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Computational design of customised nanobodies for biotechnological applications
Sara Fortuna, Ario de Marco, Miguel Soler, 2016, unpublished conference contribution

Abstract: In silico modeling to improve the biophysical characteristics of recombinant single-domain antibodies
Found in: osebi
Keywords: nanobodies, modeling, protein stability, antibody humanization, molecular dynamics
Published: 26.04.2016; Views: 1507; Downloads: 0
.pdf Fulltext (2,42 MB)

Packing patterns of silica nanoparticles on surfaces of armored polystyrene latex particles
Sara Fortuna, Catheline A. L. Colard, Stefan A. F. Bon, Alessandro Troisi, 2009, original scientific article

Abstract: Fascinating packing patterns of identical spherical and discotic objects on curved surfaces occur readily in nature and science. Examples include C60 fullerenes,(1, 2)13-atom cuboctahedral metal clusters,(3) and S-layer proteins on outer cell membranes.(4) Numerous situations with surface-arranged objects of variable size also exist, such as the lenses on insect eyes, biomineralized shells on coccolithophorids,(5) and solid-stabilized emulsion droplets(6) and bubbles.(7) The influence of size variations on these packing patterns, however, is studied sparsely. Here we investigate the packing of nanosized silica particles on the surface of polystyrene latex particles fabricated by Pickering miniemulsion polymerization of submicrometer-sized armored monomer droplets. We are able to rationalize the experimental morphology and the nearest-neighbor distribution with the help of Monte Carlo simulations. We show that broadening of the nanoparticle size distribution has pronounced effects on the self-assembled equilibrium packing structures, with original 12-point dislocations or grain-boundary scars gradually fading out.
Found in: osebi
Keywords: packing patterns, silica, simulation, Monte Carlo, order, disorder, transition, armored particles, nanoparticles, Pickering emulsion
Published: 10.10.2016; Views: 1632; Downloads: 0
.pdf Fulltext (3,85 MB)

An artificial intelligence approach for modeling molecular self-assembly: Agent Based simulations of rigid molecules
Sara Fortuna, Alessandro Troisi, 2009, original scientific article

Abstract: Agent-based simulations are rule-based models traditionally used for the simulations of complex systems. In this paper, an algorithm based on the concept of agent-based simulations is developed to predict the lowest energy packing of a set of identical rigid molecules. The agents are identified with rigid portions of the system under investigation, and they evolve following a set of rules designed to drive the system toward the lowest energy minimum. The algorithm is compared with a conventional Metropolis Monte Carlo algorithm, and it is applied on a large set of representative models of molecules. For all the systems studied, the agent-based method consistently finds a significantly lower energy minima than the Monte Carlo algorithm because the system evolution includes elements of adaptation (new configurations induce new types of moves) and learning (past successful choices are repeated).
Found in: osebi
Keywords: Self-assembly, self-organisation, agent based, Monte Carlo, rigid molecules, simulation
Published: 10.10.2016; Views: 1540; Downloads: 0
.pdf Fulltext (2,25 MB)

Hexagonal lattice model of the patterns formed by hydrogen-bonded molecules on the surface
Sara Fortuna, David L. Cheung, Alessandro Troisi, 2010, original scientific article

Abstract: We model the two-dimensional self-assembly of planar molecules capable of complementary interactions (like hydrogen bonding) as a set of hexagonal tiles on a hexagonal lattice. We use Monte Carlo simulations to study the phase diagrams of three model systems. The phases are characterized using a variety of order parameters, and they are studied as a function of the strength of the complementary interaction energy. This simplified model is proven to be capable of reproducing the phases encountered in real systems, unifying within the same framework most of the structures encountered experimentally.
Found in: osebi
Keywords: self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice
Published: 10.10.2016; Views: 1578; Downloads: 0
.pdf Fulltext (3,44 MB)

Agent based modelling for the 2D molecular self-organization of realistic molecules
Sara Fortuna, Alessandro Troisi, 2010, original scientific article

Abstract: We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.
Found in: osebi
Keywords: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram
Published: 11.10.2016; Views: 1772; Downloads: 0
.pdf Fulltext (4,00 MB)

Polymer Vesicles with a Colloidal Armor of Nanoparticles
Rong Chen, Daniel J. G. Pearce, Sara Fortuna, David L. Cheung, Stefan A. F. Bon, 2011, original scientific article

Abstract: The fabrication of polymer vesicles with a colloidal armor made from a variety of nanoparticles is demonstrated. In addition, it is shown that the armored supracolloidal structure can be postmodified through film-formation of soft polymer latex particles on the surface of the polymersome, hereby effectively wrapping the polymersome in a plastic bag, as well as through formation of a hydrogel by disintegrating an assembled polymer latex made from poly(ethyl acrylate-co-methacrylic acid) upon increasing the pH. Furthermore, ordering and packing patterns are briefly addressed with the aid of Monte Carlo simulations, including patterns observed when polymersomes are exposed to a binary mixture of colloids of different size.
Found in: osebi
Keywords: Pickering emultion, self-assemblt, Monte Carlo, simulation, nanoparticle, packing, pattern garnd canonical, colloids
Published: 11.10.2016; Views: 1418; Downloads: 0
.pdf Fulltext (1,43 MB)

Molecule-Driven Substrate Reconstruction in the Two-Dimensional Self-Organization of Fe-Phthalocyanines on Au(110)
Sara Fortuna, Pierluigi Gargiani, Maria Grazia Betti, Carlo Mariani, Arrigo Calzolari, Silvio Modesti, Stefano Fabris, 2012, original scientific article

Abstract: The structural patterns formed by molecular self-assembly at surfaces are usually controlled by the relative strengths of the intermolecular and molecule–substrate interactions. An additional steering effect is present when the substrate can easily reconstruct upon molecular adsorption, which therefore drives a self-templating effect on the metal support. This is here demonstrated for the model case of Fe-phthalocyanine molecules adsorbed on the Au(110) surface. Scanning tunneling microscopy shows that molecular adsorption promotes a local (1 × 5) surface reconstruction, which drives the assembly of molecular chains along the [11̅0] direction. The order and periodicity of the molecular assemblies are determined with low energy electron diffraction patterns. Density functional theory calculations reveal the energetic origins of the molecule-driven substrate reconstruction. Since the function of molecular overlayers at surfaces is strongly correlated to their structure, these results have implications in the design of new metal/molecular interfaces.
Found in: osebi
Keywords: self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction
Published: 11.10.2016; Views: 1579; Downloads: 0
.pdf Fulltext (2,97 MB)

Formation of Hybrid Electronic States in FePc Chains Mediated by the Au(110) Surface
Maria Grazia Betti, Pierluigi Gargiani, Carlo Mariani, Stefano Turchini, Nicola Zema, Sara Fortuna, Arrigo Calzolari, Stefano Fabris, 2012, original scientific article

Abstract: Iron–phthalocyanine (FePc) molecules deposited on the Au(110) surface self-organize in ordered chains driven by the reconstructed Au channels. The interaction process induces a rehybridization of the electronic states localized on the central metal atom, breaking the 4-fold symmetry of the molecular orbitals of the FePc molecules. The molecular adsorption is controlled by a symmetry-determined mixing between the electronic states of the Fe metal center and of the Au substrate, as deduced by photoemission and absorption spectroscopy exploiting light polarization. DFT calculations rationalize this mixing of the Fe and Au states on the basis of symmetry arguments. The calculated electronic structure reproduces the main experimental spectral features, which are associated to a distorted molecular structure displaying a trigonal bipyramidal geometry of the ligands around the metal center.
Found in: osebi
Keywords: phthalocyanine, Au(110), gold, surface, DFT, density functional theory, calculation, simulation
Published: 13.10.2016; Views: 1719; Downloads: 0
.pdf Fulltext (3,25 MB)

Structural phases of ordered FePc-nanochains self-assembled on Au(110)
Betti Maria Grazia, Pierluigi Gargiani, Carlo Mariani, Roberto Biagi, Jun Fujii, Giorgio Rossi, Andrea Resta, Stefano Fabris, Sara Fortuna, Xavier Torrelles, Manvendra Kumar, Maddalena Pedio, 2012, original scientific article

Abstract: Iron-phthalocyanine molecules deposited on the Au(110) reconstructed channels assemble into one-dimensional molecular chains, whose spatial distribution evolves into different structural phases at increasing molecular density. The plasticity of the Au channels first induces an ordered phase with a 5×5 symmetry, followed by a second long-range ordered structure composed by denser chains with a 5×7 periodicity with respect to the bare Au surface, as observed in the low-energy electron-diffraction (LEED) and grazing incidence X-ray diffraction (GIXRD) patterns. The geometry of the FePc molecular assemblies in the Au nanorails is determined by scanning tunneling microscopy (STM). For the 5×7 phases, the GIXRD analysis identifies a “4-3” rows profile along the [001] direction in the Au surface and an on-top FePc adsorption site, further confirmed by density functional theory (DFT) calculations. The latter also reveals the electronic mixing of the interface states. The chain assembly is driven by the molecule–molecule interaction and the chains interact with the Au nanorails via the central metal atom, while the chain–chain distance in the different structural phases is primarily driven by the plasticity of the Au surface.
Found in: osebi
Keywords: STM, LEED, DFT, density functional theory, phthalocyanine, Au(110), gold, surface
Published: 13.10.2016; Views: 1674; Downloads: 0
.pdf Fulltext (1,33 MB)

Spin and orbital configuration of metal phthalocyanine chains assembled on the Au(110) surface
Gargiani Pierluigi, Giorgio Rossi, Roberto Biagi, Valdis Corradini, Maddalena Pedio, Sara Fortuna, Arrigo Calzolari, Stefano Fabris, Julio Criginski Cezar, N. B. Brookes, Maria Grazia Betti, 2013, original scientific article

Abstract: The spin and orbital configuration of magnetic metal phthalocyanines (MPcs) deposited on metallic substrates are strongly influenced by the rehybridization of the molecular states with the underlying metal. FePc, CoPc, and CuPc isolated molecules are archetypal systems to investigate the interrelationship between magnetic moments and orbital symmetry after deposition on a metallic substrate. MPcs form long-range ordered chains self-assembled along the reconstructed channels of the Au(110) surface. X-ray magnetic circular dichroism from the L2,3 absorption edges of Fe, Co, and Cu shows that the orbital and spin configuration are strongly modified upon adsorption on the Au(110) surface if the orbitals responsible of the magnetic moment are involved in the interaction process. The magnetic moment for a single layer of molecular chains is completely quenched for the CoPc molecules, fully preserved for the CuPc and reduced for the FePc ones. The modified magnetic configuration is confined to the very interface layer, i.e., to the MPc molecules bound to the metal substrate up to the compact packing of the single layer. The different response can be rationalized in terms of the symmetry/orientation of the metal-ion d states interacting with the substrate states, as indicated by density functional theory calculations in agreement with experimental findings.
Found in: osebi
Keywords: phthalocyanine, Au(110), gold, self-assembly, pattern, configuration, density functional theory, DFT, CuPc, FePc
Published: 12.10.2016; Views: 1581; Downloads: 0
.pdf Fulltext (1,73 MB)

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