Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 1512.00887

Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

Pavel Malý·J. Michael Gruber·Rienk van Grondelle·Tomáš Mančal
View original source ↗Read source document ↗Export metadata ↓

Abstract

We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.

Explore related subjects

physics.bio-phphysics.chem-ph

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Pavel Malý, J. Michael Gruber, Rienk van Grondelle, Tomáš Mančal. 2015-12-02. Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory. https://arxiv.org/abs/1512.00887

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Multiscale retinal flow on a spherical cap of varying aperture

Modelling retinal haemodynamics is crucial for understanding retinal microcirculation but is computationally demanding because it involves coupling between the vasculature and surrounding tissue across multiple scales. This computational burden has been substantially alleviated by a recent analytic solution on the planar disc that enables lumping the capillary bed and surrounding tissue into an effective resistor. However, that formulation treats the retina as a flat surface, whereas the retina is a curved surface with a finite anterior aperture. In this work, we develop a nontrivial and physiologically necessary extension to spherical-cap tissue domains with varying apertures, where surface curvature and finite-aperture boundaries complicate solving coupled Darcy equations on a curved manifold. Using a stereographic projection and a decoupling transformation, we derive an analytic solution for the capillary-tissue system on the spherical cap that represents flow in both the capillary bed and interstitial tissue more realistically while retaining the efficient resistor formulation, a key advantage of the planar-disc formulation. This solution is coupled to one-dimensional (1D) arteriolar and venular flows to obtain a multiscale description of retinal haemodynamics. Using a vasculature model designed to capture retinal vascular features, we show that the multiscale model's predictions are consistent with experimental data. We further explore aperture effects using both a fixed hemispherical vasculature and aperture-dependent vasculature. The aperture affects retinal haemodynamics mainly through changes in the constructed vasculature itself, whereas the surface-averaged pressures and relative terminal flow distributions remain nearly unchanged. This framework provides a foundation for studying retinal pathophysiology on more anatomically realistic domains.

physics.bio-ph↗
arXiv2026

Double-well potentials and crucial estimations in nonlinear dynamics of microtubules

In the present work, we study the two-component model of microtubules, the basic components of the eukaryotic cytoskeleton. We introduce a couple of estimations, which tremendously simplified the model. The paper is devoted to tangential oscillations of dimers, but we explain that the model can explain the radial oscillations as well. Finally, we study the stability of all solutions of differential equations, describing the dynamics of the microtubules.

physics.bio-ph↗
arXiv2026

A thermodynamically consistent framework for finite growth of multi-constituent mixtures with application to tumor growth

Biological tissues grow by continuously producing, transporting, and reorganizing multiple interacting constituents. These processes are intrinsically coupled to finite deformation and residual stress. Existing models typically capture either finite growth kinematics or multi-constituent transport, but rarely both within a thermodynamically consistent setting. In particular, existing approaches do not consistently link the volume created by finite growth to the mass produced for each individual constituent. In this work, we develop a general continuum framework that unifies finite growth kinematics and multiphase mixture theory for fully saturated multi-constituent mixtures containing an arbitrary number of dilute dissolved solutes. Formulated in a solid-skeleton-based description, the framework rests on constituent-wise balance laws and a free-energy dissipation principle, from which thermodynamically admissible constitutive closures are derived for all mass-exchange, transport, reaction, and growth processes. The central novelty of the framework is a coupling between growth-induced volume creation and constituent mass production, expressed through volume accumulation fractions that distribute the newly created volume among the constituents while preserving saturation. We cast the resulting model in a total Lagrangian mixed weak form and specialize the general theory to a four-constituent, two-solute model of avascular tumor growth that couples nutrient transport, waste production, phenotype transitions between proliferative, hypoxic, and necrotic cells, volume growth, elastic deformation, and growth-induced residual stress. The model is implemented within a finite element setting and its capabilities are demonstrated on representative benchmark problems.

physics.bio-ph↗