligned with research goals at the faculty’s institutes. These abstracts also provide an overview of the faculty’s scientific activity, which we believe will be of interest to the broader public.

doc. RNDr. Gabriel Semanišin, PhD.

Dean of the Faculty

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Miroslava Martinková

This electronic material focuses on the subject of secondary metabolism and its products - secondary metabolites. The material gives an overview of the basic building blocks and construction mechanisms through which molecules can be synthesized in living organisms (plants). The processes of formation of the mentioned metabolites are explained using the basic mechanisms of organic reactions. Several of the secondary metabolites presented have a remarkable biological profile and are used as therapeutics or serve as lead compounds for the development of novel pharmacological agents. This electronic document is primarily intended for students of the Master's degree programme in Organic Chemistry as supporting material for the profile subject Chemistry of Natural Products.

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Vladimír Zeleňák (ed.)

Proceedings of Abstracts of the Student Scientific Conference of the Faculty of Science, Pavol Jozef Šafárik University in Košice

A characteristic feature of education at high-quality universities — among which the Faculty of Science at Pavol Jozef Šafárik University (UPJŠ) in Košice proudly belongs — is the close connection between education and scientific research. Students gain knowledge in their field of study not only through theoretical coursework in individual disciplines, but also through active involvement in solving specific scientific tasks as part of research teams. This can occur during the development of final theses or through participation in the Student Research Assistant Program (ŠPVS), which was revitalized at the faculty in 2015.

The Student Scientific Conference (ŠVK) is one of the faculty’s traditional events, organized during the Faculty’s Science Days as part of Sciencefest. By its very nature, it fits seamlessly into the aforementioned framework of combining education with research, and it has long enjoyed great popularity and student interest. In 2016, the conference featured presentations by 125 students of the Faculty of Science at UPJŠ in Košice, across 16 thematic sections. This collection of abstracts provides an overview of the focus and goals of the student projects. We believe it will serve as inspiration for other potential participants of future conferences and will also be of interest to the broader public, offering additional insight into the faculty's activities.

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Ľubomír Kováč

Učebný text „Zoogeografia“ objasňuje základné princípy a historický vývoj rozšírenia živočíchov na Zemi, a ďalej analyzuje faktory, ktoré ho ovplyvňujú. Vďaka moderným vedeckým metódam a technikám výskumu je zoogeografia veľmi dynamicky sa rozvíjajúcou disciplínou. Z geologických etáp je podrobnejšie spracovaná problematika paleoklimatických cyklov kvartéru, holocénu a vývoja postglaciálnej klímy, ktoré zohrali významnú úlohu pri dynamike vývoja živočíšnych areálov. Areálová analýza charakterizuje a triedi areály živočíchov a ich dynamiku v nadväznosti na speciáciu. Podrobne je spracovaná problematika zoogeografických oblastí s dôrazom na palearktickú oblasť. Časť zameraná na dynamickú zoogeografiu rieši najmä problematiku refúgií a reliktov v súvislosti s vývojom pleistocénnej paleoklímy. Text stručnou formou sumarizuje základné antropogénne faktory, ktoré v recentnej dobe drastickým spôsobom limitujú rozšírenie živočíchov v rýchlo ubúdajúcom prírodnom prostredí na Zemi. Text ďalej prehľadným spôsobom charakterizuje biogeografiu Karpát a faunu územia Slovenska. Záverečná časť prezentuje fylogeografiu ako modernú vednú disciplínu zameranú na rekonštrukciu migračných ciest v postglaciáli, ktorá je podložená analýzou molekulárnych markerov populácií živočíchov v širšom geografickom kontexte. 

Autor

Michal Jaščur -Michal Hnatič

In the textbook, the processes belonging to an area of  nonequilibrium physics, which make the basis for the study and analysis of compex phenomena  of statistical mechanics, are described. The Boltzmann equation for distribution function is derived and on this basis the hydrodynamic equations are constructed.  Stochastic processes are described separately and Fokker-Planck equation for density probability  is derived. Textbook is intended for the students of second year of master study at Faculty of Science of P. J. Šafarik University.   

Autors

E-book

Pavol Mártonfi

The university textbook deals with the latest knowledge from the systematics of vascular plants in a clear manner. Vascular plants arose in the Silurian period in the Paleozoic, when the first primitive plants moved from water to dry land, which required evolutionary progress in the morphological and anatomical structure of these plants. During about 420 million years of the existence of vascular plants, several of their main groups have evolved: the spore vascular plants, including the lycopods (branch Lycopodiophyta) and group of ferns and related plants (branch Monilophyta), and the seed plants, including gymnosperms (branch Gymnospermae) and angiosperms ( Angiospermae), which currently dominate among plants. The textbook provides a brief but comprehensive overview of the main groups, orders and families of plants with their description, distribution, main representatives, while also addressing the useful properties of selected species. The work is complemented by an overview of the system of plants by Cronquist, Tachtadžjan, APG and an overview of the families of the Slovak flora, as well as a taxonomic index.

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Jozef Strečka,Katarína Karľová

The 48th Conference of the Middle European Cooperation in Statistical Physics (MECO48) will be held on May 22nd-26th, 2023, in Stará Lesná, High Tatras, Slovakia. The MECO48 conference continues a long tradition of regular international meetings in the domain of statistical physics established in the early 1970s with the aim of bridging the gap between the communities of scientists from the Eastern and Western parts of Europe separated by the iron curtain. In the modern era the MECO conferences attract attention of the community of scientists who are active in the field of statistical physics including various interdisciplinary applications to biology, medicine, geography, finance, quantum information theory, and machine learning. The MECO48 conference is organized jointly by Faculty of Science of Pavol Jozef Šafárik University in Košice, Institute of Experimental Physics of Slovak Academy of Sciences in Košice, Institute of Physics, Slovak Academy of Sciences in Bratislava and Faculty of Humanities and Natural Sciences, University of Prešov under the financial support of Slovak Research and Development Agency (grant No. APVV-20-0150) and other sponsors.

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E-book

Andrej Mock

The structure of the animal body is extremely varied. Each species has its distinctive morphological features, which bears as a testimony to long-term development and belonging to the developmental lineage. At the same time, the body has been tested for a long time by natural conditions, resulting in unique adaptations to the environment and life strategy. Despite this admirable variety - which includes both recent and fossil animals and which we have far from mapped – a comparison of body parts brings knowledge we can generalize: the main building principles, and boundaries within which phenotypic diversity is realized.

Comparative animal morphology today uses the latest methodological material and knowledge from other disciplines, from genetics, molecular biology and experimental embryology, through progressive imaging methods (e.g. electron microscopy, computer micro-tomography) and the possibilities of subsequent software processing of image material (measurement, staining, etc.) to the view of physics, chemistry, statics and geometry on the structures (to nanostructures) of the living body. Detailed knowledge of historical and contemporary conditions on Earth is an important interpretative context in the study of animal morphology. Surprisingly, the knowledge accumulated after centuries of research is now rapidly supplemented by new knowledge, and often the traditional knowledge is subsequently reinterpreted. Finally, and no less important, in studying animal (and human) morphology, we learn surprising knowledge about ourselves.

The author of the presented textbook had the ambition in a simplified form to introduce the reader, especially the student of biological studies, into a dynamic and fascinating scientific discipline, as the current comparative animal morphology is.

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Tomáš Samuely

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Erik Čižmár

Textbook Automation of Laboratory Experiments in LabVIEW environment is devoted to the basics of graphical programming and shows the way how to communicate with measuring equipment and Arduino development boards in LabVIEW. The basic concepts of creating a virtual instrument and its interactive user environment are introduced. Three physical tasks are presented, the practical implementation of which takes place with the use appropriate instrumentation and LabVIEW. Practical tasks are dedicated to measuring the transmission characteristics of a low-pass RC filter, measuring the natural resonant frequency of a quartz tuning fork using the heterodyne pulse method, and mapping the magnetic field of a permanent magnet using Arduino.

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Adriana Zeleňáková - Jozef Bednarčík

Recenzovaný zborník príspevkov z vedeckej konferencie NANOVIR

Hlavným cieľom vedeckej konferencie NANOVIR bola prezentácia vedeckých výsledkov, získaných počas riešenia projektu NANOVIR – Nanočastice pre riešenie diagnosticko- terapeutických problémov s COVID-19, spolufinancovaného z Európskeho Fondu Regionálneho Rozvoja v Operačnom Programe Integrovaná Infraštruktúra 2014 – 2020, ITMS: 313011AUW7. Projekt bol riešený v období 1.1.2021 – 30.6.2023 a bol podporený sumou 1 916 004,79 EUR. Spolupodieľali sa na ňom tri spoluriešiteľské organizácie: Univerzita Pavla Jozefa Šafárika v Košiciach ako hlavný riešiteľ, Univerzita veterinárskeho lekárstva a farmácie v Košiciach ako partner č. 1 a Ústav experimentálnej fyziky Slovenskej akadémie vied ako partner č. 2.

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Valéria Skřivánková 

Predložený učebný text sa pokúša ilustrovať možné aplikácie Teórie pravdepodobnosti na príkladoch z oblastí (vo fyzike, chémii,  biológii, ekonomike, finančníctve, atď.), ktoré sú spestrené o úlohy na hľadanie optimálnej stratégie.

Text je určený predovšetkým poslucháčom Prírodovedeckej fakulty UPJŠ, budúcim učiteľom matematiky, študentom odboru matematika a informatika prípadne iným záujemcom, ktorí budú aplikovať pravdepodobnostné metódy pri riešení reálnych problémov. Obsahom pokrýva prvú časť predmetu "Pravdepodobnosť a štatistika".

Autorka

E-book

Erik Bruoth - Juraj Šebej - Ľubomír Antoni

In these university-level textbooks, we present the fundamental concepts of networks and graph theory. We explore breadth-first and depth-first graph searching. We present static and dynamic network models. We describe the issue of detecting overlapping and non-overlapping communities in directed and undirected networks. Various approaches to anomaly detection in networks also form an important part of this textbook. The final chapter is dedicated to spectral clustering, which plays a significant role in data mining in network graphs for various application domains.

These textbooks are suitable for first and second-year university students in computer science programs. The study materials are also suitable for students in non-computer science fields, with the aim of improving their knowledge and practical experience in computer science-related areas, and provide an opportunity for students to find employment in IT companies to solve practical tasks.

Download e-book for free (pdf)

E-book

Vladislav Kolarčik

Flow cytometry is a diagnostic and research technique that enables rapid analysis of cells, nuclei and organelles of plants and other organisms. In plant biology, it is most often used for DNA content analysis in a wide range of applications. It is the method of first choice and its importance is even increasing compared to competing technologies. It is unrivaled in speed, accuracy, repeatability and low cost. Flow cytometry has become a standard tool in laboratories focused on biological-ecological plant research.

This textbook provides information on the historical development of flow cytometry and its establishment in the analysis of the plant genome. It describes the procedure of sample analysis to determine the nuclear DNA content and presents the basic applications, such as determination of genome size, ploidy level and reproduction modes of plants and determination of endopolyploidy level in plant tissues. These college textbooks are intended for students, teachers and anyone interested in the use of flow cytometry in scientific work with plant cells.

Download e-book for free (pdf)

E-book

Karel Saksl

Solving crystal structures is the royal discipline of X-ray crystallography. Its primary task, with the exception of defects, is to describe the atomic structure of the motif that, by its repetition, fills the volume of the entire crystal or crystalline phase. This task is nowadays more or less routine for single-crystal X-ray diffraction, which can locate hundreds to thousands of non-hydrogen atoms in large unit cells. However, in real practice, we often have material available only in powder form instead of single crystals. Solving the atomic structure from its X-ray diffraction data is non-trivial, mainly because the three-dimensional diffraction space of a single crystal is reduced to one dimension by measuring a large number of randomly oriented microcrystals (crystallites). Therefore, the solution itself requires, in addition to proper measurement methodology, the selection of suitable tools, procedures, and strategies that, through optimization, will lead to the solution and refinement of the given crystalline phase. The current limit of this method is approximately 100 non-hydrogen atoms in the asymmetric part of the unit cell, which, however, is sufficient for most inorganic materials.

The goal of these educational texts is to provide students in the second and third levels of university studies with specific guidance on solving crystal structures from powder X-ray diffraction data. These scripts build upon my first monograph and require practical knowledge of its content. Similar to my previous monograph, I offer solved examples without a deep theoretical introduction, demonstrating procedures and strategies leading to the correct solution of crystalline phases using the freely available GSAS-II program. The examples are arranged from simpler to more complex, and the reader will find many useful pieces of information in the literature references as well as in the comments below the line. Part of these scripts are data intended for your individual practice of the described procedures. 

Karel Sakls

Download the e-book for free  (pdf)

 Andrej Oriňak - Renáta Oriňaková - Andrea Fedorková

Nanotechnology represent the fastest developing science in the present. They are based on the technologies that enable the matter manipulation at atomic level. Nanotechnology offer prepartion of the new materials with unknown and very specific properties and functions.Recent nanotechnology still stay in formative phase of their development. But more and more they are visible with nano-specific phenomenons in the fundamental control of the properties as well mater behaviour. This is quite possible that without nanotechnology will not work any science to the future, moreover that science will not exist anymore. Nanotechnolgy will give a chance and force to transform world to more environmental and comfortable. Expected is expansion of the nanotechnolgy to molecular nanosystems – heterogenous nets, in which molecules and supramolecules work as the nanodevices. The computers and robots will be reduced to the small and ultrasmall dimensions. In medicine will foremost the application of nanotechnology in genetic therapy and elimination of ageing. Nanosurgery will work at molecular level, cancer cells will be identified early and filtered , then substituted with healthy and unchanged. It is necessary to inform university or high school students  about principles of nanotechnolgy, preparation of the nanostructures, functionality of them and to offer full representation about molecular systems and nanodevices; the methods of nanostructures characterization and about application in miniaturized systems. 

Authors

E-book

Katarína Cechlárová - Eva Pitoňáková (eds.)

Proceedings of Abstracts from Contributions by Participants of the Student Scientific Conference at the Faculty of Science, UPJŠ in Košice, Held on April 26, 2017

This is the fifth edition of the proceedings from the Student Scientific Conference (ŠVK) at the Faculty of Science, Pavol Jozef Šafárik University in Košice. We are pleased that ŠVK has become an integral part of faculty life and a showcase for the quality of education provided. In 2017, ŠVK took place as part of the traditional Science Days on April 26, 2017. 105 students from the Faculty of Science presented their work. Contributions were organized into 15 sections, supplemented by an open programming competition involving 17 students and the final round of the IHRA competition, which included 27 teams from across Slovakia.

The abstracts in this proceedings demonstrate that students at the Faculty of Science, UPJŠ, acquire knowledge and skills in their field not only through theoretical study of disciplines but also through active engagement in solving partial scientific problems aligned with research goals at the faculty’s institutes. These abstracts also provide an overview of the faculty’s scientific activity, which we believe will be of interest to the broader public.

doc. RNDr. Gabriel Semanišin, PhD.

Dean of the Faculty

Download the e-book for free (pdf)