Theses | Faculty of Chemistry at the Gdańsk University of Technology

2022

1. Krzysztof Jasieński (Eng thesis): Catalytic mechanism of ATP synthase

2021

1. Antoni Marciniak (MSc thesis): Molecular mechanism of the unidirectional rotation of the c-ring in ATP synthase
2. Michał Olewniczak (MSc thesis): Mechanism of the facilitated diffusion of fatty acids through lipid membranes -- the example of the FadL protein
3. Michał Jurkowski (MSc thesis): Why do G-quadruplexes show strong preference for right-handed conformations?
4. Laura Godzwon (Eng thesis): Assessment of the possibility of extending the antimicrobial spectrum of diarylquinoline drugs using molecular docking

2020

1. Michał Olewniczak (Eng thesis): How do mutations of presenilin alter the substrate binding mode in the catalytic site of gamma-secretase?
2. Michał Jurkowski (Eng thesis): Allosteric mechanisms in model proteins studied by molecular simulations
3. Karol Jacek (Eng thesis): Interdomain communication within the hERG potassium channel using molecular dynamics simulations
4. Antoni Marciniak (Eng thesis): Coupling mechanism between the rotary motion of the membrane portion of ATP synthase with electrochemical proton gradient across the inner mitochondrial membrane

2019

1. Joanna Słabońska (MSc thesis): Mechanism of inhibition of ATP synthase by an antitubercular drug bedaquiline
2. Szymon Orkisz (MSc thesis): Energy transduction pathways within the catalytic subunit of ATP synthase
3. Miłosz Wieczór (PhD thesis): Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
4. Mateusz Kogut (PhD thesis): Thermodynamics of DNA interactions and structural transitions in water solutions based on molecular dynamics simulations
5. Łukasz Nierzwicki (PhD thesis): Biomolecular simulations as a tool for studying the recognition and binding mechanisms of proteins

2018

1. Prokopowicz Bartosz (Eng thesis): Allosteric communication pathways within ATP synthase
2. Adamczak Beata (PhD thesis): Effect of osmolytes on protein stability revealed by molecular dynamics simulations
3. Paweł Chodnicki (MSc thesis): Molecular details of the interaction between the antiviral IFITM proteins and influenza fusion peptides within a phospholipid membrane

2017

1. Chodnicki Paweł (Eng thesis): Molecular driving forces behind lateral phase separation in lipid bilayers
2. Kleist Cyprian (MSc thesis): Stability of G-quadruplexes and their aggregates characterized in molecular detail
3. Wityk Paweł (MSc thesis): Effect of local sequence on the number of strand breaks in irradiated DNA  labeled with bromouracil
4. Jurasz Jakub (MSc thesis): Development of an efficient protocol of virtual screening for identification of new inhibitors

2016

1. Dutkiewicz Mateusz (Eng thesis): Molecular mechanism of energy conversion in ATP synthase
2. Kleist Cyprian (Eng thesis): Association of G-quadruplex DNA – a numerical approach
3. Jaworski Kamil (MSc thesis): Statistical methods in analysis of numerical data from dynamic simulations of biomolecular systems
4. Wieczór Miłosz (MSc thesis): Self-association of amphotericin B in water solution

2015

1. Nierzwicki Łukasz (MSc thesis): Can specific interaction with amyloid precurssor protein underlie the cholesterol-induced acceleration of amyloidogenesis?
2. Harasimowicz Judyta (MSc thesis): Molecular determinants of the effect of osmolytes on structural stability of DNA – a Molecular Dynamics study
3. Gdaniec Paulina (MSc thesis): Stochastic processes in analysis of numerical data from dynamic simulations of biomolecular systems

2014

1. Nierzwicki Łukasz (Eng thesis): Specific binding of cholesterol to the Amyloid Precursor Protein characterized in molecular detail
2. Judyta Harasimowicz (Eng thesis): Effect of osmolytes on structural stability and dynamics of DNA – a numerical approach
3. Wityk Paweł (Eng thesis): Effect of excess electron on the stability of brominated analogs of nucleobases through ab initio Molecular Dynamics
4. Wieczór Miłosz (Eng thesis): A Molecular Dynamics analysis of TRF1/TRF2 mechanisms of sequence recognition and DNA binding
5. Tobiszewski Adrian (MSc thesis): Telomeric DNA/protein complexes as potential targets for anticancer drugs – a Molecular Dynamics study

2013

1. Toczydłowska Diana (Eng thesis): Molecular Dynamics as a method to study the effect of osmolytes on DNA structure and stability
2. Adamczak Beata (MSc thesis): Hydration of aminoacids studied by molecular dynamics
3. Kogut Mateusz (MSc thesis): Molecular determinants of stability of DNA G-quadruplexes – a computational approach