Project leader Dmitry Bocharov
Agreement No 1.1.1.2/16/I/001
Research application No 1.1.1.2/VIAA/1/16/147
The aim of this project is to develop new efficient simulation strategy for describing dynamics and anisotropic vibrational properties of advanced materials as well as chemical re-bonding and defect redistribution in complex technologically important crystals and nanomaterials. For these simulations, both density functional theory (DFT) and ab initio molecular dynamics (AIMD) have been applied. The limits of applicability of existing methods and transferability of the results obtained for regular bulk properties will be estimated on defective and low-dimensional materials. The accuracy of AIMD simulations will be validated by a direct comparison with the available temperature-dependent X-ray absorption spectra. The developed new strategy and large-scale massive parallel computer simulations will be applied for calculations on photocatalytic properties of nanostructures (nanowires, nanotubes, nanoclusters) including the calculations of the excited states and simulations of water adsorption and dissociation on photocatalyst surface for detailed understanding of the photodissociation mechanisms. The project is multidisciplinary and combines materials science, solid state chemistry, physics and computer science.
The total duration of the project is 36 months (2018. - 2021.), the total cost is 133,805.88 EUR.
Project progress
February 08, 2020
For the successful realization of the project, Dr. Alexander Sorokin and Master Maxim Sokolov were hired in the project. Together with Alexander Sorokin, the ScF3 modeling task related to the description of phonons in this material and the description of negative thermal expansion effect using Gruneisen parameters was solving. The article by P. Zguns, A. Sorokin, D. Bocharov, S. Piskunov, A. Kuzmin, J. Purans, Quantum chemistry calculations on ScF3 lattice dynamics is preparing.
Together with Maxim Sokolov the task of nanostructured photocatalysts development was studied. As part of this activity, a stepwise model of SrTiO3 was constructed to further investigate the photocatalytic properties of this nanostructure.
On November 23-26, 2020, the principal investigator attended in International conference “Functional Materials & Nanotechnology” (FM&NT) held by Vilnius University in Zoom. Poster Dmitry Bocharov, Inga Pudža, Alexei Kuzmin, Matthias Krack, „Ab initio molecular dynamics simulations of transition metal dichalcogenides” was presented.
On December 1, the project leader participated in the COST project CA18234 (Computational materials sciences for efficient water splitting with nanocrystals from abundant elements) virtual workshop "Molecular dynamics for treating nanoscale materials", where current photocatalyst design problems and approaches to use molecular dynamics to describe photocatalysts were discussed. In the workshop, the project leader presented two reports:
- Dmitry Bocharov, Alexei Kuzmin, Matthias Krack, Ab initio molecular dynamics simulations for EXAFS interpretation and development of empirical potentials
- Sergei Piskunov, Oleg Lisovski, Dmitry Bocharov, Yuri F. Zhukovskii, StephaneKenmoe, Eckhard Spohr, Modelling of nanotubes for visible-light-driven photocatalytic water splitting and development of 2D periodic model approximations for molecular dynamics simulations
On December 11, the project manager participated in the COST project CA18234 (Computational materials sciences for efficient water splitting with nanocrystals from abundant elements) virtual workshop CA18234 "First International Symposium on DFT Modeling of Materials Relevant for Water Splitting", where current problems of photocatalyst design were discussed. One report in which the author of the project participated as a co-author was presented at this workshop: “Yu.A. Mastrikov, M. Sokolov, G. Zvejnieks, D. Bocharov, E.A. Kotomin, Water adsorption on the stepped TiO2-terminated (001) SrTiO3 surface”
A draft of a popular scientific article Dmitrijs Bocharovs, Māra Putniņa, Oleg Lisovskis, Sergejs Piskunovs, "Photocatalysis and hydrogen energy: how to split water with light? was prepared for the journal "Energy and the World". Now, the authors are waiting for information from the editorial office of the journal, because in December-January the office has temporarily interrupted work due to the COVID-19 shutdown.
Calculations of CO2 and CH2 absorption were performed for the Cu-decorated graphene surface. The draft of the paper O. Lisovski, S. Piskunov, Yu.F. Zhukovskii, J. Kleperis, D. Bocharov “Copper decorated graphene for electrochemical CO2 reduction: prediction from the first principles” was written for the journal Physica E: Low-dimensional systems and nanostructures. Now, the draft is being coordinated with the co-authors.
On January 11, the project manager discussed the popularization of science on Radio Baltcom.
Project progress
November 05, 2020
Ab initio molecular dynamics calculations of ReSe2 compound were finished. Ab initio molecular dynamics calculations of Zn and Mn metals were continued.
After receiving the review, the paper M.N. Sokolov, Yu.A. Mastrikov, A. Gopejenko, D. Bocharov, Yu.F. Zhukovskii, E.A. Kotomin. Ab initio modeling of titanium impurities in α-Fe lattice. (Nucl. Instrum. Methods Phys. Res. B, 2020, 483, p. 50-54. DOI: 10.1016 / j.nimb.2020.09.013) was revised, re-submitted and accepted for publication.
A literature review “2D Slab Models of Nanotubes for Simulation of Water Adsorption” was prepared.
The preparation of a popular scientific article for the journal "Energy and the World" was continued.
In August 2020, the project manager was on annual leave.
Project progress
August 11, 2020
Ab initio molecular dynamics calculations of ReSe2 compound were started.
The paper “Dmitry Bocharov, Andris Anspoks, Janis Timoshenko, Aleksandr Kalinko, Matthias Krack, Alexei Kuzmin, Interpretation of the Cu K-edge EXAFS spectra of Cu3N using ab initio molecular dynamics” was published in Radiation Physics and Chemistry journal (175 (2020) 108100).
The manuscript Maksim N Sokolov, Yuri A. Mastrikov, Alexei V Gopejenko, Dmitry V Bocharov, Yuri F Zhukovskii, Eugene A Kotomin, “Ab initio modeling of titanium impurities in alpha-Fe lattice” was written and submitted for review to Nuclear Inst. and Methods in Physics Research, B journal.
On 7 July, the project leader participated in a virtual conference “The International Virtual Conference on New Directions for Modelling Nanocrystal Catalysts” where current challenges in the design of photocatalysts were discussed (1).
Preparation of a popular scientific article for the journal "Energy and the World" began.
At the end of May Latvian Radio 4 broadcast about the principles of modelling and scientific work (1):
At the end of May, recording of the interview on the principles of modelling and scientific work was broadcasted:
lr4.lsm.lv/lv/raksts/priroda-veschey/matematicheskoe-modelirovanie-epidemiy-i-feyki-v-nauke.a130444/
On June, 29 the project leader gave an interview for the portal rigaplus.lv, where one of the topics of discussion was a scientific work.
rigaplus.lv/ru/fizik-dmitrij-bocharov-o-kide-chto-gde-kogda-i-nauke-v-latvii/
On May 1, the author of the project commented 5G mobile technologies for Radio Baltcom broadcast:
Project progress
May 13, 2020
Together with partners from the Skolkovo Institute of Science and Technology (Skoltech), the MD-EXAFS methodology for simple bulk compounds was studied using empirical potentials, which were developed on the base of the pre-performed DFT calculations. Molecular dynamics calculations for Ti, Cu, Zn, Y, Ni and W metals were performed, and comparison of EXAFS spectra obtained from molecular dynamics calculations with EXAFS experimental results was made.
Ab initio molecular dynamics calculations for ReS2 compounds were completed.
Two poster presentations were presented at the 36th scientific conference of LU CFI:
- "First-principles molecular dynamics simulations of layered MoS2 and WS2 materials" and
- “Ab initio molecular dynamics simulations of negative thermal expansion effect in scandium fluoride”.
Additional calculations were performed for the publication “Validation of 2D constrained models for TiO2 nanotubes over a broad range of diameters”.
A review of the literature on the catalytic activity of solids, especially for the production of H2O2 peroxide from water, was performed. 29.04. Latvian Radio 4 program on the principles of modeling and scientific work was recorded (the program will be broadcast later).
Due to the COVID-19 reporting period, two mobilities to foreign partners were canceled in March and April.
Project progress
February 12, 2020
Molecular dynamics ab initio calculations for ReS2 were continued and additional calculations for MoS2 in NpT ensemble were made.
Creation of empirical MD many-parametric potentials for ScF3 compound based on pre-performed AIMD calculations were performed in collaboration with colleagues from Skolkovo Institute of Science and Technology. Testing of these potentials using molecular dynamics approach has begun. If the test will be successful, then these potentials will be used in further low-temperature calculations.
The ab initio molecular dynamics calculations of ReS2, ZnO2 and Cu3N decomposition processes were continued.
Deci-16 project "First-Principles of Molecular Dynamics Simulations of Bulk and Nanocrystalline ZnO2 Material" for Supercomputer Resources was written and submitted (the results to be announced in May 2020).
A mid-term report on the post-doctoral project was prepared and submitted.
Preparation of the manuscript “D. Bocharov, I. Jonane, A. Kuzmin, M. Krack, First-principles molecular dynamics simulations of layered MoS2 materials” for publication in the “2D materials” was started.
The paper D. Bocharov, M. Krack, Yu. Rafalski, A. Kuzmin, J. Purans, Ab initio Molecular Dynamics Simulations of Negative Thermal Expansion in ScF3: The Effect of Supercell Size, Comp. Mater. Sci. 171 (2020) 109198 was published.
On the evening of October 31, the project leader of TV broadcast "Cognitive Impulse" presented post-doctoral research project:
https://ltv.lsm.lv/lv/raksts/31.10.2019-izzinas-impulss-3.-serija.id171468/
On December 13 in the Latvian Radio 4 broadcast author discussed the history of Mendeleyev's table and current issues in quantum chemistry:
From September 23 to October 10 and from November 4 to 29, mobility took place to the Paul Sherer Institute, Switzerland.
- results of ab initio molecular dynamics for ScF3, MoS, WS2, ZnO2 bulk phase and Cu3N decomposition process were discussed.
- Poster „Dmitry Bocharov, Matthias Krack, Alexei Kuzmin, Juris Purans, Simulation of pure and Cr-doped UO2 using molecular dynamics and density functional theory” was presented at the NuFuel-MMSNF 2019 Workshop. The discussion led to the idea of studying the UF4 compound by DFT and AIMD methods.
- optPBE-vdW functional was checked for ReS2, ReSe2, WS2 un MoS2 compounds. Performed calculations showed that PBE-vdW functional previously used for calculations is preferable. The experimental data of ReSe2 compound were not reproduced in CRYSTAL and CP2K DFT calculations. Additional VASP calculations for this compound are planned.
- Slab and big void models were calculated for Cu3N decomposition process description. Both models were unsatisfactory. The model of interstitial Cu atom defect with Cu vacancy was proposed for following calculations.
- Analysis of literature for “First-principles molecular dynamics simulations of layered MoS2 material” paper was continued. The topic of the article was narrowed to a MoS2 compound. Additional NpT calculations for MoS2 compound at 300 K were started.
- Study of the documentation of the project "A Universal Force Engine for Advanced Molecular Dynamics" (http://ipi-code.org) for path integrals method implementation was started.
From January 13th to 24th, there was a mobility to the University of Duisburg-Essen.
- Activities in framework of the post-doctoral project as well as interesting results obtained in University of Duisburg-Essen, Chair of Theoretical Chemistry during last half-year were discussed on common seminar with participation of Prof. E. Spohr, Dr. S. Kenmoe and PhD student T. Kox
- The manuscript of the paper „Validation of 2D constrained models for TiO2 nanotubes over a broad range of diameters” was updated. All remarks about previous version of the paper were taken into account. Results of new calculations were added to manuscript.
- Models of Cu3N / Cu + N2 system decomposition process were discussed
- YAMBO code installation on BESKOW supercomputer (Sweden) were inspected together with Dr. S. Kemnoe for luminescence spectra modelling
Project progress
November 13, 2019
In August, following the reviewer's comments, the article D. Bocharov, M. Krack, Yu. Rafalskij, A. Kuzmin, and J. Purans «Ab initio molecular dynamics simulations of negative thermal expansion in ScF3: the effect of the supercell size» was revised and resubmitted to Computational Material Science. Article accepted for publication 11.08.2019. (Comp. Mater. Sci. 171 (2020) 109198, https://doi.org/10.1016/j.commatsci.2019.109198)
From August 26th until September 6th, a school „Hands-on DFT and beyond: high-throughput screening and big-data analytics, towards exascale computational materials science” (University of Barcelona, Spain and Fritz Haber Institute, Germany, https://th.fhi-berlin.mpg.de/meetings/d” ft2019/) was attended. The program included 33 hours of lectures and 35 workshops. A poster “D.Bocharov, M. Krack, Yu. Rafalskij, A. Kuzmin, and J. Purans «Ab initio molecular dynamics simulations of negative thermal expansion in ScF3: the effect of the supercell size»” was presented.
Calculations of WS2 and MoS2 compounds were continued and analysed.
Bulk phase DFT and molecular dynamics calculations of the ZnO2 compound were continued.
Preparation of the article „Validation of 2D constrained models for TiO2 nanotubes over a broad range of diameters” was continued.
From September 23th, until October 10th mobility at Paul Sherer Institute, Switzerland, took place. During the mobility, the results of the ScF3, MoS2, WS2, ZnO2 bulk phase and Cu3N decomposition model calculations were discussed, as well as the ReS2 and ReSe2 calculations were started.
Two interviews were recorded:
- Latvian Radio on the 150th anniversary of the Periodic Table.
- on Latvian Television about postdoctoral project for the program "Cognitive Impulse".
Both interviews will go on the air later after the montage.
Project progress
August 15, 2019
From April 29 until May 12, there was mobility to Paul Sherrer Institute, Switzerland. During the mobility, the results of the ScF3, MoS2 and WS2 calculations were discussed as well as well as ZnO2 compound calculations were started. The calculations and the analysis of the results of these compounds continued in the following months.
A paper D. Bocharov, M. Krack, Yu. Rafalskij, A. Kuzmin, and J. Purans «Ab initio molecular dynamics simulations of negative thermal expansion in ScF3: the effect of the supercell size» was finished and submitted to the journal Computational Material Science in May. Additional ScF3 calculations were performed and text partial rewriting for this article were made following reviewer's comments.
Starting from May 25 until June 1, project leader attended the 2019 EMRS Spring Meeting Conference (Nice, France). Two poster presentations “First-principles molecular dynamics simulations of layered WS2 materials” and “Ab initio molecular dynamics calculations of ScF3 temperature dependent structural properties” were presented, as well as contacts with prof. Ivano Castelli (Technical University of Denmark) were established.
On May 23 project leader participated in Radio Baltcom broadcast about Latvian Science Prospects, mentioned also a post-doctoral program in Latvia youtu.be/r2edN1PQ6XU
JIn July, a two-dimensional model of Cu3N was constructed for the study of the Cu3N / Cu + N2 chemical decomposition process.
From June 26 until July 9 in the frames of mobility the University of Duisburg-Essen was visited. The draft version of the paper „Validation of 2D constrained models for TiO2 nanotubes over a broad range of diameters” was updated and partially rewritten. Assess to Essen-Duisburg computer cluster was organized as well as common activities in framework of the post-doctoral project 1.1.1.2/VIAA/l/16/147 were discussed.
On July 25, project manager participated in a radio Baltcom program about quantum physics: https://youtu.be/d7DjSugMdLA
Project progress
May 17, 2019
In November-April ab initio molecular dynamics calculations of WS2 and MoS2 compounds were performed.
The manuscript of the Dmitry Bocharov, Janis Timoshenko, Andris Anspoks, Aleksandr Kalinko, Alexei Kuzmin, Matthias Krack, “Interpretation of the Cu K-edge EXAFS spectra of Cu3N using ab initio molecular dynamics” was updated after reviewers comments and returned to the journal “Radiation Physics and Chemistry”. This paper was accepted for publication (https://doi.org/10.1016/j.radphyschem.2018.12.020).
The paper D. Bocharov, M. Krack, Yu. Rafalskij, A. Kuzmin, J. Purans, “Ab initio molecular dynamics calculations of ScF3 temperature dependent structural properties” was preparing for submission to “Computational Materials Science” journal.
During the mobility to Paul Scherrer partner organization in January-February analysis of calculated data for ScF3 was performed. The preparation of the manuscript P. Žguns, D. Bocharov, S. Piskunov, A. Kuzmin, J. Purans, „Quantum chemistry calculations on ScF3 lattice dynamics” was started.
The oral talk D. Bocharov, J. Timoshenko, A. Anspoks, A. Kalinko, A. Kuzmin, M. Krack. "Ab initio molecular dynamics calculations of Cu3N temperature dependent structural properties" was given at annual ISSP UL conference in February.
March 9-17 post-doctoral fellow participated in 53rd Russian School on Condensed State Physics (St. Petersburg nuclear institute). The poster Dmitry Bocharov, Janis Timoshenko, Andris Anspoks, Aleksandr Kalinko, Alexei Kuzmin, Matthias Krack, „Ab initio molecular dynamics calculations of Cu3N temperature dependent structural properties” was presented.
March 18-27 in the frames of mobility the University of Duisburg-Essen was visited. During a business trip the results of TiO2 calculations were discussed with Prof. E. Spohr, a plan for the “Validation of 2D constrained models for TiO2 nanotubes over a broad range of diameters” was prepared; as well the cooperation in the framework of project 1.1.1.2/VIAA/l/16/147 was discussed.
From April 08 until April 12, there was mobility to Paul Sherrer Institute, Switzerland. During the mobility, the results of the ScF3 and WS2 calculations were discussed, as well as CP2K software installation on LASC and MARCONI supercomputers was completed.
On April,17 during the campaign "Back to School / Back to University 2019" D.Bocharov visited to J.G. Herder's Riga Grizinkalns Secondary School, where he discussed science topics and EU projects with 65 students from 3 forms.
The paper Dmitry Bocharov, Yuri Rafalskij, Matthias Krack, Mara Putnina and Alexei Kuzmin, Negative thermal expansion of ScF3: first principles vs empirical molecular dynamics. IOP Conf. Ser.: Mater. Sci. Eng. 503 (2019) 012001 was published.
Project progress
November 05, 2018
An article was published in July: D. Bocharov, S. Piskunov, Yu.F. Zhukovskii, and R.A. Evarestov. Ab initio calculations on the electronic structure and photocatalytic properties of two-dimensional WS2 (0001) nanolayers of varying thickness. Phys. Status Solidi RRL, 2018, 12, 1800253 (pp. 1-6). DOI: 10.1002/pssr.201800253, SNIP(2017)=1.017, IF(2017)=3.721. In this study we have performed hybrid DFT-LCAO calculations of WS2 nanosheets possessing stable 2H c hexagonal phase with thickness between 1 and 40 monolayers (ML) using hybrid exchange-correlation functional HSE06 adopted for this purpose. Defect less pristine WS2 nanosheets have been found to be suitable for photocatalytic applications since widths of their band gaps correspond to the range of visible light between the red and violet edges, while the top of the valence band and the bottom of the conduction band are properly aligned relative to the oxidation and reduction potentials. We found that the band gap of nanolayers decreases with growing the number of MLs in layered WS2 2D structure. The highest solar energy conversion efficiency (15–18%) usually achieved for band gap 2.0–2.2 eV (yellow range of the visible spectrum) has been found for the 2 ML thick stoichiometric WS2 (0001) nanosheet. WS2 nanolayers as prospective material for photocatalysis demand no doping or formation of vacancies as in the case of nanostructures of transition metal oxides.
From 07/21/2018 until 07/27/2018, principal investigator visited Krakow, Poland, where attended the XAFS 2018 conference. Two presentations were arranged: “Interpretation of the Cu K-edge EXAFS spectra of Cu3N using ab initio molecular dynamics” (oral presentation)) and “Validation of ab initio molecular dynamics simulations of ZnO using the Zn K-edge EXAFS spectra” (poster).
From 10/02/2018. until 10/05/2018, principal investigator attended International conference “Functional Materials & Nanotechnology” (FM&NT) held in Riga. Latvia. Poster was presented: Dmitry Bocharov, Yuri Rafalskij, Matthias Krack, Mara Putnina and Alexei Kuzmin, Negative thermal expansion of ScF3: first principles vs empirical molecular dynamics“.
In July - October, two articles were finalized and submitted for review: Dmitry Bocharov, Janis Timoshenko, Andris Anspoks, Aleksandr Kalinko, Alexei Kuzmin, Matthias Krack, “Interpretation of the Cu K-edge EXAFS spectra of Cu3N using ab initio molecular dynamics” (“Radiation Physics and Chemistry”) un Dmitry Bocharov, Yuri Rafalskij, Matthias Krack, Mara Putnina and Alexei Kuzmin, Negative thermal expansion of ScF3: first principles vs empirical molecular dynamics“ (“IOP Conference Series: Materials Science and Engineering”).
Project progress
July 13, 2018
During the first three months of the project systematic calculations of Cu3N and ZnO were performed using ab initio molecular dynamics in CP2K code framework. The test DFT and ab initio molecular dynamics calculations of WS2 and MoS2 bulk was performed for the project "First-principle molecular dynamics simulations of layered WS2 and MoS2 materials ". This project was submitted together with Swiss partner Dr. M. Krack (Paul Scherrer Institute) for CSCS Swiss supercomputer spring call (results of the project estimation will be announced in September 2018).
DFT atomic and electronic structure calculations of WS2 bulk and nanolayered structures were performed using the CRYSTAL14 software and the LCAO method. The article "D. Bocharov, S. Piskunov, Yu.F. Zhukovskii, R.A. Evarestov, Ab initio calculations on the electronic structure and photocatalytic properties of two-dimensional WS2 (0001) nanolayers of varying thickness" was written and submitted for review to the journal "Physica status solidi".
From May 13, 2018 to May 18, 2018 the author of the project participated in a scientific meeting on the photocatalytic processes in solids, nanostructures and nanotubes in Moscow (N.S. Kurnakov Institute of General and Inorganic Chemistry). During the meeting, the synergy between the project WATERSPLIT and the post-doctoral project 1.1.1.2/VIAA/l/16/147 was discussed with partner E. Spohr (The University of Duisburg-Essen).
From June 25, 2018 to July 3, 2018 first mobility took place at the Paul Scherer Institute, Switzerland. During the mobility with Swiss partner Dr. M. Krack were discussed the results of calculations for ScF3, Cu3N, UO2 and ZnO compounds, as well as discussed collaboration on first project stage.
On April 5, the project author participated in Latvian Radio 4 radio popular science broadcast http://lr4.lsm.lv/lv/raksts/priroda-veschey/smena-paradigmi-sovremennoy-latviyskoy-nauki-teorija-i-praktika.a101981/: