Molecular Dyamics and Application (MDA)

Paola Bolognesi  -

Anna Rita Casavola-

Mattea Carmen Castrovilli -

Laura Carlini  -

Jacopo Chiarinelli -

Andrea Morabito -

Lorenzo Avaldi -

Antonella Cartoni (UniSapienza) - Associato ISM

 
 

Research Activity

The Molecular Dynamics and Applications group, MDA, carries out research activities in different fields ranging from basic physical-chemistry reactions, with the study of the interaction between ionizing radiation and molecules of bio-medical interest, to more purely application sectors, with production of thin films of bioactive molecules. The main lines of research are briefly described below..

Chemical-physical characterization of systems with increasing complexity and dynamic of their processes

In this activity the radiation-matter interaction (synchrotron radiation, ultrafast FEL or HHG radiation, electrons and multiply charged ions) is used to study both the structure and the dynamics induced by the interaction in systems of increasing complexity, from isolated molecules to nanoclusters.
Multi-electron processes dominated by electronic correlations, collective excitation processes, ultra-fast charge transfer or isomerization processes, dichroic and coherent phenomena are studied using original instrumentation and innovative methodologies that involve the time-resolved measurement of the products of interaction.

 
Relevant publications

 

 

Biomolecules and their applications in radiotherapy

The first phase of radiation damage, called the physical stage, involves the interaction of ionizing radiation with the elemental components of biological systems. The activity is aimed at understanding this first phase of interaction by studying the dynamics that occur in the molecules constituents of radio-sensitizers drugs, and in some cases the drugs themselves.
The effect of the environment which surrounds these molecules, is simulated by producing homogeneous or hydrated clusters of these molecules. Their structural properties and the reactivity of the ions produced by radiation are studied by DFT methods.

 
Relevant publications

 

 

Mass spectrometry and depositions of molecules for biosensor applications

Mass spectrometry is a powerful analytical tool and it is ideal for the preparation of molecules in a well-defined charge and composition state. This technology is used in our laboratories to determine the structure of gas phase molecules and study radiation-induced fragmentation patterns via the detection and analysis of their fragmentation products.
It can be used for samples that can be brought into the gas phase from solid/liquid phase by thermal evaporation. The gas phase study of molecules with increasing complexity is instead carried out via ElectroSpray Ionization (ESI) source used for diagnostic studies, excitation/ionization experiments or controlled deposition. The same technique is used under standard conditions for the deposition of thin films of bioactive molecules, on different surfaces such as screen-printed electrodes for the production of biosensors.
The experimental study is flanked by a theoretical approach based on classical molecular dynamics, which allows information on the structural and dynamic properties of the biomolecules analyzed.

 
Relevant publications

 

 

J. Chiarinelli, P. Bolognesi, and L. Avaldi
Ion optics simulation of an ion beam set-up coupled to an electrospray ionisation source, strengths and limitations
Review Scientific Instruments 2020 (submitted)
 

Instrumentation

TOF DEPEST LAB ESI

 

 

Collaborations

  • Politecnico di Milano Physics department, as part of the PRIN project "Predicting and controlling the fate of bio-molecules driven by extreme-ultraviolet radiation". Collaborators: Mauro Nisoli, Rocio Borrego Varillas.
  • Sapienza University, as part of the study of the interaction dynamics between radical ions and molecules in the upper atmosphere. Collaborators: Antonella Cartoni
  • Universidad Autonoma de Madrid, in the context of the theoretical simulation of the molecules fragmentation (COST XLIC and COST MD-Gas Projects) Collaborators: Manuel Alcami, Fernando Martin, Sergio Tendero Diaz, Dario Barreiro Lage
  • CNRS- CIMAP, as part of the study of interactions between multiple-charged ion beams and radio-sensitizing molecules. Collaborators: Alicja Domaracka
  • Université Caen Normandie e GANIL/ Collaborators: Patrick Rousseau
  • Elettra Sincrotrone Trieste in the field of radiation-matter iteration studies with synchrotron radiation and free electron laser. Collaborators: Kevin Prince, Robert Richter, Oksana Plekan, Carlo Callegari
  • Soleil Source Optimisée de Lumière d'Énergie Intermédiaire de LURE, as part of the study of ionizing radiation interactions and homogeneous and hydrated clusters of radiosensitizing molecules. Collaborators: Aleksandar Milosavljevic
  • Stockholm University, Dept. Physics as part of the MAECI and COST projects. Collaborators: Henning Zettergren, Mark Stocket, Henning Schmidt, Eric Cederquist)
  • Institute of Physics , University of Belgrade
  • Institute of Physics , Universitè de Lorraine, in the context of the study of the double photoionization of molecules and electronic correlations. Collaborators: Ugo Ancarani
  • University of Tuscia (Viterbo) as part of molecular dynamics simulations of complex biomolecules in interaction with solvents and substrates. Collaborator: Stefano Borocci
  • CNR- Institute of Crystallography, as part of the production and characterization of biosensors. Collaborators: V. Scognamiglio, A. Antonacci
  • CNR-Institute for the Study of Nanostructured Materials Mauro Satta, Pietro Calandra
  • Biosensor Snc .T. Giardi
  • Microsis Collaborator: R. Antoniucci
  • Swiburne University of Technology (Melbourne, Australia) as part of the interpretation of valence and core photoemission spectra of molecules of biological interest

 

MDA Projects

  • ESILARANTE - ElectroSpray Immobilization of LAccase foR cANnabinoids deTEction +

    ESILARANTE - ElectroSpray Immobilization of LAccase foR cANnabinoids deTEction ESILARANTE is a project financed by the MUR as part of the PRIN 2022 call and aims to characterize and Read More
  • iSenseDNA - Computation driven development of novel vivo-like-DNA-nanotransducers for biomolecules structure identification +

    iSenseDNA - Computation driven development of novel vivo-like-DNA-nanotransducers for biomolecules structure identification Understanding how a specific molecule performs during complex biological processes is a challenge in biomedical research, despite extensive biotechnological advances Read More
  • Fabrication of a New, Low-Cost, and Environment-Friendly Laccase-Based Biosensor by Electrospray Immobilization with Unprecedented Reuse and Storage Performances +

    Fabrication of a New, Low-Cost, and Environment-Friendly Laccase-Based Biosensor by Electrospray Immobilization with Unprecedented Reuse and Storage Performances The CNR-ISM together with other Institutes such as ISMN, IGAG and IMAA and with the participation of Sapienza University of Read More
  • A “smart” molecular mechanism at the origin of life? +

    A “smart” molecular mechanism at the origin of life? An experimental and theoretical study, cover article of the J. Phys. Chem. Lett. which has involved researchers from the Institute Read More
  • Biomarkers Discovery con ElectroSpray-Mass Spectrometry - BioDivErSI +

    Biomarkers Discovery con ElectroSpray-Mass Spectrometry - BioDivErSI BioDivErSI is a project funded under the Public Call "Gruppi di Ricerca 2020" POR FESR Lazio 2014-2020 The project will Read More
  • E-CROME project is starting now! +

    E-CROME project is starting now! The #E-CROME project, for #telemedicine to assist cancer and terminal patients, is launched.The project, funded by Regione Lazio, Lazio Innova, Read More
  • SENSOCARD: SENSOrs for rapid detection CARDiovascular emergencies +

    SENSOCARD: SENSOrs for rapid detection CARDiovascular emergencies SENSOCARD aims to the optimization and  field demonstration  of an integrated prototype for the diagnosis of cardiovascular emergencies. The prototype Read More
  • Nanoscale insights in radiation damage +

    The objectives of the project are: a) the study of elementary processes of radiation damage in prototype molecules  of biological Read More
  • A nanoview of radiation-biomatter interaction +

    The project aims to exploit new opportunities to study the structure and dynamics of complex biomolecules isolated. Read More
  • NANO-IBCT - Nano-scale insights in ion beam cancer therapy +

    To combine the unique experimental and theoretical expertise available within Europe to acquire greater insight at the nanoscopic and molecular Read More
  • XLIC - XUV/X-ray light and fast ions for ultrafast chemistry +

    The scientific objective of the Action is to understand, monitor and control the nuclear dynamics. Read More
  • Nanoscale insights in radiation damage +

    The objectives of the project are the study of elementary damage processes in prototype molecules  Read More
  • nanoTOOLS - New molecular tools for exploring the nanoscopic world +

    Development of intense ESI sources and Application of the new devices. Read More
  • Chimica ionica e neutra in fase gassosa +

    The aim of the research is the study of aspects of ionic chemistry in the gaseous phase, which are of Read More
  • MD-GAS - Molecular Dynamics in the Gas Phase +

    The Action aims to develop a new physical and chemical toolbox. Read More
  • BIFACE - Biomolecular Ions: Fundamental and Applied scienCE +

    The BIFACE project aims to study fundamental properties of biomolecular ions as well as their possible applications in nanotechnology Read More
  • AttoChem - Attosecond Chemistry +

    The AttoChem network will coordinate experimental and theoretical efforts to exploit the large potential of attosecond techniques in chemistry. Read More
  • BIOX - Predicting and controlling the fate of bio-molecules driven by extreme-ultraviolet radiation +

    The target of the project is the investigation, with extreme temporal resolution, of the molecular processes initiated by the interaction Read More
  • 1
We use cookies essential for the functioning of the site. You can decide for yourself whether or not to allow cookies. Please note that if you refuse them, you may not be able to use all of the site's features.