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5122. 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: 4839; Downloads: 0
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5123. 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: 4585; Downloads: 0
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5124. 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: 4298; Downloads: 229
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5125. 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: 4760; Downloads: 244
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5126. 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: 4897; Downloads: 0
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5129. Hexagonal lattice model of the patterns formed by hydrogen-bonded molecules on the surfaceSara 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.
Keywords: self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice
Published in RUNG: 10.10.2016; Views: 4906; Downloads: 0
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5130. An artificial intelligence approach for modeling molecular self-assembly: Agent Based simulations of rigid moleculesSara 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).
Keywords: Self-assembly, self-organisation, agent based, Monte Carlo, rigid molecules, simulation
Published in RUNG: 10.10.2016; Views: 4900; Downloads: 0
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