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Research interests

My research interests are focused on the computational chemistry field, a research area that I personally find very versatile, since it allows the study of a wide range of chemical systems by means of computer simulations.

Computational chemistry comprises different types of approaches such as coarse-grained models, classical molecular dynamics (MD), semi-empirical simulations and ab initio quantum chemistry methods. Every method can assess a specific size and time scale of a system, providing different levels of accuracy.

My current research activity is specially focused on the study of chemical systems at atomistic level, using different theoretical techniques such as:

  • Classical and ab initio MD
  • Replica exchange simulations
  • Enhanced sampling techniques (e.g. metadynamics, umbrella sampling)
  • Electronic structure calculations
Exploiting these methods, I have been working specially on:

Prebiotic chemistry with atomistic computer simulations

In my current postdoctoral experience, I am interested in the origins of life research. In particular, I am studying prebiotic reactions of biochemical building blocks, such as the ribonucleotides (of great importance for the RNA world hypothesis), and amino acids.
In our computational approach (based on ab initio MD simulations), we take into account plausible prebiotic environments to model an specific chemical reaction either under exogenous (e.g. meteorites) or endogenous (e.g.hydrothermal/hot lagoons) sources.

Prebiotic chemistry of ribonucleotides: Based on de novo nucleotide synthesis (Base+PRPP), we propose a prebiotic reaction under hydrothermal conditions. From this setup, we are able to synthesize both types of beta-ribonucleotides in the absence of enzymatic catalysis.

Decomposition of aminoacids: We explore the effect of aqueous environment on the amino acids stability present in meteoritic parental bodies. In particular, we analyze the hydrothermal decomposition reactions (decarboxylation and deamination) for some of the most abundant residues in meteorites

Molecular dynamics of biomolecules

During my PhD, I have worked on the translocation mechanism of NS3 helicase from hepatitis C virus along a ssRNA. In this project, we performed MD simulations in explicit solvent coupled with enhanced sampling techniques (e.g. well-tempered metadynamics, steered MD, Hamiltonian REMD).

From this study we found an ATP-dependent stabilization for a crucial conformer along the translocation process. In addition, we got new insights about the molecular mechanism perfomed by this motor protein (NS3).