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1.
An artificial intelligence approach for modeling molecular self-assembly: Agent Based simulations of rigid molecules
Sara Fortuna, Alessandro Troisi, 2009, izvirni znanstveni članek

Opis: 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).
Najdeno v: ključnih besedah
Ključne besede: Self-assembly, self-organisation, agent based, Monte Carlo, rigid molecules, simulation
Objavljeno: 10.10.2016; Ogledov: 1458; Prenosov: 0
.pdf Polno besedilo (2,25 MB)

2.
Hexagonal lattice model of the patterns formed by hydrogen-bonded molecules on the surface
Sara Fortuna, David L. Cheung, Alessandro Troisi, 2010, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...We model the two-dimensional self-assembly of planar molecules capable of complementary interactions...
Ključne besede: self-assembly, self-organisation, Monte Carlo, simulation, lattice model, dicarboxilic acid, hexagonal lattice
Objavljeno: 10.10.2016; Ogledov: 1484; Prenosov: 0
.pdf Polno besedilo (3,44 MB)

3.
Agent based modelling for the 2D molecular self-organization of realistic molecules
Sara Fortuna, Alessandro Troisi, 2010, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...(AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental...
Ključne besede: self-assembly, self-organisation, 1, 4-benzene-dicarboxylic acid, TPA, agent based, Monte Carlo, simulation, phase diagram
Objavljeno: 11.10.2016; Ogledov: 1679; Prenosov: 0
.pdf Polno besedilo (4,00 MB)

4.
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, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...The structural patterns formed by molecular self-assembly at surfaces are usually controlled by the...
Ključne besede: self-assembly, phthalocyanine, Au(110), DFT, density functional theory, simulation, surface, recontruction
Objavljeno: 11.10.2016; Ogledov: 1498; Prenosov: 0
.pdf Polno besedilo (2,97 MB)

5.
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, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...phthalocyanine, Au(110), gold, self-assembly, pattern, configuration, density functional theory, DFT, CuPc,...
Ključne besede: phthalocyanine, Au(110), gold, self-assembly, pattern, configuration, density functional theory, DFT, CuPc, FePc
Objavljeno: 12.10.2016; Ogledov: 1494; Prenosov: 0
.pdf Polno besedilo (1,73 MB)

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