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Wojno, S., Sonker, A. K., Garg, M., Cooper, S., Rigdahl, M., Linares, M., . . . Westman, G. (2024). Cellulose nanocrystal dispersions conjugated with symmetric and asymmetric dialkylamine groups. Cellulose, 31, 6705-6718
Open this publication in new window or tab >>Cellulose nanocrystal dispersions conjugated with symmetric and asymmetric dialkylamine groups
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2024 (English)In: Cellulose, ISSN 0969-0239, E-ISSN 1572-882X, Vol. 31, p. 6705-6718Article in journal (Refereed) Published
Abstract [en]

The present study discusses the effect of symmetric and asymmetric grafting on the surface of CNCs (cellulose nanocrystals) on their dispersion properties using dialkyl azetidinium salts. Three dialkylamine of different size and chain length were successfully grafted to the sulfate groups on the surface of CNCs by conjugation of azetidinium salts. The coupling process resulted in the formation of 2-hydroxypropyl-N-dialkylamine conjugated to the CNC sulfate groups abbreviated as C n \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$_n$$\end{document} -N-C m \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$_m$$\end{document} -Prop-2-OH-CNC, where m, n are the number of carbons in the alkyl groups, each with a total of m + n = 12 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$m+n=12$$\end{document} , with ( m , n ) = ( 11 , 1 ) ; ( 9 , 3 ) ; ( 6 , 6 ) \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$(m,n) = (11,1); (9,3); (6,6)$$\end{document} . Molecular dynamics simulations were used to assess the probable morphology of the grafted chains and the interaction potential between CNCs. Steady shear simultaneously combined with polarized light imaging and oscillatory shear rheological measurements were used to evaluate for the first time the impact of the CNC surface modifications on their dispersion flow and optical properties. Overall, the results show that the different linker topologies could effectively promote different types of aggregation morphologies based on the size of the linker, their flexibility and their most probable conformation.

Place, publisher, year, edition, pages
SPRINGER, 2024
Keywords
Cellulose nanocrystals; Surface modification; Rheology; Rheo - polarized light imaging; Molecular modeling
National Category
Physical Chemistry
Identifiers
urn:nbn:se:liu:diva-206662 (URN)10.1007/s10570-024-05900-1 (DOI)001250247600001 ()
Note

Funding Agencies|Swedish Research Council [2016-05990]; Aforsk; Troedsson foundations; Advanced Functional Material Center at Linkoeping University; Wallenberg Wood Science Center (WWSC)

Available from: 2024-08-22 Created: 2024-08-22 Last updated: 2025-04-16Bibliographically approved
Sharma, M., Masood, T. B., Sidwall Thygesen, S., Linares, M., Hotz, I. & Natarajan, V. (2024). Continuous Scatterplot Operators for Bivariate Analysis and Study of Electronic Transitions. IEEE Transactions on Visualization and Computer Graphics, 30(7), 3532-3544
Open this publication in new window or tab >>Continuous Scatterplot Operators for Bivariate Analysis and Study of Electronic Transitions
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2024 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 30, no 7, p. 3532-3544Article in journal (Refereed) Published
Abstract [en]

Electronic transitions in molecules due to the 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 electronic transitions, namely 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 conformations of the molecules. In this paper, we present a novel approach for the analysis of a bivariate field and show its applicability to the study of electronic transitions. This approach is based on two novel operators, the continuous scatterplot (CSP) lens operator and the CSP peel operator, that enable effective visual analysis of bivariate fields. Both operators can be applied independently or together to facilitate analysis. The operators motivate the design of control polygon inputs to extract fiber surfaces of interest in the spatial domain. The CSPs are annotated with a quantitative measure to further support the visual analysis. We study different molecular systems and demonstrate how the CSP peel and CSP lens operators help identify and study donor and acceptor characteristics in molecular systems.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2024
Keywords
Bivariate field analysis, Continuous scatterplot, Fiber surface, Control polygon, Visual analysis, Electronic transitions
National Category
Computer Sciences Human Computer Interaction Atom and Molecular Physics and Optics Materials Chemistry
Identifiers
urn:nbn:se:liu:diva-194721 (URN)10.1109/tvcg.2023.3237768 (DOI)001258936700002 ()2-s2.0-85147261210 (Scopus ID)
Note

Funding Agencies|Indo-Swedish joint network project [DST/INT/SWD/VR/P-02/2019]; VR [2018-07085, 2018-05973]; MoE Govt. of India; Swarnajayanti Fellowship from DST India [DST/SJF/ETA-02/2015-16]; Mindtree Chair research grant; SeRC (Swedish e-Science Research Center); Swedish Research Council (VR) [2019-05487]

Available from: 2023-06-09 Created: 2023-06-09 Last updated: 2024-11-04Bibliographically approved
Skånberg, R., Falk, M., Linares, M., Ynnerman, A. & Hotz, I. (2022). Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions. IEEE Transactions on Visualization and Computer Graphics, 28(9), 3126-3137
Open this publication in new window or tab >>Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions
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2022 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 28, no 9, p. 3126-3137Article in journal (Refereed) Published
Abstract [en]

In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabschs algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin.

Place, publisher, year, edition, pages
IEEE COMPUTER SOC, 2022
Keywords
Distribution functions, Trajectory, Visualization, Graphical models, Numerical models, Shape, Periodic structures
National Category
Chemical Sciences Mathematics Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-174336 (URN)10.1109/TVCG.2021.3051632 (DOI)000833767700005 ()33444141 (PubMedID)
Note

Funding agencies: Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC)

Available from: 2021-03-20 Created: 2021-03-20 Last updated: 2025-02-28
Sharma, M., Masood, T. B., Sidwall Thygesen, S., Linares, M., Hotz, I. & Natarajan, V. (2021). Segmentation Driven Peeling for Visual Analysis of Electronic Transitions. In: 2021 IEEE Visualization Conference (VIS): . Paper presented at 2021 IEEE Visualization Conference (VIS), New Orleans, LA, USA, 24-29 Oct. 2021 (pp. 96-100). IEEE
Open this publication in new window or tab >>Segmentation Driven Peeling for Visual Analysis of Electronic Transitions
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2021 (English)In: 2021 IEEE Visualization Conference (VIS), IEEE, 2021, p. 96-100Conference paper, Published paper (Refereed)
Abstract [en]

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 conformations 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 the 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.

Place, publisher, year, edition, pages
IEEE, 2021
Keywords
Human-centered computing; Visualization; Visualization application domains; Scientific visualization
National Category
Computer Sciences Human Computer Interaction Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-182271 (URN)10.1109/VIS49827.2021.9623300 (DOI)000792590500020 ()9781665433358 (ISBN)9781665433365 (ISBN)
Conference
2021 IEEE Visualization Conference (VIS), New Orleans, LA, USA, 24-29 Oct. 2021
Funder
Swedish Research Council, 2018-07085Swedish Research Council, 2019-05487Swedish e‐Science Research CenterSwedish National Infrastructure for Computing (SNIC)
Note

Funding: Indo-Swedish joint network project [DST/INT/SWD/VR/P-02/2019, 2018-07085]; MHRD Govt.; DST India [DST/SJF/ETA-02/2015-16]; SeRC (Swedish e-Science Research Center); Swedish Research Council (VR) [2019-05487]; VR [2018-05973]

Available from: 2022-01-11 Created: 2022-01-11 Last updated: 2023-04-03Bibliographically approved
Masood, T. B., Sidwall Thygesen, S., Linares, M., Abrikosov, A. I., Natarajan, V. & Hotz, I. (2021). Visual Analysis of Electronic Densities and Transitions in Molecules. Paper presented at EuroVis 2021. Computer Graphics Forum, 40(3), 287-298
Open this publication in new window or tab >>Visual Analysis of Electronic Densities and Transitions in Molecules
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2021 (English)In: Computer Graphics Forum, ISSN 0167-7055, Vol. 40, no 3, p. 287-298Article in journal (Refereed) Published
Abstract [en]

The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials. The transitions are complex quantum mechanical processes and a detailed analysis requires a breakdown of these processes into components that can be interpreted via characteristic chemical properties. We approach these tasks by providing a detailed analysis of the electron density field. This entails methods to quantify and visualize electron localization and transfer from molecular subgroups combining spatial and abstract representations. The core of our method uses geometric segmentation of the electronic density field coupled with a graph-theoretic formulation of charge transfer between molecular subgroups. The design of the methods has been guided by the goal of providing a generic and objective analysis following fundamental concepts. We illustrate the proposed approach using several case studies involving the study of electronic transitions in different molecular systems.

Place, publisher, year, edition, pages
John Wiley & Sons, 2021
Keywords
Scientific visualization, electronic charge density, electronic transition, charge transfer
National Category
Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-178610 (URN)10.1111/cgf.14307 (DOI)000667924000024 ()2-s2.0-851111470742-s2.0-85111147074 (Scopus ID)
Conference
EuroVis 2021
Funder
Swedish Research Council, 2018-07085Swedish Research Council, 2019-05487Swedish e‐Science Research CenterSwedish National Infrastructure for Computing (SNIC)
Note

Funding: SeRC (Swedish eScience Research Center); Swedish Research Council (VR)Swedish Research Council [201905487]; Indo-Swedish joint network project [DST/INT/SWD/VR/P02/2019]; Department of Science and Technology, IndiaDepartment of Science & Technology (India) [DST/SJF/ETA-02/2015-16]; VRSwedish Research Council [2018-05973, 2018-07085]; Mindtree Chair research grant

Available from: 2021-08-24 Created: 2021-08-24 Last updated: 2023-04-03Bibliographically approved
Skånberg, R., Linares, M., Falk, M., Hotz, I. & Ynnerman, A. (2019). MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures. In: J. Byška, M. Krone, and B. Sommer (Ed.), Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA): . Paper presented at Eurovis 2019 (pp. 17-21). The Eurographics Association
Open this publication in new window or tab >>MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures
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2019 (English)In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA) / [ed] J. Byška, M. Krone, and B. Sommer, The Eurographics Association , 2019, p. 17-21Conference paper, Published paper (Refereed)
Abstract [en]

Selecting components and observing changes ofproperties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based queries with spatial selection and filtering. Morphological operations facilitate refinement of the selection by growth operators, e.g. across covalent bonds. The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events. Immediate visual feedback during interactions ensures a smooth exploration of the data. We demonstrate the utility of our selection framework by analyzing temporal changes in the secondary structure of poly-alanineand the binding ofaspirin to phospholipase A2.

Place, publisher, year, edition, pages
The Eurographics Association, 2019
Keywords
molecular dynamics, visualization, selection
National Category
Natural Sciences Computer Sciences Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:liu:diva-194524 (URN)10.2312/molva.20191096 (DOI)978-3-03868-085-7 (ISBN)
Conference
Eurovis 2019
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish e‐Science Research Center
Available from: 2023-06-07 Created: 2023-06-07 Last updated: 2025-02-28Bibliographically approved
Urbanaviciute, I., Meng, X., Biler, M., Wei, Y., Cornelissen, T. D., Bhattacharjee, S., . . . Kemerink, M. (2019). Negative piezoelectric effect in an organic supramolecular ferroelectric. Materials Horizons, 6, 1688-1698
Open this publication in new window or tab >>Negative piezoelectric effect in an organic supramolecular ferroelectric
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2019 (English)In: Materials Horizons, ISSN 2051-6347, E-ISSN 2051-6355, Vol. 6, p. 1688-1698Article in journal (Refereed) Published
Abstract [en]

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 of materials showing linear longitudinal contraction with increasing applied field (d33 < 0) is limited to few ferroelectric polymers. Here, we measure a pronounced negative piezoelectric effect in the family of organic ferroelectric small-molecular BTAs (trialkylbenzene-1,3,5-tricarboxamides), which can be tuned by mesogenic tail substitution and structural disorder. While the large- and small-signal strain in highly-ordered thin-film BTA capacitor devices are dominated by intrinsic contributions and originates from piezostriction, rising disorder introduces additional extrinsic factors that boost the large-signal d33 up to −20 pm V’1 in short-tailed molecules. Interestingly, homologues with longer mesogenic tails show a large-signal electromechanical response that is dominated by the quadratic Maxwell strain with significant mechanical softening upon polarization switching, whereas the small-signal strain remains piezostrictive. Molecular dynamics and DFT calculations both predict a positive d33 for defect-free BTA stacks. Hence, the measured negative macroscopic d33 is attributed to the presence of structural defects that enable the dimensional effect to dominate the piezoelectric response of BTA thin films.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2019
National Category
Textile, Rubber and Polymeric Materials Condensed Matter Physics Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-160355 (URN)10.1039/C9MH00094A (DOI)000486213200010 ()
Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-10-24Bibliographically approved
Skånberg, R., König, C., Norman, P., Linares, M., Jönsson, D., Hotz, I. & Ynnerman, A. (2018). VIA-MD: Visual Interactive Analysis of Molecular Dynamics. In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data: . Paper presented at Eurographics Workshop on Visual Computing for Biology and Medicine. Eurographics - European Association for Computer Graphics
Open this publication in new window or tab >>VIA-MD: Visual Interactive Analysis of Molecular Dynamics
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2018 (English)In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data, Eurographics - European Association for Computer Graphics, 2018Conference paper, Published paper (Refereed)
Abstract [en]

We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data. The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations of complex molecular systems. A key feature of our approach is the support for linked interactive 3D exploration of geometry and statistical analysis using dynamic temporal windowing and animation. Based on semantic level descriptions and hierarchical aggregation of molecular properties we enable interactive filtering, which enables the user to effectively find spatial, temporal and statistical patterns. The VIA-MD environment provides an unprecedented tool for analysis of complex microscopic interactions hidden in large data volumes. We demonstrate the utility of the VIA-MD environment with four use cases. The first two deal with simulation of amyloid plaque associated with development of Alzheimer's, and we study an aqueous solution of 100 probes and an amyloid fibril. The identification of interaction "hotspots" is achieved with the use of combined filter parameters connected with probe molecular planarity and probe-fibril interaction energetics. The third and fourth examples show the wide applicability of the environment by applying it to analysis of molecular properties in material design.

Place, publisher, year, edition, pages
Eurographics - European Association for Computer Graphics, 2018
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-160857 (URN)10.2312/molva.20181102 (DOI)978-3-03868-081-9 (ISBN)
Conference
Eurographics Workshop on Visual Computing for Biology and Medicine
Funder
Swedish Research Council, 2014-4646Swedish National Infrastructure for Computing (SNIC)National Supercomputer Centre (NSC), SwedenEU, European Research Council, 621-2014-4646Swedish e‐Science Research Center
Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2025-02-28
Elie, M., Sguerra, F., Di Meo, F., Weber, M. D., Marion, R., Grimault, A., . . . Gaillard, S. (2016). Designing NHC-Copper(I) Dipyridylamine Complexes for Blue Light-Emitting Electrochemical Cells. ACS Applied Materials and Interfaces, 8(23), 14678-14691
Open this publication in new window or tab >>Designing NHC-Copper(I) Dipyridylamine Complexes for Blue Light-Emitting Electrochemical Cells
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2016 (English)In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 8, no 23, p. 14678-14691Article in journal (Refereed) Published
Abstract [en]

This study presents the influence of various substituents on the photophysical features of heteroleptic copper(I) complexes bearing both N-heterocyclic carbene (NHC) and dipyridylamine (dpa = dipyridylamine skeleton corresponding to ligand L1) ligands. The luminescent properties have been compared to our recently reported archetypal blue emitting [Cu(IPr)(dpa)][PF6] complex. The choice of the substituents on both ligands has been guided to explore the effect of the electron donor/acceptor and "push-pull" on the emission wavelengths and photoluminescence quantum yields. A selection of the best candidates in terms of their photophysical features were applied for developing the first blue light emitting electrochemical cells (LECs) based on copper(I) complexes. The device analysis suggests that the main concern is the moderate redox stability of the complexes under high applied driving currents, leading to devices with moderate stabilities pointing to a proof-of-concept for further development. Nevertheless, under low applied driving currents the blue emission is stable, showing performance levels competitive to those reported for blue LECs baged on iridium(III) complexes. Overall, this work provides valuable guidelines to tackle the design of enhanced NHC copper complexes for lighting applications in the near future.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2016
Keywords
copper(I) complexes; blue emitters; electroluminescence; light-emitting electrochemical cells; TADF; TD-DFT
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:liu:diva-130285 (URN)10.1021/acsami.6b04647 (DOI)000378195000048 ()27224961 (PubMedID)
Note

Funding Agencies|Ministere de la Recherche et des Nouvelles Technologies; CNRS (Centre National de la Recherche Scientifique); LABEX SynOrg [ANR-11-LABX-0029]; "Agence Nationale de la Recherche", within the CSOSG program [ANR-12-SECU-0002-02]; ANR program [ANR-15-CE39-0006]; Region Basse-Normandie; SeRC (Swedish e-Science Research Center); Swedish Research Council [621-2014-4646]; "Fonds der Chemischen Industrie" (FCI); EAM Starting Grant of the Cluster of Excellence Engineering of Advanced Materials (EAM)

Available from: 2016-08-01 Created: 2016-07-28 Last updated: 2018-03-22
Volpi, R., Kottravel, S., Norby, M. S., Stafström, S. & Linares, M. (2016). Effect of Polarization on the Mobility of C60: A Kinetic Monte-Carlo Study. Journal of Chemical Theory and Computation, 12(2), 812-824
Open this publication in new window or tab >>Effect of Polarization on the Mobility of C60: A Kinetic Monte-Carlo Study
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2016 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 2, p. 812-824Article in journal (Refereed) Published
Abstract [en]

We present a study of mobility field and temperature dependence for C60 with Kinetic Monte-Carlo simulations. We propose a new scheme to take into account polarization effects in organic materials through atomic induced dipoles on nearby molecules. This leads to an energy correction for the single site energies and to an external reorganization happening after each hopping. The inclusion of polarization allows us to obtain a good agreement with experiments for both mobility field and temperature dependence.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-122989 (URN)10.1021/acs.jctc.5b00975 (DOI)000370112900032 ()
Note

Vid tiden för disputation förelåg publikationen endast som manuskript

Funding agencies:  SeRC (Swedish e-Science Research Center)

Available from: 2015-12-01 Created: 2015-12-01 Last updated: 2017-12-01Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9720-5429

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