Interakce peptidů s modifikovanými lipidovými membránami (Počítačová studie)
| Thesis title in Czech: | Interakce peptidů s modifikovanými lipidovými membránami (Počítačová studie) |
|---|---|
| Thesis title in English: | Interactions of peptides with modified lipid membranes (Computer study) |
| Key words: | peptidy; lipidové membrány; disipativní částicová dynamika; zhrubený model; |
| English key words: | peptides; lipid membrane; dissipative particle dynamics; coarse-grained model; |
| Academic year of topic announcement: | 2019/2020 |
| Thesis type: | Bachelor's thesis |
| Thesis language: | čeština |
| Department: | Department of Biochemistry (31-250) |
| Supervisor: | doc. Ing. Zuzana Limpouchová, CSc. |
| Author: | hidden - assigned by the advisor, waiting for guarantor's approval |
| Date of registration: | 22.11.2019 |
| Date of assignment: | 22.11.2019 |
| Date of electronic submission: | 15.06.2020 |
| Date of proceeded defence: | 27.07.2020 |
| Opponents: | Mgr. Petr Jeřábek, Ph.D. |
| Advisors: | prof. RNDr. Jiří Hudeček, CSc. |
| Guidelines |
| Termodynamika a statisticka fyzika Vybrane partie z matematiky |
| References |
| [1] D. Ciumac, H.N. Gong, X.Z. Hu, J.R. Lu, Membrane targeting cationic antimicrobial peptides, Journal of Colloid and Interface Science 537 (2019) 163-185. [2] A. Bunker, A. Magarkar, T. Viitala, Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation, Biochimica Et Biophysica Acta-Biomembranes 1858(10) (2016) 2334-2352. [3] S. Hezaveh, S. Samanta, A. De Nicola, G. Milano, D. Roccatano, Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer Using Coarse-Grained Molecular Dynamics Simulations, Journal of Physical Chemistry B 116(49) (2012) 14333-14345. [4] R.D. Groot, P.B. Warren, Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation, Journal of Chemical Physics 107(11) (1997) 4423-4435. [5] M. Mueller, K. Katsov, M. Schick, Biological and synthetic membranes: What can be learned from a coarse-grained description?, Physics Reports-Review Section of Physics Letters 434(5-6) (2006) 113-176. [6] R.S. Katiyar, P.K. Jha, Molecular simulations in drug delivery: Opportunities and challenges, Wiley Interdisciplinary Reviews- Computational Molecular Science 8(4) (2018). |
| Preliminary scope of work |
| V rámci navrhovaného bakalářského projektu bude studována interakce peptidů a biopolymerů s povrchy membrán modifikovanými různými receptory. Simulace budou prováděny pomocí disipativní částicové dynamiky (DPD), což je jedna z variant molekulární dynamiky. Vzhledem k tomu, že DPD pracuje se zhrubeným modelem látek a s tzv. měkkým potenciálem, umožňuje dostatečně dlouhé simulace dostatečně velkých systémů. |
| Preliminary scope of work in English |
| This bachelor project will be focused on the interaction of peptides and of other biopolymers with membrane surfaces modified by receptors. The simulations will be performed by means of dissipative particle dynamics (DPD), which belongs to the family of molecular dynamics methods. As the DPD method uses coarse-grained model of compounds and so called soft potential, it enables the simulations of large enough systems for sufficiently long times to study above mention effects. |