Papers by Valentina Tozzini
Journal of Materials Chemistry C
Spatially selective functionalization of monolayer graphene is achieved by combining electron bea... more Spatially selective functionalization of monolayer graphene is achieved by combining electron beam irradiation patterning with 1,3-dipolar cycloaddition of azomethine ylide and shown to be reversible via focused laser irradiation-induced desorption.
Graphene’s strength and extreme flexibility allow sustained ripples in a wide range of amplitudes... more Graphene’s strength and extreme flexibility allow sustained ripples in a wide range of amplitudes and wavelengths [1]. Ripples produce a modulation of the local curvature, which is strongly correlated with the stability of chemisorbed hydrogen atoms [2]. Curvature induced local pyramidalisation, i.e. pushing a carbon site towards the sp3 configuration, contributes to the increase of graphene's reactivity [3]. Thus, the functionalization of curved graphene with hydrogen, or other adatoms, gives the possibility to tune its chemical and adsorption properties for storage and other applications [4].
Quasi free standing monolayer graphene (QFMLG) grown on SiC by selective Si evaporation from the ... more Quasi free standing monolayer graphene (QFMLG) grown on SiC by selective Si evaporation from the Si-rich SiC(0001) face and H intercalation displays irregularities in STM and AFM analysis, appearing as localized features, which we previously identified as vacancies in the H layer coverage [Y Murata, et al. Nano Res, in press, DOI: 10.1007/s12274-017-1697-x]. The size, shape, brightness, location, and concentration of these features, however, are variable, depending on the hydrogenation conditions. In order to shed light on the nature of these features, in this work we perform a systematic Density Functional Theory study on the structural and electronic properties of QFMLG with defects in the H coverage arranged in different configurations including up to 13 vacant H atoms, and show that these generate localized electronic states with specific electronic structure. Based on the comparison of simulated and measured STM images we are able to associate different vacancies of large size ...
Graphene monolayer grown by Si evaporation from the 0001 surface of SiC displays a moir\'e pa... more Graphene monolayer grown by Si evaporation from the 0001 surface of SiC displays a moir\'e pattern of corrugation whose structure is ambiguous: different measurements and theoretical studies show either protruding bumps surrounded by valleys, or, reversely, wells surrounded by crests. Here we address the fine structure of monolayer graphene on SiC by means of Density Functional Theory, using a model including the full symmetry of the system and the substrate (1648 atoms) and therefore realistically reproducing the experimental sample. We find that accurate treatment of the vdW interactions between monolayer and the underlying substrate-bound buffer layer is crucial in stabilizing one or the opposite corrugation pattern, which explain the different results and measurement available in the literature. Our study indicates that at low temperature a state more closely following the topography of the underneath buffer layer is stabilized, while others are metastable. Since environment...
Frontiers in Molecular Biosciences
Nano Research
We report the superlubric sliding of monolayer tungsten disulfide (WS 2 ) on epitaxial graphene (... more We report the superlubric sliding of monolayer tungsten disulfide (WS 2 ) on epitaxial graphene (EG) grown on silicon carbide (SiC). Single-crystalline WS 2 flakes with lateral size of hundreds of nanometers are obtained via chemical vapor deposition (CVD) on EG. Microscopic and diffraction analyses indicate that the WS 2 /EG stack is predominantly aligned with zero azimuthal rotation. The present experiments show that, when perturbed by a scanning probe microscopy (SPM) tip, the WS 2 flakes are prone to slide over the graphene surfaces at room temperature. Atomistic force field-based molecular dynamics simulations indicate that, through local physical deformation of the WS 2 flake, the scanning tip releases enough energy to the flake to overcome the motion activation barrier and trigger an ultralow-friction rototranslational displacement, that is superlubric. Experimental observations show that, after sliding, the WS 2 flakes come to rest with a rotation of n/3 with respect to graphene. Moreover, atomically resolved measurements show that the interface is atomically sharp and the WS 2 lattice is strain-free. These results help to shed light on nanotribological phenomena in van der Waals (vdW) heterostacks, and suggest that the applicative potential of the WS 2 /graphene heterostructure can be extended by novel mechanical prospects.
Nanoscale, Jan 2, 2017
This work reports an electronic and micro-structural study of an appealing system for optoelectro... more This work reports an electronic and micro-structural study of an appealing system for optoelectronics: tungsten disulfide (WS2) on epitaxial graphene (EG) on SiC(0001). The WS2 is grown via chemical vapor deposition (CVD) onto the EG. Low-energy electron diffraction (LEED) measurements assign the zero-degree orientation as the preferential azimuthal alignment for WS2/EG. The valence-band (VB) structure emerging from this alignment is investigated by means of photoelectron spectroscopy measurements, with both high space and energy resolution. We find that the spin-orbit splitting of monolayer WS2 on graphene is of 462 meV, larger than what is reported to date for other substrates. We determine the value of the work function for the WS2/EG to be 4.5 ± 0.1 eV. A large shift of the WS2 VB maximum is observed as well, due to the lowering of the WS2 work function caused by the donor-like interfacial states of EG. Density functional theory (DFT) calculations carried out on a coincidence su...
Nano Research
Si dangling bonds at the interface of quasi-free-standing monolayer graphene (QFMLG) are known to... more Si dangling bonds at the interface of quasi-free-standing monolayer graphene (QFMLG) are known to act as scattering centers that can severely affect carrier mobility. Herein, we investigate the atomic and electronic structure of Si dangling bonds in QFMLG using low-temperature scanning tunneling microscopy/ spectroscopy (STM/STS), atomic force microscopy (AFM), and density functional theory (DFT) calculations. Two types of defects with different contrast were observed on a flat graphene terrace by STM and AFM; in particular, their STM contrast varied with the bias voltage. Moreover, these defects showed characteristic STS peaks at different energies, 1.1 and 1.4 eV. The comparison of the experimental data with the DFT calculations indicates that the defects with STS peak energies of 1.1 and 1.4 eV consist of clusters of three and four Si dangling bonds, respectively. The relevance of the present results for the optimization of graphene synthesis is discussed.
Applied Physics Letters, 2015
Fluorescent Proteins (FPs) offer a wide palette of colors for imaging applications. One purpose o... more Fluorescent Proteins (FPs) offer a wide palette of colors for imaging applications. One purpose of this chapter is to review the variety of FP spectral properties, with a focus on their structural basis. Fluorescence in FPs originates from the autocatalytically-formed chromophore. Several studies exist on synthetic chromophore analogs in gas phase and in solution. Together with the X-ray structures of many Fluorescent Proteins, these studies help to understand how excitation and emission energies are tuned by chromophore structure, protonation state, and interactions with the surrounding environment, either solvent molecules or aminoacids residues. The increasing use of Fluorescent Proteins in two-photon microscopy also prompted detailed investigations of their two-photon excitation properties. The comparison with one-photon excitation reveals non-trivial features, which are relevant both for their implications in understanding multiphoton properties of fluorophores and for application purposes. Contents
Festschrift in Honor of Naseem K Rahman's 60th Birthday, 2004
Springer Series on Fluorescence, 2011
Fluorescent Proteins (FPs) offer a wide palette of colors for imaging applications. One purpose o... more Fluorescent Proteins (FPs) offer a wide palette of colors for imaging applications. One purpose of this chapter is to review the variety of FP spectral properties, with a focus on their structural basis. Fluorescence in FPs originates from the autocatalytically-formed chromophore. Several studies exist on synthetic chromophore analogs in gas phase and in solution. Together with the X-ray structures of many Fluorescent Proteins, these studies help to understand how excitation and emission energies are tuned by chromophore structure, protonation state, and interactions with the surrounding environment, either solvent molecules or aminoacids residues. The increasing use of Fluorescent Proteins in two-photon microscopy also prompted detailed investigations of their two-photon excitation properties. The comparison with one-photon excitation reveals non-trivial features, which are relevant both for their implications in understanding multiphoton properties of fluorophores and for application purposes. Contents
MRS Proceedings, 2001
ABSTRACTWe report the spontaneous formation of a GaP fullerene cage in ab-initio Molecular Dynami... more ABSTRACTWe report the spontaneous formation of a GaP fullerene cage in ab-initio Molecular Dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of neutral and ionized III-V (GaP, GaAs, AlAs, AIP) clusters suggests the stability of hetero-fullerenes formed by compounds with zincblend bulk structure. Our prediction is supported by several indicators: these clusters show closed electronic shells and relatively large energy gaps; the ratio between the cohesive energy per atom in the cluster and in the bulk is very close to the value found for carbon fullerenes of the same size; the clusters are thermally stable up to a temperature range of 1500–2000 K and they do not dissociate when ionized.
The Journal of Physical Chemistry B, 2006
The Journal of Physical Chemistry B, 2001
ABSTRACT
The Journal of Physical Chemistry B, 2003
The reversible photoinduced structural changes of a green fluorescent protein (GFP) mutant and th... more The reversible photoinduced structural changes of a green fluorescent protein (GFP) mutant and their optical control are reported. A photoreversible optically inactive configuration is demonstrated with the absorption peak at 365 nm, which is consistent with a photoisomerization pathway associated with hydrogen-bond breaking in the chromophore environment. We show that this state is involved in the switching dynamics recently discovered in these molecules and we determine the transition rates of the reversible photoconversion processes. These experiments combine to provide the framework for the implementation and optimization of efficient room-temperature GFP-based all-optical memories that use the fluorescent properties of these proteins.
Retrovirology, 2009
Background: An essential event during the replication cycle of HIV-1 is the integration of the re... more Background: An essential event during the replication cycle of HIV-1 is the integration of the reverse transcribed viral DNA into the host cellular genome. Our former report revealed that HIV-1 integrase (IN), the enzyme that catalyzes the integration reaction, is positively regulated by acetylation mediated by the histone acetyltransferase (HAT) p300. Results: In this study we demonstrate that another cellular HAT, GCN5, acetylates IN leading to enhanced 3'-end processing and strand transfer activities. GCN5 participates in the integration step of HIV-1 replication cycle as demonstrated by the reduced infectivity, due to inefficient provirus formation, in GCN5 knockdown cells. Within the C-terminal domain of IN, four lysines (K258, K264, K266, and K273) are targeted by GCN5 acetylation, three of which (K264, K266, and K273) are also modified by p300. Replication analysis of HIV-1 clones carrying substitutions at the IN lysines acetylated by both GCN5 and p300, or exclusively by GCN5, demonstrated that these residues are required for efficient viral integration. In addition, a comparative analysis of the replication efficiencies of the IN triple-and quadruple-mutant viruses revealed that even though the lysines targeted by both GCN5 and p300 are required for efficient virus integration, the residue exclusively modified by GCN5 (K258) does not affect this process. Conclusions: The results presented here further demonstrate the relevance of IN post-translational modification by acetylation, which results from the catalytic activities of multiple HATs during the viral replication cycle. Finally, this study contributes to clarifying the recent debate raised on the role of IN acetylated lysines during HIV-1 infection.
Proteins: Structure, Function, and Genetics, 2003
Molecular dynamics simulations with the Amber force field are carried out to study two mutants of... more Molecular dynamics simulations with the Amber force field are carried out to study two mutants of the green fluorescent protein (GFP), namely EGFP (F64L/S65T) and T203Y-EGFP (E 2 GFP). Those variants display an opposite equilibrium between the structural A and B states, associated with neutral and anionic protonation forms of the chromophore. Configurations of those two states are simulated for each variant and the energetics of their equilibrium in the two mutants is studied by evaluating the change in the relative free energy of A and B states (⌬G AB ) upon T203Y mutation. The resulting ⌬⌬G AB agrees with the value inferred from absorption measurements. A comparison of the hydrogen bond network around the chromophore rationalizes the different population of state A and B in EGFP and E 2 GFP. On the basis of structural and energetic considerations, a mechanism for destabilization of the neutral chromophore in S65T mutants is proposed. Simulations of the B state of the S65T variant and of WT GFP are also performed for comparison and to test the force field parameters of the chromophore derived for the present calculations. Possible paths of proton transfer leading to nonfluorescent states of the chromophore are discussed in light of the photodynamical behavior of GFP, as revealed by fluorescence correlation spectroscopy and single-molecule experiments. Proteins 2003;51:378 -389.
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Papers by Valentina Tozzini