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Computational Chemistry

The Department of Chemical Sciences hosts the Computational Chemistry Community at Padua / Comunità di Chimica Computazionale di Padova, or C3P.

In silico design or high-throughput computational approaches are actually familiar tasks in the scientific community activities.  In addition to the theoretical method developers, chemists are by now computer science experts as they modify chemistry software to run on massively parallel machines with dozens, even hundreds, of processors, design general tools to make clusters and their ilk run better, highlight new research on ways to visualize data, design new hardware to speed up lengthy calculations, and test numerous parallel versions of computational chemistry software on new hardware architectures.

C3P aims to provide an efficient environment for chemists in Padova, utilizing complementary simulation and modelling tools, starting from static and dynamic ab initio quantum simulations (e.g. density functional theory), atomistic simulations based on detailed many-body inter-atomic potentials, steady-state and big-bang Monte Carlo methods, coarse-grained approaches based on molecular, brownian and dissipative particle dynamics and mesoscopic approaches. Besides C3P is a framework to develop general computational tools for nanoscience applications characterized by multiscale approaches and it is meant to be readily available for experimental research and for industrial applications of the specific computational tools developed in research academic environments.

The  C3P main activities are devoted to computational and theoretical chemistry through a wide range of theoretical approaches and computational techniques, all focused on the interpretation, simulation, characterization and rationalization of complex molecular systems, functionalized materials at nanoscale, biomolecular processes.

A repository of locally developed software is available for diverse chemical applications, under open source license.
In particular suites programs dedicated to magnetic spectroscopies are made available for the interpretation of relaxation properties from nuclear magnetic resonance (NMR) and simulation of electron spin resonance spectra (ESR). The link between theoretical predictive methodologies and MR spectroscopies dates back to several decades, and it is due to a happy coincidence between experimental needs and available interpretative tools. MR spectroscopies are intrinsically amenable to an advanced theoretical interpretation: the tools needed are based on quantum chemistry, as far as the parameters of the spin Hamiltonian are concerned, and on statistical thermodynamics, for the spectral lineshapes.

Presently, the main home-made available software packages are:

  • E-SpiReS: an integrated approach to electron spin resonance;
  • C++OPPS: a two-body stochastic approach to NMR relaxation in bio-molecules;
  • DITE: evaluation of diffusion and friction tensors of flexible molecules;
  • JEMDI: stochastic evaluation of multi-dimensional integrals;
  • JEFREE: a C++ library for free-energy calculations within the framework of non-equilibrium transformations.

Commercial and open source software are also commonly running at C3P. Among others, the following tools are available: Adf, Amber, Comsol, Gaussian, Gromacs, Lammps, Mathematica, Materials Studio, Namd, Orca, Quantum espresso.

 

      

 

 

All-atom molecular dynamics simulation study of the mechanism, at atomic level, of the transport of Ca2+ ions through the channel of connexin. The latter is a trans-membrane protein consisting of about 10000 atoms. The simulations were carried out including a portion of phospholipidic bilayer, and explicit water molecules and calcium ions for a total of 100000 atoms.

  

  

C3p is composed of 4 computing clusters:

  1. Avogadro: 90 computing nodes, 546 xeon cores, about 2000GB Ram, ca. 50TB hard-disk capacity, 1Gb ethernet and 20Gb infiniband net;
  2. Dalton: 140 cores (xeon and ppc), 680GB Ram, 6TB hard-disk capacity, 1Gb ethernet and 40Gb infiniband net;
  3. Curie: 204 core amd, 480GB Ram, 8TB hard-disk capacity, 25 GPU Nvidia Tesla, 1Gb ethernet and 40Gb infiniband net;
  4. Pierre: 44 core xeon, 304GB Ram, 3TB hard-disk capacity, 1Gb ethernet.

The C3P main room is equipped with four uninterruptible power supply (UPS) units, ranging from 20KVA monophase to 15KVA monophase and 20KVA triphase and three air conditioning systems for a global power of 80KVA.

 

 

Coarse grained molecular dynamics simulation of the self assembly of poly(gamma-benzyl-L-glutammate) in water. Coarse graining has been carried out both on the polymer molecules, representing each monomer and the two fullerene cappings as single beads, and on the water molecules, using beads to represent the collective properties of 4 water molecules. Starting from a box with 1600 polymer molecules randomly placed and 1600000 water beads, the system evolved to form hollow spherical aggregates compatible in dimensions to those observed experimentally by TEM.

The C3P facility is open to researchers of the University of Padova and managed by a scientific committee composed of:

  • prof Antonino Polimeno (e-mail: antonino.polimeno@unipd.it )
  • prof Maurizio Casarin (e-mail: maurizio.casarin@unipd.it )

A description, in Italian, of the terms and conditions of usage is reported here :
(http://www.chimica.unipd.it/sites/dipartimenti.it/files/regolamento_LICC.pdf)