Position: Post doctoral fellow
Affiliation: Physics Dept. University of Rome "La Sapienza", P.le A. Moro 2, I-00185 Rome, Italy
Office: Ed. Marconi , Room 339 B
Telephone: +39 06 4969 4282
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Email:   adolfoDOTpomaDOTbernaolaATroma1DOTinfnDOTit

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Curriculum Vitae

Research Interest

1. Adaptive Resolution Scheme (AdResS): Quantum/Classical coupling
2. Rare events simulation: TAMD, Single Sweep method, TPS/Importance Sampling
3. Coarse-Grained modeling for soft matter applications
4. Ab initio Molecular Dynamics simulations 

Current Research Projects

•  Quantum free energy reconstruction of rare events:

The sodium alanate has been initially studied by an anelastic spectrocopy (AS) [1] and measured a typical activation barrier of F=0.126 eV, however  microscopic species associated to this particular signal could not be identified. To explain the signal the existence of hydrogen defects in one of the crystals units is assumed plus a possible rearrangement of the H around the defective AlH(6-x) (i.e. local vacancy diffusion). To investigate the origin of that signal, a study of defective Na3AlH(6-x) by combining neutron scattering (NS)  and  DFT calculation was carried out [2]. In that work was introduced mainly two new suspects: the exchange of the hydrogen vacancy among a defective AlH(6-x) unit and a fully hexacoordinated aluminum  (i.e. non-local vacancy diffusion) and secondly the diffusion of a sodium vacancy. The NS experiment provided an energy barrier of about 0.4 eV. DFT calculations lead to associate this barrier to the local vacancy diffusion, in spite of the results of [1]. These two studies have created a controversy and certainly a theoretical description of this system may be required to interpret or guide the experiments.    To solve this controversy a new theoretical approach [3] has been used to calculate the free energy barrier of an activated processes (local and non-local diffusion). The authors concluded from their simulations that free energy barrier associated to the local diffusion is simply negligible compared to the non-local diffusion and so it is not responsible for the signal observed either in the AS or NS experiments. The estimative of the activation barrier for the non local diffusion is about 0.41-0.45 eV. Therefore they attributed this signal to the NS experiment.

Fig 1: Path integral representation of  ahydrogen diffusion in sodium alanate

In this work we aim to go further an include nuclear quantum effects by the path integral formalism. This will lead us to a better reconstruction of the  energy profile. The "Path Integral single sweep method (PI-TAMD) [4]" will be used to overcome the limitation of the poor sampling of the free energy in the presence of a rare event. 

[1] J. Voss et al., J. Phys. Chem. B, 111, 3886 (2007).

[2] O. Palumbo et al., J. Phys. Chem. B 109, 1168 (2005).                         

[3] M. Monteferrate, S. Bonella and G. Ciccotti, Phys. Chem. Chem. Phys., 13, 10546 (2011).

[4] S. Bonella and R. Vuilleumier, ``Path Integral single sweep method for quantum free energy reconstruction" (to be published).

• Prediction of membrane-protein structures

Several large proteins confined in membrane can not be crystallize in the lab. Although small systems such as the trans-membrane helix dimer (i.e. glycophorin A) can be successfully crystalized in normal condition, the same does not occure for larger systems.
	Fig 2: Transmembrane protein of Glyp A.

Publications

1. A. B. Poma and L. Delle Site, “Adaptive Resolution Simulation of Liquid Para-Hydrogen: Testing the robustness of the Quantum-Classical Adaptive Coupling.”, Phys. Chem. Chem. Phys 13, 10510 (2011). 
2. A. B. Poma and L. Delle Site, “Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling”, Phys. Rev. Lett. 104, 250201 (2011).
3. A. B. Poma and L. Delle Site, “
   Separation of variables in MD simulation: A
   criterion to estimate the quality of the approximation
   Separation of variables in MD simulation: Acriterion to estimate the quality of the approximation”, Phys. Rev. E. 78,  056703 (2008).
4. A. Poma, M. Monteferrante, S. Bonella and G. Ciccotti, “ 
   Separation of variables in MD simulation: A
   criterion to estimate the quality of the approximation
   Quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6”, accepted in Phys. Chem. Chem. Phys. 14, 15458 (2012).
5. A. Poma, A. Deiana, A. Giansanti and G. Ciccotti,"Assessment the quality of transmembrane protein models: a free energy study", in preparation (2013).

Related links

• Coarse-graining and quantum-classical adaptive coupling in soft matter (pdf - PhD thesis)
• Atomistic Simulation of rare events using Transition Path Sampling ((pdf - Master thesis))