Diego Prada-Gracia

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Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape(More)
A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schrödinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time(More)
Molecular simulations as well as single molecule experiments have been widely analyzed in terms of order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive, mounting evidence showed that such descriptions are inaccurate, leading to ambiguous definitions of states and(More)
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter(More)
Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water(More)
Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead to a straightforward interpretation of the mechanism. For the case of the Fip35 WW-domain where multiple long(More)
The concentration of macromolecules inside the cell is high with respect to conventional in vitro experiments or simulations. In an effort to characterize the effects of crowding on the thermodynamics and kinetics of disordered peptides, molecular dynamics simulations were run at different concentrations by varying the number of identical weakly interacting(More)
A large number of water models exist for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient. Past analysis mostly concentrated on ensemble quantities, while few data were reported on the different microscopic(More)
Quantum transport is strongly influenced by interference with phase relations that depend on the scattering medium. As even small changes in the geometry of the medium can turn constructive interference to destructive, a clear relation between structure and fast, efficient transport is difficult to identify. Here we present a complex network analysis of(More)
In the last decades several hydrogen-bond definitions were proposed by classical computer simulations. Aiming at validating their self-consistency on a wide range of conditions, here we present a comparative study of six among the most common hydrogen-bond definitions for temperatures ranging from 220 K to 400 K and six classical water models. Our results(More)