Visualization and Molecular Dynamics

The research interests are related to the development and application of computational methods for the description and interpretation of chemical phenomena. Our approach combines classical computational chemistry techniques (Molecular Dynamics and Monte Carlo simulations) with scientific visualization applications for desktop and Immersive Virtual Reality (IVR) systems.

Force Fields development

Computational methods such as Molecular Dynamics (MD) and Monte Carlo (MC) are powerful tools to estimate macroscopic properties from microscopic models. These methodologies have shown to be especially useful to investigate the structure of several systems such as organic liquids and biological macromolecules. MD calculations make use of a set of parameters to describe the potential energy of a system of particles, named as force field (FF), usually extracted from spectroscopic experiments or from quantum mechanical (QM) calculations of isolated molecules for a selected set of molecular targets.
Our aim is focused on the development of novel parameterization strategies for new FF strictly based on QM computations, in order to correctly describe hydrogen bonding directionality in hydrogen bonded liquids and to reproduce experimental values of target properties. Moreover, we are involved in the implementation of such methods in Gaussian software and combine them with other methodologies in order to study new challenging problems in complex systems.



Caffeine

Caffeine is a new molecular viewer for Immersive Virtual Reality (IVR) systems developed at the SMART Laboratory of Scuola Normale Superiore. Currently Caffeine supports both standard desktop computers as well as multi-screen IVR systems such as the CAVE theater installed at SNS. It allows to visualize both static and dynamic structures using the most widespread representations (all-atoms and ribbons), isosurfaces extracted interactively by volume data sets, and line charts displaying additional scalar data resulting from further data analysis. Support for Oculus Rift DK1 was implemented in a previous version of the software, but it has been discontinued for technical reasons. Support for latest generation of HDMs is currently being developed and will be introduced soon.

VMS-Draw

A major research effort of our group is focused on the development of a virtual multifrequency spectrometer (VMS) providing user-friendly access to the latest developments of computational spectroscopy also to non-specialists.

VMS (Virtual Multifrequency Spectrometer) is composed of two parts: a simulation module, based on quantum-chemical calculations (VMS-Comp) and graphical module (VMS-Draw) which offers a number of high level features not present at the same time in pre- and post-processing facilities for ESCs.

VMS Comp is released within the Gaussian ESC and provides support for state-of-the art computational spectroscopy (e.g. different vibrational spectroscopies including anharmonic effects, electronic spectroscopies including vibronic effect).

VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it allows the analysis of Electronic Spin Resonance (ESR), nuclear magnetic resonance (NMR) and rotational spectra by interfacing with dedicated software, thus providing a unique integrated platform able to cover a wide range of spectroscopic techniques.

VMS-Draw increases the productivity of both computationally and experimentally-oriented researchers and allows an easier and faster sharing of results. It offers, in an all-in-one package, all the tools to analyze the rich information produced by quantum chemical calculations and use them for the interpretation of experimental observations.

Virtual Multifrequency Spectrometer VMS-Draw pipeline

Selected publications

  • M. Pagliai, G. Mancini, I. Carnimeo, N. De Mitri, V. Barone, “Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach”, Journal of Computational Chemistry, 38 (6), 319–335 (2017), DOI: 10.1002/jcc.24683
  • A. Salvadori, G. Del Frate, M. Pagliai, G. Mancini, V. Barone, “Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data”, International Journal of Quantum Chemistry, 116 (22), 1731–1746 (2016), DOI: 10.1002/qua.25207
  • G. Del Frate, F. Bellina, G. Mancini, G. Marianetti, P. Minei, A. Pucci, V. Barone, “Tuning of dye optical properties by environmental effects: a QM/MM and experimental study”, Phys. Chem. Chem. Phys., 18, 9724-9733 (2016), DOI: 10.1039/C6CP00841K
  • M. Macchiagodena, G. Mancini, M. Pagliai, V. Barone, “Accurate prediction of bulk properties in hydrogen bonded liquids: amides as case studies”, Phys. Chem. Chem. Phys., 18, 25342-25354 (2016), DOI: 10.1039/C6CP04666E
  • D. Licari, A. Baiardi, M. Biczysko, F. Egidi, C. Latouche, V. Barone, “Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool”, Journal of Computational Chemistry, 36, 321–334 (2015), DOI: 10.1002/jcc.23785
  • A. Salvadori, A. Brogni, G. Mancini, V. Barone, “Moka: Designing a Simple Scene Graph Library for Cluster-Based Virtual Reality Systems Inproceedings”, De Paolis, Lucio Tommaso ; Mongelli, Antonio (Ed.): Augmented and Virtual Reality: First International Conference, AVR 2014, Lecce, Italy, September 17-20, 2014, Revised Selected Papers, Springer International Publishing, 333–350 (2014), DOI: 10.1007/978-3-319-13969-2_25
  • A. Salvadori, D. Licari, G. Mancini, A. Brogni, N. De Mitri, V. Barone, “Graphical Interfaces and Virtual Reality for Molecular Sciences Incollection”, Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, Elsevier, (2014), DOI: 10.1016/B978-0-12-409547-2.11045-5


People

Vincenzo Barone

Professor
Carovana - Director's Office
Scuola Normale Superiore, Pisa
vincenzo.barone@sns.it

Giordano Mancini

Researcher
Piazza San Silvestro, 7 - Office 1.2
Scuola Normale Superiore, Pisa
giordano.mancini@sns.it

Oliver Carrillo

Postdoc Fellow
Palazzo D'Ancona
Scuola Normale Superiore, Pisa
oliver.carrillo@sns.it

Sara Del Galdo

Postdoc Fellow
Palazzo D'Ancona
Scuola Normale Superiore, Pisa
sara.delgaldo@sns.it

Francesco Fracchia

Postdoc Fellow
Piazza San Silvestro, 7 - Office 1.2
Scuola Normale Superiore, Pisa
francesco.fracchia@sns.it

Daniele Licari

Postdoc Fellow
Palazzo D'Ancona - Office 2.7
Scuola Normale Superiore, Pisa
daniele.licari@sns.it

Marina Macchiagodena

Postdoc Fellow
Piazza San Silvestro, 7 - Office 1.2
Scuola Normale Superiore, Pisa
marina.macchiagodena@sns.it

Duilio Malorgio

Postdoc Fellow
Carovana - Office Altana
Scuola Normale Superiore, Pisa
duilio.malorgio@sns.it

Alexey Nikitin

Postdoc Fellow
Piazza San Silvestro, 7 - Office 1.2
Scuola Normale Superiore, Pisa
alexey.nikitin@sns.it

Andrea Salvadori

Postdoc Fellow
Palazzo D'Ancona - Office Altana
Scuola Normale Superiore, Pisa
andrea.salvadori@sns.it

Akash Deep Biswas

PhD Student
Palazzo D'Ancona
Scuola Normale Superiore, Pisa
akash.biswas@sns.it

Gianluca Del Frate

PhD Student
Piazza San Silvestro, 7 - Office 1.2
Scuola Normale Superiore, Pisa
gianluca.delfrate@sns.it

Federico Lazzari

Graduate Student
Palazzo D'Ancona - Office Altana
Scuola Normale Superiore, Pisa
federico.lazzari@sns.it