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Use this search facility to find out more about the profile of our HPC-Europa2 visitors, the type of work they have been doing, and their project achievements.
During my visit in CINECA initially I have taken advantage of the extensive experience of the local host and the staff of CINECA in order to optimize and benchmark my large scale simulations (aproximetely 50000 atoms) in order to obtain the most optimum efficiency. The first week of the visit the objective was to to prepare the initial structures for use in the production runs. This procedure involved designing the structures and then perform energy minimization on them which followed by a small duration (a few tens of ns) of parallel simulation in order to obtain reliable initial structures. A second objective was to be completed within the next weeks of my staying was the benchmarking and optimizing the system so as to start our large scale atomistic simulations. In order to fully equilibrate our structures more than 200 ns of simulation time is required, corresponding in parallel simulations of single day duration using 256 processors. The last objective was about to be completed at the last week of the visit and this time was used for analyzing the trajectories obtained from our production runs and investigation of dynamical and rheological properties (e.g local dynamics, relaxation spectrum of the Rouse modes, terminal relaxation properties, self-diffusion and friction coefficient) of the resulting systems and comparison of our results with available experimental data.
The first objective was completed since we managed to prepare the structures of our under study simulations. The systems we designed were melts of three different molecular weight linear and ring polyethylene oxide ranging in molecular length from N=340 up to N=1400 atoms per molecule. For studying the structure, dynamics, and rheology of ring, linear polymer blends we constructed these considered lengths of equal chain length as the above pure melts. Three mixtures have been prepared with 25%,50%,75% contamination in linear chains. Energy minimization also conducted in each of the above systems concluding with this action the last part of our first objective. Benchmarking and optimizing the system in the available HPC machines provided by CINECA (FERMI and PLX) was also achieved and with this last step we started our production simulations at PLX machine. Our systems of polyethylene oxide with low molecular weight have fully equilibrated while the equilibration of the larger systems is in progress surpassing the limit of 200 nanoseconds.
(S)-Glutamic acid adsorbed on Ag(100) organizes in different self-assembled structures depending on surface temperature [M. Smerieri et al., Langmuir 2011, 27, 2393]. In particular two of these structures, referred to as “square” and “flower” geometries, are found to co-exist on the surface upon deposition at T=350 K. The former assembly was fully resolved at the atomic level in ref. [M. Smerieri et al., Langmuir 2010, 26, 7208], in which we proved that the driving force for adsorption are the VdW interactions between the molecules and the Ag surface, i.e. that molecules are in a physisorbed state. This was done thanks to a previous application to the HPC-Europa2 program (appl. N. 14).
The goal of the present application is to expand this work, providing a full DFT description of the more complex “flower” structure, for which a strong chemical bond between glutamic radicals and the surface is expected on the basis of experimental data.
The “flower” type molecular self assembly obtained after adsorption of GLU on Ag(100) surface has been investigated using a combination of experiments and DFT calculations. It was shown previously that GLU deposited on Ag(100) at T=350 K can arrange in two different and co-existing patterns, indicated as “square” and “flower” structures. The former was previously investigated in details in [M. Smerieri et al. Langmuir 2010, 26, 7208]. For the latter, we have calculated within the present application a molecular model based on a unit cell containing the organized assembly of eight GLU molecules. Calculated interaction energies and STM images were confronted with experimental STM images. It was concluded that the “flower” structure is adsorbed much more strongly than the “square” assembly, due to the radical/anionic GLU units forming the heart of the flower structure. However entropic contributions disfavor this assembly compared with the less strongly adsorbed “squares”. The excellent agreement between experimental and simulated STM images confirms the validity of our results.
The present system is another example in which the Ag(100) surface is shown to allows the stabilization of a self-assembled biological layer which is not chemically perturbed by the substrate.
We also started a detailed description and analysis of the free energy of interaction comparing both competing assemblies, which is however still running.
Drug delivery systems are extensively studied due to their possible use in anticancer therapy. We proposed very interesting solution, the so called “nanocapsule” - nanodevice composed of open-ended carbon nanotube and two ferromagnetic nanoparticles attached to its tips. The aim of our research was to study influence of its structure on properties and behaviour under external magnetic field. We studied behaviour of such nanocapsule composed of single-walled carbon nanotube (25,0) and ferromagnetic nanoparticles by means of Monte Carlo simulations. The results have shown very promising properties, that is capping the nanotube in the absence of EMF and uncapping when large enough EMF is applied. Moreover, applying lower EMFs give no change of the structure, making it possible to use low EMFs for targeted delivery.
The next step of our research was to study properties of similar structures. Finding optimal structure of nanocarrier is very important for future synthesis. Therefore, we focused on studies of the dependence of the nanocapsule properties on its parameters, i.e. type of nanotube (its diameter, chirality), size and magnetic state of nanoparticles, how nanoparticles are bound to the nanotube tips, etc. We were also interested in dynamic properties of the nanocapsule under the external magnetic field. Time-scale of the structural transformation is the crucial parameter making the nanocapsule applicable as drug delivery system. Behaviour of the nanocapsule under the alternating magnetic fields was also of our interest. Therefore, the Molecular Dynamics code with the implemented Brenner potential was being developed for such purposes. During my visit I planned to finish its development and optimize it. Next step would be code parallelization using OpenMP.
Further, with help of Dr Philip Camp, I planned to choose appropriate approach to study the behaviour of such a nanocapsule when composed of superparamagnetic nanoparticles and modify the MD code accordingly.
I started research as planned and worked on developing and optimizing the Molecular Dynamics code. Using the software available on Hector I managed to optimize it. Improvement of the most time-consuming part of the code made the whole code worked more than 10x faster.
Discussions with Dr Philip Camp resulted in choice of the appropriate potential for description of magnetic interactions of superparamagnetic nanoparticles with the external magnetic field and modification of the MD code accordingly.
Preliminary calculations based on the MD code revealed an enormous sensitivity to the choice of the initial structure of the nanocapsule which resulted in the program crash. After performing careful debugging and testing we stated that the best approach will be to find a relaxed structure by means of Monte Carlo simulations of to perform the total energy minimization before the MD run. Finally we decided to implement MC code which additionaly gave us a notion about the influence of size parameter on the behaviour of the nanocapsule.
Additionally, I started to use different, more realistic potential to describe nanoparticles-nanotube interactions. Previously, they were described by Lennard-Jones potential which is regarded as crude approximation in this case. Currently the Hamaker potential is implemented in the code. Results obtained from the MC simulations for both potentials seemed to be very promising, therefore we kept using this approach to obtain more information about the influence of various factors on the properties and behaviour of the nanocapsule with and without the external magnetic field. I determined how the size and type of the nanoparticles and type of the nanotube affects the nanodevice behaviour. I also developed an auxiliary code that is capable of creating various structures of nanodevice, making possible to prepare a lot of simulation runs quickly. These studies will be continued and their results will be published.
Moreover, as soon as that part of research will be completed, we will continue to study the dynamic properties of the nanocapsule.