5071. Phase behaviour of self-assembled monolayers controlled by tuning physisorbed and chemisorbed states: a lattice-model viewSara Fortuna, David L. Cheung, Karen Johnston, 2016, original scientific article Abstract: The self-assembly of molecules on surfaces into 2D structures is important for the bottom-up fabrication of functional nanomaterials, and the self-assembledstructure depends on the interplay between molecule-molecule interactions and molecule-surface interactions. Halogenated benzene derivatives on platinum have been shown to have two distinct adsorption states: a physisorbed state and a chemisorbed state, and the interplay between the two can be expected to have a profound effect on the self-assembly and phase behaviour of these systems. We developed a lattice model that explicitly includes both adsorption states, with representative interactions parameterised using density functional theory calculations. This model was used in Monte Carlo simulations to investigate pattern formation of hexahalogenated benzene molecules on the platinumsurface. Molecules that prefer the physisorbed state were found to self-assemble with ease, depending on the interactions between physisorbed molecules. In contrast, molecules that preferentially chemisorb tend to get arrested in disordered phases. However, changing the interactions between chemisorbed and physisorbed molecules affects the phase behaviour. We propose functionalising molecules in order to tune their adsorption states, as an innovative way to control monolayer structure, leading to a promising avenue for directed assembly of novel 2D structures.
Keywords: lattice model, hexagonal lattice, Monte Carlo, DFT, density functional theory, benzene, physisorption, chemisorption, halogenated
Published in RUNG: 11.10.2016; Views: 4606; Downloads: 0
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5072. 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.
Keywords: self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction
Published in RUNG: 11.10.2016; Views: 4743; Downloads: 0
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5076. Polymer Vesicles with a Colloidal Armor of NanoparticlesRong 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.
Keywords: Pickering emultion, self-assemblt, Monte Carlo, simulation, nanoparticle, packing, pattern garnd canonical, colloids
Published in RUNG: 11.10.2016; Views: 4835; Downloads: 0
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5077. Oxalic acid adsorption states on the clean Cu(110) surfaceSara Fortuna, 2016, original scientific article Abstract: Carboxylic acids are known to assume a variety of configurations on metallic surfaces. In particular oxalic acid on the Cu(110) surface has been proposed to assume a number of upright configurations. Here we explore with DFT calculations the possible structures that oxalic acid can form on copper 110 at different protonation states, with particular attention at the possibility of forming structures composed of vertically standing molecules. In its fully protonated form it is capable of anchoring itself on the surface thanks to one of its hydrogen-free oxygens. We show the monodeprotonated upright molecule with two oxygens anchoring it on the surface to be the lowest energy conformation of a single oxalic molecules on the Cu(110) surface. We further show that it is possible for this configuration to form dense hexagonally arranged patterns in the unlikely scenario in which adatoms are not involved.
Keywords: oxalic acid, oxalate, cu(110), copper, surface, adsorption, density functional theory, DFT
Published in RUNG: 11.10.2016; Views: 4583; Downloads: 0
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5078. Bodo naslednje volitve legalne in legitimne?Zoran Božič, 2016, professional article Abstract: Prispevek govori o neustavnosti slovenske volilne zakonodaje, predvsem o neuresničenem določilu ustave, da imajo volivci odločilen vpliv na izbiro kandidatov. Avtor kot najprimernejši volilni sistem zagovarja dvokrožni večinski sistem, ki je dobil potrditev ljudstva na referendumu leta 1996.
Keywords: volilni sistemi, demokracija, državni zbor, Slovenija, večinski volilni sistem
Published in RUNG: 11.10.2016; Views: 4290; Downloads: 229
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5079. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodiesMiguel Soler, Ario De Marco, Sara Fortuna, 2016, original scientific article Abstract: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular
recognition. Their small size represents a precious advantage for rational mutagenesis based on
modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate
mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule
docking. The method was tested on two sets of nanobodies characterized experimentally
for their biophysical features. One set contained point mutations introduced to humanize a wild type
sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae
and human hallmarks. The method resulted in accurate scoring approaches to predict experimental
yields and enabled to identify the structural modifications induced by mutations. This work is a
promising tool for the in silico development of single-domain antibodies and opens the opportunity to
customize single functional domains of larger macromolecules
Keywords: nanobodies, molecular dynamics, modeling, antibody solubility
Published in RUNG: 11.10.2016; Views: 4747; Downloads: 244
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5080. Agent based modelling for the 2D molecular self-organization of realistic moleculesSara 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.
Keywords: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram
Published in RUNG: 11.10.2016; Views: 4892; Downloads: 0
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