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Knijff, L. (2025). Dipole and Charge Prediction for Electrochemical Systems from Atomistic Machine Learning. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Dipole and Charge Prediction for Electrochemical Systems from Atomistic Machine Learning
2025 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Due to the increasing demand for energy, sustainable energy generation and storage are becoming more and more important in society and research. Electrochemical energy storage devices such as electrochemical double-layer capacitors (EDLCs) play an important role in fulfilling this need. To understand, control and design EDLCs at atomic precision, physical insights from atomistic simulation are clearly needed. However, atomistic simulation of EDLCs faces challenges such as the large system size and the complex chemistry involved at electrified solid-liquid interfaces. To address these challenges, machine learning models for charge prediction have been developed to aid the atomistic simulations of EDLCs in this thesis. Here, a divide-and-conquer approach was taken, and the electrolyte and electrode component were investigated separately.

Initially, a neural network approach called PiNet-dipole was developed to model the supercell polarization in liquid water using two constraints. First, the displacement of the atomic charges is proportional to the itinerant polarization. Second, each water molecule has a net charge of zero. In doing so, a molecular dipole moment distribution can be inferred for liquid water that is surprisingly similar to that computed from Wannier centers. More importantly, PiNet-dipole provides a way to predict atomic charge without resorting to any predefined charge partition schemes. This is followed by using a class of machine learning models called PiNet-chi to predict the response charge as the result of an applied electric field for both organic electrolyte molecules and graphene analogues. Both of these models were then upgraded through the addition of equivariant features in PiNet2. This opened up new ways of predicting dipole moment for both small molecules and condensed phase systems, allowing expansion to the PiNet2-dipole family and enabling a more expressive atomic charge prediction model.

Finally, by combining the PiNet(2)-dipole and the PiNet(2)-chi models and integrating them with the semi-classical molecular dynamics code MetalWalls, the PiNNwall interface was developed to model polarizable and heterogeneous electrodes. PiNNwall was then used to study chemically doped graphene and graphene oxide under different electrical boundary conditions, as well as to investigate the influence of the proton charge on aqueous EDLCs.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2025. p. 70
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2484
Keywords
electrochemical energy storage, double-layer capacitor, charge response kernel, molecular dipole moment, atomic charge, machine learning, atomistic simulation
National Category
Materials Chemistry
Research subject
Chemistry with specialization in Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-544810 (URN)978-91-513-2334-3 (ISBN)
Public defence
2025-02-11, Å101121, Sonja-Lyttkens, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2025-01-10 Created: 2024-12-09 Last updated: 2025-01-16Bibliographically approved
Li, J., Knijff, L., Zhang, Z.-Y., Andersson, L. & Zhang, C. (2025). PiNN: Equivariant Neural Network Suite for Modeling Electrochemical Systems. Journal of Chemical Theory and Computation, 21(3), 1382-1395
Open this publication in new window or tab >>PiNN: Equivariant Neural Network Suite for Modeling Electrochemical Systems
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2025 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 21, no 3, p. 1382-1395Article in journal (Refereed) Published
Abstract [en]

Electrochemical energy storage and conversion play increasingly important roles in electrification and sustainable development across the globe. A key challenge therein is to understand, control, and design electrochemical energy materials with atomistic precision. This requires inputs from molecular modeling powered by machine learning (ML) techniques. In this work, we have upgraded our pairwise interaction neural network Python package PiNN via introducing equivariant features to the PiNet2 architecture for fitting potential energy surfaces along with PiNet2-dipole for dipole and charge predictions as well as PiNet2-chi for generating atom-condensed charge response kernels. By benchmarking publicly accessible data sets of small molecules, crystalline materials, and liquid electrolytes, we found that the equivariant PiNet2 shows significant improvements over the original PiNet architecture and provides a state-of-the-art overall performance. Furthermore, leveraging on plug-ins such as PiNNAcLe for an adaptive learn-on-the-fly workflow in generating ML potentials and PiNNwall for modeling heterogeneous electrodes under external bias, we expect PiNN to serve as a versatile and high-performing ML-accelerated platform for molecular modeling of electrochemical systems.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2025
National Category
Materials Chemistry Computer Sciences Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-554781 (URN)10.1021/acs.jctc.4c01570 (DOI)001409940900001 ()39883580 (PubMedID)2-s2.0-85216813378 (Scopus ID)
Funder
EU, Horizon 2020, 949012EU, European Research CouncilKnut and Alice Wallenberg Foundation, 2022-06725Swedish Research Council
Available from: 2025-04-16 Created: 2025-04-16 Last updated: 2025-04-16Bibliographically approved
Li, J., Knijff, L., Zhang, Z.-Y., Andersson, L. & Zhang, C. (2025). PiNN: equivariant neural network suite for modelling electrochemical systems. Journal of Chemical Theory and Computation, 21(3), 1382-1395
Open this publication in new window or tab >>PiNN: equivariant neural network suite for modelling electrochemical systems
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2025 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 21, no 3, p. 1382-1395Article in journal (Refereed) Published
Abstract [en]

Electrochemical energy storage and conversion play increasingly important roles in electrification and sustainable development across the globe. A key challenge therein is to understand, control, and design electrochemical energy materials with atomistic precision. This requires inputs from molecular modeling powered by machine learning (ML) techniques. In this work, we have upgraded our pairwise interaction neural network Python package PiNN via introducing equivariant features to the PiNet2 architecture for fitting potential energy surfaces along with PiNet2-dipole for dipole and charge predictions as well as PiNet2-χ for generating atom-condensed charge response kernels. By benchmarking publicly accessible data sets of small molecules, crystalline materials, and liquid electrolytes, we found that the equivariant PiNet2 shows significant improvements over the original PiNet architecture and provides a state-of-the-art overall performance. Furthermore, leveraging on plug-ins such as PiNNAcLe for an adaptive learn-on-the-fly workflow in generating ML potentials and PiNNwall for modeling heterogeneous electrodes under external bias, we expect PiNN to serve as a versatile and high-performing ML-accelerated platform for molecular modeling of electrochemical systems.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2025
Keywords
machine learning, molecular dynamics, liquid electrolyte, ion transport, proton transfer, double layer, supercapacitor
National Category
Materials Chemistry Computer Sciences
Research subject
Chemistry with specialization in Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-544807 (URN)10.1021/acs.jctc.4c01570 (DOI)001409940900001 ()39883580 (PubMedID)2-s2.0-85216813378 (Scopus ID)
Funder
EU, European Research Council, 949012Knut and Alice Wallenberg Foundation, WISE-AP01- PD37
Note

De två första författarna delar förstaförfattarskapet

Available from: 2024-12-09 Created: 2024-12-09 Last updated: 2026-04-22Bibliographically approved
Bi, S., Knijff, L., Lian, X., van Hees, A., Zhang, C. & Salanne, M. (2024). Modeling of Nanomaterials for Supercapacitors: Beyond Carbon Electrodes. ACS Nano, 18(31), 19931-19949
Open this publication in new window or tab >>Modeling of Nanomaterials for Supercapacitors: Beyond Carbon Electrodes
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2024 (English)In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 18, no 31, p. 19931-19949Article, review/survey (Refereed) Published
Abstract [en]

Capacitive storage devices allow for fast charge and discharge cycles, making them the perfect complements to batteries for high power applications. Many materials display interesting capacitive properties when they are put in contact with ionic solutions despite their very different structures and (surface) reactivity. Among them, nanocarbons are the most important for practical applications, but many nanomaterials have recently emerged, such as conductive metal-organic frameworks, 2D materials, and a wide variety of metal oxides. These heterogeneous and complex electrode materials are difficult to model with conventional approaches. However, the development of computational methods, the incorporation of machine learning techniques, and the increasing power in high performance computing now allow us to tackle these types of systems. In this Review, we summarize the current efforts in this direction. We show that depending on the nature of the materials and of the charging mechanisms, different methods, or combinations of them, can provide desirable atomic-scale insight on the interactions at play. We mainly focus on two important aspects: (i) the study of ion adsorption in complex nanoporous materials, which require the extension of constant potential molecular dynamics to multicomponent systems, and (ii) the characterization of Faradaic processes in pseudocapacitors, that involves the use of electronic structure-based methods. We also discuss how recently developed simulation methods will allow bridges to be made between double-layer capacitors and pseudocapacitors for future high power electricity storage devices.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
Keywords
Pseudocapacitors, Doublelayer, MXene, Metal-organic framework, 2D materials, Metaloxides, Molecular dynamics, Machine-learning
National Category
Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-544551 (URN)10.1021/acsnano.4c01787 (DOI)001279682400001 ()39053903 (PubMedID)2-s2.0-85199565614 (Scopus ID)
Funder
EU, Horizon 2020, 945298EU, Horizon 2020, 949012Uppsala UniversityKnut and Alice Wallenberg Foundation
Available from: 2024-12-05 Created: 2024-12-05 Last updated: 2024-12-10Bibliographically approved
Zhang, L., Kühling, F., Mattsson, A.-M., Knijff, L., Hou, X., Ek, G., . . . Berg, E. J. (2024). Reversible Hydration Enabling High-Rate Aqueous Li-Ion Batteries. ACS Energy Letters, 9, 959-966
Open this publication in new window or tab >>Reversible Hydration Enabling High-Rate Aqueous Li-Ion Batteries
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2024 (English)In: ACS Energy Letters, E-ISSN 2380-8195, Vol. 9, p. 959-966Article in journal (Refereed) Published
Abstract [en]

Layered TiS2 has been proposed as a versatile host material for various battery chemistries. Nevertheless, its compatibility with aqueous electrolytes has not been thoroughly understood. Herein, we report on a reversible hydration process to account for the electrochemical activity and structural evolution of TiS2 in a relatively dilute electrolyte for sustainable aqueous Li-ion batteries. Solvated water molecules intercalate in TiS2 layers together with Li+ cations, forming a hydrated phase with a nominal formula unit of Li0.38(H2O)2−δTiS2 as the end-product. We unambiguously confirm the presence of two layers of intercalated water by complementary electrochemical cycling, operando structural characterization, and computational simulation. Such a process is fast and reversible, delivering 60 mAh g–1 discharge capacity at a current density of 1250 mA g–1. Our work provides further design principles for high-rate aqueous Li-ion batteries based on reversible water cointercalation.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
National Category
Materials Chemistry Other Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:uu:diva-524300 (URN)10.1021/acsenergylett.4c00224 (DOI)001167199600001 ()
Funder
Swedish Research Council Formas, 2019-02496Swedish Research Council, 2016-04069Swedish Research Council, 2022-03856Swedish Research Council, 2018-07152Swedish Energy Agency, 50119-1Vinnova, 2018-04969Knut and Alice Wallenberg Foundation, 2017.0204Swedish Foundation for Strategic Research, FFL18-0269StandUp
Available from: 2024-03-01 Created: 2024-03-01 Last updated: 2024-03-04Bibliographically approved
Knijff, L., Jia, M. & Zhang, C. (2023). Electric double layer at the metal-oxide/electrolyte interface. In: Gunther Andersson; David Starr; Hendrik Bluhm (Ed.), Encyclopedia of Solid Liquid Interfaces: (pp. 567-575). Elsevier, 1-3
Open this publication in new window or tab >>Electric double layer at the metal-oxide/electrolyte interface
2023 (English)In: Encyclopedia of Solid Liquid Interfaces / [ed] Gunther Andersson; David Starr; Hendrik Bluhm, Elsevier, 2023, Vol. 1-3, p. 567-575Chapter in book (Other academic)
Abstract [en]

Metal-oxide surfaces act as both Brønsted acids and bases, which allows the exchange of protons with the electrolyte solution and generates either positive or negative proton charges depending on the environmental pH. These interfacial proton charges are then compensated by counter-ions from the electrolyte solution, which leads to the formation of the electric double layer (EDL). Because the EDL plays a crucial role in electrochemistry, geochemistry and colloid science, understanding the structure-property relationship of the EDL in metal-oxide systems from both experimental and theoretical approaches is necessary. This article focuses on the physical chemistry of the protonic double layer at the metal-oxide/electrolyte interface. In particular, determinations of the EDL capacitance and the double-layer potential from potentiometric titration experiments, electrochemical methods, surface-sensitive vibrational spectroscopy and X-ray photoelectron spectroscopy are summarized. This is followed by discussions from the atomistic modeling aspect of the EDL, with an emphasis on the density-functional theory-based molecular dynamics simulations. A conclusion and outlook for future works on this topic are also given.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
Capacitance, Density-functional theory, Double layer, Metal oxide, Molecular dynamics, Surface charge
National Category
Physical Chemistry Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-581049 (URN)10.1016/B978-0-323-85669-0.00012-X (DOI)2-s2.0-85191853046 (Scopus ID)9780323856690 (ISBN)
Available from: 2026-03-03 Created: 2026-03-03 Last updated: 2026-03-03Bibliographically approved
Dufils, T., Knijff, L., Shao, Y. & Zhang, C. (2023). PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation. Journal of Chemical Theory and Computation, 19(15), 5199-5209
Open this publication in new window or tab >>PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation
2023 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 15, p. 5199-5209Article in journal (Refereed) Published
Abstract [en]

Electrochemical energy storage always involves the capacitive process. The prevailing electrode model used in the molecular simulation of polarizable electrode–electrolyte systems is the Siepmann–Sprik model developed for perfect metal electrodes. This model has been recently extended to study the metallicity in the electrode by including the Thomas–Fermi screening length. Nevertheless, a further extension to heterogeneous electrode models requires introducing chemical specificity, which does not have any analytical recipes. Here, we address this challenge by integrating the atomistic machine learning code (PiNN) for generating the base charge and response kernel and the classical molecular dynamics code (MetalWalls) dedicated to the modeling of electrochemical systems, and this leads to the development of the PiNNwall interface. Apart from the cases of chemically doped graphene and graphene oxide electrodes as shown in this study, the PiNNwall interface also allows us to probe polarized oxide surfaces in which both the proton charge and the electronic charge can coexist. Therefore, this work opens the door for modeling heterogeneous and complex electrode materials often found in energy storage systems.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-510937 (URN)10.1021/acs.jctc.3c00359 (DOI)001033844500001 ()37477645 (PubMedID)
Funder
EU, Horizon 2020, 949012Swedish Research Council, 2022-06725
Available from: 2023-09-13 Created: 2023-09-13 Last updated: 2024-12-09Bibliographically approved
Shao, Y., Andersson, L., Knijff, L. & Zhang, C. (2022). Finite-field coupling via learning the charge response kernel. Electronic Structure, 4(1), Article ID 014012.
Open this publication in new window or tab >>Finite-field coupling via learning the charge response kernel
2022 (English)In: Electronic Structure, E-ISSN 2516-1075, Vol. 4, no 1, article id 014012Article in journal (Refereed) Published
Abstract [en]

Response of the electronic density at the electrode–electrolyte interface to the external field (potential) is fundamental in electrochemistry. In density-functional theory, this is captured by the so-called charge response kernel (CRK). Projecting the CRK to its atom-condensed form is an essential step for obtaining the response charge of atoms. In this work, the atom-condensed CRK is learnt from the molecular polarizability using machine learning (ML) models and subsequently used for the response-charge prediction under an external field (potential). As the machine-learnt CRK shows a physical scaling of polarizability over the molecular size and does not (necessarily) require the matrix-inversion operation in practice, this opens up a viable and efficient route for introducing finite-field coupling in the atomistic simulation of electrochemical systems powered by ML models.

Place, publisher, year, edition, pages
Institute of Physics Publishing (IOPP), 2022
National Category
Theoretical Chemistry
Research subject
Chemistry with specialization in Physical Chemistry; Chemistry with Specialisation in Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-481503 (URN)10.1088/2516-1075/ac59ca (DOI)000897703700001 ()
Funder
EU, Horizon 2020, 949012
Available from: 2022-08-11 Created: 2022-08-11 Last updated: 2024-12-09Bibliographically approved
Knijff, L. & Zhang, C. (2021). Machine learning inference of molecular dipole moment in liquid water. Machine Learning: Science and Technology, 2(3), Article ID 03LT03.
Open this publication in new window or tab >>Machine learning inference of molecular dipole moment in liquid water
2021 (English)In: Machine Learning: Science and Technology, E-ISSN 2632-2153, Vol. 2, no 3, article id 03LT03Article in journal (Refereed) Published
Abstract [en]

Molecular dipole moment in liquid water is an intriguing property, partly due to the fact that there is no unique way to partition the total electron density into individual molecular contributions. The prevailing method to circumvent this problem is to use maximally localized Wannier functions, which perform a unitary transformation of the occupied molecular orbitals by minimizing the spread function of Boys. Here we revisit this problem using a data-driven approach satisfying two physical constraints, namely: (a) The displacement of the atomic charges is proportional to the Berry phase polarization; (b) Each water molecule has a formal charge of zero. It turns out that the distribution of molecular dipole moments in liquid water inferred from latent variables is surprisingly similar to that obtained from maximally localized Wannier functions. Apart from putting a maximum-likelihood footnote to the established method, this work highlights the capability of graph convolution based charge models and the importance of physical constraints on improving the model interpretability.

National Category
Theoretical Chemistry Physical Chemistry Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-464076 (URN)10.1088/2632-2153/ac0123 (DOI)
Funder
EU, Horizon 2020, 949012
Available from: 2022-01-13 Created: 2022-01-13 Last updated: 2024-12-09Bibliographically approved
Shao, Y., Knijff, L., Dietrich, F. M., Hermansson, K. & Zhang, C. (2021). Modelling Bulk Electrolytes and Electrolyte Interfaces with Atomistic Machine Learning. Batteries & Supercaps, 4(4), 585-595
Open this publication in new window or tab >>Modelling Bulk Electrolytes and Electrolyte Interfaces with Atomistic Machine Learning
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2021 (English)In: Batteries & Supercaps, E-ISSN 2566-6223, Vol. 4, no 4, p. 585-595Article, review/survey (Refereed) Published
Abstract [en]

Batteries and supercapacitors are electrochemical energy storage systems which involve multiple time-scales and length-scales. In terms of the electrolyte which serves as the ionic conductor, a molecular-level understanding of the corresponding transport phenomena, electrochemical (thermal) stability and interfacial properties is crucial for optimizing the device performance and achieving safety requirements. To this end, atomistic machine learning is a promising technology for bridging microscopic models and macroscopic phenomena. Here, we provide a timely snapshot of recent advances in this area. This includes technical considerations that are particularly relevant for modelling electrolytes as well as specific examples of both bulk electrolytes and associated interfaces. A perspective on methodological challenges and new applications is also discussed.

Place, publisher, year, edition, pages
John Wiley & SonsWILEY-V C H VERLAG GMBH, 2021
Keywords
Materials Modelling, Machine Learning, Neural Network, Electrolyte, Interface
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-454621 (URN)10.1002/batt.202000262 (DOI)000604327200001 ()
Funder
Swedish Research Council, 2019-05012Swedish Research Council, 2019-04824
Available from: 2021-09-29 Created: 2021-09-29 Last updated: 2024-01-15Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0009-0007-8171-3983

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