How Static Disorder Mimics Decoherence in Anisotropy Pump–Probe Experiments on Purple-Bacteria Light Harvesting Complexes

Stross, Clement; Kamp, Marc W. van der; Oliver, Thomas A. A.; Harvey, Jeremy N.; Linden, Noah; Manby, Frederick R.

doi:10.1021/acs.jpcb.6b09916

Cited by 10 publications

(12 citation statements)

References 81 publications

(239 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The QM/MM computations indicate a selective broadening of the B800 absorption band relative to B850 (Figures 3C and S2) as well as a wider distribution of the ring-averaged excitation energies. The 10-meV width of the excitation energy distribution (Figure S3) is similar to values of 7.4 and 9.4 meV previously extracted from pump-probe experiments (Stross et al, 2016). Our simulation identifies two factors that influence reorientation and spectral broadening of B800.…”

Section: Segregation Of Proteins Enables Heterogeneous Membrane Curvaturesupporting

confidence: 85%

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy

Maffeo

Delgado-Magnero

et al. 2019

Cell

140

119

View full text Add to dashboard Cite

show abstract

Section: Segregation Of Proteins Enables Heterogeneous Membrane Curvaturesupporting

confidence: 85%

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy

Maffeo

Delgado-Magnero

et al. 2019

Cell

140

119

View full text Add to dashboard Cite

show abstract

“…The 10-meV width of the excitation energy distribution (Fig. S23) is similar to those previously extracted from pump-probe experiments, namely 7.4 and 9.4 meV (Stross et al, 2016). Our simulation identifies two factors that influence reorientation and spectral broadening of B800.…”

Section: Segregation Of Proteins Enables Heterogeneous Membrane Curvasupporting

confidence: 84%

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

et al. 2019

View full text Add to dashboard Cite

Bioenergetic membranes are the key cellular structures responsible for coupled energy-conversion processes, which supply ATP and important metabolites to the cell. Here, we report the first 100million atom-scale model of an entire photosynthetic organelle, a chromatophore membrane vesicle from a purple bacterium, which reveals the rate-determining steps of membrane-mediated energy conversion. Molecular dynamics simulations of this bioenergetic organelle elucidate how the network of bioenergetic proteins influences membrane curvature and demonstrates the impact of thermal disorder on photosynthetic excitation transfer. Brownian dynamics simulations of the quinone and cytochrome c2 charge carriers within the chromatophore interior probe the mechanisms of nanoscale charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a rate-kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore's structural integrity and robust energy conversion. Put together, the hybrid structure determination and systems-level modeling of the chromatophore, in conjunction with optical spectroscopy, illuminate the chemical and organizational design principles of biological membranes that foster energy storage and transduction in living cells. Parallels are drawn with the more universal mitochondrial bioenergetic machinery, from whence molecular-scale insights on the mechanism of cellular aging are inferred. This endeavor made feasible through the advent of petascale supercomputers, paves the way to first-principles modeling of whole living cells.

show abstract

“…After extracting chromophore geometries from the MD simulations, ab initio methods have been used to calculate ground and excited-state chromophore site energies and couplings. 17,19,27,28 Although these approaches include some atomistic detail in the dynamical propagation, they nevertheless average over many of the constituent atomic motions of both the environment and the system. The quantum system is collapsed onto a set of site energies, the environment is collapsed into a spectral density function, and the system-environment coupling is collapsed into a set of simple functional forms -e.g., bilinear coupling.…”

Section: Introductionmentioning

confidence: 99%

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

Sisto

Stross

Kamp

et al. 2017

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail - enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck-Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τ) between 650-1050 fs, and B800 population decay (τ) between 10-50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.

show abstract

How Static Disorder Mimics Decoherence in Anisotropy Pump–Probe Experiments on Purple-Bacteria Light Harvesting Complexes

Cited by 10 publications

References 81 publications

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

Contact Info

Product

Resources

About