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Segmentation Driven Peeling for Visual Analysis of Electronic Transitions [article]

Mohit Sharma, Talha Bin Masood, Signe S. Thygesen, Mathieu Linares, Ingrid Hotz, Vijay Natarajan
2021 arXiv   pre-print
Electronic transitions in molecules due to absorption or emission of light is a complex quantum mechanical process. Their study plays an important role in the design of novel materials. A common yet challenging task in the study is to determine the nature of those electronic transitions, i.e. which subgroups of the molecule are involved in the transition by donating or accepting electrons, followed by an investigation of the variation in the donor-acceptor behavior for different transitions or
more » ... onformations of the molecules. In this paper, we present a novel approach towards the study of electronic transitions based on the visual analysis of a bivariate field, namely the electron density in the hole and particle Natural Transition Orbital (NTO). The visual analysis focuses on the continuous scatter plots (CSPs) of the bivariate field linked to their spatial domain. The method supports selections in the CSP visualized as fiber surfaces in the spatial domain, the grouping of atoms, and segmentation of the density fields to peel the CSP. This peeling operator is central to the visual analysis process and helps identify donors and acceptors. We study different molecular systems, identifying local excitation and charge transfer excitations to demonstrate the utility of the method.
arXiv:2109.08987v1 fatcat:qhj3mtynonafphsynpkganmxmu

Understanding morphology-mobility dependence in PEDOT:Tos

Nicolas Rolland, Juan Felipe Franco-Gonzalez, Riccardo Volpi, Mathieu Linares, Igor V. Zozoulenko
doi:10.1103/physrevmaterials.2.045605 fatcat:zexzkht3xnfk7lj6up4pqtd7py

A novel supra coarse-grained model for cellulose

Aleksandar Y. Mehandzhiyski, Nicolas Rolland, Mohit Garg, Jakob Wohlert, Mathieu Linares, Igor Zozoulenko
2020 Cellulose  
Cellulose being the most widely available biopolymer on Earth is attracting significant interest from the industry and research communities. While molecular simulations can be used to understand fundamental aspects of cellulose nanocrystal selfassembly, a model that can perform on the experimental scale is currently missing. In our study we develop a supra coarse-grained (sCG) model of cellulose nanocrystal which aims to bridge the gap between molecular simulations and experiments. The sCG
more » ... is based on atomistic molecular dynamics simulations and it is developed with the forcematching coarse-graining procedure. The validity of the model is shown through comparison with experimental and simulation results of the elastic modulus, self-diffusion coefficients and cellulose fiber twisting angle. We also present two representative case studies, self-assembly of nanocrystal during solvent evaporation and simulation of a chiral nematic phase ordering. Finally, we discuss possible future applications for our model. Electronic supplementary material The online version of this article ( contains supplementary material, which is available to authorized users.
doi:10.1007/s10570-020-03068-y fatcat:mecq67rujbbsvmtktqstzmggcu

Visual Analysis of Stochastic Trajectory Ensembles in Organic Solar Cell Design

Sathish Kottravel, Riccardo Volpi, Mathieu Linares, Timo Ropinski, Ingrid Hotz
2017 Informatics  
Mathieu Linares and Riccardo Volpi are the Physicists that performed the simulation of the charge transport and are responsible for the data generation.  ... 
doi:10.3390/informatics4030025 fatcat:f25e3t5rbfgcrcez2nuazcivhm

π-Extended perylene diimide double-heterohelicenes as ambipolar organic semiconductors for broadband circularly polarized light detection

Li Zhang, Inho Song, Jaeyong Ahn, Myeonggeun Han, Mathieu Linares, Mathieu Surin, Hui-Jun Zhang, Joon Hak Oh, Jianbin Lin
2021 Nature Communications  
AbstractDespite great challenges, the development of new molecular structures with multiple and even conflicting characteristics are eagerly pursued for exploring advanced applications. To develop high-performance chiral organic semiconducting molecules, a distorted π-system is required for strong coupling with circularly polarized light (CPL), whereas planar π-stacking systems are necessary for high charge-carrier mobility. To address this dilemma, in this work, we introduce a skeleton merging
more » ... approach through distortion of a perylene diimide (PDI) core with four fused heteroaromatics to form an ortho-π-extended PDI double-[7]heterohelicene. PDI double helicene inherits a high dissymmetry factor from the helicene skeleton, and the extended π-planar system concurrently maintains a high level of charge transport properties. In addition, ortho-π-extension of the PDI skeleton brings about near-infrared (NIR) light absorption and ambipolar charge transport abilities, endowing the corresponding organic phototransistors with high photoresponsivity of 450 and 120 mA W−1 in p- and n-type modes respectively, along with a high external quantum efficiency (89%) under NIR light irradiations. Remarkably, these multiple characteristics enable high-performance broadband CPL detections up to NIR spectral region with chiral organic semiconductors.
doi:10.1038/s41467-020-20390-y pmid:33420007 fatcat:ngbffpsorjafbkecqlwejbqhde

Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes

Jenifer Rubio-Magnieto, Florent Di Meo, Mamadou Lo, Cécile Delcourt, Sébastien Clément, Patrick Norman, Sébastien Richeter, Mathieu Linares, Mathieu Surin
2015 Organic and biomolecular chemistry  
A novel π-extended NiII-porphyrin shows a high selectivity towards human telomeric G-quadruplexes.
doi:10.1039/c4ob02097a pmid:25563845 fatcat:n3qgusrkybbujeyuyvv4wog244

Quantifying resonance through a Lewis Valence Bond approach: application to haloallyl and carbonylcations

Mathieu Linares, Stéphane Humbel, Benoît Braïda
2007 Faraday discussions  
Linares, B. Braida and S. Humbel, J. Phys. Chem. A, 2006, 110, 2505-2509 1 is applied to resonance effect quantification.  ... 
doi:10.1039/b605325d pmid:17328433 fatcat:zvhpqyyczrg67lvxaefuw3yzgy

Negative piezoelectric effect in an organic supramolecular ferroelectric

Indre Urbanaviciute, Xiao Meng, Michal Biler, Yingfen Wei, Tim D. Cornelissen, Subham Bhattacharjee, Mathieu Linares, Martijn Kemerink
2019 Materials Horizons  
The vast majority of ferroelectric materials demonstrate a positive piezoelectric effect. Theoretically, the negative piezoelectric coefficient d33 could be found in certain classes of ferroelectrics, yet in practice, the number...
doi:10.1039/c9mh00094a fatcat:efwj7jdkkvh4vibwlrkhsttaqa

Kinetic Monte Carlo simulations of organic ferroelectrics

Tim D. Cornelissen, Michal Biler, Indre Urbanaviciute, Patrick Norman, Mathieu Linares, Martijn Kemerink
2019 Physical Chemistry, Chemical Physics - PCCP  
A newly developed kinetic Monte Carlo model for organic ferroelectrics gives insight into switching kinetics.
doi:10.1039/c8cp06716c fatcat:en6sgq4u75b7xnwvafmawgrvti

Optical properties of wine pigments: theoretical guidelines with new methodological perspectives

Patrick Trouillas, Florent Di Meo, Johannes Gierschner, Mathieu Linares, Juan Carlos Sancho-García, Michal Otyepka
2015 Tetrahedron  
Linares, c Juan Carlos Sancho-García, e and Michal Otyepka b a INSERM S850, Université de Limoges, 2 rue du Dr Marcland, F-87025 Limoges, France b Regional Centre of Advanced Technologies and Materials  ...  vDW-DF van der Waals Density Functional; Optical properties of wine pigments: theoretical guidelines with new methodological perspectives Patrick Trouillas, a,b,1 Florent Di Meo, c Johannes Gierschner, d Mathieu  ... 
doi:10.1016/j.tet.2014.10.046 fatcat:q3cml7m67fhcfging6fs3myqjm

Orthohalogen substituents dramatically enhance hydrogen bonding of aromatic ureas in solution

Ilaria Giannicchi, Benjamin Jouvelet, Benjamin Isare, Mathieu Linares, Antonella Dalla Cort, Laurent Bouteiller
2014 Chemical Communications  
The phenylurea moiety is a ubiquitous synthon in supramolecular chemistry. Here we report that the introduction of chlorine or bromine atoms in the ortho positions to the urea unit is a simple and very efficient way to improve its intermolecular hydrogen bond (HB) donor character. This effect was demonstrated in solution both in the context of bis-ureas self-association and of mono-ureas hydrogen bonding to strong HB acceptors. Notes and references
doi:10.1039/c3cc47447j pmid:24280764 fatcat:2snncrol7fcelibaji5ozsvrhu

Monte Carlo simulations of charge transport in organic systems with true off-diagonal disorder

Mattias Jakobsson, Mathieu Linares, Sven Stafström
2012 Journal of Chemical Physics  
Redistribution subject to AIP license or copyright; see Jakobsson, Linares, and Stafström J. Chem. Phys. 137, 114901 (2012)  ... 
doi:10.1063/1.4748796 pmid:22998284 fatcat:t3wibgxeabdira2ddzunpltw5a

Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions

Robin Skanberg, Martin Falk, Mathieu Linares, Anders Ynnerman, Ingrid Hotz
2021 IEEE Transactions on Visualization and Computer Graphics  
Mathieu Linares  ... 
doi:10.1109/tvcg.2021.3051632 pmid:33444141 fatcat:w26oyymzyben3iehccqihruyii

Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra

Mathieu Linares, Haofan Sun, Michal Biler, Joakim Andréasson, Patrick Norman
2019 Physical Chemistry, Chemical Physics - PCCP  
DNA intercalation and groove binding of two photoswitching dithienylethene derivatives have been studied and characterized by means of molecular dynamics and electronic circular dichroism.
doi:10.1039/c8cp05326j fatcat:m5s6rirghzbpjnfyz5rl23mcmu

Humidity-Dependent Thermal Boundary Conductance Controls Heat Transport of Super-Insulating Nanofibrillar Foams

Varvara Apostolopoulou-Kalkavoura, Shiqian Hu, Nathalie Lavoine, Mohit Garg, Mathieu Linares, Pierre Munier, Igor Zozoulenko, Junichiro Shiomi, Lennart Bergström
2020 Matter  
We show that anisotropic foams based on aligned cellulose nanofibrils are superinsulating also at high relative humidity (RH). Thermal conductivity measurements and non-equilibrium molecular dynamic simulations show that the moistureinduced swelling and increase of the inter-fibrillar distance results in a reduction of the thermal boundary conductance that exceeds the thermal conductivity increase due to water uptake up to 75% RH. Phonon engineering by moisture could be used to tailor the heat
more » ... ransfer properties of hygroscopic nanofibrillar materials.
doi:10.1016/j.matt.2020.11.007 fatcat:37ml3wzqmjhrzg4ykhte2iatji
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