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1703 Publications visible to you, out of a total of 1703
Linear Dimensionality Reduction for Time Series

Abstract (Expand)

Visualisation by dimensionality reduction is an important tool for data exploration. In this work we are interested in visualising time series. To that end we formulate a latent variable model that … mirrors probabilistic principal component analysis (PPCA). However, as opposed to PPCA which maps the latent variables directly to the data space, we first map the latent variables to the parameter space of a recurrent neural network, i.e. each latent projection instantiates a recurrent network. Each instantiated recurrent network in turn is responsible for modelling a time series in the dataset. Hence, each latent variable is indirectly mapped to a time series. Incorporating the recurrent network in the latent variable model helps us account for the temporal nature of the time series and capture their underlying dynamics. The proposed algorithm is demonstrated on two benchmark problems and a real world dataset.

Author: Nikolaos Gianniotis

Date Published: 2017

Publication Type: InProceedings

Computational Design of pH-Switchable Control Agents for Nitroxide Mediated Polymerization

Abstract (Expand)

In the present work we use accurate quantum chemistry to evaluate several known and novel nitroxides bearing acid–base groups as pH-switchable control agents for room temperature NMP. Based on … G3(MP2,CC)(+)//M06-2X/6-31+G(d) calculations with UAKS-CPCM/M06-2X/6-31+G(d) solvation corrections, a number of novel nitroxides are predicted to be suitable for controlled polymerization of bulk styrene at room temperature when deprotonated (i.e. negatively charged), while remaining inert when neutral. These include an α-ethyl analogue of 3-carboxy-PROXYL and novel derivatives of 2,2,5-trimethyl-4-phenyl-3-azahexane-3-nitroxide (TIPNO) that have been modified to include acidic groups. Among the other species evaluated, 3,4-dicarboxy-PROXYL, α-carboxylated PROXYL and the phosphoric acid derivative of N-(2-methylpropyl)-N-(1-diethylphosphono-2,2-dimethylpropyl)-N-oxyl (SG1) are predicted to undergo suitable pH-switching at around 60 °C, and may also be fitting for some applications.

Authors: Ganna Gryn’ova, Leesa M. Smith, Michelle L. Coote

Date Published: 2017

Publication Type: Journal

Guidelines and Diagnostics for Charge Carrier Tuning in Thiophene-Based Wires

Abstract (Expand)

Reported experimental trends in charge carrier tuning in single molecule junctions of oligothiophene-based wires are rationalized by means of frontier molecular orbital theory. The length and substituent … effects on the energy levels of the frontier orbitals have been shown to translate to the computed transmission spectra – with a caveat of the role of the linker group. The resulting transport (charge carrier) type – n- (electrons) or p- (holes) – is easily identifiable from the in silico charge transfer trends.

Authors: Ganna Gryn'ova, Pauline J. Ollitrault, Clémence Corminboeuf

Date Published: 2017

Publication Type: Journal

Enhancing the Power Conversion Efficiency of Dye-Sensitized Solar Cells via Molecular Plasmon-Like Excitations

Abstract (Expand)

We introduce a tactic for employing molecular plasmon-like excitations to enhance solar-to-electric power conversion efficiency of dye-sensitized solar cells. We offer general design principles of … dimeric dyes, in which a strong plasmonic interaction between two π-conjugated moieties is promoted. The π-stacked conformations of these dimeric dyes result in a desirable broadened absorption and a longer absorption onset wavelength.

Authors: Jian-Hao Li, Ganna Gryn'ova, Antonio Prlj, Clémence Corminboeuf

Date Published: 2017

Publication Type: Journal

Directionality and the Role of Polarization in Electric Field Effects on Radical Stability

Abstract (Expand)

ccurate quantum-chemical calculations are used to analyze the effects of charges on the kinetics and thermodynamics of radical reactions, with specific attention given to the origin and directionality … of the effects. Conventionally, large effects of the charges are expected to occur in systems with pronounced charge-separated resonance contributors. The nature (stabilization or destabilization) and magnitude of these effects thus depend on the orientation of the interacting multipoles. However, we show that a significant component of the stabilizing effects of the external electric field is largely independent of the orientation of external electric field (e.g. a charged functional group, a point charge, or an electrode) and occurs even in the absence of any pre-existing charge separation. This effect arises from polarization of the electron density of the molecule induced by the electric field. This polarization effect is greater for highly delocalized species such as resonance-stabilized radicals and transition states of radical reactions. We show that this effect on the stability of such species is preserved in chemical reaction energies, leading to lower bond-dissociation energies and barrier heights. Finally, our simplified modelling of the diol dehydratase-catalyzed 1,2-hydroxyl shift indicates that such stabilizing polarization is likely to contribute to the catalytic activity of enzymes.

Authors: Ganna Gryn'ova, Michelle L. Coote

Date Published: 2017

Publication Type: Journal

Charge Transport in Highly Ordered Organic Nanofibrils: Lessons from Modelling

Abstract (Expand)

H-Aggregates featuring tight π-stacks of the conjugated heterocyclic cores represent ideal morphologies for 1D organic semiconductors. Such nanofibrils have larger electronic couplings between the … adjacent cores compared to the herringbone crystal or amorphous assemblies. In this work, we show that for a set of seven structurally and electronically distinct cores, including quaterthiophene and oligothienoacenes, the co-planar dimer model captures the impact of the monomer's electronic structure on charge transport, but more advanced multiscale modelling, featuring molecular dynamics and kinetic Monte-Carlo simulations, is needed to account for the packing and disorder effects. The differences in the results between these two computational approaches arise from the sensitivity of the electronic coupling strength to the relative alignment of adjacent cores, in particular the long-axis shift between them, imposed by the oligopeptide side chains. Our results demonstrate the dependence of the performance of H-aggregates on the chemical nature of the cores and the presence of the side chains, as well as the limitations in using the simple dimer model for a rapid computational pre-screening of the conjugated cores.

Authors: Ganna Gryn’ova, Adrien Nicolaï, Antonio Prlj, Pauline Ollitrault, Denis Andrienko, Clemence Corminboeuf

Date Published: 2017

Publication Type: Journal

Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems

Abstract

Not specified

Author: Martin Reinhardt

Date Published: 2017

Publication Type: Master's Thesis

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