High Conductance Ratio in Molecular Optical Switching of Functionalized Nanoparticle Self-Assembled Nanodevices

Self-assembled functionalized nano particles are at the focus of a number of potential applications, in particular for molecular scale electronics devices. Here we perform experiments of self-assembly of 10 nm Au nano particles (NPs), functionalized by a dense layer of azobenzene-bithiophene (AzBT) molecules, with the aim of building a light-switchable device with memristive properties. We fabricate planar nanodevices consisting of NP self-assembled network (NPSANs) contacted by nanoelectrodes separated by interelectrode gaps ranging from 30 to 100 nm. We demonstrate the light-induced reversible switching of the electrical conductance in these AzBT NPSANs with a record on/off conductance ratio up to 620, an average value of ca. 30 and with 85% of the devices having a ratio above 10. Molecular dynamics simulation of the structure and dynamics of the interface between molecular monolayers chemisorbed on the nano particle surface are performed and compared to the experimental findings. The properties of the contact interface are shown to be strongly correlated to the molecular conformation which in the case of AzBT molecules, can reversibly switched between a cis and a trans form by means of light irradiations of well-defined wavelength. Molecular dynamics simulations provide a microscopic explanation for the experimental observation of the reduction of the on/off current ratio between the two isomers, compared to experiments performed on flat self-assembled monolayers contacted by a conducting cAFM tip.Comment: pdf files : publication and supporting informatio

From modulational instability to focusing dam breaks in water waves

We report water wave experiments performed in a long tank where we consider the evolution of nonlinear deep-water surface gravity waves with the envelope in the form of a large-scale rectangular barrier. Our experiments reveal that, for a range of initial parameters, the nonlinear wave packet is not disintegrated by the Benjamin-Feir instability but exhibits a specific, strongly nonlinear modulation, which propagates from the edges of the wavepacket towards the center with finite speed. Using numerical tools of nonlinear spectral analysis of experimental data we identify the observed envelope wave structures with focusing dispersive dam break flows, a peculiar type of dispersive shock waves recently described in the framework of the semi-classical limit of the 1D focusing nonlinear Schr"odinger equation (1D-NLSE). Our experimental results are shown to be in a good quantitative agreement with the predictions of the semi-classical 1D-NLSE theory. This is the first observation of the persisting dispersive shock wave dynamics in a modulationally unstable water wave system

Nonlinear Spectral Synthesis of Soliton Gas in Deep-Water Surface Gravity Waves

Soliton gases represent large random soliton ensembles in physical systems that exhibit integrable dynamics at the leading order. Despite significant theoretical developments and observational evidence of ubiquity of soliton gases in fluids and optical media, their controlled experimental realization has been missing. We report a controlled synthesis of a dense soliton gas in deep-water surface gravity waves using the tools of nonlinear spectral theory [inverse scattering transform (IST)] for the one-dimensional focusing nonlinear Schrödinger equation. The soliton gas is experimentally generated in a one-dimensional water tank where we demonstrate that we can control and measure the density of states, i.e., the probability density function parametrizing the soliton gas in the IST spectral phase space. Nonlinear spectral analysis of the generated hydrodynamic soliton gas reveals that the density of states slowly changes under the influence of perturbative higher-order effects that break the integrability of the wave dynamics

Prediction and manipulation of hydrodynamic rogue waves via nonlinear spectral engineering

Peregrine soliton (PS) is widely regarded as a prototype nonlinear structure capturing properties of rogue waves that emerge in the nonlinear propagation of unidirectional wave trains. It has been recently demonstrated that PS can emerge locally, as an asymptotic structure arising from the propagation of an arbitrary large decaying pulse, independently of its solitonic content. This mathematical discovery has changed the widely accepted paradigm of the solitonic nature of rogue waves by enabling the PS to emerge from partially radiative or even completely solitonless initial data. In this work, we realize this scenario in a water tank experiment with a particular aim to control the point of the PS occurrence in space-time by imposing an appropriately chosen initial chirp. By employing the inverse scattering transform for the synthesis of the initial data, we are able to engineer a localized wave packet with a prescribed solitonic and radiative content. This enabled us to control the position of the emergence of the rogue wave by adjusting the inverse scattering spectrum. The proposed method of nonlinear spectral engineering is found to be robust to higher-order nonlinear effects, preceding the wave breaking dynamics, that are inevitable in realistic wave propagation conditions

Multi-scale modelling of nanostructures self-assembly on surfaces

Le développement des méthodes de simulations numériques a permis de modéliser des systèmes physiques de plus en plus complexes et de les étudier à des échelles de taille et de temps importantes en appliquant une démarche multi-échelle.Ainsi, dans le cadre de cette thèse, un premier travail a regardé l’étude de l’auto-organisation de trois types de molécules organiques aromatiques sur une surface semi-conductrice à l’aide de différents outils numériques. Dynamique moléculaire empirique, métadynamique, et simulations de type Monte-Carlo ont été judicieusement combinées pour permettre l’étude multi-échelle de ces systèmes permettant ainsi d’explorer l’importance des interactions non-covalentes inter- moléculaires et molécule-surface, dans la structure et stabilité des réseaux 2 dimensions. A noter que, pour l‘une d’entre elles un comportement cinétique a également pu être mis en évidence, pouvant conduire à la coexistence de phases de symétries différentes sur la surface. Dans tous les cas, la comparaison avec les résultats expérimentaux est excellente.Dans une deuxième partie de ces travaux, l’étude du comportement de couches denses de molécules chimisorbées à l’interface entre des nanoparticules d’Au auto-assemblées sur surface a été abordée. Deux types de molécules ont été étudiés. Pour la première, un comportement différent de la jonction moléculaire, suivant la configuration des molécules (cis ou trans), a pu être mis en évidence, permettant de proposer des explications microscopiques pour la réponse électronique des jonctions entre nanoparticules auto-assemblées, utilisées dans des dispositifs d’électronique moléculaire. Pour la seconde molécule, nous avons pu étudier le comportement des couches moléculaires à l’interface entre couches de nano-particules, quand celles-ci sont soumises à une contrainte mécanique de type compression. Un module de Young efficace pour ces couches moléculaires a pu être estimé.The development of computer simulation methods allows to model physical systems of ever growing complexity, and to study their behavior over unprecedentedly large scales of time and length, by applying a multi-scale strategy.In the framework of this thesis, we firstly studied the self-organization of three dif- ferent kinds of organic aromatic molecules (THBB, TBBB, TCNBB) on a boron-doped semi-conductor surface, (Si:B(111)), by means of different numerical simulation methods. Empirical molecular dynamics, metadynamics and Monte Carlo simulations were adequa- tely combined, in order to explore the multi-scale behavior of such systems, allowing to elucidate the role of weak intermolecular and molecule-surface interactions, in the struc- ture and stability of the resulting bi-dimensional supramolecular lattices. In particular, for the TCNBB molecule a kinetic pathway has been demonstrated, which may lead to the coexistence of phases with different symmetry on the surface. In all cases, an excellent agreement with experiments was demonstrated.In a second part of this thesis, we studied the behavior of dense layers of molecules chemisorbed at the surface of nanometer-sized Au particles, in driving their self-assembly. Two kind of molecules, AzBT and MUDA, were studied. For the first one, the response of the junctions formed between the adjoining Au nanoparticles has been shown to de- pend on the conformation of the molecules, in their cis or trans form. This allowed to propose microscopic explanations for the experimentally observed electronic behavior of the junctions. For the second molecule, we studied the mechanical response of the self- assembled Au nanoparticle layers subject to a compressive load, leading to an estimate of the effective Young’s modulus of the nanostructure

On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes

Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior. We characterize the waters at the interface and in the core of the Maxi protein by the statistics of correctly predicted positions with respect to crystallographic water positions in the PDB files as well as the dynamic measures of diffusion constants and position lifetimes. Our approach provides a methodology for the evaluation of predicted interfacial water positions through an investigation of water-mediated inter-chain contacts. While our results show satisfactory behaviour for molecular dynamics simulation, they also highlight the need for improvement of continuum methods

Structural transitions in ordered supramolecular networks on a semiconductor surface

We report the experimental and theoretical study of the self-assembly of planar organic molecules of the type tris-X-biphenyl-benzene (with X=N, I, Br, CH) on a passivated, boron-doped Si(111)-√3x√3 (R=30°) surface. Ordered molecular structures are observed by high-resolution STM. We perform multi-scale atomistic simulations, by DFT structure relaxation (Gaussian), metadynamics, molecular dynamics (MD) with empirical forces, and kinetic Monte Carlo with condensed degrees of freedom. Al low coverage, we identify by metadynamics the lowest-energy adsorption sites consistently with the STM images. Upon increasing molecular coverage, structural phase transitions of the molecular network are observed, in excellent agreement with experimental STM data. Our theoretical models allow to elucidate the subtle interplay between dispersion forces and hydrogen bonding, leading to some unexpected phenomena. Biasing the MD by a simple elastic-band constraint method, we identify the kinetic path leading from a low-density to a high-density ordered phase. Next, kinetic Monte Carlo simulations over a frozen Si:B surface, with energy parameters derived from the MD, help explaining the apparently striking experimental observations, according to which lower-density phases are favoured over higher-density phases

Modelling Of Supramolecular Network Deposited On A Semiconductor Surface

POSTER Journées Surfaces et Interfaces, Orléans, France, 30 Janvier - 1er février 2013.We investigated the self-assembly mechanisms and electronic properties of highly- symmetric organic molecules based on a substituted 1,2,5-tri(4-phenyl)benzene core[1], deposited on a passivated boron-doped Si(111)-√3x√3 R30° surface, by using ab-initio calculations, empirical molecular dynamics and metadynamics. The electronic properties of the isolated molecules in vacuo have been calculated using GAUSSIAN03 software. The different molecular conformations have been optimized assuming the highest symmetry group (D3h) for all the molecules. Very similar electronic properties (HOMO-LUMO gap, Mülliken charge distribution, vertical ionization potential, adiabatic electronic affinity) have been observed for the different molecules, despite the presence of various terminations (such as H, bromine, iodine, biphenyl, cyanobiphenyl, phenylpyridin, iodobiphenyl). The minor variation in the electronic properties does not explain the large differences observed in the experimental STM images of supramolecular networks [1,2]. Next, combination of empirical molecular dynamics using DLPOLY software and metadynamics using the PLUMED plugin with the MM3 molecular force field have been undertaken for the cyanobiphenyl substituted molecule, by using the results of ab-initio calculations as input for the molecular structure. The first simulations allowed us to reconstruct a very similar network with that observed on the STM images. By calculating the ratio of interaction molecule-network and molecule-surface, we highlight the influence of Van der Waals interactions for the stability of the supramolecular network. Current molecular dynamics simulations focus on the monolayer vs. bilayer assembly mechanisms in order to explain the structural differences of the network between a single and a double deposition of the molecule visible on STM images

Modelisation of supramolecular network on semiconductor

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