1. Coil-globule transition of a homopolymer chain in a square-well potentialArtem Badasyan, Achille Giacometti, Rudolf Podgornik, Trinh Xuan Hoang, 2012, other component parts Found in: ključnih besedah Summary of found: ...Monte Carlo simulation, biopolymers, coil-globule transition, Wang-Landau sampling, ... Keywords: Monte Carlo simulation, biopolymers, coil-globule transition, Wang-Landau sampling Published: 25.04.2014; Views: 3644; Downloads: 12 Fulltext (0,00 KB) |
2. INNOVATIVE METHODS FOR IMAGING WITH THE USE OF X-RAY FREE ELECTRON LASER (XFEL) AND SYNCHROTRON SOURCESBoštjan Mavrič, Grega Belšak, Marjan Maček, N. Talat, Rizwan Zahoor, Božidar Šarler, 2016, project documentation (preliminary design, working design) Found in: ključnih besedah Summary of found: ...XFEL, simulation, microjet, gas, method of fundamental solutions... Keywords: XFEL, simulation, microjet, gas, method of fundamental solutions Published: 20.06.2016; Views: 3866; Downloads: 0 Fulltext (66,05 KB) |
3. Packing patterns of silica nanoparticles on surfaces of armored polystyrene latex particlesSara 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: ključnih besedah Summary of found: ...packing patterns, silica, simulation, Monte Carlo, order, disorder, transition, armored particles,... Keywords: packing patterns, silica, simulation, Monte Carlo, order, disorder, transition, armored particles, nanoparticles, Pickering emulsion Published: 10.10.2016; Views: 2878; Downloads: 0 Fulltext (3,85 MB) |
4. 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). Found in: ključnih besedah Keywords: Self-assembly, self-organisation, agent based, Monte Carlo, rigid molecules, simulation Published: 10.10.2016; Views: 2800; Downloads: 0 Fulltext (2,25 MB) |
5. 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. Found in: ključnih besedah Summary of found: ...self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice... Keywords: self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice Published: 10.10.2016; Views: 2802; Downloads: 0 Fulltext (3,44 MB) |
6. 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. Found in: ključnih besedah Summary of found: ...a lower energy configuration in the same simulation time than both of the MC simulation... Keywords: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram Published: 11.10.2016; Views: 2970; Downloads: 0 Fulltext (4,00 MB) |
7. 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. Found in: ključnih besedah Summary of found: ...Pickering emultion, self-assemblt, Monte Carlo, simulation, nanoparticle, packing, pattern garnd canonical, colloids... Keywords: Pickering emultion, self-assemblt, Monte Carlo, simulation, nanoparticle, packing, pattern garnd canonical, colloids Published: 11.10.2016; Views: 2700; Downloads: 0 Fulltext (1,43 MB) |
8. 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: ključnih besedah Summary of found: ...self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction... Keywords: self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction Published: 11.10.2016; Views: 2810; Downloads: 0 Fulltext (2,97 MB) |
9. Formation of Hybrid Electronic States in FePc Chains Mediated by the Au(110) SurfaceMaria 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: ključnih besedah Keywords: phthalocyanine, Au(110), gold, surface, DFT, density functional theory, calculation, simulation Published: 13.10.2016; Views: 2947; Downloads: 0 Fulltext (3,25 MB) |
10. ROBAST: Development of a Non-Sequential Ray-Tracing Simulation Library and its Applications in the Cherenkov Telescope ArrayMarko Zavrtanik, Danilo Zavrtanik, Gabrijela Zaharijas, Lili Yang, Serguei Vorobiov, Samo Stanič, Gašper Kukec Mezek, Andrej Filipčič, Akira Okumura, 2015, published scientific conference contribution Found in: ključnih besedah Keywords: Cherenkov Telescope Array (CTA), simulation of optical systems of CTA telescopes, ROBAST: a Non-Sequential Ray-Tracing Simulation Library Published: 16.02.2017; Views: 2215; Downloads: 198 Fulltext (4,32 MB) |