Effect of Intra-molecular Disorder and Inter-molecular Electronic Interactions on the Electronic Structure of Poly-p-Phenylene Vinylene (PPV)

We investigate the role of intra-molecular conformational disorder and inter-molecular electronic interactions on the electronic structure of disorder clusters of poly-p-phenylene vinylene (PPV) oligomers. Classical molecular dynamics is used to determine probable molecular geometries, and first-principle density functional theory (DFT) calculations are used to determine electronic structure. Intra-molecular and inter-molecular effects are disentangled by contrasting results for densely packed oligomer clusters with those for ensembles of isolated oligomers with the same intra-molecular geometries. We find that electron trap states are induced primarily by intra-molecular configuration disorder, while the hole trap states are generated primarily from inter-molecular electronic interactions.Comment: 4 pages, 4 figures. Compile with pdflate

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism

Turbulent Velocity Structure in Molecular Clouds

We compare velocity structure in the Polaris Flare molecular cloud at scales ranging from 0.015 pc to 20 pc to simulations of supersonic hydrodynamic and MHD turbulence computed with the ZEUS MHD code. We use several different statistical methods to compare models and observations. The Delta-variance wavelet transform is most sensitive to characteristic scales and scaling laws, but is limited by a lack of intensity weighting. The scanning-beam size-linewidth relation is more robust with respect to noisy data. Obtaining the global velocity scaling behaviour requires that large-scale trends in the maps not be removed but treated as part of the turbulent cascade. We compare the true velocity PDF in our models to velocity centroids and average line profiles in optically thin lines, and find that the line profiles reflect the true PDF better unless the map size is comparable to the total line-of-sight thickness of the cloud. Comparison of line profiles to velocity centroid PDFs can thus be used to measure the line-of-sight depth of a cloud. The observed density and velocity structure is consistent with supersonic turbulence with a driving scale at or above the size of the molecular cloud and dissipative processes below 0.05 pc. Ambipolar diffusion could explain the dissipation. The velocity PDFs exclude small-scale driving such as that from stellar outflows as a dominant process in the observed region. In the models, large-scale driving is the only process that produces deviations from a Gaussian PDF shape consistent with observations. Strong magnetic fields impose a clear anisotropy on the velocity field, reducing the velocity variance in directions perpendicular to the field. (abridged)Comment: 21 pages, 24 figures, accepted by A&A, with some modifications, including change of claimed direct detection of dissipation scale to an upper limi

Molecular ferroelectric contributions to anomalous hysteresis in hybrid perovskite solar cells

We report a model describing the molecular orientation disorder in CH3NH3PbI3, solving a classical Hamiltonian parametrised with electronic structure calculations, with the nature of the motions informed by ab-initio molecular dynamics. We investigate the temperature and static electric field dependence of the equilibrium ferroelectric (molecular) domain structure and resulting polarisability. A rich domain structure of twinned molecular dipoles is observed, strongly varying as a function of temperature and applied electric field. We propose that the internal electrical fields associated with microscopic polarisation domains contribute to hysteretic anomalies in the current--voltage response of hybrid organic-inorganic perovskite solar cells due to variations in electron-hole recombination in the bulk.Comment: 10 pages; 4 figures, 2 SI figure

Charge mobility of discotic mesophases: A multiscale quantum/classical study

A correlation is established between the molecular structure and charge mobility of discotic mesophases of hexabenzocoronene derivatives by combining electronic structure calculations, Molecular Dynamics, and kinetic Monte Carlo simulations. It is demonstrated that this multiscale approach can provide an accurate ab-initio description of charge transport in organic materials

Quasimolecular structure in elastic O16 + O16 scattering

It is suggested that the experimentally observed intermediate structure in the cross section of elastic O16 + O16 scattering is due to quasibound molecular states of the ion-ion system while the gross structure originates from virtually bound molecular states

First-Principles Based Matrix-Green's Function Approach to Molecular Electronic Devices: General Formalism

Transport in molecular electronic devices is different from that in semiconductor mesoscopic devices in two important aspects: (1) the effect of the electronic structure and (2) the effect of the interface to the external contact. A rigorous treatment of molecular electronic devices will require the inclusion of these effects in the context of an open system exchanging particle and energy with the external environment. This calls for combining the theory of quantum transport with the theory of electronic structure starting from the first-principles. We present a rigorous yet tractable matrix Green's function approach for studying transport in molecular electronic devices, based on the Non-Equilibrium Green's Function Formalism of quantum transport and the density-functional theory of electronic structure using local orbital basis sets. By separating the device rigorously into the molecular region and the contact region, we can take full advantage of the natural spatial locality associated with the metallic screening in the electrodes and focus on the physical processes in the finite molecular region. This not only opens up the possibility of using the existing well-established technique of molecular electronic structure theory in transport calculations with little change, but also allows us to use the language of qualitative molecular orbital theory to interpret and rationalize the results of the computation. For the device at equilibrium, our method provides an alternative approach for solving the molecular chemisorption problem. For the device out of equilibrium, we show that the calculation of elastic current transport through molecules, both conceptually and computationally, is no more difficult than solving the chemisorption problem.Comment: To appear in Chemical Physic

The simulation of molecular clouds formation in the Milky Way

Using 3D hydrodynamic calculations we simulate formation of molecular clouds in the Galaxy. The simulations take into account molecular hydrogen chemical kinetics, cooling and heating processes. Comprehensive gravitational potential accounts for contributions from the stellar bulge, two and four armed spiral structure, stellar disk, dark halo and takes into account self-gravitation of the gaseous component. Gas clouds in our model form in the spiral arms due to shear and wiggle instabilities and turn into molecular clouds after t\simgt 100 Myr. At the times $t\sim 100 - 300$ Myr the clouds form hierarchical structures and agglomerations with the sizes of 100 pc and greater. We analyze physical properties of the simulated clouds and find that synthetic statistical distributions like mass spectrum, "mass-size" relation and velocity dispersion are close to those observed in the Galaxy. The synthetic $l-v$ (galactic longitude - radial velocity) diagram of the simulated molecular gas distribution resembles observed one and displays a structure with appearance similar to Molecular Ring of the Galaxy. Existence of this structure in our modelling can be explained by superposition of emission from the galactic bar and the spiral arms at $\sim$3-4 kpc.Comment: 10 pages, 8 figure