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National Repository of Grey Literature 2 records found  Search took 0.01 seconds. 
Non-adiabatic molecular dynamics of photochemical processes accelerated by machine learning
 Martinka, Jakub ; Pittner, Jiří (advisor) ; Sršeň, Štěpán (referee)
Nonadiabatic molecular dynamics is an important approach for the study of photochemical phenomena. Using a stochastic algorithm and a set of trajectories, it is possible to study phenomena where the Born-Oppenheimer approximation breaks down. This approach is limited by the size of the molecule and the length of time intervals that can be studied. Machine learning techniques, which have proven themselves in many different fields, can be a helpful tool. In this thesis, I focus on the applicability of a kernel ridge regression technique as a potential tool for accelerating nonadiabatic molecular dynamics simulations. Vinyl bromide is a small molecule with a heavy bromine atom, which from a computational point of view represents a suitable test system for nonadiabatic molecular dynamics with the inclusion of non-adiabatic and spinorbital couplings.
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Study of naphthalene access pathways to cytochrome P450 1A2.
 Martinka, Jakub ; Jeřábek, Petr (advisor) ; Kulhánek, Petr (referee)
Cytochrome P450 1A2 is a human liver enzyme of a hemoprotein nature that belongs to the evolutionarily ancient group of cytochromes P450. Cytochrome P450 substrates include a wide range of drugs and most procarcinogens, making it a crucial enzyme for the study of carcinogenesis. The main reaction catalyzed by cytochrome P450 1A2 is monooxygenation, in which an oxygen atom is incorporated into a substrate molecule. This reaction takes place at an active site which, in the case of published structure of cytochrome P450 1A2, is buried in the core of the catalytic domain without an accessible tunnels. Molecular modeling techniques allow the study of dynamic phenomena in large systems and are therefore also suitable for simulations of the transport of substrate molecules to the active site. The tunnels are being made accessible due to structural fluctuations. In this work, molecular modeling techniques were used to study the pathways that the naphthalene molecule uses to enter the active site of cytochrome P450 1A2. A system consisting of cytochrome P450 1A2 anchored in a phospholipid membrane, water, ion and naphthalene molecules was simulated. The simulations yielded trajectories with a total length of 8 µs and the analysis identified seven tunnels that can be used to transport substrates....
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See also: similar author names
2 Martinka, Jan
1 Martinka, Jiří
2 Martinka, Jozef
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