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Rinkevicius, ZilvinasORCID iD iconorcid.org/0000-0003-2729-0290
Publications (10 of 78) Show all publications
Ahmadzadeh, K., Li, X., Rinkevicius, Z., Norman, P. & Zaleśny, R. (2024). Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation. The Journal of Physical Chemistry Letters, 15(4), 969-974
Open this publication in new window or tab >>Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation
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2024 (English)In: The Journal of Physical Chemistry Letters, E-ISSN 1948-7185, Vol. 15, no 4, p. 969-974Article in journal (Refereed) Published
Abstract [en]

In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
National Category
Theoretical Chemistry Organic Chemistry
Identifiers
urn:nbn:se:kth:diva-343471 (URN)10.1021/acs.jpclett.3c03513 (DOI)001156015800001 ()38252270 (PubMedID)2-s2.0-85184138546 (Scopus ID)
Note

QC 20240215

Available from: 2024-02-15 Created: 2024-02-15 Last updated: 2024-07-04Bibliographically approved
Fransson, T., Delcey, M. G., Brumboiu, I. E., Hodecker, M., Li, X., Rinkevicius, Z., . . . Norman, P. (2023). eChem: A Notebook Exploration of Quantum Chemistry. Journal of Chemical Education, 100(4), 1664-1671
Open this publication in new window or tab >>eChem: A Notebook Exploration of Quantum Chemistry
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2023 (English)In: Journal of Chemical Education, ISSN 0021-9584, E-ISSN 1938-1328, Vol. 100, no 4, p. 1664-1671Article in journal (Refereed) Published
Abstract [en]

The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
Keywords
chemistry education, computational chemistry, interactive, Jupyter, notebook, Python, theoretical chemistry, visualization
National Category
Chemical Sciences Learning
Identifiers
urn:nbn:se:kth:diva-331091 (URN)10.1021/acs.jchemed.2c01103 (DOI)000954538900001 ()2-s2.0-85150424886 (Scopus ID)
Note

QC 20230705

Available from: 2023-07-05 Created: 2023-07-05 Last updated: 2024-03-15Bibliographically approved
Masys, S., Jonauskas, V. & Rinkevicius, Z. (2023). Geometries of defects in nanodiamonds optimized with the low-cost methods: How good are they for the electronic g-tensor calculations?. Diamond and related materials, 136, Article ID 110009.
Open this publication in new window or tab >>Geometries of defects in nanodiamonds optimized with the low-cost methods: How good are they for the electronic g-tensor calculations?
2023 (English)In: Diamond and related materials, ISSN 0925-9635, E-ISSN 1879-0062, Vol. 136, article id 110009Article in journal (Refereed) Published
Abstract [en]

The geometry optimization of 30 paramagnetic defects, including biomedically attractive nitrogen-, silicon-, germanium-, and nickel-related color centers, is performed after their incorporation into hydrogenated nano -diamond (ND) of C84H64 size. The main aim is to examine the effectiveness of the low-cost methods, namely, PBEh-3c, r2SCAN-3c, B97-3c, HF-3c, and GFN2-xTB, in reproducing the geometries of these defects basing on the similarity between the results of the subsequent electronic g-tensor calculations. It is revealed that the overall performance of PBEh-3c, r2SCAN-3c, and B97-3c is very alike and can be considered as good, however, none of these "3c" approaches is able to cope with all tested geometries. The results of HF-3c, on the other hand, are disappointing, as this method is outperformed by computationally much more lighter GFN2-xTB. Additional calculations carried out for dangling bonds introduced into hydroxylated and aminated NDs show that all low-cost methods perform reasonably well for this type of defect but the largest quantitative discrepancies once again are demonstrated by HF-3c. The obtained findings lay the foundations for the future studies of larger NDs with the purpose to figure out the magnetic properties dependence on the size of NDs or defect positions within NDs.

Place, publisher, year, edition, pages
Elsevier BV, 2023
Keywords
Nanodiamonds, Electronic g -tensor, Density functional theory
National Category
Materials Engineering
Identifiers
urn:nbn:se:kth:diva-330498 (URN)10.1016/j.diamond.2023.110009 (DOI)001007859400001 ()2-s2.0-85159096482 (Scopus ID)
Note

QC 20230630

Available from: 2023-06-30 Created: 2023-06-30 Last updated: 2023-06-30Bibliographically approved
Sevcik, A., Rinkevicius, Z. & Adliene, D. (2023). Radiation-Driven Polymerisation of Methacrylic Acid in Aqueous Solution: A Chemical Events Monte Carlo Study. Gels, 9(12), Article ID 947.
Open this publication in new window or tab >>Radiation-Driven Polymerisation of Methacrylic Acid in Aqueous Solution: A Chemical Events Monte Carlo Study
2023 (English)In: Gels, E-ISSN 2310-2861, Vol. 9, no 12, article id 947Article in journal (Refereed) Published
Abstract [en]

This study employed a coarse-grained Monte Carlo (MC) simulation to investigate the radiation-induced polymerisation of methacrylic acid (MAA) in an aqueous solution. This method provides an alternative to traditional kinetic models, enabling a detailed examination of the micro-structure and growth patterns of MAA polymers, which are often not captured in other approaches. In this work, we generated multiple clones of a simulation box, each containing a specific chemical composition. In these simulations, every coarse-grained (CG) bead represents an entire monomer. The growth function, defined by the chemical behaviour of interacting substances, was determined through repeated random sampling. This approach allowed us to simulate the complex process of radiation-induced polymerisation, enhancing our understanding of the formation of poly(methacrylic acid) hydrogels at a microscopic level; while Monte Carlo simulations have been applied in various contexts of polymerisation, this study’s specific approach to modelling the radiation-induced polymerisation of MAA in an aqueous environment, utilising the data obtained by quantum chemistry modelling, with an emphasis on micro-structural growth, has not been extensively explored in existing studies. This understanding is important for advancing the synthesis of these hydrogels, which have potential applications in diverse fields such as materials science and medicine.

Place, publisher, year, edition, pages
MDPI AG, 2023
Keywords
growth pattern, hydrogels, methacrylic acid, micro-structure simulation, Monte Carlo, polymer chemistry, radiation-induced polymerisation
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:kth:diva-342149 (URN)10.3390/gels9120947 (DOI)001131348600001 ()2-s2.0-85180713154 (Scopus ID)
Note

QC 20240115

Available from: 2024-01-15 Created: 2024-01-15 Last updated: 2024-02-29Bibliographically approved
Rinkevicius, Z., Kaminskas, M., Palevičius, P., Ragulskis, M., Bočkutė, K., Sriubas, M. & Laukaitis, G. (2022). A polarizable coarse-grained model for metal, metal oxide and composite metal/metal oxide nanoparticles and its applications. Physical Chemistry, Chemical Physics - PCCP, 24(45), 27742-27750
Open this publication in new window or tab >>A polarizable coarse-grained model for metal, metal oxide and composite metal/metal oxide nanoparticles and its applications
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2022 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 45, p. 27742-27750Article in journal (Refereed) Published
Abstract [en]

We present a selected set of exemplifying applications of the novel polarizable coarse-grained model [see the first part] to various outstanding problems in the physics and chemistry of nanoparticles: electrostatic potential around silver and gold nanoparticles; spontaneous and external electric field-driven self-organization of gold and silver nanoparticle systems; and physisorption of carbon dioxide on titanium dioxide nanoparticles decorated with a gold catalyst. In the first application, the developed model has shown capabilities of predicting long-range potential with accuracy comparable to the tight-binding density functional theory methods. Furthermore, the electrostatic potential analysis in hot spot regions allowed us to identify twin defect lines in a silver nanostar as a promising candidate for an enhancer in surface-enhanced Raman spectroscopy. In the second application, the developed model has facilitated the elucidation of the microscopic mechanisms responsible for the self-organization of gold and silver nanoparticles. Analysis of Monte-Carlo simulations established that the self-organization process is driven by van der Waals interactions in the absence of an external electric field, and that it becomes gradually driven by electrostatic interactions in the presence of an external electric field with increasing strength of the external electric field. In the third application, the developed model combined with Monte-Carlo simulations has identified the dominant mechanism responsible for carbon dioxide transfer to the catalytic sites. Analysis of the obtained results indicates that surface diffusion is the dominant mechanism for the transport of carbon dioxide to the catalytic sites, and only in exceptional situations, direct physisorption becomes a competitive mechanism with the surface diffusion mechanism. These successful applications of the developed model indicate its wide range of applicability to various problems in the chemistry and physics of nanoparticles.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2022
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-328849 (URN)10.1039/d2cp03462j (DOI)000883077500001 ()36354371 (PubMedID)2-s2.0-85142918610 (Scopus ID)
Note

QC 20230615

Available from: 2023-06-15 Created: 2023-06-15 Last updated: 2023-06-15Bibliographically approved
Rinkevicius, Z., Kaminskas, M., Palevičius, P., Ragulskis, M., Bočkutė, K., Sriubas, M. & Laukaitis, G. (2022). A polarizable coarse-grained model for metal, metal oxide and composite metal/metal oxide nanoparticles: development and implementation. Physical Chemistry, Chemical Physics - PCCP, 24(45), 27731-27741
Open this publication in new window or tab >>A polarizable coarse-grained model for metal, metal oxide and composite metal/metal oxide nanoparticles: development and implementation
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2022 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 45, p. 27731-27741Article in journal (Refereed) Published
Abstract [en]

We present a polarizable coarse-grained model for metal, metal oxide, and composite metal/metal oxide nanoparticles with well-defined crystalline surfaces. The developed model uses a low-resolution polarizable “surface beads” representation of the nanoparticle's geometry and pairwise cross nanoparticle potential consisting of van der Waals and electrostatic interaction terms. The electrostatic interaction term of the cross nanoparticle potential incorporates a crucial physical aspect of electrostatic interaction into the metal and metal oxide systems, such as induced surface charges, making it possible to explore the nanoparticles’ behavior in complex environments as well as investigate the interplay between electrostatic and van der Waals interactions in nanoparticle systems. The iterative stability, computational scaling, and performance of the presented model was tested on selected systems of gold, titanium dioxide, and composite gold/titanium dioxide nanoparticle systems. The model exhibits robust iterative stability and is able to converge the charge equilibration equation for fluctuating induced charges and dipoles within 10-60 “tug-tow” iterations in challenging situations, like crowded nanoparticle systems or nanoparticle systems in extreme external electric fields. The computation scaling of the presented model is semi-linear with respect to the number of nanoparticles in the system. It slightly varies depending on the size distribution of nanoparticles in a specific nanoparticle system. The computation cost of the model is significantly lower than that of conventional atomistic polarizable force field models and enables the treatment of large nanoparticle systems that are beyond the reach of currently existing atomistic force field models. 

Place, publisher, year, edition, pages
Royal Society of Chemistry (RSC), 2022
Keywords
Coarse-grained modeling, Coulomb interactions, Electric fields, Gold compounds, Metal nanoparticles, System stability, Titanium dioxide, Van der Waals forces, Atomistics, Crystalline surfaces, Force field models, Interaction term, Metal composites, Metal oxide nanoparticles, Metal-oxide, Nanoparticle systems, Scalings, Metals, gold, metal nanoparticle, oxide, titanium, Oxides
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-328894 (URN)10.1039/d2cp03461a (DOI)000883961800001 ()36367108 (PubMedID)2-s2.0-85142534805 (Scopus ID)
Note

QC 20230613

Available from: 2023-06-13 Created: 2023-06-13 Last updated: 2023-06-13Bibliographically approved
Sriubas, M., Bockute, K., Palevicius, P., Kaminskas, M., Rinkevicius, Z., Ragulskis, M., . . . Laukaitis, G. (2022). Antibacterial Activity of Silver and Gold Particles Formed on Titania Thin Films. Nanomaterials, 12(7), 1190, Article ID 1190.
Open this publication in new window or tab >>Antibacterial Activity of Silver and Gold Particles Formed on Titania Thin Films
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2022 (English)In: Nanomaterials, E-ISSN 2079-4991, Vol. 12, no 7, p. 1190-, article id 1190Article in journal (Refereed) Published
Abstract [en]

Metal-based nanoparticles with antimicrobial activity are gaining a lot of attention in recent years due to the increased antibiotics resistance. The development and the pathogenesis of oral diseases are usually associated with the formation of bacteria biofilms on the surfaces; therefore, it is crucial to investigate the materials and their properties that would reduce bacterial attachment and biofilm formation. This work provides a systematic investigation of the physical-chemical properties and the antibacterial activity of TiO2 thin films decorated by Ag and Au nanoparticles (NP) against Veillonella parvula and Neisseria sicca species associated with oral diseases. TiO2 thin films were formed using reactive magnetron sputtering by obtaining as-deposited amorphous and crystalline TiO2 thin films after annealing. Au and Ag NP were formed using a two-step process: magnetron sputtering of thin metal films and solid-state dewetting. The surface properties and crystallographic nature of TiO2/NP structures were investigated by SEM, XPS, XRD, and optical microscopy. It was found that the higher thickness of Au and Ag thin films results in the formation of the enlarged NPs and increased distance between them, influencing the antibacterial activity of the formed structures. TiO2 surface with AgNP exhibited higher antibacterial efficiency than Au nanostructured titania surfaces and effectively reduced the concentration of the bacteria. The process of the observation and identification of the presence of bacteria using the deep learning technique was realized.

Place, publisher, year, edition, pages
MDPI AG, 2022
Keywords
TiO2 thin films, silver nanoparticles, gold nanoparticles, Gram-negative bacteria
National Category
Materials Chemistry
Identifiers
urn:nbn:se:kth:diva-311521 (URN)10.3390/nano12071190 (DOI)000781080300001 ()35407308 (PubMedID)2-s2.0-85127378713 (Scopus ID)
Note

QC 20220503

Available from: 2022-05-03 Created: 2022-05-03 Last updated: 2022-06-25Bibliographically approved
Fransson, T., Delcey, M. G., Brumboiu, I. E., Hodecker, M., Li, X., Rinkevicius, Z., . . . Norman, P. (2022). Computational Chemistry from Laptop to HPC: A notebook exploration of quantum chemistry (1ed.). Stockholm: KTH Royal Institute of Technology
Open this publication in new window or tab >>Computational Chemistry from Laptop to HPC: A notebook exploration of quantum chemistry
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2022 (English)Book (Other academic)
Abstract [en]

Quantum chemistry is a powerful tool. It is now possible to model complex chemical processes even on a laptop getting insights into matter at its fundamental scale.

But quantum chemistry is also very complex. Answering a chemical question requires selecting parameters among a wide variety of choices. Choosing a model system, an electronic structure method, a basis set, a set of properties, and a wide array of parameters which can affect the results in small but sometimes meaningful way… It can be a very daunting task, even for veterans of the field.

Similarly, for those who wish to get a deeper understanding of a method, going through the pages of equation often riddled with inconsistent notations and formulations is very challenging. And at the end, the link between the equation and the computer implementation found in existing softwares can be vague at best.

We believe that a core issue is that humans are not good at learning in abstract terms. We can get very far with a lecture or a textbook, but we will never build as much intuition about how a clock work as by simply breaking one apart and rebuilding it from scratch.

This is exactly the aim of this page, allowing a hands-on approach to computational chemistry. Together we will dismantle the black box that a computational chemistry code often seems to be, go through all the cogs and gears, and build back together some of the main computational methods of modern computational chemistry. We will do this by presenting the underlying equations, all expressed with consistent notations, as well as by suggesting a simple python implementation, to really display in action how the theory is implemented into a practical tool. Additionally, we will put these methods in context by showing how they can be used to address concrete chemical questions, discussing the strengths and weaknesses of each method and how to best use them to solve practical problems.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2022 Edition: 1
Keywords
theoretical chemistry; spectroscopy; computational chemistry; molecular physics
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-316346 (URN)10.30746/978-91-988114-0-7 (DOI)978-91-988114-0-7 (ISBN)
Note

QC 20220819

Available from: 2022-08-15 Created: 2022-08-15 Last updated: 2022-11-11Bibliographically approved
Ahmadzadeh, K., Li, X., Rinkevicius, Z. & Norman, P. (2022). Efficient Kohn-Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions. Electronic Structure, 4(4), Article ID 044004.
Open this publication in new window or tab >>Efficient Kohn-Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions
2022 (English)In: Electronic Structure, E-ISSN 2516-1075, Vol. 4, no 4, article id 044004Article in journal (Refereed) Published
Abstract [en]

For general exchange-correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only similar to 25% (one-photon off-resonance regions) and similar to 50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.

Place, publisher, year, edition, pages
IOP Publishing, 2022
Keywords
density functional theory, response theory, nonlinear optics
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-324057 (URN)10.1088/2516-1075/aca859 (DOI)000919217600001 ()2-s2.0-85145257235 (Scopus ID)
Note

QC 20230222

Available from: 2023-02-22 Created: 2023-02-22 Last updated: 2023-10-03Bibliographically approved
Timofejeva, I., Laukaitis, G., Rinkevicius, Z. & Ragulskis, M. (2022). Finite-Time Stabilization of the Fractional Model of the Driven Dissipative Nonlinear Pendulum. International Journal of Bifurcation and Chaos in Applied Sciences and Engineering, 32(04), Article ID 2250056.
Open this publication in new window or tab >>Finite-Time Stabilization of the Fractional Model of the Driven Dissipative Nonlinear Pendulum
2022 (English)In: International Journal of Bifurcation and Chaos in Applied Sciences and Engineering, ISSN 0218-1274, Vol. 32, no 04, article id 2250056Article in journal (Refereed) Published
Abstract [en]

Finite-time stabilization of the driven dissipative nonlinear pendulum is investigated in this paper. First, asymptotic and nonasymptotic convergence towards stable and unstable orbits of the ordinary model of the driven dissipative nonlinear pendulum is considered. It is shown that the existence of nonasymptotic convergence does not contradict the fact that time-reversal invariance holds true for the ordinary model of the driven dissipative nonlinear pendulum. Then, finite-time stabilization of unstable orbits of the fractional model of the driven dissipative nonlinear pendulum is discussed. The proposed stabilization technique is based on a proper selection of initial conditions and does not require any feedback loops. Computational experiments are used to illustrate the efficacy of the proposed finite-time stabilization techniques.

Place, publisher, year, edition, pages
World Scientific Pub Co Pte Ltd, 2022
Keywords
Driven dissipative nonlinear pendulum, finite-time stabilization, nonasymptotic convergence, unstable orbit
National Category
Control Engineering
Identifiers
urn:nbn:se:kth:diva-310999 (URN)10.1142/S0218127422500560 (DOI)000776249200014 ()2-s2.0-85128134890 (Scopus ID)
Note

QC 20220420

Available from: 2022-04-20 Created: 2022-04-20 Last updated: 2022-06-25Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0003-2729-0290

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