Leonardo Pacifici

VMSLab-G: a virtual laboratory prototype for molecular science on the grid

A Grid-based Virtual Molecular Science Laboratory (VMSLab-G) based on both human (meter scale) and molecular (nanometer scale) virtual reality aimed at facilitating ubiquitous laboratory practice and stimulate insight in scientific research is illustrated. Details are given of its structure, prototypical implementation and illustrative examples.

Modeling of energy transfer from vibrationally excited CO2 molecules: cross sections and probabilities for kinetic modeling of atmospheres, flows, and plasmas.

We present extended applications of an established theoretical and computational machinery suitable for the study of the dynamics of CO2+CO2 collisions, focusing on vibrational energy exchange, considered over a wide range of energies and rotational temperatures. Calculations are based on quasi-classical trajectories on a potential energy function (a critical component of dynamics simulations), tailored to accurately describe the intermolecular interactions, modeled by the recently proposed bond-bond semiempirical formulation that allows the colliding molecules to be stretchable, rather than frozen at their equilibrium geometry. In a previous work, the same potential energy surface has been used to show that modifications in the geometry (and in physical properties such as polarizability and charge distribution) of the colliding partners affect the intermolecular interaction and determine the features of the energy exchange, to a large extent driven by long-range forces. As initial partitioning of the energy among the molecular degrees of freedom, we consider the excitation of the vibrational bending mode, assuming an initial rotational distribution and a rotational temperature. The role of the vibrational angular momentum is also carefully assessed. Results are obtained by portable implementations of this approach in a Grid-computing framework and on high performance platforms. Cross sections are basic ingredients to obtain rate constants of use in advanced state-to-state kinetic models, under equilibrium or nonequilibrium conditions, and this approach is suitable for gas dynamics applications to plasmas and modeling of hypersonic flows.

Time-dependent wavepacket calculations for the system on a LEPS surface: inelastic and reactive probabilities

A time-dependent wavepacket program has been used to determine rotationally and vibrationally inelastic and reactive probabilities for collisions between a N atom and a N2 molecule in their ground electronic states (4S and respectively). The calculation is performed on a single LEPS surface and therefore any spin effects (expected to be negligibly small) are neglected. Complete rovibrational product state resolution is achieved. The collision is found to be to a large extent vibrationally adiabatic, while there is significant mixing of rotational states. An interesting interference effect is observed.A time-dependent wavepacket program has been used to determine rotationally and vibrationally inelastic and reactive probabilities for collisions between a N atom and a N2 molecule in their ground electronic states (4S and respectively). The calculation is performed on a single LEPS surface and therefore any spin effects (expected to be negligibly small) are neglected. Complete rovibrational product state resolution is achieved. The collision is found to be to a large extent vibrationally adiabatic, while there is significant mixing of rotational states. An interesting interference effect is observed.

An innovative synergistic grid approach to the computational study of protein aggregation mechanisms

Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.

Energy transfer upon collision of selectively excited CO2 molecules: State-to-state cross sections and probabilities for modeling of atmospheres and gaseous flows

Carbon dioxide molecules can store and release tens of kcal/mol upon collisions, and such an energy transfer strongly influences the energy disposal and the chemical processes in gases under the extreme conditions typical of plasmas and hypersonic flows. Moreover, the energy transfer involving CO2 characterizes the global dynamics of the Earth-atmosphere system and the energy balance of other planetary atmospheres. Contemporary developments in kinetic modeling of gaseous mixtures are connected to progress in the description of the energy transfer, and, in particular, the attempts to include non-equilibrium effects require to consider state-specific energy exchanges. A systematic study of the state-to-state vibrational energy transfer in CO2 + CO2 collisions is the focus of the present work, aided by a theoretical and computational tool based on quasiclassical trajectory simulations and an accurate full-dimension model of the intermolecular interactions. In this model, the accuracy of the description of the intermolecular forces (that determine the probability of energy transfer in molecular collisions) is enhanced by explicit account of the specific effects of the distortion of the CO2 structure due to vibrations. Results show that these effects are important for the energy transfer probabilities. Moreover, the role of rotational and vibrational degrees of freedom is found to be dominant in the energy exchange, while the average contribution of translations, under the temperature and energy conditions considered, is negligible. Remarkable is the fact that the intramolecular energy transfer only involves stretching and bending, unless one of the colliding molecules has an initial symmetric stretching quantum number greater than a threshold value estimated to be equal to 7.

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.

Quantum reactive scattering on innovative computing platforms

Abstract The possibility of implementing quantum reactive scattering programs on cheap platforms, originally used for graphic purposes only, has been investigated using a NVIDIA GPU. After a conversion of the code considered from Fortran to C and its deep restructuring for exploiting the GPU key features, significant speedups have been obtained for RWAVEPR, a time dependent quantum reactive scattering code propagating in time a complex wavepacket. As benchmark calculations those concerned with the evaluation of the reactive probabilities of the Cl+H2 and the N+N2 reactions have been considered.

A Time Dependent Study of the Nitrogen Atom Nitrogen Molecule Reaction

In this paper a preliminary study of the N + N2 reaction making use of quantum time-dependent calculations in Jacobi coordinates is 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.

Quantum reactive scattering calculations on GPU

An atom diatom time dependent reactive scattering code has been implemented on a platform made of a CPU and a GPU. The detailed analysis of the implemented code led to its restructuring to exploit the architectural features of graphic processors. Resulting gains of efficiency of the code when used for a prototype case study are compared.