Investigation area: Molecular dynamics, Biomolecular simulations, free-energy calculations and small-molecules confinement within narrow nanotubes.
During the last 20 years, computational techniques have become an indispensable tool for the understanding of chemical processes at the nanoscale level, which, even though the huge advancements in the manipulation of matter at the molecular level (e.g. single-molecule techniques), in general remains hardly accessible by traditional experimental means. The popularity and acceptance of Molecular Simulation as a well established fi eld, is thanks to its contributions in physics, chemistry, biology between others, expanding the knowledge on the aforementioned fields and, in practice, bridging the gap between “pure theory” and the empirical world. Its rapid development, thanks to the interdisciplinary combined efforts of chemists, physicists and computational scientists has triggered the generation of novel algorithms, new software and faster computational resources, rendering molecular simulation a widespread technique easy accessible to wider audiences. Among the great many methodologies belonging to this field, Molecular Dynamics is widely used for the study and characterization of molecules at an atomic resolution. MD deals with the numerical solution of the N -body problem for atomic and molecular systems, elegantly combining statical mechanics and classical physics through the time-dependent integration of Newtons equations of motion. These equations, even in the simplest systems, are of such complexity that the integration must be done with numerical methods over a huge quantity of discrete time-steps, instead of being performed in an analytical, continuous fashion. For atomistic simulations, the magnitude of these time steps is in the range of femtoseconds (fs ). At each time-step, the coordinates are used to calculate the potential energy of the system (V ) and the negative rst derivative (with respect to the position of each atom), the force, using a molecular mechanics force field (FF). A long series of these calculations allows for the generation of a trajectory through phase space, 6N dimensional space (where N is the total number of atoms of the system), defined by the three atomic spatial position and velocity arrays, as representative of a statistical mechanical ensemble of microstates.
MD is very versatile technique, thus as a group focused on MD we are interested in broad and interdisciplinary range of topic; among such are:
- Method development.
- Free-energy calculations.
- Small molecules confined within narrow pores and nanotubes.
- Biomolecular channels such as Aquaporins.
- Carbon-based nanoparticles nanotoxicity.
- Mechanical unfolding of knotted proteins.
Selected Peer-reviewed Publications:
- Sebastian E. Gutierrez-Maldonado, Jose Antonio Garate, Maria Jose Retamal, Marcelo Cisternas, Ulrich G. Volkmann, Tomas Perez-Acle “Accessing the structural and thermodynamic properties of ultra-thin layers of C32 adsorbed on a SiO2 surface” Chem. Phys. Lett, accepted (2017).
- F Villanelo, Y Escalona, C Pareja-Barrueto, JA Garate, IM Skerrett, T Perez-Acle “Accessing gap-junction channel structure-function relationships through molecular modelling and simulations” BMC Cell Biology, 18(Suppl 1):5 (2017).
- Niall J. English and Jose Antonio Garate “Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Nonequilibrium molecular dynamics” J. Chem.
- Marracino Paolo,Liberti Micaela, Trapani Erika, Burnham Christian J,Avena, Massimiliano, Garate, José-Antonio, Apollonio Francesca, English, Niall J”Human Aquaporin 4 Gating Dynamics under Perpendicularly-Oriented Electric-Field Impulses: A Molecular Dynamics Study.” IJMS, 1422-0067 (2016).
- Yerko Escalona, Jose A. Garate, Raul Araya-Secchi, Tien Huynh, Ruhong Zhou and Tomas Perez-Acle, “Exploring the membrane potential of simple dual-membrane systems as models for Gap-junction channels.” Biophys J. accepted (2016).
B.S Biotechnology, University of Chile (2005)
Molecular Biotechnology Engineer, University of Chile (2007)
PhD in Chemical and Bioprocess Engineering , University College Dublin (2010)
E-mail: jose.garate at uv.cl
Address: Pasaje Harrington 287, Playa Ancha, Valparaíso, Chile.