Machine Learning Optimization of Non-Kasha Behavior and of Transient Dynamics in Model Retinal Isomerization.

Designing a model of retinal isomerization in rhodopsin, the first step in vision, that accounts for both experimental transient and stationary state observables is challenging. Here, multiobjective Bayesian optimization is employed to refine the parameters of a minimal two-state-two-mode () model describing the photoisomerization of retinal in rhodopsin. The optimized retinal model predicts excitation wavelength-dependent fluorescence spectra that closely align with experimentally observed non-Kasha behavior in the nonequilibrium steady state.

Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes.

Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.

Coherent Spatial Control of Wave Packet Dynamics on Quantum Lattices.

Quantum lattices are pivotal in the burgeoning fields of quantum materials and information science. Novel experimental techniques allow the preparation and monitoring of wave packet dynamics on quantum lattices with high spatiotemporal resolution. We present an analytical study of wave packet diffusivity and diffusion length on tight-binding quantum lattices subject to stochastic noise.

Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria.

In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps.

Electronic-Vibrational Resonance Does Not Significantly Alter Steady-State Transport in Natural Light-Harvesting Systems.

Oscillations in time-dependent two-dimensional electronic spectra appear as evidence of quantum coherence in light-harvesting systems related to electronic-vibrational resonant interactions. Nature, however, takes place in a non-equilibrium steady-state; therefore, the relevance of these arguments to the natural process is unclear. Here, we examine the role of intramolecular vibrations in the non-equilibrium steady-state of photosynthetic dimers in the natural scenario of incoherent light excitation.

Steady State Photoisomerization Quantum Yield of Model Rhodopsin: Insights from Wavepacket Dynamics?

We simulate the nonequilibrium steady state photoisomerization of retinal chromophore in rhodopsin on the basis of a two-state, two-mode model coupled to a thermal environment. By analyzing the systematic trends within an inhomogeneously broadened ensemble of systems, we find that the steady state reaction quantum yield (QY) correlates strongly with the excess energy above the crossing point of the system, in agreement with the prediction of the short-time dynamical wavepacket picture. However, the nontrivial dependence of the QY on the system-environment interaction indicates that a pure dynamical picture is insufficient and that environment-induced partial internal energy redistribution takes place before the reaction concludes.

Multi-objective optimization for retinal photoisomerization models with respect to experimental observables.

The fitting of physical models is often done only using a single target observable. However, when multiple targets are considered, the fitting procedure becomes cumbersome, there being no easy way to quantify the robustness of the model for all different observables. Here, we illustrate that one can jointly search for the best model for each desired observable through multi-objective optimization.

Universal Scalings in Two-Dimensional Anisotropic Dipolar Excitonic Systems.

Low-dimensional excitonic materials have inspired much interest owing to their novel physical and technological prospects. In particular, those with strong in-plane anisotropy are among the most intriguing but short of general analyses. We establish the universal functional form of the anisotropic dispersion in the small k limit for 2D dipolar excitonic systems.

Extreme Parametric Sensitivity in the Steady-State Photoisomerization of Two-Dimensional Model Rhodopsin.

We computationally studied the photoisomerization reaction of the retinal chromophore in rhodopsin using a two-state two-mode model coupled to thermal baths. Reaction quantum yields at the steady state (10 ps and beyond) were found to be considerably different than their transient values, suggesting a weak correlation between transient and steady-state dynamics in these systems. Significantly, the steady-state quantum yield was highly sensitive to minute changes in system parameters, while transient dynamics was nearly unaffected.

Stochastically Realized Observables for Excitonic Molecular Aggregates.

We show that a stochastic approach enables calculations of the optical properties of large 2-dimensional and nanotubular excitonic molecular aggregates. Previous studies of such systems relied on numerically diagonalizing the dense and disordered Frenkel Hamiltonian, which scales approximately as for dye molecules. Our approach scales much more efficiently as , enabling quick study of systems with a million of coupled molecules on the micrometer size scale.

LH1-RC light-harvesting photocycle under realistic light-matter conditions.

Quantum master equations are used to simulate the photocycle of the light-harvesting complex 1 (LH1) and the associated reaction center (RC) in purple bacteria excited with natural incoherent light. The influence of the radiation and protein environments and the full photocycle of the complexes, including the charge separation and RC recovery processes, are taken into account. Particular emphasis is placed on the steady state excitation energy transfer rate between the LH1 and the RC and the steady state dependence on the light intensity.

Photochemical Control of Exciton Superradiance in Light-Harvesting Nanotubes.

Photosynthetic antennae and organic electronic materials use topological, structural, and molecular control of delocalized excitons to enhance and direct energy transfer. Interactions between the transition dipoles of individual chromophore units allow for coherent delocalization across multiple molecular sites. This delocalization, for specific geometries, greatly enhances the transition dipole moment of the lowest energy excitonic state relative to the chromophore and increases its radiative rate, a phenomenon known as superradiance.

Quantum Diffusion on Molecular Tubes: Universal Scaling of the 1D to 2D Transition.

The transport properties of disordered systems are known to depend critically on dimensionality. We study the diffusion coefficient of a quantum particle confined to a lattice on the surface of a tube, where it scales between the 1D and 2D limits. It is found that the scaling relation is universal and independent of the temperature, disorder, and noise parameters, and the essential order parameter is the ratio between the localization length in 2D and the circumference of the tube.

Excitonic effects from geometric order and disorder explain broadband optical absorption in eumelanin.

Eumelanin is a ubiquitous biological pigment, and the origin of its broadband absorption spectrum has long been a topic of scientific debate. Here, we report a first-principles computational investigation to explain its broadband absorption feature. These computations are complemented by experimental results showing a broadening of the absorption spectra of dopamine solutions upon their oxidation.

Scaling relations and optimization of excitonic energy transfer rates between one-dimensional molecular aggregates.

We theoretically study the distance, chain length, and temperature dependence of the electronic couplings as well as the excitonic energy transfer rates between one-dimensional (1D) chromophore aggregates. In addition to the well-known geometry dependent factor that leads to the deviation from Förster’s classic R(DA)(–6) scaling on the donor–acceptor separation, nonmonotonic dependence on aggregate size and the breakdown of far-field dipole selection rules are also investigated in detail and compared to prior calculations. Our analysis provides a simple, unifying framework to bridge the results of the ground state electronic couplings at low temperatures and those from the classical rate-summation at high temperatures.

Optimal fold symmetry of LH2 rings on a photosynthetic membrane.

An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a hexagonal lattice and establish two related mechanisms for the promotion of maximum excitation energy transfer (EET). (i) For certain fold numbers, there exist optimal basis cells with rotational symmetry, extendable to the entire lattice for the global optimization of the EET network.

Hypothetical toroidal, cylindrical, and helical analogs of C60.

Toroidal, cylindrical, and helical analogs of C(60) buckyball are theoretically constructed and analyzed. In these structures, pentagons and heptagons are separated compactly by hexagons in analogy to pentagons in C(60) and heptagons in C(168) proposed by Vanderbilt and Tersoff (1992) [2]. Specifically, all nonhexagons therein are surrounded by hexagons and hexagons are surrounded alternatively by hexagons and nonhexagons, i.

Dual space approach to the classification of toroidal carbon nanotubes.

We apply the dual space approach to the classification of toroidal carbon nanotubes. We show that the realizations of most of the geometric manipulations described in the literature become explicit in the dual space of the original molecular graph. In particular, dual graph can be easily constructed on a rectangular strip in the parametric plane of the torus.

Systematics of high-genus fullerenes.

In this article, we present a systematic way to classify a family of high-genus fullerenes (HGFs) by decomposing them into two types of necklike structures, which are the negatively curved parts of parent toroidal carbon nanotubes. By replacing the faces of a uniform polyhedron with these necks, an HGF polyhedron corresponding to the vertex configuration of the polyhedron can be obtained. HGF polyhedra including tetrahedron, cube, octahedron, dodecahedron, icosahedron, and truncated icosahedron are proposed under the same construction scheme, which contains nonhexagons other than heptagons.

Generalized classification scheme of toroidal and helical carbon nanotubes.

In this study, we develop a generalized classification scheme for toroidal (TCNT) and helical carbon nanotubes (HCNT) containing both pentagons and heptagons simultaneously. We show that a particular class of TCNTs with n-fold rotational symmetry and well-defined latitude coordinates can be uniquely characterized by a set of four indices, and each of the indices can be linked to the relative arrangement of pentagons and heptagons in the corresponding torus. Chiral isomers or the corresponding helical derivatives, HCNTs, can also be readily derived either by introducing a chiral vector or dissecting a distorted TCNT through certain longitude.