Institute of Physics, Polish Academy of Sciences
32/46 Lotników Ave., 02-668 Warsaw
tel. +48 22 116 3365; e-mail: email@example.com
Head: Marek Cieplak
The Computer Laboratory operates using an integrated cluster of servers with about 200 cores. 72 of them, with accessories, has been funded by the NanoFun project.
The research activities are focused on modeling biological and nanotechnological systems. A big part of studies involve molecular dynamics simulations either within all-atom or coarse–grained models. The former are employed primarily in the context of interactions of proteins and amino acids with solids, such as gold, mica, ZnO, and ZnS. We determine the potentiais of the mean force for amino acids and determine structural deformations of proteins adsorbed to the solid. The coarsegrained models are used for studies of large conformational changes in biomolecules, such as that take place during protein folding, unfolding and stretching. These processes involve time scales which are well beyond capabilities of atomic-level approaches.
Our greatest expertise is in understanding the mechanisms of unraveling proteins through mechanical pulling, e.g. by a tip of the atomic force microscope. We have made surveys of almost 20 000 proteins and discovered novel modes of resistance to stretching. We have identified proteins with a particularly high mechanostability – higher than in the muscle protein titin and in the proteins that are present in the silk produced by spiders.
Publications based on the research performed in this NanoFun Laboratory:
- Mateusz Chwastyk, Mariusz Jaskolski, and Marek Cieplak, The volume of cavities in proteins and virus capsids, Proteins 2016; 84:1275–1286, link
- Mateusz Chwastyk et al. Theoretical tests of the mechanical protection strategy in protein nanomechanics, Proteins: Structure, Function, and Bioinformatics, 19 Feb 2014, link
- Marek Cieplak, Mechanostability of virus capsids and their proteins in structure-based Models, Computational methods to study the structure and dynamics of biomolecules and biomolecular processes - from bioinformatics to molecular quantum mechanics - Spriger, link
- Mateusz Chwastyk, Mariusz Jaskolski, Marek Cieplak, Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins – case study of plant pathogenesis-related proteins of class 10, FEBS Journal, 2013, 281, 1, 416–429, link
- Marek Cieplak, Jayanth R. Banavar, Energy landscape and dynamics of an HP lattice model of proteins – the role of anisotropy, Europhysics Letters, 104 (2013) 58001, link
- Marek Cieplak, Jayanth R. Banavar, Energy landscape and dynamics of proteins: An exact analysis of a simplified lattice model, Physical Review E, 88, 040702(R) –22 Oct 2013, link
- Grzegorz Nawrocki, Marek Cieplak, Amino acids and proteins at ZnO–water interfaces in molecular dynamics simulations, Physical Chemistry Chemical Physics, 14 Jun 2013, 15, 8132-8143, link
- Marek Cieplak, Mark O. Robbins, Nanoindentation of 35 virus capsids in a molecular model: Relating mechanical properties to structure, PLOS ONE, 13 June 2013, link
- Damien Thompson et al. A multi-scale molecular dynamics study of micron-size supraparticle assembly from alkyl-coated 30 nm nanoparticles, Physical Chemistry Chemical Physics, 2013 Jun 7;15(21):8132-43, link
- M. Sikora, M. Cieplak, Formation of cystine slipknots in dimeric proteins, PLOS ONE, 2013, link
- Mateusz Sikora, Marek Cieplak, Cystine plug and other novel mechanisms of large mechanical stability in dimeric proteins, Physical Review Letters, 109, 208101, 13 Nov 2012, link
- Mateusz Sikora et al., Geometrical and electrical properties of indium tin oxide clusters in ink dispersions, Langmuir, 2012, 28 (2), pp 1523–1530, link