Research Groups

RESEARCH UNIT: Theory and Simulation

Soft Matter Theory Group (SOFTMATTER)

As a response to the world-wide COVID-19 pandemic, this year we added a new Research line about the interaction between SARS-CoV-2 virus and materials. We also continued on the planned Research in different aspects of Self-Assembly and SoftMatter.

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
  • Dalinda Quingatuña - PhD researcher

Interaction of SARS-CoV-2 virus with different materials. (a) Typical image of a SARS-CoV-2 virion colored to emphasize its supramolecular structure (b) Atomistic model of a spike (S) protein of the virus protruding from a membrane (c) Result of a computer simulation of the interaction of the S protein with cellulose, showing stable adsorption (d) Result of a computer simulation of the interaction between the S protein and graphite, showing a strong deformation of the protein (e) Detail of the results in (c) showing the hydrogen bonds responsible for the observed stable adsorption in cellulose.

Achievements

During year 2020 we not only obtained substantial results in our active research lines but also we started a new research line on the interaction between the SARS-CoV-2 virus and materials. It is also remarkable that all our publications during this year have been featured in one or several ways such as editor’s choice or highlighted in Chemistry World or Scilight. In our traditional field of magnetic nanoparticles we have published a featured review of our works in magnetophoresis. In our traditional research line of self-assembly, we have obtained new results by combining implicit solvent DFT calculations and force field Molecular Dynamics.

We have demonstrated that the unexpected self-assembly behavior of certain molecules (COSAN) is due a charge separation in water between a polar and apolar region, as in classical surfactants. Using Reactive Molecular Dynamics we have unveiled the role of metal surfaces in de-fluorination of fluorinated buckyballs. Concerning the new line of the interaction of the new SARS-CoV-2 virus and surfaces, it has to be emphasized that this is a topic of fundamental importance, given the role of interfaces in many aspects of virus transmission, from filters and face masks to surface contamination.

Since the interaction of the SARS-CoV-2 virus with the environment is mediated by its large protruding spike S protein that covers the viral particle (hence the name “corona”), we have considered the interaction of the S protein (protruding from a virion) with different materials.We found that graphite substantially deforms the spike protein of the virus. On the contrary, the spike protein adsorbs over cellulose with little deformation, by forming hydrogen bonds between its receptor binding domain and adjacent residues and the cellulose (some of them mediated by hydration).

Publications

Computer Simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces
David C Malaspina and Jordi Faraudo
Biointerphases 2020, 15, 5, 051008, 10.1116/6.0000502

Unified view of magnetic nanoparticle separation under magnetophoresis
SS Leong, Z Ahmad, SC Low, J Camacho, J Faraudo, JK Lim
Langmuir 2020, 36, 28, 8033-8055, 10.1021/acs.langmuir.0c00839

Atomistic Simulations of COSAN: Amphiphiles without a Head and Tail Design Display “Head and Tail” Surfactant Behavior
DC Malaspina, C Viñas, F Teixidor, J Faraudo
Angewandte Chemie International Edition 2020, 59, 8, 3088-3092, 10.1002/anie.201913257

Surface specificity and mechanistic pathway of de-fluorination of C 60 F 48 on coinage metals
R Palacios-Rivera, DC Malaspina, N Tessler, O Solomeshch, J Faraudo, E Barrena and C Ocal
Nanoscale Advances 2020, 2, 10, 4529-4538, 10.1039/D0NA00513D

Outreach activities

Participation in the events “Bojos per la Física” and “Nit Europea de la Recerca”

Main projects

Main projects in which the group has participated in 2020:

Rising the impact of Selected Engineered Bacterial Cellulose Composites (RISE-BC)
RTI2018-096273-B-I00
Anna Laromaine and Anna Roig
180.000€

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.
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