- Title: Self-assembly of sticky nanoparticles and patchy proteins: Molecular Dynamics simulations.

The project is offered as a Master Thesis (Trabajo Final de Master) within the Master of Computational & Applied  Physics, or within the Master of Nanoscience and Nanotechnology, or within the Master of Biophysics. It can be extended for a Ph.D. thesis and could be included in the proposal for a joint project between UB, CSIC, University of Cambridge, University College of Dublin, and Rome University "La Sapienza". The project involves experiments at the CSIC  (Barcelona) and theory and simulations at UB and Rome.

- Short Summary

New exciting experiments show how sticky metal nonoparticles coated with organic compounds can aggregate and be molded to any shape. Patchy (localized sticky) interactions could be responsible  of protein aggregation diseases, such as eye cataracts. Sticky interactions with step repulsion display metastable phase transition (MPT) and can give rise to string-like assembly or stripe formations. I propose to explore, by Molecular Dynamics simulations, the effect of patchy interactions to produce the self-assembly of specific structures as in proteins. Importance: Combining patchy interactions and the effect of a MPT could be a powerful method to regulate the self-assembly at the nanoscale, opening new horizons for applications, such as delivery of drugs or imaging agents for curing diseases, and could allow the optimization of the conditions for protein crystallization.

- Contact: Please, follow the contact informations here

Examples of

self-assembly in organic

semiconductors (left)

and protein (right).

Click the figures

for further

informations. 

- Title: Supercooled water and glass formers.

The project is offered as a Master Thesis (Trabajo Final de Master) within the Master of Computational & Applied  Physics.  It can be extended for a Ph.D. thesis and could be included in the group’s collaborations with Boston University, University College of Dublin, Universidad Federal do Rio Grande do Sul (Porto Alegre) and Universidad de Granada. These collaborations are funded by different agencies, including the Spanish Ministerio de Ciencia e Innovación, and the USA National Science Foundation.

- Short Summary

Supercooled water is a metastable state of the liquid with respect to the crystal. Many molecular liquids, such as glycerol, at low temperatures do not crystallize and slowly form glasses. The analogy of the dynamic crossover found in the supercooled water and the dynamic crossover of intramolecular relaxation of glass formers is intriguing and only partially understood. We propose to generalize a recently introduced model for water in such a way to describe more complex molecular liquids and explore their similarities and differences in the thermodynamics and the dynamics, by using mean field approach and simple simulations. Importance: A general theoretical understanding of the phenomenology of glasses is a challenge. An effective strategy for the fabrication of new materials based on glass formers will stand on the comprehension of their general properties.

- Contact: Please, follow the contact informations here

A molecule of glycerol,

a glass former, with C in gray, 

O in red, H in white

and the lone electrons

in pink (left).

A video showing the

phenomenon of

supercooling

(right). Click the figures

for more informations.

- Title: Dynamic scaling in water at biological interfaces and under confinement: theory and Monte Carlo simulations.

The project is offered as a Master Thesis (Trabajo Final de Master) within the Master of Computational & Applied  Physics and the Master of Biophysics.  It can be extended for a Ph.D. thesis and could be included in the group’s collaborations with University of Cambridge, University College of Dublin, Boston University, Universidad Federal do Rio Grande do Sul (Porto Alegre) and Universidad de Granada. These collaborations are funded by different agencies, including the Spanish Ministerio de Ciencia e Innovación, and the USA National Science Foundation.

- Short Summary

Proteins and biological macromolecules (DNA, RNA) are suspended in water to fold and work. Recent experiments show that dynamics of the biomolecules is regulated by the surrounding water. The driving force is related to the structural changes of water, with macroscopic manifestations such as the hydrophobic effect. With this project we want to analyze the relation between the dynamics of surface water and the extension of the correlation length in the water Hydrogen bond network, by using Monte Carlo simulations and percolation theory. Importance: Water dynamics is connected to the protein function, as can be observed in a wide variety of systems from small soluble globular proteins to membrane proteins. Therefore, the characterization of the dynamic of the solvent in terms of a general parameter such as the correlation length could represent the key for a general understanding of the interplay of water and protein dynamics.

- Contact: Please, follow the contact informations here

Proteins (red and green)

suspended in the cell

water-solution (left:

click for more

information)

and the macroscopic

manifestation of the

hydrophobic effect on

my table cloth.