Potential Mean Force for Chitosan and Glyphosate

Glyphosate is the most widely consumed herbicide in the world and has threatening and harmful properties to living beings due to its chronic toxicity and carcinogenic activity. That is why the proposal to remove glyphosate through chitosan in an aqueous medium arose, due to the high capacity of the biopolymer to chelate contaminants. This can be achieved computationally, simulating models representing real systems, such as the Molecular Dynamics (MD) methodology, mainly in models of atomistic force fields such as OPLS-AA (Optimized Potentials for Atomistic Liquid Simulations) used here, through the computational software GROMACS 4.6 (Groningen Machine for Chemical Simulations). However, this work aims to calculate the Potential Mean Force (PMF) of chitosan and glyphosate binding through 594 simulations by Steered Molecular Dynamics (SMD) using umbrella sampling method, performing the gradual removal of the herbicide in 3 different Cartesian axes ( + x; + y; + z) and in 3 different temperatures (288 K, 298 K, and 308 K) adding 9 systems with 66 simulations for each axis and 198 simulations for each temperature. The glyphosate adsorption process occurs mainly by formation of electrostatic interactions caused by its high polarity groups, such as phosphonate, carboxylate, and amine with the chitosan's groups such as non-acetylated amine groups, primary and secondary hydroxyls. The energy barriers showed very close values in all systems, indicating enough disturbance samples to satisfy Jarzynski's equality. This fact suggested the lack of specificity regarding the axis of untying of the herbicide in relation to chitosan since the great proximity between all the PMF calculations performed was evident. Therefore, the promising potential of chitosan as a glyphosate adsorbent was theoretically confirmed, it agrees with experimental studies of the attempt to remove the herbicide glyphosate in chitosan in desorption processes.

The equation of state with non-equilibrium methods

Jarzynski’s equality provides an elegant and powerful tool to directly compute differences in free energy in Monte Carlo simulations and it can be readily extended to lattice gauge theories to compute a large set of physically interesting observables. In this talk we present a novel technique to determine the thermodynamics of stronglyinteracting matter based on this relation, which allows for a direct and efficient determination of the pressure using out-of-equilibrium Monte Carlo simulations on the lattice. We present results for the equation of state of the SU(3) Yang-Mills theory in the confined and deconfined phases. Finally, we briefly discuss the generalization of this method for theories with fermions, with particular focus on the equation of state of QCD.