Research Groups

RESEARCH UNIT: Theory and Simulation

Soft Matter Theory Group (SOFTMATTER)

During this year we have developed theory, modelling and simulation studies for proteins and nanomaterials interactions, and we have unveiled the nature and properties of bacterial cellulose, and explored the techniques in new and diverse fields

The Soft Matter Theory Group develops theory, modelling and simulation studies of Soft Matter. This is a field in which Physics, Chemistry, Biology and Material Science meet. Soft Matter includes materials as diverse as biological structures and biopolymers, membranes, nanoparticles, colloids or self-assembled supramolecular materials such as vesicles or liposomes for drug delivery. This broad area of materials is characterized by highly tunable properties and collective behavior driven by weak interactions (hydrogen bonds, hydrophobic effect, solvent mediated interactions…) which have magnitudes of the order of the thermal energy.

Our task is to predict and model the interactions and properties of these materials from an atomistic or molecular perspective with the help of supercomputers using basic physical and chemical laws. In our simulations, we consider both atomistically detailed models and coarse-grain molecular models. These models provide a fundamental understanding of a variety of complex phenomena observed experimentally and they can be employed to modify or tune materials for desired properties or in the rational design of new materials.

Members

  • Dr. Jordi Faraudo - Tenured Scientist
  • Dr. David Malaspina - Postdoctoral Researcher
  • Dr. Yamila García- Postdoctoral Researcher
  • Dr. Ivana Malvacio - Visiting Postdoctoral Researcher
  • Sílvia Illa Tuset - PhD researcher

Development of the atomistic implicit-solvent MD simulations. Atomistic simulations of proteins in water (top left) can be used to parametrize atomistic force fields with implicit solvent (top right). These force fields are suitable for use in atomistic simulations involving large systems (millions of atoms) such as those found in the simulation of the formation of protein corona over a nanoparticle (bottom left) or protein films over inorganic surfaces (bottom right)

Achievements

From the scientific perspective, this year 2019 we have consolidated our developments in certain areas in which we have been active the last years, started new experimental-theory collaborations and explored the use of our techniques in fields in which we were not previously active. As an example of consolidation, we should mention the publication of a review article about the modelling of the interactions between proteins and nanomaterials in collaboration with researchers from the University of Granada (Spain) and CNRS (France). In a new collaboration with Durham University (UK) we explored the use of Molecular Dynamics simulations to interpret AFM data in solution. We were able to identify the presence of individual ions at the surface of membranes and the effect they produce on nanostructuration and on mechanical properties.

Collaborations with experimental groups within ICMAB allowed joint theoretical-experimental advances in several fields. For example, the ongoing collaboration with the Nanoparticles and Nanocomposites group at ICMAB fueled developments in fields as diverse as nanoparticles (how to add a bio-identity to inorganic nanoparticles by covering them with proteins)  or the properties of cellulose (for example adhesion in dry or wet cellulose). Another substantial advancement was related to the use of Molecular Dynamics simulations to solve a long-standing controversy related to the possible amphiphilic nature of cellulose.

From the technical side, we developed a computational tool (Chitin builder) useful for the preparation of simulations of crystals of this organic material. This tool was made freely available for download from the group GitHub repository.

Publications

Long-lived ionic nano-domains can modulate the stiffness of soft interfaces
Trewby, W; Faraudo, J; Voitchovsky, K
Nanoscale 11, 10, 4376-4384, 2019

Molecular insight into the wetting behavior and amphiphilic character of cellulose nanocrystals
Malaspina, DC; Faraudo, J
Advances in Colloid and Interface Science 267, 15-25, 2019

Nanocellulose films with multiple functional nanoparticles in confined spatial distribution
Roig-Sanchez, S; Jungstedt, E; Anton-Sales, I; Malaspina, DC; Faraudo, J; Berglund, LA; Laromaine, A; Roig, A
Nanoscale Horizons 4, 3, 634-641, 2019

Insights into Preformed Human Serum Albumin Corona on Iron Oxide Nanoparticles: Structure, Effect of Particle Size, Impact on MRI Efficiency, and Metabolizatio
Carlos Moya, Remei Escudero, David C Malaspina, Maria de la Mata, Jesús Hernández-Saz, Jordi Faraudo, Anna Roig
ACS Applied Bio Materials 2, 3084-3094, 2019

Protein-surface interactions at the nanoscale: Atomistic simulations with implicit solvent models
Malaspina, DC; Perez-Fuentes, L; Drummond, C; Bastos-Gonzalez, D; Faraudo, J
Current Opinion in Colloid & Interface Science 41, 40-49, 2019

Using evolved gas analysis - mass spectrometry to characterize adsorption on a nanoparticle surface
Martinez-Esain, J; Puig, T; Obradors, X; Ros, J; Farjas, J; Roura-Grabulosa, P; Faraudo, J; Yanez, R; Ricart, S
Nanoscale Advances 1, 7, 2740-2747, 2019 

Coordination
Anna May-Masnou This email address is being protected from spambots. You need JavaScript enabled to view it.
Redaction
Anna May-Masnou This email address is being protected from spambots. You need JavaScript enabled to view it.
Web & Graphic Editor
José Antonio Gómez  This email address is being protected from spambots. You need JavaScript enabled to view it.

Webmasters
José Antonio Gómez This email address is being protected from spambots. You need JavaScript enabled to view it.
Albert Moreno     This email address is being protected from spambots. You need JavaScript enabled to view it.
ICMAB