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Publications (10 of 64) Show all publications
Ali, A., Laaksonen, A., Huang, G., Hussain, S., Luo, S., Chen, W., . . . Ji, X. (2024). Emerging strategies and developments in oxygen reduction reaction using high-performance Platinum-based electrocatalysts. Nano Reseach, 17(5), 3516-3532
Open this publication in new window or tab >>Emerging strategies and developments in oxygen reduction reaction using high-performance Platinum-based electrocatalysts
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2024 (English)In: Nano Reseach, ISSN 1998-0124, E-ISSN 1998-0000, Vol. 17, no 5, p. 3516-3532Article, review/survey (Refereed) Published
Place, publisher, year, edition, pages
Tsinghua University Press, 2024
National Category
Materials Chemistry
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-102482 (URN)10.1007/s12274-023-6310-x (DOI)001115229400003 ()2-s2.0-85178965214 (Scopus ID)
Funder
The Kempe Foundations, SMK21-0011, SMK21-0020Swedish Research Council, 2019-03865EU, Horizon Europe, 101086667
Note

Validerad;2024;Nivå 2;2024-04-08 (joosat);

Funder: Horizon-EIC and Pathfinder challenges (101070976)

Available from: 2023-11-16 Created: 2023-11-16 Last updated: 2024-04-09Bibliographically approved
Carbonaro, C. M., Engelbrecht, L., Olla, C., Cappai, A., Casula, M. F., Melis, C., . . . Mocci, F. (2024). Graphene quantum dots and carbon nanodots: modeling of zero-dimensional carbon nanomaterials. In: Kuruvilla Joseph; Runcy Wilson; Gejo George; Saritha Appukuttan (Ed.), Zero-Dimensional Carbon Nanomaterials: Material Design Methods, Properties, and Applications (pp. 411-482). Elsevier
Open this publication in new window or tab >>Graphene quantum dots and carbon nanodots: modeling of zero-dimensional carbon nanomaterials
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2024 (English)In: Zero-Dimensional Carbon Nanomaterials: Material Design Methods, Properties, and Applications / [ed] Kuruvilla Joseph; Runcy Wilson; Gejo George; Saritha Appukuttan, Elsevier , 2024, p. 411-482Chapter in book (Other academic)
Place, publisher, year, edition, pages
Elsevier, 2024
Series
Woodhead Publishing Series in Electronic and Optical Materials
National Category
Chemical Sciences Nano Technology
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-105302 (URN)10.1016/B978-0-323-99535-1.00014-7 (DOI)2-s2.0-85190038790 (Scopus ID)
Note

ISBN for host publication: 978-0-323-99535-1

Available from: 2024-05-03 Created: 2024-05-03 Last updated: 2024-05-03Bibliographically approved
Lyubartsev, A. & Laaksonen, A. (2024). Hierarchical Multiscale Modeling Through Inverse Problem Solving (1ed.). In: Manuel Yáñez; Russell J. Boyd (Ed.), Comprehensive Computational Chemistry: (pp. 622-635). Elsevier
Open this publication in new window or tab >>Hierarchical Multiscale Modeling Through Inverse Problem Solving
2024 (English)In: Comprehensive Computational Chemistry / [ed] Manuel Yáñez; Russell J. Boyd, Elsevier , 2024, 1, p. 622-635Chapter in book (Other academic)
Place, publisher, year, edition, pages
Elsevier, 2024 Edition: 1
National Category
Computational Mathematics Applied Mechanics
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-102665 (URN)10.1016/B978-0-12-821978-2.00121-5 (DOI)978-0-12-823256-9 (ISBN)
Available from: 2023-11-23 Created: 2023-11-23 Last updated: 2023-11-23Bibliographically approved
An, R., Wu, N., Gao, Q., Dong, Y., Laaksonen, A., Shah, F. U., . . . Fuchs, H. (2024). Integrative studies of ionic liquid interface layers: bridging experiments, theoretical models and simulations. Nanoscale Horizons, 9(4), 506-535
Open this publication in new window or tab >>Integrative studies of ionic liquid interface layers: bridging experiments, theoretical models and simulations
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2024 (English)In: Nanoscale Horizons, ISSN 2055-6756, Vol. 9, no 4, p. 506-535Article, review/survey (Refereed) Published
Place, publisher, year, edition, pages
Royal Society of Chemistry, 2024
National Category
Physical Chemistry
Research subject
Energy Engineering; Chemistry of Interfaces
Identifiers
urn:nbn:se:ltu:diva-104260 (URN)10.1039/d4nh00007b (DOI)001162334600001 ()38356335 (PubMedID)2-s2.0-85185438821 (Scopus ID)
Funder
Swedish Research Council, 2020-03899The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), CH2019-8287EU, Horizon Europe, 101070976Swedish Research Council, 2018-04133The Kempe Foundations, SMK21-0011Swedish Research Council, 2019-03865EU, Horizon Europe, 101086667
Note

Validerad;2024;Nivå 2;2024-04-03 (joosat);

Funder: China Post-doctoral Science Foundation and the National Natural Science Foundation of China (Grant No. 21838004, 22108015,21978134);

Available from: 2024-02-12 Created: 2024-02-12 Last updated: 2024-04-03Bibliographically approved
Wang, X., Gao, Q., Li, L., Tatrari, G., Shah, F. U., Laaksonen, A., . . . An, R. (2024). Quantifying and Decoupling Molecular Interactions of Ionic Liquids with Gold Electrodes. Langmuir
Open this publication in new window or tab >>Quantifying and Decoupling Molecular Interactions of Ionic Liquids with Gold Electrodes
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2024 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827Article in journal (Refereed) Published
Abstract [en]

This work combined gold colloid probe atomic force microscopy (AFM) with a quartz crystal microbalance (QCM) to accurately quantify the molecular interactions of fluorine-free phosphonium-based ionic liquids (ILs) with gold electrode surfaces. First, the interactions of ILs with the gold electrode per unit area (𝐹′A𝐹A′, N/m2) were obtained via the force–distance curves measured by gold probe AFM. Second, a QCM was employed to detect the IL amount to acquire the equilibrium number of IL molecules adsorbed onto the gold electrode per unit area (NIL, Num/m2). Finally, the quantified molecular interactions of ILs with the gold electrode (F0, nN/Num) were estimated. F0 is closely related to the IL composition, in which the IL with the same anion but a longer phosphonium cation exhibits a stronger molecular interaction. The changes in the quantified interactions of gold with different ILs are consistent with the interactions predicted by the extended Derjaguin–Landau–Verwey–Overbeek theory, and the van der Waals interaction was identified as the major contribution of the overall interaction. The quantified molecular interaction is expected to enable the direct experimental-derived interaction parameters for molecular simulations and provide the virtual design of novel ILs for energy storage applications.

Place, publisher, year, edition, pages
American Chemical Society, 2024
National Category
Physical Chemistry Analytical Chemistry
Research subject
Chemistry of Interfaces; Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-106152 (URN)10.1021/acs.langmuir.4c00688 (DOI)001234453200001 ()38804259 (PubMedID)2-s2.0-85194483556 (Scopus ID)
Funder
Swedish Research Council, 2018-04133, 2019-03865EU, Horizon Europe, 101086667
Note

Validerad;2024;Nivå 2;2024-07-03 (hanlid);

Funder: Science Fund of Shandong Laboratory of Advanced Materials and Green Manufacturing (AMGM2024F18); China Postdoctoral Science Foundation; National Natural Science Foundation of China (21978134, 21838004); Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX23_0460); Horizon-EIC, Pathfinder challenges (101070976)

Available from: 2024-06-10 Created: 2024-06-10 Last updated: 2024-07-03Bibliographically approved
Laaksonen, A. & Mocci, F. (2024). Section Introduction: Molecular Dynamics Simulations and Reaction Rates (1ed.). In: Manuel Yáñez; Russell J. Boyd (Ed.), Comprehensive Computational Chemistry: (pp. 315-328). Elsevier
Open this publication in new window or tab >>Section Introduction: Molecular Dynamics Simulations and Reaction Rates
2024 (English)In: Comprehensive Computational Chemistry / [ed] Manuel Yáñez; Russell J. Boyd, Elsevier , 2024, 1, p. 315-328Chapter in book (Other academic)
Place, publisher, year, edition, pages
Elsevier, 2024 Edition: 1
National Category
Energy Engineering
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-102667 (URN)10.1016/B978-0-12-821978-2.00130-6 (DOI)978-0-12-823256-9 (ISBN)
Available from: 2023-11-23 Created: 2023-11-23 Last updated: 2023-11-23Bibliographically approved
Perepelytsya, S., Vasiliu, T., Laaksonen, A., Engelbrecht, L. d. & Mocci, F. (2024). Unusual bending patterns of spermidine3+ bound to DNA double helix. Low temperature physics (Woodbury, N.Y., Print), 50(3), 204-214
Open this publication in new window or tab >>Unusual bending patterns of spermidine3+ bound to DNA double helix
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2024 (English)In: Low temperature physics (Woodbury, N.Y., Print), ISSN 1063-777X, E-ISSN 1090-6517, Vol. 50, no 3, p. 204-214Article in journal (Refereed) Published
Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2024
National Category
Chemical Sciences
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-104988 (URN)10.1063/10.0024969 (DOI)2-s2.0-85189093745 (Scopus ID)
Projects
BioMat4CAST
Funder
EU, Horizon Europe, 101086667Swedish Research Council
Note

Validerad;2024;Nivå 2;2024-04-05 (marisr);

Originally published in: Fiz. Nizk. Temp. 2024, 50, 219–230. doi: https://doi.org/10.1063/10.0024969;

Funder: National Academy of Sciences of Ukraine (0120U100855)

Available from: 2024-04-05 Created: 2024-04-05 Last updated: 2024-04-05Bibliographically approved
Perepelytsya, S., Vasiliu, T., Laaksonen, A., Engelbrecht, L. d. & Mocci, F. (2024). Unusual bending patterns of spermidine3+ bound to DNA double helix: [Незвичайні форми вигину спермідину3+, зв’язаного з ДНК]. Fizika Nizkih Temperatur, 50(3), 219-230
Open this publication in new window or tab >>Unusual bending patterns of spermidine3+ bound to DNA double helix: [Незвичайні форми вигину спермідину3+, зв’язаного з ДНК]
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2024 (English)In: Fizika Nizkih Temperatur, ISSN 0132-6414, E-ISSN 1816-0328, Vol. 50, no 3, p. 219-230Article in journal (Refereed) Published
Place, publisher, year, edition, pages
B.Verkin Institute for Low Temperature Physics and Engineering of the NAS of Ukraine, 2024
National Category
Chemical Sciences
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-104640 (URN)2-s2.0-85186919877 (Scopus ID)
Funder
EU, Horizon Europe, 101086667
Note

Godkänd;2024;Nivå 0;2024-04-05 (marisr);

Also published in Low Temp. Phys. 50, 204 (2024); doi: 10.1063/10.0024969;

Funder: European Cooperation in Science and Technology (CA21101); National Academy of Sciences of Ukraine (0120U100855);

Available from: 2024-03-18 Created: 2024-03-18 Last updated: 2024-04-05Bibliographically approved
Perepelytsya, S., Vasiliu, T., Laaksonen, A., Engelbrecht, L. D., Brancato, G. & Mocci, F. (2023). Conformational flexibility of spermidine3+ interacting with DNA double helix. Journal of Molecular Liquids, 389, Article ID 122828.
Open this publication in new window or tab >>Conformational flexibility of spermidine3+ interacting with DNA double helix
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2023 (English)In: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 389, article id 122828Article in journal (Refereed) Published
Abstract [en]

Natural polyamines play a key role in many biological processes, particularly in the stabilization of DNA double helix structure in the cell nucleus. Among others, the conformational flexibility of polyamines, such as spermidine, is an essential property for the formation of complexes with DNA. Yet, the characterization of the conformational space of polyamines has not been fully elucidated. Using atomistic molecular dynamics (MD) simulations, we present a detailed study of the conformational space of spermidine3+ both in solution and in interaction with DNA. We have identified more than 2000 distinct conformations, which can be grouped into seven modes. Notably, the relative population of these modes is highly affected by the interaction of spermidine3+ with DNA, thus representing a fingerprint of complex formation. In particular, three of the seven dihedral angles of spermidine3+ are predominantly in trans conformation (with or without DNA), while the other four dihedral angles are observed to switch between trans, gauche+ and gauche-. The preference between the latter conformational states was analyzed in terms of the distinct energy contributions composing the potential energy. Overall, our results shed some light on the conformational equilibrium and dynamics of spermidine3+, which in turn is important for understanding the nature of its interaction with DNA.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
polyamine, spermidine3+, DNA double helix, molecular dynamics, conformation, dihedral angle
National Category
Organic Chemistry
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-99687 (URN)10.1016/j.molliq.2023.122828 (DOI)001064981700001 ()2-s2.0-85168410056 (Scopus ID)
Projects
BioMat4CAST
Funder
EU, Horizon Europe, 101086667Swedish Research Council, 2019-03865
Note

Validerad;2023;Nivå 2;2023-12-12 (marisr);

Funder: National Academy of Sciences of Ukraine (0123U102290); COST Action CA21101, COST (European Cooperation in Science and Technology);

Full text license: CC BY

Available from: 2023-08-15 Created: 2023-08-15 Last updated: 2023-12-12Bibliographically approved
Giron, C. C., Laaksonen, A. & Barroso da Silva, F. L. (2023). Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. Journal of Biomolecular Structure and Dynamics, 41(12), 5707-5727
Open this publication in new window or tab >>Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies
2023 (English)In: Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, E-ISSN 1538-0254, Vol. 41, no 12, p. 5707-5727Article in journal (Refereed) Published
Abstract [en]

SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.

Place, publisher, year, edition, pages
Taylor & Francis, 2023
Keywords
Protein-protein interactions, host-pathogen interaction, ACE2 polymorphism, molecular recognition, antibody, development, binding affinities, Covid-19, Monte Carlo
National Category
Biophysics Biochemistry and Molecular Biology Public Health, Global Health, Social Medicine and Epidemiology
Research subject
Energy Engineering
Identifiers
urn:nbn:se:ltu:diva-92153 (URN)10.1080/07391102.2022.2095305 (DOI)000822640300001 ()35815535 (PubMedID)2-s2.0-85133669820 (Scopus ID)
Funder
Swedish Research Council
Note

Validerad;2023;Nivå 2;2023-12-12 (marisr);

Funder: Fundação de Amparo à Pesquisa do Estado de São Paulo (Fapesp 2020/07158-2); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq 305393/2020-0, PIBIC/CNPq 2020-1732); Ministry of Research and Innovation of Romania (PN-III-P4-ID-PCCF-2016-0050)

Available from: 2022-07-13 Created: 2022-07-13 Last updated: 2023-12-12Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9783-4535

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