Theory and computer simulation of interactions between lipid membranes and nano-objects
Modelling of interactions of nanostructured surface patterns with cells and proteins
Development of new scientific methods and efficient parallel codes for GPU using CUDA and machine learning. (Recent publications)
The direct proof of this size-dependent translocation was provided by an in situ observation of a single event of a nanoparticle quitting the bilayer. We identified the threshold size for translocation: nanoparticles with diameters <5 nm stay trapped in the bilayer, whereas those with diameters >5 nm insert into the bilayer. (Science Advances DOI: 10.1126/sciadv.1600261).
The nanopattern on the surface of Clanger cicada wings represents the first example of a new class of biomaterials that can kill bacteria on contact based solely on their physical surface structure. We propose a biophysical model of the interactions between bacterial cells and cicada wing surface nanopatterned structure. (Nature DOI: 10.1038/nature.2013.12533)
First reported physical bactericidal activity of black silicon nanopattern. We show that the nanoprotrusions on the surfaces of black silicon structures generate a mechanical bactericidal effect, independent of chemical composition. It represents an excellent prospect for the development of a new generation of mechano-responsive, antibacterial nanomaterials. (Nature Com. DOI: 10.1038/ncomms3838).
We find that the energy cost of the bilayer rupture is quite high compared to that of the energy of thermal motion. This conclusion may indirectly support other energy-dependent translocation mechanisms, such as, for example, endocytosis. (ACS Nano DOI: 10.1021/nn1016549).
Together with Prof. Elena Ivanova from RMIT University, Australia, we develop theoretical models to understend the mechanism of bacteria killing mechanism due to mechanical cell rupture by nanostructures. The goal of this project is to identify the criteria for cell toxicity and biocidal activity of a nanopatterned surfaces.
Dragonfly expedition to Massif Els Ports in collaboration between Museu de les Terres de l'Ebre, Amposta and Universitat Rovira i Virgili, Tarragona.
SCMF method is one of the theoretical tools exploited in the Soft Matter theory group in Tarragona. The SCMF theory describes a single molecule surrounded by the mean fields. It takes explicitly into account the structure of an individual molecule at a coarse-grained level similar to coarse-grained MC or MD simulations.
The SCMF theory is particularly suitable for the description of nano-objects like polymeric drug carriers: it gives a detailed microscopic information on the configurations of the chains, the optimal shape and structure of drug delivery systems, the distribution of chains in the aggregate, the critical micellar concentrations as well as the critical aggregation concentration, the optimal aggregation number and the size distributions.
Suggested mechanism of a lipid-covered hydrophobic nanoparticle spontaneously crossing lipid bilayer. In contrast to expectations, we demonstrate that lipid-covered hydrophobic nanoparticles may translocate through lipid membranes by direct penetration within milliseconds. We identified the threshold size for translocation: nanoparticles with diameters smaller than 5 nm stay trapped in the bilayer, whereas those with diameters larger than 5 nm insert into the bilayer, opening pores in the bilayer.
We demonstrate an efficient method of polymer conformations generation massively in parallel. The mean field nature of the method allows for discarding the correlations between molecules, thus eliminating the need of communication between the cores. The method allows for evolutionary optimization of a molecule's architecture for biotechnological applications.
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