Theoretical modelling and methods for data analysis


  • Prof. Leonas Valkūnas 
  • Dr. Jevgenij Chmeliov 
  • Dr. Andrius Gelžinis 
  • Dr. Gediminas Trinkūnas 
  • Jakov Braver 
Various theoretical modelling approaches are used to explain and predict dynamic phenomena in different molecular systems. The simplest yet still effective is the phenomenological approach. Even though it often allows one to better understand the processes under consideration, it does not reveal the exact mechanisms behind these processes. This can be achieved by using microscopic modeling, based on structural data and quantum mechanical description. The task, however, is complicated due to the fact that the electronic degrees of freedom of the molecules interact with vibrational degrees of freedom of the molecules themselves and their surroundings. Due to these difficulties the exact description of dynamic processes or spectral properties becomes almost impossible, thus forcing researchers to utilize approximate approaches. Development of the latter is therefore an important scientific problem.
Theoretical modelling is one of the pillars of the studies performed in the Biophysical research laboratory. In recent years theoretical research was performed in several directions: modeling of electronic spectra and their properties [1, 3, 4, 7, 8, 12, 18], creation of coarse-grained models for the migration of electronic excitation [5, 14], influence of vibrational degrees of freedom to the electronic excitation dynamics [6], methods of open quantum systems [9], research of the origin of selected properties of molecular compounds [10], quantum chemical calculations [2, 11, 15], analysis of spectroscopic signals of molecular systems [13, 17].
In the laboratory, we aim to develop convenient and informative methods for analysis of spectroscopic data as well as accurate and effective microscopic description of molecular compounds, that would allow us to model both dynamical properties and spectral response of such systems.

Publications (2015–2019)
  1. A. Gelzinis, D. Abramavicius, L. Valkunas, Absorption lineshapes of molecular aggregates revisited, J. Chem. Phys. 142, 154107, 2015.
  2. M. Macernis, D. Galzerano, J. Sulskus, E. Kish, Y.-H. Kim, S. Koo, L. Valkunas, B. Robert, Resonance Raman Spectra of Carotenoid Molecules: Influence of Methyl Substitutions, J. Phys. Chem. A 119, 56–66, 2015.
  3. V. Balevičius Jr., L. Valkunas, and D. Abramavicius, Modeling of ultrafast time-resolved fluorescence applied to a weakly coupled chromophore pair, J. Chem. Phys. 143, 074101, 2015.
  4. V. Chorošajev, A. Gelzinis, L. Valkunas, D. Abramavicius, Benchmarking the stochastic time-dependent variational approach for excitation dynamics in molecular aggregates, Chem. Phys. 481, 108-116, 2016.
  5. J. Chmeliov, G. Trinkunas, H. van Amerongen, L. Valkunas, Excitation migration in fluctuating light-harvesting antenna systems, Phot. Res. 127, 49-60, 2016.
  6. D. Abramavicius, L. Valkunas, Role of coherent vibrations in energy transfer and conversion in photosynthetic pigment–protein complexes, Phot. Res. 127, 33-47, 2016.
  7. V. Butkus, H. Dong, G. R. Fleming, D. Abramavicius, L. Valkunas, Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules, J. Phys. Chem. Lett. 7, 277-282, 2016.
  8. A. Gelzinis, D. Abramavicius, J. P. Ogilvie, L. Valkunas, Spectroscopic properties of photosystem II reaction center revisited, J. Chem. Phys. 147, 115102, 2017.
  9. A. Gelzinis, E. Rybakovas, L. Valkunas, Applicability of transfer tensor method for open quantum system dynamics, J. Chem. Phys. 147, 234108, 2017.
  10. O. Rancova, M. Jakučionis, L. Valkunas, D. Abramavicius, Origin of non-Gaussian site energy disorder in molecular aggregates, Chem. Phys. Lett. 674, 120-124, 2017.
  11. K. F. Fox, V. Balevičius, Jr., J. Chmeliov, L. Valkunas, A. V. Ruban, C. D. P. Duffy, The carotenoid pathway: what is important for excitation quenching in plant antenna complexes?, Phys. Chem. Chem. Phys. 19, 22957-22968, 2017.
  12. E. Rybakovas, A. Gelzinis, L. Valkunas, Simulations of absorption and fluorescence lineshapes using the reaction coordinate method, Chem. Phys. 515, 242–251, 2018.
  13. A. Gelzinis, Y. Braver, J. Chmeliov, L. Valkunas, Decay- and evolution-associated spectra of time-resolved fluorescence of LHCII aggregates, Lith. J. Phys. 58, 295-306, 2018.
  14. G. Trinkūnas, J. Chmeliov, Fluctuating antenna model: Applications and prospects, Lith. J. Phys. 58, 379–390, 2018.
  15. Y. A. Dyakov, S. Toliautas, L. I. Trakhtenberg, L. Valkunas, Excited state photodissociation dynamics of 2-, 3-, 4-hydroxyacetophenone: Theoretical study, Chem. Phys. 515, 672-678, 2018.
  16. D. Abramavicius, V. Chorošajev, L. Valkunas, Tracing feed-back driven exciton dynamics in molecular aggregates, Phys. Chem. Chem. Phys. 20, 21225-21240, 2018.
  17. Y. Braver, A. Gelzinis, J. Chmeliov, L. Valkunas, Application of decay- and evolution-associated spectra for molecular systems with spectral shifts or inherent inhomogeneities, Chem. Phys. 525, 110403, 2019.
  18. A. Gelzinis, R. Augulis, V. Butkus, B. Robert, L. Valkunas, Two-dimensional spectroscopy for non-specialists, Biochim. Biophys. Acta 1860, 271-285, 2019.