Noelia Faginas Lago

COMPCHEM: Progress Towards GEMS a Grid Empowered Molecular Simulator and Beyond

Foundations and structure of the building blocks of GEMS, the ab initio molecular simulator designed for implementation on the EGEE computing Grid, are analyzed. The impact of the computational characteristics of the codes composing its blocks (the calculation of the ab initio potential energy values, the integration of the dynamics equations of the nuclear motion, and the statistical averaging of microscopic information to evaluate the relevant observable properties) on their Grid implementation when using rigorous ab initio quantum methods are discussed. The requests prompted by this approach for new computational developments are also examined by considering the present implementation of the simulator that is specialized in atom diatom reactive exchange processes.

Modeling the intermolecular interactions and characterization of the dynamics of collisional autoionization processes

The autoionization dynamics of triatomic molecules induced by He*(23,1S1,0) and Ne*(3P2,0) collisions has been discussed. The systems are analyzed by using an optical potential model within a semiclassical approach. The real part of the potential is formulated applying a semiempirical method, while the imaginary part has been used in the fitting procedure of the data adjusting its pre-exponential factor. The good agreement between calculations and experiment confirms the attractive nature of the potential energy surface driving the He* and Ne*-H2O dynamics.

A bond-bond portable approach to intermolecular interactions: simulations for n-methylacetamide and carbon dioxide dimers

In this paper we present two applications of a recently developed method for obtaining analytical potential energy surfaces describing the intermolecular interaction of pairs of molecules made up of three or more atoms. The method is based on an empirical formulation of the intermolecular terms of the potential based on the idea that pairwise interaction terms, usually appearing in the many-body expansion of the potential energy, must be referred to pairs of interacting centers (group of atoms and/or bonds) of the molecular monomers, rather than, as traditionally done, to atomic centers. Such representation is incorporated in a grid empowered molecular simulator and coupled with dynamical calculations to evaluate observable properties of a simple CO2 dimer and a more complex chemical system (the N-methylacetamide dimer).

Distributed and collaborative learning objects repositories on grid networks

The paper deals with the design and a prototype implementation of a collaborative repository of scientific learning objects based on an efficient mechanism of filing and retrieving distributed knowledge on the Grid. The proposed repository can deal with a large variety of different learning contents. Its prototype implementation, developed for Chemistry contents, is part of an extended architecture consisting of a federation of autonomous local repositories. The federation is led by a coordinator who keeps track of the repository in which the learning objects are directly stored or referenced. In each repository server, a locally hosted Web Portal allows a easy management of the repository through a CMS front-end.

Carbon Oxides in Gas Flows and Earth and Planetary Atmospheres: State-to-State Simulations of Energy Transfer and Dissociation Reactions

In this paper we illustrate an approach to the study of the molecular collision dynamics, suited for massive calculations of vibrational state-specific collision cross sections and rate constants of elementary gas phase processes involving carbon oxides. These data are used in the theoretical modeling of the Earth and planetary atmospheres and of non-equilibrium reactive gas flows containing the CO2 and CO molecules. The approach is based on classical trajectory simulations of the collision dynamics and on the bond-bond semi-empirical description of the intermolecular interaction potential, that allows the formulation of full dimension potential energy surfaces (the main input of simulations) for small and medium size systems. The bond-bond potential energy surfaces account for the dependence of the intermolecular interaction on some basic physical properties of the colliding partners, including modulations induced by the monomer deformation. The approach has been incorporated into a Grid empowered simulator able to handle the modeling of the CO2 + CO2 collisions, while extensions to other processes relevant for the modeling of gaseous flows and atmospheres, such as CO + CO → C + CO2 and CO2 + N2, are object of current work. Here the case of CO2 + CO2 collisions will be illustrated in detail to exemplify an application of the method.

Thermal rate coefficients in collinear versus bent transition state reactions: the N+N2 case study

Zero total angular momentum exact quantum calculations of the probabilities of the N+N2 reaction have been performed on the L3 potential energy surface having a bent transition state. This has allowed us to work out J-shifting estimates of the thermal rate coefficient based on the calculation of either detailed (state-to-state) or cumulative (multiconfiguration) probabilities. The results obtained are used to compare the numerical outcomes and the concurrent computational machineries of both quantum and semiclassical approaches as well as to exploit the potentialities of the J-shifting model. The implications of moving the barrier to reaction from the previously proposed collinear geometry of the LEPS to the bent one of L3 are also investigated by comparing the related detailed reactive probabilities.

A high-level ab initio study of the N2 + N2 reaction channel.

A new six‐dimensional (6D) global potential energy surface (PES) is proposed for the full range description of the interaction of the N2(1Σg+)+N2(1Σg+) system governing collisional processes, including N atom exchange. The related potential energy values were determined using high‐level ab initio methods. The calculations were performed at a coupled‐cluster with single and double and perturbative triple excitations level of theory in order to have a first full range picture of the PES. Subsequently, in order to accurately describe the stretching of the bonds of the two interacting N2 molecules by releasing the constraints of being considered as rigid rotors, for the same molecular geometries higher level of theory multi reference calculations were performed. Out of the calculated values a 6D 4‐atoms global PES was produced for use in dynamical calculations. The ab initio calculations were made possible by the combined use of High Throughput Computing and High Performance Computing techniques within the frame of a computing grid empowered molecular simulator.

An extension of the grid empowered molecular simulator to quantum reactive scattering.

Within the activities of the D37 COST Action, we have further developed the quantum dynamics framework of the grid empowered molecular simulator (GEMS) implemented on the segment of the European grid available to the COMPCHEM (computational chemistry) virtual organization. GEMS does now include in a full ab initio approach, the evaluation of the detailed quantum (both time dependent and time independent) dynamics of small systems starting from the calculation of the electronic structure properties as well as the direct calculation of thermalized properties. Illustrative, full dimensional applications of the extended simulator to the H + H2, N + N2, and O + O2 systems are presented.

The Molecular Stirrer Catalytic Effect in Methane Ice Formation

The use of the high throughput European Grid Infrastructure, of the synergistic workflow-directed Grid Empowered Molecular Simulator, of the molecular polarizability driven formulation of the intermolecular interaction, has been exploited to the end of rationalizing the Sodium Docecyl Sulfate (SDS) catalyzed formation of methane clathrate hydrates. The mild distortion undergone by the SDS additive when interacting with CH4 in water solution still allows such molecule to act as a molecular stirrer and catalyze the caging of the solvent molecule around methane. On the contrary, this is not found to occur for CO2 because its strong interaction with the SDS molecule makes the additive fold and lose the stirring ability.

A High-Level Ab Initio Study of the N-2 + N-2 Reaction Channel

A new six‐dimensional (6D) global potential energy surface (PES) is proposed for the full range description of the interaction of the N2(1Σg+)+N2(1Σg+) system governing collisional processes, including N atom exchange. The related potential energy values were determined using high‐level ab initio methods. The calculations were performed at a coupled‐cluster with single and double and perturbative triple excitations level of theory in order to have a first full range picture of the PES. Subsequently, in order to accurately describe the stretching of the bonds of the two interacting N2 molecules by releasing the constraints of being considered as rigid rotors, for the same molecular geometries higher level of theory multi reference calculations were performed. Out of the calculated values a 6D 4‐atoms global PES was produced for use in dynamical calculations. The ab initio calculations were made possible by the combined use of High Throughput Computing and High Performance Computing techniques within the frame of a computing grid empowered molecular simulator.