Recently observed quantum emitters in hexagonal boron nitride (hBN) membranes have a potential fo... more Recently observed quantum emitters in hexagonal boron nitride (hBN) membranes have a potential for achieving high accessibility and controllability thanks to the lower spatial dimension. Moreover, these objects naturally have a high sensitivity to vibrations of the hosting membrane due to its low mass density and high elasticity modulus. Here, we propose and analyze a spin-mechanical system based on color centers in a suspended hBN mechanical resonator. Through group theoretical analyses and ab initio calculation of the electronic and spin properties of such a system, we identify a spin doublet ground state and demonstrate that a spin-motion interaction can be engineered which enables ground state cooling of the mechanical resonator. We also present a toolbox for initialization, rotation, and readout of the defect spin qubit. As a result the proposed setup presents the possibility for studying a wide range of physics. To illustrate its assets, we show that a fast and noise resilient preparation of a multicomponent cat state and a squeezed state of the mechanical resonator is possible; the latter is achieved by realizing the extremely detuned, ultrastrong coupling regime of the Rabi model, where a phonon superradiant phase transition is expected to occur.
The journal of physical chemistry. B, Jan 16, 2017
Temperature-dependent fluctuations of both site energies and electronic couplings are known to af... more Temperature-dependent fluctuations of both site energies and electronic couplings are known to affect the excitation energy transfer in light-harvesting complexes. Environment effects on such fluctuations as well as possible spatial correlations among them are investigated here in the PE545 complex from cryptophyte algae using ensemble-averaged wave packet dynamics to extract the exciton dynamics. This strategy directly uses the time-dependent fluctuations of the system Hamiltonian, as described by quantum mechanics/molecular mechanics calculations performed along a classical MD trajectory. Neither the fluctuations in the couplings nor spatial correlations including cross-correlations between site energies and couplings are found to be important in the exciton dynamics of the complex. This finding does not change if a polarizable embedding is used instead of its electrostatic counterpart. The impact of variations in spectral densities and screening of excitonic couplings based on th...
The journal of physical chemistry letters, Jan 7, 2016
Excitation energy and charge transfer are fundamental processes in biological systems. Because of... more Excitation energy and charge transfer are fundamental processes in biological systems. Because of their quantum nature, the effect of dephasing on these processes is of interest especially when trying to understand their efficiency. Moreover, recent experiments have shown quantum coherences in such systems. As a first step toward a better understanding, we studied the relationship between dephasing time and energy gap fluctuations of the individual molecular subunits. A larger set of molecular simulations has been investigated to shed light on this dependence. This set includes bacterio-chlorophylls in Fenna-Matthews-Olson complexes, the PE545 aggregate, the LH2 complexes, DNA, photolyase, and cryptochromes. For the individual molecular subunits of these aggregates it has been confirmed quantitatively that an inverse proportionality exists between dephasing time and average gap energy fluctuation. However, for entire complexes including the respective intermolecular couplings, such ...
Density functional theory (DFT) calculations have been employed for a systematic study of electro... more Density functional theory (DFT) calculations have been employed for a systematic study of electronic dispersion and morphologic characteristics (length and angle of chemical bonds) of bare and hydrogenated narrow zigzag single walled carbon nanotubes (SWCNTs), d < 7 angstrom. For these narrow tubes, the "band gap" and the bond character show a strong dependence on the diameter of the tubes. Our results show that exo-hydrogenation changes the band gap substantially. The gap shows essential dependence on the coverage of the exo-hydrogenation and increases with decreasing tube diameter. These properties can be useful in sensing and characterising applications. However, endo-hydrogenation in wider tubes occurs mainly by storing H(2) gas molecules inside them and their electronic structure changes slightly whereas for very narrow tubes, there is an interplay between the curvature and chirality effects. The nature of hydrogen adsorption in these cases can be a mixture of the ...
The interest in the phycoerythrin 545 (PE545) photosynthetic antenna system of marine algae and t... more The interest in the phycoerythrin 545 (PE545) photosynthetic antenna system of marine algae and the Fenna-Matthews-Olson (FMO) complex of green sulfur bacteria has drastically increased since long-lived quantum coherences were reported for these complexes. For the PE545 complex, this phenomenon is clearly visible even at ambient temperatures, while for the FMO system it is more prominent at lower temperatures. The key to elucidate the role of the environment in these long-lived quantum effects is the spectral density. Here, we employ molecular dynamics simulations combined with quantum chemistry calculations to study the coupling between the biological environment and the vertical excitation energies of the bilin pigment molecules in PE545 and compare them to prior calculations on the FMO complex. It is found that the overall strength of the resulting spectral densities for the PE545 system is similar to the experiment-based counterpart but also to those in the FMO complex. Molecular analysis, however, reveals that the origin for the spectral densities in the low frequency range, which is most important for excitonic transitions, is entirely different. In the case of FMO, this part of the spectral density is due to environmental fluctuations, while, in case of PE545, it is essentially only due to internal modes of the bilin molecules. This finding sheds new light on possible explanations of the long-lived quantum coherences and that the reasons might actually be different in dissimilar systems.
Plants can safely dissipate excess excitation energy during light harvesting to prevent the forma... more Plants can safely dissipate excess excitation energy during light harvesting to prevent the formation of triplet chlorophyll, which can generate deleterious singlet oxygen. With this regulation, known as non-photochemical quenching
ABSTRACT Long-lived quantum coherences have been shown experimentally in the Fenna–Matthews–Olson... more ABSTRACT Long-lived quantum coherences have been shown experimentally in the Fenna–Matthews–Olson (FMO) complex of green sulfur bacteria as well as in the phycoerythrin 545 (PE545) photosynthetic antenna system of marine algae. A combination of classical molecular dynamics simulations, quantum chemistry and quantum dynamical calculations is employed to determine the excitation transfer dynamics in PE545. One key property of the light-harvesting system concerning the excitation transfer and dephasing phenomena is the spectral density. This quantity is determined from time series of the vertical excitation energies of the aggregate. In the present study we focus on the quantum dynamical simulations using the earlier QM/MM calculations as input. Employing an ensemble-averaged classical path-based wave packet dynamics, the excitation transfer dynamics between the different bilins in the PE545 complex is determined and analyzed. Furthermore, the nature of the environmental fluctuations determining the transfer dynamics is discussed.
Plants can safely dissipate excess excitation energy during light harvesting to prevent the forma... more Plants can safely dissipate excess excitation energy during light harvesting to prevent the formation of triplet chlorophyll, which can generate deleterious singlet oxygen. With this regulation, known as non-photochemical quenching
Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for... more Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion.
The experimental observation of long-lived quantum coherences in the FennaÀMatthewsÀOlson (FMO) l... more The experimental observation of long-lived quantum coherences in the FennaÀMatthewsÀOlson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search of explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings is analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian, linear and two-dimensional spectra are determined. The thus-obtained linear absorption line shape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.
Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex a... more Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex and other photosynthetic complexes have led to theoretical studies searching for an explanation of this unexpected phenomenon. Extending in this regard our own earlier calculations, we performed simulations of the FMO complex in a glycerol-water mixture at 310 K as well as 77 K, matching the conditions of earlier 2D spectroscopic experiments by Engel et al. The calculations, based on an improved quantum procedure employed by us already, yielded spectral densities of each individual pigment of FMO, in water and glycerol-water solvents at ambient temperature that compare well to prior experimental estimates. Due to the slow solvent dynamics at 77 K, the present results strongly indicate the presence of static disorder, i.e., disorder on a time scale beyond that relevant for the construction of spectral densities.
ABSTRACT Density functional theory (DFT) calculations have been employed for a systematic study o... more ABSTRACT Density functional theory (DFT) calculations have been employed for a systematic study of electronic dispersion and morphologic characteristics (length and angle of chemical bonds) of bare and hydrogenated narrow zigzag single walled carbon nanotubes (SWCNTs), d &lt; 7 angstrom. For these narrow tubes, the &quot;band gap&quot; and the bond character show a strong dependence on the diameter of the tubes. Our results show that exo-hydrogenation changes the band gap substantially. The gap shows essential dependence on the coverage of the exo-hydrogenation and increases with decreasing tube diameter. These properties can be useful in sensing and characterising applications. However, endo-hydrogenation in wider tubes occurs mainly by storing H(2) gas molecules inside them and their electronic structure changes slightly whereas for very narrow tubes, there is an interplay between the curvature and chirality effects. The nature of hydrogen adsorption in these cases can be a mixture of the internal C H bonds and H(2) molecules and existence of free atomic hydrogen gas inside the tubes cannot be ruled out. (C) 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.
In many physical, chemical, and biological systems energy and charge transfer processes are of ut... more In many physical, chemical, and biological systems energy and charge transfer processes are of utmost importance. To determine the influence of the environment on these transport processes, equilibrium molecular dynamics simulations become more and more popular. From these simulations, one usually determines the thermal fluctuations of certain energy gaps, which are then either used to perform ensemble-averaged wave packet simulations, also called Ehrenfest dynamics, or to employ a density matrix approach via spectral densities. These two approaches are analyzed through energy gap fluctuations that are generated to correspond to a predetermined spectral density. Subsequently, density matrix and wave packet simulations are compared through population dynamics and absorption spectra for different parameter regimes. Furthermore, a previously proposed approach to enforce the correct long-time behavior in the wave packet simulations is probed and an improvement is proposed.
Recently observed quantum emitters in hexagonal boron nitride (hBN) membranes have a potential fo... more Recently observed quantum emitters in hexagonal boron nitride (hBN) membranes have a potential for achieving high accessibility and controllability thanks to the lower spatial dimension. Moreover, these objects naturally have a high sensitivity to vibrations of the hosting membrane due to its low mass density and high elasticity modulus. Here, we propose and analyze a spin-mechanical system based on color centers in a suspended hBN mechanical resonator. Through group theoretical analyses and ab initio calculation of the electronic and spin properties of such a system, we identify a spin doublet ground state and demonstrate that a spin-motion interaction can be engineered which enables ground state cooling of the mechanical resonator. We also present a toolbox for initialization, rotation, and readout of the defect spin qubit. As a result the proposed setup presents the possibility for studying a wide range of physics. To illustrate its assets, we show that a fast and noise resilient preparation of a multicomponent cat state and a squeezed state of the mechanical resonator is possible; the latter is achieved by realizing the extremely detuned, ultrastrong coupling regime of the Rabi model, where a phonon superradiant phase transition is expected to occur.
The journal of physical chemistry. B, Jan 16, 2017
Temperature-dependent fluctuations of both site energies and electronic couplings are known to af... more Temperature-dependent fluctuations of both site energies and electronic couplings are known to affect the excitation energy transfer in light-harvesting complexes. Environment effects on such fluctuations as well as possible spatial correlations among them are investigated here in the PE545 complex from cryptophyte algae using ensemble-averaged wave packet dynamics to extract the exciton dynamics. This strategy directly uses the time-dependent fluctuations of the system Hamiltonian, as described by quantum mechanics/molecular mechanics calculations performed along a classical MD trajectory. Neither the fluctuations in the couplings nor spatial correlations including cross-correlations between site energies and couplings are found to be important in the exciton dynamics of the complex. This finding does not change if a polarizable embedding is used instead of its electrostatic counterpart. The impact of variations in spectral densities and screening of excitonic couplings based on th...
The journal of physical chemistry letters, Jan 7, 2016
Excitation energy and charge transfer are fundamental processes in biological systems. Because of... more Excitation energy and charge transfer are fundamental processes in biological systems. Because of their quantum nature, the effect of dephasing on these processes is of interest especially when trying to understand their efficiency. Moreover, recent experiments have shown quantum coherences in such systems. As a first step toward a better understanding, we studied the relationship between dephasing time and energy gap fluctuations of the individual molecular subunits. A larger set of molecular simulations has been investigated to shed light on this dependence. This set includes bacterio-chlorophylls in Fenna-Matthews-Olson complexes, the PE545 aggregate, the LH2 complexes, DNA, photolyase, and cryptochromes. For the individual molecular subunits of these aggregates it has been confirmed quantitatively that an inverse proportionality exists between dephasing time and average gap energy fluctuation. However, for entire complexes including the respective intermolecular couplings, such ...
Density functional theory (DFT) calculations have been employed for a systematic study of electro... more Density functional theory (DFT) calculations have been employed for a systematic study of electronic dispersion and morphologic characteristics (length and angle of chemical bonds) of bare and hydrogenated narrow zigzag single walled carbon nanotubes (SWCNTs), d < 7 angstrom. For these narrow tubes, the "band gap" and the bond character show a strong dependence on the diameter of the tubes. Our results show that exo-hydrogenation changes the band gap substantially. The gap shows essential dependence on the coverage of the exo-hydrogenation and increases with decreasing tube diameter. These properties can be useful in sensing and characterising applications. However, endo-hydrogenation in wider tubes occurs mainly by storing H(2) gas molecules inside them and their electronic structure changes slightly whereas for very narrow tubes, there is an interplay between the curvature and chirality effects. The nature of hydrogen adsorption in these cases can be a mixture of the ...
The interest in the phycoerythrin 545 (PE545) photosynthetic antenna system of marine algae and t... more The interest in the phycoerythrin 545 (PE545) photosynthetic antenna system of marine algae and the Fenna-Matthews-Olson (FMO) complex of green sulfur bacteria has drastically increased since long-lived quantum coherences were reported for these complexes. For the PE545 complex, this phenomenon is clearly visible even at ambient temperatures, while for the FMO system it is more prominent at lower temperatures. The key to elucidate the role of the environment in these long-lived quantum effects is the spectral density. Here, we employ molecular dynamics simulations combined with quantum chemistry calculations to study the coupling between the biological environment and the vertical excitation energies of the bilin pigment molecules in PE545 and compare them to prior calculations on the FMO complex. It is found that the overall strength of the resulting spectral densities for the PE545 system is similar to the experiment-based counterpart but also to those in the FMO complex. Molecular analysis, however, reveals that the origin for the spectral densities in the low frequency range, which is most important for excitonic transitions, is entirely different. In the case of FMO, this part of the spectral density is due to environmental fluctuations, while, in case of PE545, it is essentially only due to internal modes of the bilin molecules. This finding sheds new light on possible explanations of the long-lived quantum coherences and that the reasons might actually be different in dissimilar systems.
Plants can safely dissipate excess excitation energy during light harvesting to prevent the forma... more Plants can safely dissipate excess excitation energy during light harvesting to prevent the formation of triplet chlorophyll, which can generate deleterious singlet oxygen. With this regulation, known as non-photochemical quenching
ABSTRACT Long-lived quantum coherences have been shown experimentally in the Fenna–Matthews–Olson... more ABSTRACT Long-lived quantum coherences have been shown experimentally in the Fenna–Matthews–Olson (FMO) complex of green sulfur bacteria as well as in the phycoerythrin 545 (PE545) photosynthetic antenna system of marine algae. A combination of classical molecular dynamics simulations, quantum chemistry and quantum dynamical calculations is employed to determine the excitation transfer dynamics in PE545. One key property of the light-harvesting system concerning the excitation transfer and dephasing phenomena is the spectral density. This quantity is determined from time series of the vertical excitation energies of the aggregate. In the present study we focus on the quantum dynamical simulations using the earlier QM/MM calculations as input. Employing an ensemble-averaged classical path-based wave packet dynamics, the excitation transfer dynamics between the different bilins in the PE545 complex is determined and analyzed. Furthermore, the nature of the environmental fluctuations determining the transfer dynamics is discussed.
Plants can safely dissipate excess excitation energy during light harvesting to prevent the forma... more Plants can safely dissipate excess excitation energy during light harvesting to prevent the formation of triplet chlorophyll, which can generate deleterious singlet oxygen. With this regulation, known as non-photochemical quenching
Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for... more Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion.
The experimental observation of long-lived quantum coherences in the FennaÀMatthewsÀOlson (FMO) l... more The experimental observation of long-lived quantum coherences in the FennaÀMatthewsÀOlson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search of explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings is analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian, linear and two-dimensional spectra are determined. The thus-obtained linear absorption line shape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.
Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex a... more Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex and other photosynthetic complexes have led to theoretical studies searching for an explanation of this unexpected phenomenon. Extending in this regard our own earlier calculations, we performed simulations of the FMO complex in a glycerol-water mixture at 310 K as well as 77 K, matching the conditions of earlier 2D spectroscopic experiments by Engel et al. The calculations, based on an improved quantum procedure employed by us already, yielded spectral densities of each individual pigment of FMO, in water and glycerol-water solvents at ambient temperature that compare well to prior experimental estimates. Due to the slow solvent dynamics at 77 K, the present results strongly indicate the presence of static disorder, i.e., disorder on a time scale beyond that relevant for the construction of spectral densities.
ABSTRACT Density functional theory (DFT) calculations have been employed for a systematic study o... more ABSTRACT Density functional theory (DFT) calculations have been employed for a systematic study of electronic dispersion and morphologic characteristics (length and angle of chemical bonds) of bare and hydrogenated narrow zigzag single walled carbon nanotubes (SWCNTs), d &lt; 7 angstrom. For these narrow tubes, the &quot;band gap&quot; and the bond character show a strong dependence on the diameter of the tubes. Our results show that exo-hydrogenation changes the band gap substantially. The gap shows essential dependence on the coverage of the exo-hydrogenation and increases with decreasing tube diameter. These properties can be useful in sensing and characterising applications. However, endo-hydrogenation in wider tubes occurs mainly by storing H(2) gas molecules inside them and their electronic structure changes slightly whereas for very narrow tubes, there is an interplay between the curvature and chirality effects. The nature of hydrogen adsorption in these cases can be a mixture of the internal C H bonds and H(2) molecules and existence of free atomic hydrogen gas inside the tubes cannot be ruled out. (C) 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.
In many physical, chemical, and biological systems energy and charge transfer processes are of ut... more In many physical, chemical, and biological systems energy and charge transfer processes are of utmost importance. To determine the influence of the environment on these transport processes, equilibrium molecular dynamics simulations become more and more popular. From these simulations, one usually determines the thermal fluctuations of certain energy gaps, which are then either used to perform ensemble-averaged wave packet simulations, also called Ehrenfest dynamics, or to employ a density matrix approach via spectral densities. These two approaches are analyzed through energy gap fluctuations that are generated to correspond to a predetermined spectral density. Subsequently, density matrix and wave packet simulations are compared through population dynamics and absorption spectra for different parameter regimes. Furthermore, a previously proposed approach to enforce the correct long-time behavior in the wave packet simulations is probed and an improvement is proposed.
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Papers by Mortaza Aghtar