arXiv subjects

Tomáš Mančal

Publications and source records attributed to Tomáš Mančal.

At least 19 recordsLinked to original sources

arXiv2026

Photo-thermal 2D spectroscopy: a different type of action

Advances in multidimensional spectroscopy have seen the rise of action detection, where coherent response is encoded into incoherent signals. These are typically proportional to the excited-state population, an example in 2D electronic spectroscopy (2DES) is fluorescence-detected 2DES (F-2DES), and in 2D infrared (2DIR) tag-loss 2DIR (TL-2DIR). Very recently, a new type of photo-thermal action signal has been introduced in 2DIR, detecting the generated heat by atomic force microscopy-based 2DIR (AFM-2DIR). We present a unified theoretical framework for population- and heat-based 2D spectroscopy, highlighting their complementary features. In the infrared, TL-2DIR reflects the system linear response, whereas AFM-2DIR produces spectra resembling conventional 2DIR, with sensitivity to anharmonicity and mode coupling. Our model reproduces key experimental AFM-2DIR features, confirming measurement in a highly nonlinear regime. Extending photothermal detection to electronic spectroscopy, we compare F-2DES with proposed photo-thermal 2DES (PT-2DES). PT-2DES closely resembles conventional 2DES, while enjoying the advantages of action detection.

physics.chem-ph↗

arXiv2026

Förster resonance energy transfer with transient coherent effects

We formulate the weak intramolecular coupling Förster resonance energy transfer theory in a form suitable for calculating ultrafast nonlinear response of molecular systems. We introduce a formally exact time-dependent factorization of the molecular statistical operator into the system and bath components. Combining this factorization with unperturbed environment evolution, we generalize the traditional Förster master equation for the state population probabilities into a complete master equation for the system's reduced statistical operator. The traditional Förster theory applies in the limit where the intermolecular coupling is weak, and the system-bath coupling is strong. Our technique of derivation explicitly leads to a time non-local Förster type master equation, which remains valid also in the limit of vanishing system-bath coupling. The theory predicts a rapid initial coherent evolution of populations arising from a transient initial coherence-dependent term, which induces a slippage of the initial condition that persists during subsequent rate-controlled transfer. Comparison with exact numerical results confirms the clear improvement of the present generalization over earlier formulations of the Förster theory and delineates its range of validity.

physics.chem-ph↗

arXiv2024

Self-consistent approach to the dynamics of excitation energy transfer in multichromophoric systems

Computationally tractable and reliable, albeit approximate, methods for studying exciton transport in molecular aggregates immersed in structured bosonic environments have been actively developed. Going beyond the lowest-order (Born) approximation for the memory kernel of the quantum master equation typically results in complicated and possibly divergent expressions. Starting from the memory kernel in the Born approximation, and recognizing the quantum master equation as the Dyson equation of Green's functions theory, we formulate the self-consistent Born approximation to resum the memory-kernel perturbation series in powers of the exciton--environment interaction. Our formulation is in the Liouville space and frequency domain and handles arbitrary exciton--environment spectral densities. In a molecular dimer coupled to an overdamped oscillator environment, we conclude that the self-consistent cycle significantly improves the Born-approximation energy-transfer dynamics. The dynamics in the self-consistent Born approximation agree well with the solutions of hierarchical equations of motion over a wide range of parameters, including the most challenging regimes of strong exciton--environment interactions, slow environments, and low temperatures. This is rationalized by the analytical considerations of coherence-dephasing dynamics in the pure-dephasing model. We find that the self-consistent Born approximation is good (poor) at describing energy transfer modulated by an underdamped vibration resonant (off-resonant) with the exciton energy gap. Nevertheless, it reasonably describes exciton dynamics in the seven-site model of the Fenna--Matthews--Olson complex in a realistic environment comprising both an overdamped continuum and underdamped vibrations.

physics.chem-ph↗

arXiv2022

Accuracy of approximate methods for the calculation of absorption-type linear spectra with a complex system-bath coupling

The accuracy of approximate methods for calculating linear optical spectra depends on many variables. In this study, we fix most of these parameters to typical values found in photosynthetic light-harvesting complexes of plants and determine the accuracy of approximate spectra with respect to exact calculation as a function of the energy gap and interpigment coupling in a pigment dimer. We use a spectral density with the first eight intramolecular modes of chlorophyll a and include inhomogeneous disorder for the calculation of spectra. We compare the accuracy of absorption, linear dichroism, and circular dichroism spectra calculated using the Full Cumulant Expansion (FCE), coherent time-dependent Redfield (ctR), and time-independent Redfield and modified Redfield methods. As a reference we use spectra calculated with the Exact Stochastic Path Integral Evaluation method. We find the FCE method to be the most accurate for the calculation of all spectra. The ctR method performs well for the qualitative calculation of absorption and linear dichroism spectra when pigments are moderately coupled ($\sim 15\text{ cm}^{-1}$), but ctR spectra may differ significantly from exact spectra when strong interpigment coupling ($\sim 100\text{ cm}^{-1}$) is present. The dependence of the quality of Redfield and modified Redfield spectra on molecular parameters is similar, and these methods almost always perform worse than ctR, especially when the interpigment coupling is strong or the excitonic energy gap is small (for a given coupling). The accuracy of approximate spectra is not affected by resonance between the excitonic energy gap and intramolecular modes when realistic inhomogeneous disorder is included.

physics.chem-ph↗

arXiv2021

Translation of Werner Heisenberg's Paper "Quantum-Theoretical Reinterpretation of Kinematic and Mechanical Relations" Zeitschrift für Physik 33, 1925, 879-893 into Czech language

To facilitate teaching of quantum mechanics on undergraduate and even advanced secondary school levels, we present an unabridged translation of the original German text of the famous Werner Heisenberg's breakthrough paper of 1925 into Czech language. While the paper introduces fundamentally new concepts into mechanics, and it contains a relatively large number of equations, its conceptual side is surprisingly lightweight when it comes to the use of advanced mathematics. The discussions contained in its Section 1 allow students of quantum mechanics to contemplate the reasons for the inadequacy of classical kinematic concepts in the micro-world. Understanding of the kinematic transition from real valued functions to complex valued "matrices", which is the central point of the paper, can be reached with relatively elementary mathematics. Translations of the Heisenberg's work into languages other than English provide a unique opportunity to introduce the great scientific concepts of quantum mechanics first hand to a broader audience of students who have yet to reach proficiency in the current scientific lingua franca. The present translation is equipped with footnotes explaining the notation, identifying several typos and pointing out sudden changes in notation in the original paper.

physics.ed-ph↗

arXiv2021

Hidden Vibronic and Excitonic Structure and Vibronic Coherence Transfer in the Bacterial Reaction Center

We report two-dimensional electronic spectroscopy (2DES) experiments on the bacterial reaction center (BRC) from purple bacteria, revealing hidden excitonic and vibronic structure. Through analysis of the coherent dynamics of the BRC we resolve specific coherent signatures that allow us to definitively assign the upper exciton energy of the "special pair." This assignment is supported by simulations of coherent dynamics of a reduced excitonic model of the BRC. The simulations also identify nonsecular vibronic coherence transfer processes neglected in standard models of photosynthetic energy transfer and charge separation. In addition, the coherent dynamics reveal multiple quasi-resonances between key intramolecular pigment vibrations and excited state energy gaps in the BRC. The functional significance of such electronic-vibrational resonances for photosynthetic energy transfer and charge separation remains an open question.

physics.chem-ph↗

arXiv2020

Exact description of excitonic dynamics in molecular aggregates weakly driven by light

We present a rigorous theoretical description of excitonic dynamics in molecular light-harvesting aggregates photoexcited by weak-intensity radiation of arbitrary properties. While the interaction with light is included up to the second order, the treatment of the excitation-environment coupling is exact and results in an exact expression for the reduced excitonic density matrix that is manifestly related to the spectroscopic picture of the photoexcitation process. This expression takes fully into account the environmental reorganization processes triggered by the two interactions with light. This is particularly important for slow environments and/or strong excitation-environment coupling. Within the exponential decomposition scheme, we demonstrate how our result can be recast as the hierarchy of equations of motion (HEOM) that explicitly and consistently includes the photoexcitation step. We analytically describe the environmental reorganization dynamics triggered by a delta-like excitation of a single chromophore, and demonstrate how our HEOM, in appropriate limits, reduces to the Redfield equations comprising a pulsed photoexcitation and the nonequilibrium Foerster theory. We also discuss the relation of our formalism to the combined Born-Markov-HEOM approaches in the case of excitation by thermal light.

physics.chem-ph↗

arXiv2020

Nonequilibrium steady-state picture of incoherent light-induced excitation harvesting

We formulate a comprehensive theoretical description of excitation harvesting in molecular aggregates photoexcited by weak incoherent radiation. An efficient numerical scheme that respects the continuity equation for excitation fluxes is developed to compute the nonequilibrium steady state (NESS) arising from the interplay between excitation generation, excitation relaxation, dephasing, trapping at the load, and recombination. The NESS is most conveniently described in the so-called preferred basis in which the steady-state excitonic density matrix is diagonal. The NESS properties are examined by relating the preferred-basis description to the descriptions in the site or excitonic bases. Focusing on a model photosynthetic dimer, we find that the NESS in the limit of long trapping time is quite similar to the excited-state equilibrium in which the stationary coherences originate from the excitation-environment entanglement. For shorter trapping times, we demonstrate how the properties of the NESS can be extracted from the time-dependent description of an incoherently driven but unloaded dimer. This relation between stationary and time-dependent pictures is valid, provided that the trapping time is longer than the decay time of dynamic coherences accessible in femtosecond spectroscopy experiments.

physics.chem-ph↗

arXiv2020

Plasmonic Quantum Yield Enhancement of a Single Molecule Near a Nanoegg

We investigate the impact of the dipole-active modes formed via the mode-mixing of the dipole mode with higher-order surface plasmon modes of a nanoegg on the radiative decay rate and quantum yield of an excited molecule near the nanoegg. The Purcell factor, rate of power dissipation by the emitter, antenna efficiency of the nanoegg, as well as quantum yield enhancement of the emitter, were studied using the quasistatic approximation and the semiclassical theory of radiation, following the Gersten-Nitzan and Ford-Weber approaches. Compared to the concentric nanoshell, we show that the dielectric core-metallic shell nanoegg is a more efficient plasmonic nanoantenna for radiative decay rate enhancement of single emitters. The quantum yield of the emitter was found to be more enhanced near the nanoshell, while its emission rate was found to be more enhanced near the nanoegg.

physics.optics↗

arXiv2019

Energy Transfer Times in Fluorographene-based Biomimetic Light Harvesting Antennae

It has been demonstrated earlier that graphene-like defects on fluorographene can act as molecules in biomimetic molecular light-harvesting antennae. In competition with radiative and non-radiative losses, transfer time of excitations in an antenna measures its performance. We report on the optimal conditions for excitation energy transfer in artificial antennae built from selected types of fluorographene defects. The excitation transfer dynamics is calculated based on the Frenkel exciton model using hierarchical equations of motion for different values of temperature, system-environment reorganization energy and bath correlation time to study a possible range of parameters pertaining to the fluorographene material. We also study possible energy funnelling in the third dimension for two parallel fluorographene sheets with defects. We conclude that the strength of system-environment interaction is more important for the efficient energy funnelling in our proposed material than a precise control over the structure of artificial antennae.

physics.chem-ph↗

arXiv2019

Localized Surface Plasmon Resonances of Simple Tunable Plasmonic Nanostructures

We derive and present systematic relationships between the analytical formulas for calculation of the localized surface plasmon resonances (LSPR) of some plasmonic nano-structures which we have categorized as simple. These relationships, including some new formulas, are summarized in a tree diagram which highlights the core-shell plasmons as the generators of solid and cavity plasmons. In addition, we show that the LSPR of complex structures can be reduced to that of simpler ones, using the LSPR of a nanorice as a case study, in the dipole limit. All the formulas were derived using a combination of the Drude model, the Rayleigh approximation, and the Fröhlich condition. The formulas are handy and they are in good agreement with the results of the plasmon hybridization theory. The formulas also account for dielectric effects, which provide versatility in the tuning of the LSPR of the nanostructures. A simplified model of plasmon hybridization is presented, allowing us to investigate the weak-coupling regimes of solid and cavity plasmons in the core-shell nanostructures we have studied.

physics.optics↗

arXiv2018

Role of enviromental dynamic polarizability in static excited state properties of embedded molecular systems: Application to disordered fluorographene systems

We present an extension of the standard polarizable quantum mechanic/molecular mechanics (QM/MM) approach for treating environmental effects on excited state properties of embedded systems. A quantum polarizable atom model is derived from a full quantum description of the environment using perturbation theory for the system-environment coupling. Our model provides a more general description of the environment, including frequency dependent atomic polarizabilities, without loss of computational simplicity of the QM/MM approach. The classical polarizable atom description used in polarizable QM/MM approach can be obtained as a limiting case of the present model. This enables us to pinpoint approximations and assumptions about the system inherent to classical polarizable atom description of the environment. We apply our method to fluorographene (FG) based systems to investigate effects of the FG sheet on excited state properties of impurities on the FG surface. Comparison to full quantum chemistry calculations and to the standard polarizable QM/MM approach on disordered fluorograhene clusters reveals the importance of frequency dependence of atomic polarizabilities for the proper treatment of the effects of the environment on both the transition energy shifts and the interaction energies.

physics.chem-ph↗

arXiv2018

Geometric dependencies of vibronically mediated excitation transfer in rylene dyads

We study the excitation transfer in various geometric arrangements of rylene dimers using absorption, fluorescence and transient absorption spectra. Polarization and detection frequency dependencies of transient absorption track the interplay of transfer and vibrational relaxation within the dyads. We have resolved microscopic parametrization of intermolecular coupling between rylenes and reproduced transport data. Dynamical sampling of molecular geometries captures thermal fluctuations for Quantum Chemical estimate of couplings for orthogonally arranged dyad, where static estimates vanish and normal mode analysis of fluctuations underestimates them by an order of magnitude. Nonperturbative accounts for the modulation of transport by strongly coupled anharmonic vibrational modes is provided by a vibronic dimer model. Vibronic dynamics is demonstrated to cover both the Förster transport regime of orthogonally arranged dyads and the strong coupling regime of parallel chromophores and allows us to model signal variations along the detection frequency.

physics.chem-ph↗

arXiv2018

Treatment of Herzberg-Teller and non-Condon effects in optical spectra with Hierarchical Equations of Motion

We derive a Hierarchical Equations of Motion (HEOM) description of nonadiabatic Herzberg-Teller type coupling effects and of non-Condon effects in a system of electronic transitions interacting with intra- and inter-molecular vibrational modes. We point out analogies between the auxiliary density operators (ADOs) of the hierarchy and the terms arising from explicit description of the vibrational modes in the Hamiltonian. In comparison with the standard formulation of HEOM, our equations contain additional connections between ADOs in the hierarchy scheme, which account for the dependence of the nonadiabatic coupling elements on the vibrational coordinates. We compare absorption spectra calculated with our HEOM methodology and with explicit treatment of vibrational DOF for a dimer system in the strong resonance coupling regime. Furthermore, we show that for sufficiently strong excitonic coupling, the corresponding effects in linear absorption spectra of vibronic dimers can be captured very well by the concept of effective Huang-Rhys factors.

physics.chem-ph↗

arXiv2018

Signatures of Exciton Delocalization and Exciton-Exciton Annihilation in Fluorescence-Detected Two-Dimensional Coherent Spectroscopy

We present calculations of the fluorescence-detected coherent two-dimensional (F-2DES) spectra of a molecular heterodimer. We compare how the F-2DES technique differs from the standard coherently detected two-dimensional (2DES) spectroscopy in measuring exciton delocalization. We analyze which processes contribute to cross-peaks in the zero-waiting-time spectra obtained by the two methods. Based strictly on time-dependent perturbation theory, we study how in both methods varying degree of cancellation between perturbative contributions gives rise to cross-peaks, and identify exciton annihilation and exciton relaxation contributions to the cross-peak in the zero-waiting-time F-2DES. We propose that time-gated fluorescence detection can be used to isolate the annihilation contribution to F-2DES both to retrieve information equivalent to 2DES spectroscopy and to study annihilation contribution itself.

physics.chem-ph↗

arXiv2018

Fluorographene with Impurities as a Biomimetic Light-Harvesting Medium

We investigate the prospect of using a two-dimensional material, fluorographene, to mimic light-harvesting function of natural photosynthetic antennae. We show by quantum chemical calculations that isles of graphene in a fluorographene sheet can act as quasi-molecules similar to natural pigments from which structures similar in function to photosynthetic antennae can be built. The graphene isles retain enough identity so that they can be used as building blocks to which intuitive design principles of natural photosynthetic antennae can be applied. We examine excited state properties, stability and interactions of these building blocks. Constraints put on the antenna structure by the two-dimensionality of the material as well as the discrete nature of fluorographene sheet are studied. We construct a hypothetical energetic funnel out of two types of quasi-molecules to show how a limited number of building blocks can be arranged to bridge the energy gap and spatial separation in excitation energy transfer. Energy transfer rates for a wide range of the system-environment interaction strengths are predicted. We conclude that conditions for the near unity quantum efficiency of energy transfer are likely to be fulfilled in fluorographene with controlled arrangement of quasi-molecules.

physics.chem-ph↗

arXiv2015

Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.

physics.bio-ph↗

arXiv2015

Ultrafast Energy Relaxation in Single Light-Harvesting Complexes

Energy relaxation in light-harvesting complexes has been extensively studied by various ultrafast spectroscopic techniques, the fastest processes being in the sub-100 fs range. At the same time much slower dynamics have been observed in individual complexes by single-molecule fluorescence spectroscopy (SMS). In this work we employ a pump-probe type SMS technique to observe the ultrafast energy relaxation in single light-harvesting complexes LH2 of purple bacteria. After excitation at 800 nm, the measured relaxation time distribution of multiple complexes has a peak at 95 fs and is asymmetric, with a tail at slower relaxation times. When tuning the excitation wavelength, the distribution changes in both its shape and position. The observed behaviour agrees with what is to be expected from the LH2 excited states structure. As we show by a Redfield theory calculation of the relaxation times, the distribution shape corresponds to the expected effect of Gaussian disorder of the pigment transition energies. By repeatedly measuring few individual complexes for minutes, we find that complexes sample the relaxation time distribution on a timescale of seconds. Furthermore, by comparing the distribution from three long-lived complexes with the whole ensemble, we demonstrate that the ensemble can be considered ergodic. Our findings thus agree with the commonly used notion of an ensemble of identical LH2 complexes experiencing slow random fluctuations.

physics.bio-ph↗