1,720,966 research outputs found
A fast method for electronic couplings in embedded multichromophoric systems
Full text linkElectronic couplings are key to understanding exciton delocalization and transport in natural and artificial light harvesting processes. We develop a method to compute couplings in multichromophoric aggregates embedded in complex environments without running expensive quantum chemical calculations. We use a transition charge approximation to represent the quantum mechanical transition densities of the chromophores and an atomistic and polarizable classical model to describe the environment atoms. We extend our framework to estimate transition charges directly from the chromophore geometry, i.e., bypassing completely the quantum mechanical calculations using a regression approach. The method allows to rapidly compute accurate couplings for a large number of geometries along molecular dynamics trajectories
The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol
Full text linkThe 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 the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant. (c) 2022 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).2022 Author(s)
The energy transfer model of nonphotochemical quenching: Lessons from the minor CP29 antenna complex of plants
Full text linkAntenna complexes in photosystems of plants and green algae are able to switch between a light-harvesting unquenched conformation and a quenched conformation so to avoid photodamage. When the switch is activated, nonphotochemical quenching (NPQ) mechanisms take place for an efficient deactivation of excess excitation energy. The molecular details of these mechanisms have not been fully clarified but different hypotheses have been proposed. Among them, a popular one involves excitation energy transfer (EET) from the singlet excited Chls to the lowest singlet state (S1) of carotenoids. In this work, we combine such model with μs-long molecular dynamics simulations of the CP29 minor antenna complex to investigate how conformational fluctuations affect the electronic couplings and the final EET quenching. The computational framework is applied to both CP29 embedding violaxanthin and zeaxantin in its L2 site. Our results demonstrate that the EET model is rather insensitive to physically reasonable variations in single chlorophyll-carotenoid couplings, and that very large conformational changes would be needed to see the large variation of the complex lifetime expected in the switch from light-harvesting to quenched state. We show, however, that a major role in regulating the EET quenching is played by the S1 energy of the carotenoid, in line with very recent spectroscopy experiments
Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes
Full text linkWe propose a machine
learning (ML)-based strategy for an inexpensive
calculation of excitonic properties of light-harvesting complexes
(LHCs). The strategy uses classical molecular dynamics simulations
of LHCs in their natural environment in combination with ML prediction
of the excitonic Hamiltonian of the embedded aggregate of pigments.
The proposed ML model can reproduce the effects of geometrical fluctuations
together with those due to electrostatic and polarization interactions
between the pigments and the protein. The training is performed on
the chlorophylls of the major LHC of plants, but we demonstrate that
the model is able to extrapolate well beyond the initial training
set. Moreover, the accuracy in predicting the effects of the environment
is tested on the simulation of the small changes observed in the absorption
spectra of the wild-type and a mutant of a minor LHC
How the pH Controls Photoprotection in the Light-Harvesting Complex of Mosses
Full text linkIn 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 light irradiation in a strategy known as non-photochemical quenching (NPQ). NPQ is activated by an acidification of the thylakoid lumen, which is sensed directly or indirectly by the LHC, resulting in a conformational change of the complex that leads to the quenched state. The conformational changes responsible for NPQ activation and their connection to specific quenching mechanisms are still unknown. Here, we investigate the pH-triggered conformational changes in the light-harvesting complex stress-related (LHCSR) of mosses. By combining constant-pH molecular dynamics and enhanced sampling techniques, we find that the pH sensitivity of the complex is driven by the coupled protonation of three residues modulating the conformation of the short amphipathic helix placed at the lumen side of the embedding membrane. Combining these results with quantum mechanics/molecular mechanics calculations, we show that the quenching mechanism sensitive to the pH goes through a charge-transfer between a carotenoid and an excited chlorophyll, which is controlled by the protein conformation
Electronic Excited States from Physically Constrained Machine Learning
No full textData-driven techniques are increasingly used to replace electronic-structure calculations of matter. In this context, a relevant question is whether machine learning (ML) should be applied directly to predict the desired properties or combined explicitly with physically grounded operations. We present an example of an integrated modeling approach in which a symmetry-adapted ML model of an effective Hamiltonian is trained to reproduce electronic excitations from a quantum-mechanical calculation. The resulting model can make predictions for molecules that are much larger and more complex than those on which it is trained and allows for dramatic computational savings by indirectly targeting the outputs of well-converged calculations while using a parametrization corresponding to a minimal atom-centered basis. These results emphasize the merits of intertwining data-driven techniques with physical approximations, improving the transferability and interpretability of ML models without affecting their accuracy and computational efficiency and providing a blueprint for developing ML-augmented electronic-structure methods
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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