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  • 1. Atzori, Alessio
    et al.
    Liggi, Sonia
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). University of Cagliari, Italy.
    Porcu, Massimiliano
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Università di Cagliari, Italy.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Saba, Giuseppe
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Università di Cagliari, Italy.
    Base sequence specificity of counterion binding to DNA: what can MD simulations tell us?2016In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 94, no 12, 1181-1188 p.Article in journal (Refereed)
    Abstract [en]

    Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan-Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the A. qvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.

  • 2.
    Smania, Massimiliano
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Elhassan, Ashraf M.
    Stockholm University, Faculty of Science, Department of Physics.
    Tavakoli, Armin
    Stockholm University, Faculty of Science, Department of Physics.
    Bourennane, Mohamed
    Stockholm University, Faculty of Science, Department of Physics.
    Experimental quantum multiparty communication protocols2016In: npj Quantum Information, ISSN 2056-6387, Vol. 2, 16010Article in journal (Refereed)
    Abstract [en]

    Quantum information science breaks limitations of conventional information transfer, cryptography and computation by using quantum superpositions or entanglement as resources for information processing. Here we report on the experimental realisation of three-party quantum communication protocols using single three-level quantum system (qutrit) communication: secret-sharing, detectable Byzantine agreement and communication complexity reduction for a three-valued function. We have implemented these three schemes using the same optical fibre interferometric setup. Our realisation is easily scalable without compromising on detection efficiency or generating extremely complex many-particle entangled states.

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