arXiv subjects

Bertus van Heerden

Publications and source records attributed to Bertus van Heerden.

6 recordsLinked to original sources

arXiv2026

Objective clustering protocol for single-molecule data: A lifetime vs. intensity study

Single-molecule spectroscopy (SMS) is an exceptionally sensitive technique, but its inherently limited photon budget produces noisy data that can readily lead to subjective analyses, fitting errors, and reduced statistical power, obscuring true subpopulations and their dynamics. Here, we present an unbiased, objective method to cluster two-dimensional single-molecule data and demonstrate it on fluorescence lifetime--intensity correlations. The clustering method is based on Gaussian mixture modeling, with the optimal number of clusters determined through {information criteria (the Akaike and Bayesian information criteria and integrated completed likelihood) and supplemented by cluster quality metrics such as average cluster tightness and the fraction of points outside confidence ellipses, which guide the selection of statistically robust and physically meaningful clusters. The protocol was benchmarked on simulated datasets spanning clean, smeared, and noisy overlap-limited regimes, and applied to experimental data from Alexa Fluor 647 and QD 605. This approach reliably recovers relevant subpopulations even in the presence of noise and overlapping distributions, providing an objective framework for analyzing single-molecule heterogeneity, with limitations arising primarily under severe geometric overlap or extreme state-occupancy imbalance where distinct populations are no longer separable.

physics.bio-ph↗

arXiv2026

Size-Dependent Fluorescence Kinetics Reveal Contributions of Intrinsic Quenching and Singlet-Triplet Annihilation during LHCII Aggregation

Aggregation of the main antenna complex of higher plants, Light-Harvesting Complex II (LHCII), is widely used as an in vitro model for energy-dependent quenching (qE), yet fluorescence reduction in aggregates is frequently interpreted without a quantitative separation of intrinsic quenching from excitation-induced annihilation. Here, we address this ambiguity by directly correlating aggregate size, concentration, steady-state fluorescence intensity, and decay kinetics during controlled, incremental aggregation of isolated LHCII. By combining fluorescence correlation spectroscopy (FCS) with TCSPC in a unified experimental framework, we monitored structural and photophysical changes in real time as detergent removal drives biphasic aggregation. We quantified the aggregate composition from the particle concentrations, enabling direct scaling of the absorption cross-section with aggregate size. The average fluorescence lifetime decreased semi-logarithmically with increases in hydrodynamic radius, whereas steady-state fluorescence intensities deviated strongly from this trend. Intensitydependent measurements and steady-state kinetic modeling reveal that singlet-triplet annihilation (STA) emerges at moderate excitation intensities and rapidly becomes the dominant contributor to fluorescence quenching, even for relatively small aggregates. In contrast, intrinsic quenching increases more gradually with aggregate size. By quantitatively disentangling intrinsic excitation quenching from annihilation processes, this work demonstrates that STA can govern the apparent photophysical response of aggregated LHCII across excitation regimes commonly considered non-annihilating. The size-dependent mechanistic framework presented here provides a basis for distinguishing intrinsic quenching from annihilation effects in aggregation-based studies of photosynthetic antenna complexes.

physics.bio-ph↗

arXiv2024

Advanced analysis of single-molecule spectroscopic data

We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analysing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data -- such as fluorescence brightness, lifetime, and spectra -- of molecular- or nanometre-scale particles such as single dye molecules, quantum dots, or fluorescently labelled biological macromolecules. Full SMS allows an unbiased statistical analysis of fluorescence brightness through level resolution and clustering, analysis of fluorescence lifetimes through decay fitting, as well as the calculation of second-order correlation functions and the display of fluorescence spectra and raster-scan images. Additional features include extensive data filtering options, a custom HDF5-based file format, and flexible data export options. The software is open source and written in Python but GUI-based so it may be used without any programming knowledge. A multi-process architecture was employed for computational efficiency. The software is also designed to be easily extendable to include additional import data types and analysis capabilities.

physics.bio-ph↗

arXiv2022

Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective

Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. We then systematically discuss each of the core components of RT-FD-SPT in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. We then introduce a collection of metrics for RT-FD-SPT to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, we conclude with a discussion on future perspectives in the field.

physics.chem-ph↗

arXiv2022

Theoretical comparison of real-time feedback-driven single-particle tracking techniques

Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in native or near-native environments. A number of different RT-FD-SPT approaches exist, and comparisons between methods based on experimental results are of limited use due to differences in samples and setups. In this study, we used statistical calculations and dynamical simulations to directly compare the performance of different methods. The methods considered were the orbital method, the Knight`s Tour (grid scan) method and MINFLUX, and we considered both fluorescence-based and interferometric scattering (iSCAT) approaches. There is a fundamental trade-off between precision and speed, with the Knight`s Tour method being able to track the fastest diffusion but with low precision, and MINFLUX being the most precise but only tracking slow diffusion. To compare iSCAT and fluorescence, different biological samples were considered, including labeled and intrinsically fluorescent samples. The success of iSCAT as compared to fluorescence is strongly dependent on the particle size and the density and photophysical properties of the fluorescent particles. Using a wavelength for iSCAT that is negligibly absorbed by the tracked particle allows an increased illumination intensity, which results in iSCAT providing better tracking for most samples. This work highlights the fundamental aspects of performance in RT-FD-SPT and should assist with the selection of an appropriate method for a particular application. The approach used can easily be extended to other RT-FD-SPT methods.

physics.ins-det↗

arXiv2019

Strong plasmonic fluorescence enhancement of individual plant light-harvesting complexes

Plasmonic coupling of metallic nanoparticles and adjacent pigments can dramatically increase the brightness of the pigments due to the enhanced local electric field. Here, we demonstrate that the fluorescence brightness of a single plant light-harvesting complex (LHCII) can be significantly enhanced when coupled to single gold nanorods (AuNRs). The AuNRs utilized in this study were prepared via chemical reactions, and the hybrid system was constructed using a simple and economical spin-assisted layer-by-layer technique. Enhancement of fluorescence brightness of up to 240-fold was observed, accompanied by a 109-fold decrease in the average (amplitude-weighted) fluorescence lifetime from approximately 3.5 ns down to 32 ps, corresponding to an excitation enhancement of 63-fold and emission enhancement of up to 3.8-fold. This large enhancement is due to the strong spectral overlap of the longitudinal localized surface plasmon resonance of the utilized AuNRs and the absorption or emission bands of LHCII. This study provides an inexpensive strategy to explore the fluorescence dynamics of weakly emitting photosynthetic light-harvesting complexes at the single molecule level.

physics.bio-ph↗