Quantum mechanics of excitation transport in photosynthetic complexes: a key issues review

Optimal conditions for environment-assisted quantum transport on the fully connected network

We present a theoretical analysis of the efficiency and rate of excitation transport on a network described by a complete graph in which every site is connected to every other. The long-time transport properties are analytically calculated for networks of arbitrary size that are symmetric except for the trapping site, start with a range of initial states, and are subject to dephasing and excitation decay. Conditions for which dephasing increases transport are identified, and optimal conditions are found for various physical parameters. The optimal conditions demonstrate robustness and a convergence of timescales previously observed in the context of light-harvesting complexes.

Phase coherent quasi-particle formation in biological systems

The problem of the origin of canonical and aberrant DNA mutations and the contribution of protons to genetic stability is an essential topic in molecular biology. Based on the empirical results, we reconsidered canonical and tautomeric mutations under the two-fluid model of quantum physics. We assumed that the pressure exerted by protons (H+) in the DNA environment, through changes in pH, could alter the concentration ratio of canonical and tautomeric base pairs, which were found to be different at and beyond the criticality level, respectively. We anticipate that the deviation of the cellular system from a specific (critical) temperature at which dynamic entropy reaches a minimum and a critical pH occurs could result in tautomerization and point mutations.

The influence of a Hamiltonian vibration vs a bath vibration on the 2D electronic spectra of a homodimer

We elucidate the influence of the system–bath boundary placement within an open quantum system, with emphasis on the two-dimensional electronic spectra, through the application of the hierarchical equations of motion formalism for an exciton system. We apply two different models, the Hamiltonian vibration model (HVM) and bath vibration model (BVM), to a monomer and a homodimer. In the HVM, we specifically include the vibronic states in the Hamiltonian capturing vibronic quenching, whereas in the BVM, all vibrational details are contained within the bath and described by an underdamped spectral density. The resultant spectra are analyzed in terms of energetic peak position and thermodynamic broadening precision in order to evaluate the efficacy of the two models. The HVM produces 2D spectra with accurate peak positional information, while the BVM is well suited to modeling dynamic peak broadening. For the monomer, both models produce equivalent spectra in the limit where additional damping associated with the underdamped vibration in the BVM approaches zero. This is supported by analytical results. However, for the homodimer, the BVM spectra are redshifted with respect to the HVM due to an absence of vibronic quenching in the BVM. The computational efficiency of the two models is also discussed in order to inform us of the most appropriate use of each method.

Classification of Coherent Enhancements of Light-Harvesting Processes

Several kinds of coherence have recently been shown to affect the performance of light-harvesting systems, in some cases significantly improving their efficiency. Here, we classify the possible mechanisms of coherent efficiency enhancements, based on the types of coherence that can characterize a light-harvesting system and the types of processes these coherences can affect. We show that enhancements are possible only when coherences and dissipative effects are best described in different bases of states. Our classification allows us to predict a previously unreported coherent enhancement mechanism, where coherence between delocalized eigenstates can be used to localize excitons away from dissipation, thus reducing the rate of recombination and increasing efficiency.

Dynamical disorder and resonance energy transfer: a novel quantum-classical approach

A novel quantum-classical approach demonstrates that dynamic disorder, as induced by a liquid polar solvent, boosts RET efficiency.

Real-Time Propagation TDDFT and Density Analysis for Exciton Coupling Calculations in Large Systems

Photoactive systems are characterized by their capacity to absorb the energy of light and transform it. Usually, more than one chromophore is involved in the light absorption and excitation transport processes in complex systems. Linear-Response Time-Dependent Density Functional (LR-TDDFT) is commonly used to identify excitation energies and transition properties by solving the well-known Casida’s equation for single molecules. However, in practice, LR-TDDFT presents some disadvantages when dealing with multichromophore systems due to the increasing size of the electron–hole pairwise basis required for accurate evaluation of the absorption spectrum. In this work, we extend our local density decomposition method that enables us to disentangle individual contributions into the absorption spectrum to computation of exciton dynamic properties, such as exciton coupling parameters. We derive an analytical expression for the transition density from Real-Time Propagation TDDFT (P-TDDFT) based on Linear Response theorems. We demonstrate the validity of our method to determine transition dipole moments, transition densities, and exciton coupling for systems of increasing complexity. We start from the isolated benzaldehyde molecule, perform a distance analysis for π-stacked dimers, and finally map the exciton coupling for a 14 benzaldehyde cluster.

Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili

The electrically conductive pili of Geobacter sulfurreducens are of both fundamental and practical interest. They facilitate extracellular and interspecies electron transfer (ET) and also provide an electrical interface between living and nonliving systems. We examine the possible mechanisms of G. sulfurreducens electron transfer in regimes ranging from incoherent to coherent transport. For plausible ET parameters, electron transfer in G. sulfurreducens bacterial nanowires mediated only by the protein is predicted to be dominated by incoherent hopping between phenylalanine (Phe) and tyrosine (Tyr) residues that are 3 to 4 Å apart, where Phe residues in the hopping pathways may create delocalized "islands." This mechanism could be accessible in the presence of strong oxidants that are capable of oxidizing Phe and Tyr residues. We also examine the physical requirements needed to sustain biological respiration via nanowires. We find that the hopping regimes with ET rates on the order of 10⁸ s^-1 between Phe islands and Tyr residues, and conductivities on the order of mS/cm, can support ET fluxes that are compatible with cellular respiration rates, although sustaining this delocalization in the heterogeneous protein environment may be challenging. Computed values of fully coherent electron fluxes through the pili are orders of magnitude too low to support microbial respiration. We suggest experimental probes of the transport mechanism based on mutant studies to examine the roles of aromatic amino acids and yet to be identified redox cofactors.

Robust and Fragile Quantum Effects in the Transfer Kinetics of Delocalized Excitons between B850 Units of LH2 Complexes

Aggregates of light harvesting 2 (LH2) complexes form the major exciton-relaying domain in the photosynthetic unit of purple bacteria. Application of a generalized master equation to pairs of the B850 units of LH2 complexes, where excitons predominantly reside, provides quantitative information on how the inter-LH2 exciton transfer depends on the distance, relative rotational angle, and the relative energies of the two LH2s. The distance dependence demonstrates significant enhancement of the rate due to quantum delocalization of excitons, the qualitative nature of which remains robust against the disorder. The angle dependence reflects isotropic nature of exciton transfer, which remains similar for the ensemble of disorder. The variation of the rate on relative excitation energies of LH2 exhibits resonance peaks, which, however, is fragile as the disorder becomes significant. Overall, the average transfer times between two LH2s are estimated to be in the range of 4-25 ps for physically plausible inter-LH2 distances.

Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory

The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.

Vibration-Assisted and Vibration-Hampered Excitonic Quantum Transport

The interplay between excitons and vibrations is considered to be a key factor in determining the exciton-transfer properties in light-harvesting complexes. Here we study this interplay theoretically in a model for exciton transport, composed of two chromophores coupled to an exciton source and sink in the presence of vibrations. We consider two cases that show qualitatively distinct transport features. In the first, the vibrations are global and affect the two chromophores simultaneously. In the second case, the vibrations are localized on each chromophore. For global vibrations, the current exhibits antiresonances as a function of the chromophore energy difference, which are due to exciton-polaron interference. For local vibrations, on the contrary, the currents show tunneling resonances at multiples of the vibration energy. Counterintuitively, both effects increase with increasing temperature. Our results demonstrate that an environment can either assist or hamper exciton transport and is in accord with the current understanding of energy transfer in natural exciton-transfer complexes.

Quantum interference in multi-branched molecules: The exact transfer matrix solutions

We present a transfer matrix formalism for studying quantum interference in a single molecule electronic system with internal branched structures. Based on the Schrödinger equation with the Bethe ansatz and employing Kirchhoff's rule for quantum wires, we derive a general closed-form expression for the transmission and reflection amplitudes of a two-port quantum network. We show that the transport through a molecule with complex internal structures can be reduced to that of a single two-port scattering unit, which contains all the information of the original composite molecule. Our method allows for the calculation of the transmission coefficient for various types of individual molecular modules giving rise to different resonant transport behaviors such as the Breit-Wigner, Fano, and Mach-Zehnder resonances. As an illustration, we first re-derive the transmittance of the Aharonov-Bohm ring, and then we apply our formulation to N identical parity-time (PT)-symmetric potentials, connected in series as well as in parallel. It is shown that the spectral singularities and PT-symmetric transitions of single scattering cells may be observed in coupled systems. Such transitions may occur at the same or distinct values of the critical parameters, depending on the connection modes under which the scattering objects are coupled.

Functional window of the avian compass

The functional window is an experimentally observed property of the avian compass that refers to its selectivity around the geomagnetic-field strength. We show that the simple radical-pair model, using biologically feasible hyperfine parameters, can qualitatively explain the salient features of the avian compass as observed in behavioral experiments: its functional window, as well as disruption of the compass action by radio-frequency fields of specific frequencies. Further, we show that adjustment of the hyperfine parameters can tune the functional window, suggesting a possible mechanism for its observed adaptation to field variation. While these lend support to the radical-pair model, we find that in its simplest form-or even with minor augmentations-it cannot quantitatively explain the observed width of the functional window. This suggests deeper generalization of the model, possibly in terms of more nuclei or more subtle environmental interaction than has been considered hitherto. Finally, we examine a possible biological purpose for the functional window; even assuming evolutionary benefit from radical-pair magnetoreception, it seems likely that the functional window could be just a corollary thereof, imparting no additional advantage.

Plasmonic bio-sensing for the Fenna-Matthews-Olson complex

We study theoretically the bio-sensing capabilities of metal nanowire surface plasmons. As a specific example, we couple the nanowire to specific sites (bacteriochlorophyll) of the Fenna-Matthews-Olson (FMO) photosynthetic pigment protein complex. In this hybrid system, we find that when certain sites of the FMO complex are subject to either the suppression of inter-site transitions or are entirely disconnected from the complex, the resulting variations in the excitation transfer rates through the complex can be monitored through the corresponding changes in the scattering spectra of the incident nanowire surface plasmons. We also find that these changes can be further enhanced by changing the ratio of plasmon-site couplings. The change of the Fano lineshape in the scattering spectra further reveals that “site 5” in the FMO complex plays a distinct role from other sites. Our results provide a feasible way, using single photons, to detect mutation-induced, or bleaching-induced, local defects or modifications of the FMO complex, and allows access to both the local and global properties of the excitation transfer in such systems.

Light Absorption and Energy Transfer in the Antenna Complexes of Photosynthetic Organisms

The process of photosynthesis is initiated by the capture of sunlight by a network of light-absorbing molecules (chromophores), which are also responsible for the subsequent funneling of the excitation energy to the reaction centers. Through evolution, genetic drift, and speciation, photosynthetic organisms have discovered many solutions for light harvesting. In this review, we describe the underlying photophysical principles by which this energy is absorbed, as well as the mechanisms of electronic excitation energy transfer (EET). First, optical properties of the individual pigment chromophores present in light-harvesting antenna complexes are introduced, and then we examine the collective behavior of pigment-pigment and pigment-protein interactions. The description of energy transfer, in particular multichromophoric antenna structures, is shown to vary depending on the spatial and energetic landscape, which dictates the relative coupling strength between constituent pigment molecules. In the latter half of the article, we focus on the light-harvesting complexes of purple bacteria as a model to illustrate the present understanding of the synergetic effects leading to EET optimization of light-harvesting antenna systems while exploring the structure and function of the integral chromophores. We end this review with a brief overview of the energy-transfer dynamics and pathways in the light-harvesting antennas of various photosynthetic organisms.

Quantum Coherence Facilitates Efficient Charge Separation at a MoS2/MoSe2 van der Waals Junction

Two-dimensional transition metal dichalcogenides (MX2, M = Mo, W; X = S, Se) hold great potential in optoelectronics and photovoltaics. To achieve efficient light-to-electricity conversion, electron-hole pairs must dissociate into free charges. Coulomb interaction in MX2 often exceeds the charge transfer driving force, leading one to expect inefficient charge separation at a MX2 heterojunction. Experiments defy the expectation. Using time-domain density functional theory and nonadiabatic (NA) molecular dynamics, we show that quantum coherence and donor-acceptor delocalization facilitate rapid charge transfer at a MoS2/MoSe2 interface. The delocalization is larger for electron than hole, resulting in longer coherence and faster transfer. Stronger NA coupling and higher acceptor state density accelerate electron transfer further. Both electron and hole transfers are subpicosecond, which is in agreement with experiments. The transfers are promoted primarily by the out-of-plane Mo-X modes of the acceptors. Lighter S atoms, compared to Se, create larger NA coupling for electrons than holes. The relatively slow relaxation of the "hot" hole suggests long-distance bandlike transport, observed in organic photovoltaics. The electron-hole recombination is notably longer across the MoS2/MoSe2 interface than in isolated MoS2 and MoSe2, favoring long-lived charge separation. The atomistic, time-domain studies provide valuable insights into excitation dynamics in two-dimensional transition metal dichalcogenides.

Energy transfer cascade in bio-inspired chlorophyll-a/polyacrylamide hydrogel: towards a new class of biomimetic solar cells

Efficient solar energy harvesting in natural photosystem inspired chlorophyll-a/hydrogel based soft, simple system, revealing the effect of coherence-dephasing interpaly.