Max Planck

In the group of Biophysics of Tropical Diseases (BioTD) there are three main research lines:

Nano-biomolecular interaction and dynamics

We apply state-of-the art computational methods to determine interaction mechanisms between nanosystems and molecules to biomolecules of microorganisms causing infectious diseases. 

Projects: 

• Variation of hemozoin physico-chemical properties when formed in presence of antimalarials. 
• Interaction of Silver nanoparticles and biomolecules and implication in the antibacterial mechanisms.
   

Research highlight:
Atomic structure and origin of chirality of DNA-stabilized silver clusters, X Chen, M Boero, O Lopez-Acevedo, Physical Review Materials 4 (6), 065601 (2020)

Design of high-affinity molecules and binding peptides

We develop computational methods for the rational design of binding peptides and molecules to a protein target using hybrid molecular dynamics / Monte Carlo simulations and knowledge-based potentials.

Projects:

• Optimization and application of a computational peptide-design protocol.
• Mechanistic study of membrane-pore formation for one new Croatolicidin-derived peptide as therapeutic against Staphylococcus aureus.
• Optimization of a peptide design protocol for using non-natural amino acids.
   

Research highlight: 
PARCE: Protocol for amino acid refinement through computational evolution, R Ochoa, MA Soler, A Laio, P Cossio, Computer Physics Communications 260, 107716 (2021)

Method developments

We develop algorithms and codes for increasing the accuracy and speed of used methods and therefore the range of the systems we can study.

Projects:

• Methods for the analysis of electron microscopy (EM) images.
• Interfacing ab-initio and enhancing sampling methods.
• Kinetic functionals for Orbital-free Density Functional Theory.
   

Research highlight: 
A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments J Giraldo-Barreto, S Ortiz, EH Thiede, K Palacio-Rodriguez, B Carpenter, et al Scientific Reports 11 (1), 1-15 (2021)