
Selfassembled polymer systems responsive to external stimuli for biomedicine
Babuka, David ; Štěpánek, Petr (advisor) ; Pánek, Jiří (referee) ; Sedláček, Jan (referee)
Stimuliresponsive selfassembled polymer nanoparticles are becoming increasingly more important tools in nanomedicine. In this thesis we studied two large sets of polymer samples designed to be capable of such selfassembly. Polymers in the first set, containing poly(2methyl2oxazoline) or poly[N(2hydroxypropyl) methacrylamide] hydrophilic blocks and poly[N(2,2difluoroethyl)acrylamide] thermoresponsive block, were designed to act as 19F MRI contrast agents. Polymers in the second set were designed as drug delivery systems and were based on 2methyl2oxazine for hydrophilic parts and 2propyl2oxazoline for thermoresponsive or 2butyl2oxazoline for hydrophobic parts. Both sets of copolymers were prepared with various ratios of monomers in their blocks and the second set was also prepared with gradient chain architecture. Properties of their selfassembled systems were studied in detail and compared with regard to their potential for biomedical applications. The primary used method of analysis was dynamic light scattering supported by a vast array of methods including static light scattering, small angle Xray and neutron scattering, nuclear magnetic resonance and others. From the investigated copolymers the most promising candidates for biomedical applications were selected and highlighted.


BEHAVIOR OF THE CONCRETETOCONCRETE INTERFACE WITHOUT SHEAR REINFORCEMENT
Čairovič, Dorde ; Terzijski, Ivailo (referee) ; Čajka,, Radim (referee) ; Štěpánek, Petr (advisor)
Doctoral thesis focuses on behavior of the interface between two concrete layers cast at different times and without shear reinforcement. By means of both experimental and numerical analysis, some of the factors affecting interface strength have been assessed. Namely, surface roughness and suitability of different roughness parameters used for its characterization, effects of overlay mechanical properties and collateral effects of surface preparation methods. Also, different tests to assess interface strength have been investigated in detail and mutually compared. The most suitable roughness parameters have been chosen, based on its overall stability. Correlation between mean texture depth and other parameters have been defined. Results of the experimental program intended to further investigate abovementioned effects on interface strength, led to proposition of extended semi quantitative design approach and introduction of coefficient of surface preparation. Based on the extensive experimental program, correlation between different test setups, including its main advantages and disadvantages, has been presented, together with roughness characterization and failure envelope of the dimpled interface.


Molecular dynamics simulations of complexes consisting of proteins and nucleic acids
Šmít, Daniel ; Barvík, Ivan (advisor) ; Štěpánek, Petr (referee)
Na/ev pracc: Molekularnedynamicke simulace komplcxu sestavajicich z nukleovyeh kyselin a proleinu Autor: Daniel Snu't Katedra (ustav): Fy/ikalni ustav UK Vedouci hukalafskc prace: RNDr. Ivan Barvik. Ph.D. email vedoueiho: iharvikiY/'karlov.mff.euni.c/ Abstrakt: Prace od /akladu se/namujc s biochemickymi principy. struklurou nukleovych kysclin a aminokyselin, stavbou proleinu a mechanismem jejich synte/y. /vlastni zfetel jc kladen na /pusoby replikacc nukleovych kysclin ruznyeh viru a na mo/nosli lerapie zalozene na interferenci s toulo replikaci. Dale jsou nastmeny i jine moderni melody lerapie spoci'vajici v modulaci imunity ei vyu/ili RNA interference. Struklura viru IICV je podrobne popsana. Replikacni en7\'in viru. IK'V RNA depcndenlni KNA polymcra/a, je podrt>bne popsan spolu s pfedpokladunym prubehcm jelut iniciace a poKmeracni akiiviiy. Dale jsou popsans /aklady molekularne dynamickych (Ml)) simulaci. ktere jsou v ranici bakalafske prace denionstrovany na jednoduchem modelovem systemu argonoveho clusteru. V druhe polovinc prace jsou provedeny MD simulace inhihice IK'V RclRp prostrednictvim lalek PMIXi, PMPG a IIPMPG. Struklura a stabilita komplexu je dctailnc analy/ovana na atomarni urovni. Klicova slova: molekularni dynamika. nuklcove kyseliny, IICV. IIPMIJ(j Title: Molecular dynamics simulations...


Koordinace mezi logickými agenty
Krištofič, Milutín ; Štěpánek, Petr (advisor) ; Vojtáš, Peter (referee)
In this thesis, we study the recent models for coordination and we propose a new model based on argumentation system. This system, named Argumentation BlackBoard for Coordination (ABBC), and its extension, Abstract ABBC, are based on successful argumentation approaches, such as abstract argumentation framework and defeasible logic programming. Our aim is to present necessary argumentation elements in open multiagent system that consists of logic agents. In this work, we also describe a brief software design for the system.


Communication in MultiAgent Systems
Bosík, Andrej ; Štěpánek, Petr (advisor) ; Gregor, Petr (referee)
This thesis analyses the questions of communication between agents in MAS. Firstly, I tried to introduce a logic agents, particularly logic rational agents. For rational logic agents characterization I used LORA logic. I illustrated the syntax and the semantic of LORA. Then I concentrated on architecture MAS according to a FIPA specification. I used the JADE environment as implementation of this architecture. JADE is fully implemented in the JAVA language. I described how the communication between two JADE agents works and what form and parameters the messages according to the ACL language have. FIPA developed the ACL language for communication between agents. I described how agents use the protocols. JADE didn't contain any protocol for negotiation. That is why I integrated a new VETO protocol into JADE. This protocol can use all the JADE agents. In order to do it, I integrated new message parameters into JADE. This message parameters extend the ACL message parameters. For demonstration I implemented two classes in the JADE (one for the initiator and one for the responder) using a Veto protocol. Further, I described how new negotiation protocols could be add to JADE. For example I added to JADE another negotiation protocol, called NEGO. At last I used my new implemented ability to negotiation on...


Verefication of Mathematical Proofs
Pudlák, Petr ; Štěpánek, Petr (advisor) ; Haniková, Zuzana (referee) ; Plátek, Martin (referee)
In this thesis we deal with the problem of automatic proving (or disproving) mathematical conjectures using computer programs (usually called automated theorem provers). We address several issues that are important for a successful utilization of such programs. In Chapter 3 we examine how to store and reuse important pieces of mathematical knowledge in the form of lemmas. We investigate how this process can be automatized, i.e. how a computer can construct and use lemmas without human guidance. The program we develop tries to shorten or to speed up the proofs of several conjectures from a common theory. It repeatedly extracts lemmas from the proofs it has already completed and uses the lemmas to improve the sets of premisses to produce more efficient proofs of the conjectures. In Chapter 4 we develop a new algorithm that tries to construct the optimal sets of premisses for proving and disproving mathematical conjectures. The algorithm semantically analyzes the conjectures and the set of premisses of the given theory to find the optimal subsets of the premisses. The algorithm uses an automated model finder to construct models that serve as counterexamples that guide the algorithm to find the optimal set of premisses. In Chapter 5 we use the algorithm to decide formulae in a wide range of modal systems. We...


Formal description of board games
Nowak, Stanislav ; Štěpánek, Petr (advisor) ; Kunčar, Ondřej (referee)
The aim of thesis was to design a mathematical formalism that allows describing and exploring the properties of board games. The work benefits from the findings of automata theory and logic programming. First part of thesis deals with finite automata and their possible applications for the needs of board games. The result is an extension of finitestate automaton covering the specifics of board games called game automaton. Board games are a complex domain hight level tools should be used. Such a tools is a logical programming. Using logic programming was designed instrument that allows declarative descriptions of games, named gaming system. This declarative description is used as an framework for the implementation of interactive games. Linking the two worlds will be demonstrated by conversion of the gaming system to the game automaton.


MultiAgent systems and organizations
Kúdela, Lukáš ; Štěpánek, Petr (advisor) ; Neruda, Roman (referee)
Multiagent systems (MAS) are emerging as a promising paradigm for conceptualizing, designing and implementing largescale heterogeneous software systems. The key advantage of looking at components in such systems as autonomous agents is that as agents they are capable of flexible selforganization, instead of being rigidly organized by the system's architect. However, selforganization is like evolutionit takes a lot of time and the results are not guaranteed. More often than not, the system's architect has an idea about how the agents should organize themselveswhat types of organizations they should form. In our work, we tried to solve the problem of modelling organizations and their roles in a MAS, independent of the particular agent platform on which the MAS will eventually run. First and foremost, we have proposed a metamodel for expressing platformindependent organization models. Furthermore, we have implemented the proposed metamodel for the Jade agent platform as a module extending this framework. Finally, we have demonstrated the use of our module by modelling three specific organizations: remote function invocation, arithmetic expression evaluation and sealedbid auction. Our work shows how to separate the behaviour acquired through a role from the behaviour intrinsic to an agent. This...


Transformation of Logic Programs
Vyskočil, Jiří ; Štěpánek, Petr (advisor) ; Vomlelová, Marta (referee) ; Mařík, Radek (referee)
This paper is a contribution to improving computational e fficiency of de nite Prolog programs using Unfold/Fold (U/F) strategy with homeomorphic embedding as a control heuristic. Unfold/Fold strategy is an alternative to so called conjunctive partial deduction (CPD). The ECCE system is one of the best system for program transformations based on CPD. In this thesis is presented a new fully automated system of program transformations based on U/F strategy. The experimental results, namely CPU times, the number of inferences, and the size of the transformed programs are included. These results are compared to the ECCE system and indicate that in many cases both systems have produced programs with similar or complementary e fficiency. Moreover, a new method based on a simple combination of both systems is presented. This combination represents, to our best knowledge, the most effective transformation program for normal logic programs. In most cases, the combination signi cantly exceeds both the Unfold/Fold algorithm presented here and the results of the ECCE system. The experimental results with a complete comparison among these algorithms are included.


Data and Ontologies
Kotowski, Jakub ; Štěpánek, Petr (advisor) ; Vojtáš, Peter (referee)
In the core of current semantic web efforts is the notion of ontology. Although ontologies have been explored since times of the Greek philosopher Aristotle already there is still much to learn in this area. There are many tutorials and introductory texts both into the semantic web as whole and into its individual technologies but the learning curve is still very steep and developers have to seek answers to questions that are often topic of current research or the answer is simply not known yet. Much of these difficulties one encounters at what is often the very first step towards building a semantic web application  creating an ontology. In this work I point out some of the difficulties I encountered myself during the work on an ontology for a Sun Microsystems website. I review current research on the problems and suggest a solution. I particularly analyze the notion of role concepts, suggest an improvment of a normalisation technique which can then be used to avoid some of the rolerelated problems. I also present the process of creating the example Sun ontology.
