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Coordinated pathfinding with formations
Obrázek, Václav ; Surynek, Pavel (advisor) ; Balyo, Tomáš (referee)
The topic of cooperative pathfinding with the extension of formations is addressed in this thesis. The problem of cooperative pathfinding with formations was formally defined and a new scalable hierarchical modular solving algorithm named APriCA was introduced and implemented. For testing and benchmarking purposes an environment called ChessWars was developed. In order to measure the quality of maintaining formations we introduced a new quantity named "fragmentation". The APriCA algorithm performed better than external domain independent planners such as LPG, Blackbox and SASE in all aspects. In comparison with the LRA* algorithm the solutions found by APriCA were of better quality and with certain parameters settings were found faster.
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Theoretical study of enzymes related to carcinogenesis: DNA polymerase β and cytochromes P450
Jeřábek, Petr ; Martínek, Václav (advisor) ; Entlicher, Gustav (referee) ; Ettrich, Rüdiger (referee)
Present doctoral thesis contributed to understanding of mechanistic principles of two enzymes participating in the process of carcinogenesis; DNA polymerase (pol ) and cytochromes P450 (CYP). Pol is part of the DNA base-excision repair mechanism (BER). The primary role of pol in, the BER mechanism, is inserting a new nucleotide into a DNA strand according to Watson-Crick base pairing rules. Pol plays an important role in the process of carcinogenesis, approximately 30 % of human tumors express pol mutants. The ability of pol to discriminate between "right" and "wrong" nucleotide during the insertion process is called fidelity. We employed computational methods to elucidate molecular basis of the fidelity of pol . First, the relative free energy calculation method LRA was employed to compare differences in free energies between the "right" and "wrong" nucleotide during its insertion into DNA. The results indicated a better stabilization of transition-state of the nucleophilic substitution catalyzed by pol in the case of the "right" versus "wrong" nucleotide. This difference resulted in an 80-fold contribution to its fidelity. Further, computational methods FEP and LIE were used to examine how mutations effect fidelity of pol . Results were than correlated with experimental data...
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Coordinated pathfinding with formations
Obrázek, Václav ; Surynek, Pavel (advisor) ; Balyo, Tomáš (referee)
The topic of cooperative pathfinding with the extension of formations is addressed in this thesis. The problem of cooperative pathfinding with formations was formally defined and a new scalable hierarchical modular solving algorithm named APriCA was introduced and implemented. For testing and benchmarking purposes an environment called ChessWars was developed. In order to measure the quality of maintaining formations we introduced a new quantity named "fragmentation". The APriCA algorithm performed better than external domain independent planners such as LPG, Blackbox and SASE in all aspects. In comparison with the LRA* algorithm the solutions found by APriCA were of better quality and with certain parameters settings were found faster.
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