Jakub Višňák | Charles University, Prague (original) (raw)

Papers by Jakub Višňák

Geologica Acta

This study shows a comparison and analysis of results from a modelling exercise concerning a fiel... more This study shows a comparison and analysis of results from a modelling exercise concerning a field experiment involving the transport and retention of different radionuclide tracers in crystalline rock. This exercise was performed within the Swedish Nuclear Fuel and Waste Management Company (SKB) Task Force on Modelling of Groundwater Flow and Transport of Solutes (Task Force GWFTS).Task 9B of the Task Force GWFTS was the second subtask within Task 9 and focused on the modelling of experimental results from the Long Term Sorption Diffusion Experiment in situ tracer test. The test had been performed at a depth of about 410m in the Äspö Hard Rock Laboratory. Synthetic groundwater containing a cocktail of radionuclide tracers was circulated for 198 days on the natural surface of a fracture and in a narrow slim hole drilled in unaltered rock matrix. Overcoring of the rock after the end of the test allowed for the measurement of tracer distribution profiles in the rock from the fracture ...

Department of Mathematical AnalysisKatedra matematické analýzyFaculty of Mathematics and PhysicsM... more Department of Mathematical AnalysisKatedra matematické analýzyFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Task 9B of the SKB Task Force on Modelling of Groundwater Flow and Transport of Solutes (Task For... more Task 9B of the SKB Task Force on Modelling of Groundwater Flow and Transport of Solutes (Task Force GWFTS) was the second subtask within Task 9 and focused on the modelling of experimental results from the LTDE-SD in situ tracer test. The test had been performed at a depth of about 410 m in the Äspö Hard Rock Laboratory. Synthetic groundwater containing a cocktail of radionuclide tracers was circulated for 198 days on the natural surface of a fracture and in a narrow slim hole drilled in unaltered rock matrix. Overcoring of the rock after the end of the test allowed for the measurement of tracer distribution profiles in the rock from the fracture surface (A cores) and also from the slim hole (D cores). The measured tracer activities in the rock samples showed long profiles (several cm) for non- or weakly-sorbing tracers (Cl-36, Na-22), but also for many of the more strongly-sorbing radionuclides. The understanding of this unexpected feature was one of the main motivations for this m...

Title: Quantum computing algorithms for quantum chemistry Author: Jakub Višňák Abstract: The topi... more Title: Quantum computing algorithms for quantum chemistry Author: Jakub Višňák Abstract: The topic of this study is the simulation of the quantum algorithm for the diagonalization of the matrix representation of the all-electron Dirac-Coulomb hamiltonian of the SbH molecule. Two different limited CI expansions were used to describe both the ground state (X 0+ ) and the first excited doublet (A 1) by simulating the Iterative Phase Estinamtion Algorith (IPEA). In the simulations numerically performed in this work, the "compact mapping" has been employed for the representation of the evolution operator exp(i Hˆ t); in the theoretical part of the work, the "direct mapping" is described as well. The influence of the metodics for choosing the initial eigenvector estimate is studied in both IPEA A and IPEA B variants. For those variants, the success probabilities pm are computed for different single-points on the SbH dissociation curves. The initial eigenvector estimate...

Journal of Chemical Physics, May 7, 2020

There are three essential problems in computational relativistic chemistry: electrons moving at r... more There are three essential problems in computational relativistic chemistry: electrons moving at relativistic speeds, close lying states and dynamical correlation. Currently available quantum-chemical methods are capable of solving systems with one or two of these issues. However, there is a significant class of molecules, in which all the three effects are present. These are the heavier transition metal compounds, lanthanides and actinides with open d or f shells. For such systems, sufficiently accurate numerical methods are not available, which hinders the application of theoretical chemistry in this field. In this paper, we combine two numerical methods in order to address this challenging class of molecules. These are the relativistic versions of coupled cluster methods and density matrix renormalization group (DMRG) method. To the best of our knowledge, this is the first relativistic implementation of the coupled cluster method externally corrected by DMRG. The method brings a s...

arXiv: Chemical Physics, 2018

Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS) and cryo-TRLFS are sensitive tools ... more Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS) and cryo-TRLFS are sensitive tools for \textit{in situ} speciation of low-level uranium in aqueous samples, including natural waters. To tailor, often ill-conditioned (i.e., leading to ambiguous interpretations), multi-linear analysis, first-principles based theoretical computation (Molecular Dynamics and Quantum Chemistry) of luminescence spectra would be beneficial. We present a methodology to simulate TRLFS and cryo-TRLFS spectra and present vibrationally resolved luminescence spectra for aquo complex [UO$_2$(H$_2$O)$_5$]$^{2+}$(aq). Comparison to experimental data, interpretation of spectra in the terms of a minimal non-redundant set of spectroscopic parameters (peak spacing \omega, the 0' rightarrow\rightarrowrightarrow 0 peak position T$_{00}$, envelope shape parameter \Delta R, average peak width \sigma and luminescence life-times) and shifts due to ligand coordination are discussed. The minimum theory-experiment deviation in T$...

EPJ Web of Conferences, 2017

EPJ Web of Conferences, 2016

International Journal of Quantum Chemistry, 2016

EPJ Web of Conferences, 2015

J. Chem. Phys. 152, 174107, 2020

Brandejs J., Višňák J., Veis L., Maté M., Legeza Ö., Pittner J.: Toward DMRG-tailored coupled clu... more Brandejs J., Višňák J., Veis L., Maté M., Legeza Ö., Pittner J.: Toward DMRG-tailored coupled cluster method in the 4c-relativistic domain

There are three essential problems in computational relativistic chemistry: Electrons moving at relativistic speeds, close lying states, and dynamical correlation. Currently available quantum-chemical methods are capable of solving systems with one or two of these issues. However, there is a significant class of molecules in which all the three effects are present. These are the heavier transition metal compounds, lanthanides, and actinides with open d or f shells. For such systems, sufficiently accurate numerical methods are not available, which hinders the application of theoretical chemistry in this field. In this paper, we combine two numerical methods in order to address this challenging class of molecules. These are the relativistic versions of coupled cluster methods and the density matrix renormalization group (DMRG) method. To the best of our knowledge, this is the first relativistic implementation of the coupled cluster method externally corrected by DMRG. The method brings a significant reduction of computational costs as we demonstrate on the system of TlH, AsH, and SbH.

For arxiv version, see: https://arxiv.org/pdf/2001.05352.pdf

EPJ Web of Conferences, Volume 154, p. 01030 (2017), 2017

No core Full Configurational Interaction (NCFCI) calculations of Nuclear Bonding energy are resou... more No core Full Configurational Interaction (NCFCI) calculations of Nuclear Bonding energy are resource demanding, in particular, computational time scales exponentially with the nucleon number A. In contrast to that, usage of quantum computers would allow an efficient (in polynomial time) NCFCI calculation and speed-up for other beyond-Mean-Field (correlation energy including) methods. To initiate feasibility studies of given quantum algorithms, we present an introduction to preliminary classical-computer simulation for the case of spherical nuclei (and 4He in particular) within NCFCI with realistic chiral NNLO_opt potential.

EPJ Web of Conferences, Volume 154, p. 01029 (2017), 2017

Authors: Višňák, J.; Steudtner, R.; Kassahun, A.; Hoth, N. Natural waters’ uranium level monitor... more Authors: Višňák, J.; Steudtner, R.; Kassahun, A.; Hoth, N.
Natural waters’ uranium level monitoring is of great importance for health and environmental protection. One possible detection method is the Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS), which offers the possibility to distinguish different uranium species. The analytical identification of aqueous uranium species in natural water samples is of distinct importance since individual species differ significantly in sorption properties and mobility in the environment. Samples originate from former uranium mine sites and have been provided by Wismut GmbH, Germany. They have been characterized by total elemental concentrations and TRLFS spectra. Uranium in the samples is supposed to be in form of uranyl(VI) complexes mostly with carbonate (CO3(2-)) and bicarbonate (HCO3(-)) and to a lesser extent with sulphate (SO4(2-)), arsenate (AsO4(3-)), hydroxo (OH(-)), nitrate (NO3(-)) and other ligands. Presence of alkaline earth metal dications (M = Ca(2+), Mg(2+), Sr(2+)) will cause most of uranyl to prefer ternary complex species, e.g. Mn(UO2)(CO3)3(2n-4) (n = 1, 2). From species quenching the luminescence, Cl- and Fe2+ should be mentioned. Measurement has been done under cryogenic conditions to increase the luminescence signal. Data analysis has been based on Singular Value Decomposition and monoexponential fit of corresponding loadings (for separate TRLFS spectra, the “Factor analysis of Time Series” (FATS) method) and Parallel Factor Analysis (PARAFAC, all data analysed simultaneously). From individual component spectra, excitation energies T_{00}, uranyl symmetric mode vibrational frequencies omega_{gs} and excitation driven U-Oyl bond elongation DeltaR have been determined and compared with quasirelativistic (TD)DFT/B3LYP theoretical predictions to cross-check experimental data interpretation.

For co-authors, please see the pdf Comparison of uranyl-sulfate and uranyl-selenate stability co... more For co-authors, please see the pdf

Comparison of uranyl-sulfate and uranyl-selenate stability constants, enthalpy and enthropy of complexation, uranyl group symmetrical mode vibrational frequency, adiabatic excitation energy (main luminescence active transition) by TRLFS and UV-VIS spectrophotometric means. Results from my 2014 IAA proceedings contribution in English.

(for co-autors, please see the pdf). The whole Annual Report of DNC (FNSPE, CTU) 2011/2012 is ava... more (for co-autors, please see the pdf). The whole Annual Report of DNC (FNSPE, CTU) 2011/2012 is available at the website of the Department - http://www.jaderna-chemie.cz/data/documents/vyrocni_zpravy/AR2011-2012.pdf

The UO2(2+) - SO4(2-) - H2O system is important for uranium
mining studies, safety studies of radioactive waste repository, geochemical modelling and several other fields.
Aim of our work was to obtain parameters of the speciation
(log β° for the individual uranyl-sulfate complexes and SIT
coefficients ε(i, j) where i is an uranyl specie) by factor
analysis based fit of the spectral data.

Please, see also IAA 2014 Proceedings paper -
(The IAA 2014 Proceedings contribution cite part of this research, compare it with TRLFS based speciation studies of both uranyl-sulfates and uranyl-selenates and further discuss the uranyl-sulfates stability constant data overestimation in this work - the need for a precise preceding uranyl hydrolytic study under similar conditions is stressed there).

Geologica Acta

Journal of Chemical Physics, May 7, 2020

arXiv: Chemical Physics, 2018

EPJ Web of Conferences, 2017

EPJ Web of Conferences, 2016

International Journal of Quantum Chemistry, 2016

EPJ Web of Conferences, 2015

J. Chem. Phys. 152, 174107, 2020

For arxiv version, see: https://arxiv.org/pdf/2001.05352.pdf

EPJ Web of Conferences, Volume 154, p. 01030 (2017), 2017

EPJ Web of Conferences, Volume 154, p. 01029 (2017), 2017

For co-authors, please see the pdf Comparison of uranyl-sulfate and uranyl-selenate stability co... more For co-authors, please see the pdf

EPJ Web of Conferences 128, 02002 (2016), 2016

A brief introduction into computational methodology and preliminary results for spectroscopic (ex... more A brief introduction into computational methodology and preliminary results for spectroscopic (excitation energies, vibrational frequencies in ground and excited electronic states) and thermodynamic (stability constants, standard enthalpies and enthropies of complexation reactions) properties of some 1:1, 1:2 and 1:3 uranyl sulphato-and selenato-complexes in aqueos solutions will be given. The relativistic effects are included via Effective Core Potential (ECP), electron correlation via (TD)DFT/B3LYP (dispersion interaction corrected) and solvatation is described via explicit inclusion of one hydratation sphere beyond the coordinated water molecules. We acknowledge limits of this approximate description – more accurate calculations (ranging from semiphenomenological two-component spin-orbit coupling up to four-component Dirac-Coulomb-Breit hamiltonian) and Molecular Dynamics simulations are in preparation. The computational results are compared with the experimental results from Time-resolved Laser-induced Fluorescence Spectroscopy (TRLFS) and UV-VIS spectroscopic studies (including our original experimental research on this topic). In case of the TRLFS and UV-VIS speciation studies, the problem of complex solution spectra decomposition into individual components is ill-conditioned and hints from theoretical chemistry could be very important. Qualitative agreement between our quantum chemical calculations of the spectroscopic properties and experimental data was achieved. Possible applications for geochemical modelling (e.g. safety studies of nuclear waste repositories, modelling of a future mining site) and analytical chemical studies (including natural samples) are dissucussed.

PhD thesis, 2018

Submitted dissertation thesis is concerned with application of Time-Resolved Laser-Induced Fluore... more Submitted dissertation thesis is concerned with application of Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS) for uranyl(VI) direct speciation in laboratory-prepared aqueous samples (systems UO22+ - SO42- and UO22+ - SeO42-, with an aim to determine binary 1:1, 1:2 and 1:3 complex stability constants, as well as individual component spectra) and natural water samples (measurement has been done under cryogenic setup in collaboration with TU Freiberg, Germany. I did the multilinear analysis of time-resolved spectra and developed methodology of result interpretation connected with quantum chemical modelling of dominant species, i.e. Ca2UO2(CO3)30, CaUO2(CO3)32-, MgUO2(CO3)32-, UO2SO4 and UO2(CO3)n2-2n)). I performed TRLFS speciation study of UO22+ - SO42- system under cryogenic conditions (T = 153 K) in order to study swift liquid sample cooling (by liquid nitrogen, into ice-block) influence on its speciation. A preliminary study is attached. Importance of stability constant determination for further geochemical modelling is discussed in „Preface“ (and [T1]-[T4]) together with the discussion of natural water sample direct speciation importance for environmental monitoring, protection and remediation or for mining prospection.
In the second part of my thesis, „Theoretical Chemistry Modelling“, the possibility for determination of spectroscopic parameters of the above mentioned experimentally studied complex species „from first principles“ is probed. I have studied many-atomic supramolecular systems resulting from explicitly modelled solvation (needed due to the directional character of aqueous H-bonds) by computational protocol connecting Classical Molecular Dynamics (CMD), Time-dependent Density Functional Theory (TDDFT/CAM-B3LYP and other functionals. Scalar quasi-relativistic, spin-orbit coupling including quasi-relativistic description have been compared to computations based on Dirac-Coulomb-Gaunt Hamiltonian and corresponding four-component one-particle wave-functions (bispinors)) and double-harmonic approximation for Franck-Condon factor estimation (Duschinsky effect included [DOKetal]). From truly ab initio (i.e. wave-function theory as opposed to DFT) quantum chemical methods, I have used Delta-SCF method for comparison. Simulated and experimental vibrationally resolved luminescence spectra show qualitative agreement, discussion of possibilities to achieve quantitative agreement follows. More accurate description of electron correlation, crucial for a quantitative agreement would require post-HF ab initio methods. Their large computational demands are an obstacle avoidable in future through quantum computer usage. Some of the respective quantum algorithms are briefly reviewed in the chapter „Preword to following publication lists“ as this topic is connected to publications [O1], [O2] co-authored by me.
In the chapters „Preface“ and „Motivation“ current common luminescence spectra tabulation praxis (band maxima wavelengths in nm, integer precision) is critically reviewed. I propose an alternative, non-redundant, yet more complete set of spectroscopic parameters with a direct physical meaning supported by theoretical chemistry.