[HTML][HTML] The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol

E Cignoni, V Slama, L Cupellini… - The Journal of Chemical …, 2022 - pubs.aip.org
The function of light-harvesting complexes is determined by a complex network of dynamic
interactions among all the different components: the aggregate of pigments, the protein, and …

Growing Spicy ONIOMs: Extending and generalizing concepts of ONIOM and many body expansions

P Seeber, S Seidenath, J Steinmetzer… - Wiley Interdisciplinary …, 2023 - Wiley Online Library
The ONIOM method and many extensions to it provide capabilities to treat challenging
multiscale problems in catalysis and material science. Our open‐source program Spicy is a …

Design principles for energy transfer in the photosystem II supercomplex from kinetic transition networks

SJ Yang, DJ Wales, EJ Woods, GR Fleming - Nature Communications, 2024 - nature.com
Photosystem II (PSII) has the unique ability to perform water-splitting. With light-harvesting
complexes, it forms the PSII supercomplex (PSII-SC) which is a functional unit that can …

Machine learning exciton Hamiltonians in light-harvesting complexes

E Cignoni, L Cupellini, B Mennucci - Journal of Chemical Theory …, 2023 - ACS Publications
We propose a machine learning (ML)-based strategy for an inexpensive calculation of
excitonic properties of light-harvesting complexes (LHCs). The strategy uses classical …

A different perspective for nonphotochemical quenching in plant antenna complexes

E Cignoni, M Lapillo, L Cupellini… - Nature …, 2021 - nature.com
Light-harvesting complexes of plants exert a dual function of light-harvesting (LH) and
photoprotection through processes collectively called nonphotochemical quenching (NPQ) …

[HTML][HTML] Coupled charge and energy transfer dynamics in light harvesting complexes from a hybrid hierarchical equations of motion approach

TP Fay, DT Limmer - The Journal of Chemical Physics, 2022 - pubs.aip.org
We describe a method for simulating exciton dynamics in protein–pigment complexes,
including effects from charge transfer as well as fluorescence. The method combines the …

Impact of structure, coupling scheme, and state of interest on the energy transfer in CP29

S Petry, JC Tremblay, JP Götze - The Journal of Physical …, 2023 - ACS Publications
The Qy and Bx excitation energy transfer (EET) in the minor light-harvesting complex CP29
(LHCII B4. 1) antenna complex of Pisum sativum was characterized using a computational …

Kinetics of the xanthophyll cycle and its role in photoprotective memory and response

A Short, TP Fay, T Crisanto, R Mangal… - Nature …, 2023 - nature.com
Efficiently balancing photochemistry and photoprotection is crucial for survival and
productivity of photosynthetic organisms in the rapidly fluctuating light levels found in natural …

How the pH controls photoprotection in the light-harvesting complex of mosses

L Pedraza-González, E Cignoni… - Journal of the …, 2023 - ACS Publications
In response to varying light conditions, light-harvesting complexes (LHCs) switch from a light-
harvesting state to a quenched state to protect the photosynthetic organism from excessive …

A perspective on the major light-harvesting complex dynamics under the effect of pH, salts, and the photoprotective PsbS protein

E Navakoudis, T Stergiannakos, V Daskalakis - Photosynthesis Research, 2023 - Springer
The photosynthetic apparatus is a highly modular assembly of large pigment-binding
proteins. Complexes called antennae can capture the sunlight and direct it from the …