Article
Multidisciplinary Sciences
J. J. Erik Maris, Freddy T. Rabouw, Bert M. Weckhuysen, Florian Meirer
Summary: Single-particle tracking is a powerful method for studying the motion of individual molecules and particles. The DiffusionLab software package provides motion analysis tools for challenging data sets, allowing trajectory classification based on motion type and computation of diffusion constants.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Teun A. P. M. Huijben, Hamidreza Heydarian, Alexander Auer, Florian Schueder, Ralf Jungmann, Sjoerd Stallinga, Bernd Rieger
Summary: Particle fusion in single molecule localization microscopy can improve signal-to-noise ratio, but is limited by structural heterogeneity. The authors demonstrate an unsupervised classification method that can differentiate structurally different DNA origami structures without prior knowledge.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Qi Pan, Daxiao Sun, Jianfeng Xue, Jie Hao, Hansen Zhao, Xijian Lin, Li Yu, Yan He
Summary: The study introduced a dark-field microscopy based single plasmonic nanoparticle tracking technique to monitor and characterize the spatial-temporal heterogeneity of protein LLPS condensates.
Article
Biochemical Research Methods
Fabian Hauser, Jaroslaw Jacak
Summary: The algorithm presented in this study allows real-time analysis of 3D single molecule localization microscopy images with minimal impact on fitting accuracy, utilizing lookup-tables with discrete xyz-positions. Real-time visualization during acquisition is achieved, with performance demonstrated on both simulated and measured data. Furthermore, a feedback loop controlling the activation laser pulse maintains a constant number of emitters per image frame.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Physics, Multidisciplinary
Hamim Mahmud Rivy, Syed A. A. Aljunid, Emmanuel Lassalle, Nikolay I. I. Zheludev, David Wilkowski
Summary: Optical tweezers, which are essential tools for manipulating atoms or molecules at a single particle level, are limited by the transverse size of the trap determined by the optical wavelength. In this study, a superoscillatory trapping method is used to create a subwavelength hotspot, smaller than the usual diffraction limit, for trapping a single ultracold atom. This technique not only enables the generation of compact and tenable ensembles of trapped atoms for quantum simulators but also has applications in single molecule quantum chemistry and the study of cooperative atom-photon interactions within subwavelength arrays of quantum emitters.
COMMUNICATIONS PHYSICS
(2023)
Article
Biochemical Research Methods
Koen J. A. Martens, Abbas Jabermoradi, Suyeon Yang, Johannes Hohlbein
Summary: In single-molecule localization microscopy, integrating various PSF modalities into the phasor-based framework enables fast and accurate localization of single-molecule emitters in three dimensions. This approach is crucial for analyzing complex PSFs and achieving high precision in localization.
Article
Chemistry, Physical
John S. H. Danial, Andreas Jenner, Ana J. Garcia-Saez, Katia Cosentino
Summary: Single molecule fluorescence microscopy allows real-time analysis of protein complex assembly in cellular membranes. A new automated analysis software has been developed to accurately measure the assembly kinetics of high-order oligomer complexes. The software is user-friendly and can analyze data sets of several hundred to thousand molecules in less than 2 minutes. This tool provides biologists with a fast and efficient way to study the compositional evolution of macromolecular assemblies and their underlying mechanisms.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Physics, Applied
Tal I. Sommer, Gil Weinberg, Ori Katz
Summary: In recent years, image-scanning microscopy (ISM) has been developed as a technique that enhances the resolution and signal-to-noise ratio in microscopy. It utilizes a detector array at the image plane of a confocal laser scanning microscope. Through k-space analysis, we show that ISM is equivalent to spotlight synthetic-aperture radar and oblique-illumination microscopy, indicating that ISM can be performed with a single detector placed in the k-space of the sample, as demonstrated numerically.
APPLIED PHYSICS LETTERS
(2023)
Article
Biology
Alec Heckert, Liza Dahal, Robert Tijan, Xavier Darzacq
Summary: Single-particle tracking (SPT) is a powerful tool for studying molecular mechanisms of cellular regulation. However, there are technical limitations in interpreting SPT data for fast-diffusing proteins. Researchers have proposed methods based on Bayesian nonparametrics to address these limitations.
Article
Multidisciplinary Sciences
Esley Torres-Garcia, Raul Pinto-Camara, Alejandro Linares, Damian Martinez, Victor Abonza, Eduardo Brito-Alarcon, Carlos Calcines-Cruz, Gustavo Valdes-Galindo, David Torres, Martina Jablonski, Hector H. Torres-Martinez, Jose L. Martinez, Haydee O. Hernandez, Jose P. Ocelotl-Oviedo, Yasel Garces, Marco Barchi, Rocco D'Antuono, Ana Boskovic, Joseph G. Dubrovsky, Alberto Darszon, Mariano G. Buffone, Roberto Rodriguez Morales, Juan Manuel Rendon-Mancha, Christopher D. Wood, Armando Hernandez-Garcia, Diego Krapf, Alvaro H. Crevenna, Adan Guerrero
Summary: This study presents a new super-resolution microscopy algorithm called Mean-Shift Super Resolution (MSSR), which extends the spatial resolution of single fluorescence images beyond the diffraction limit. MSSR works on various fluorophore densities and optical setups, and has denoising capabilities.
NATURE COMMUNICATIONS
(2022)
Article
Automation & Control Systems
Hu Liang, Shengrong Zhao, Na Li
Summary: This paper introduces a super-resolution image reconstruction method using a plug-and-play framework, which improves the challenges of detail and artifact enhancement by introducing a multi-fidelity term and learned prior knowledge. Experimental results demonstrate that the proposed method outperforms other comparison methods in subjective and objective metrics.
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS
(2022)
Article
Chemistry, Physical
Irina V. Gopich, Jae-Yeol Kim, Hoi Sung Chung
Summary: In single-molecule free diffusion experiments, accurate determination of individual molecule species' brightness and diffusivity from selected bursts of photons is crucial. New methods are presented to analyze the bursts, considering the bias introduced by the burst selection criteria. These methods, utilizing Maximum Likelihood (ML) approach, perform well on simulated photon trajectories and experimental data.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Nanoscience & Nanotechnology
Abhinav Banerjee, Micky Anand, Simanta Kalita, Mahipal Ganji
Summary: DNA-PAINT super-resolution imaging is used to measure the free energy of dinucleotide base stacking at the single-molecule level. Results show that addition of a single dinucleotide base stacking can greatly stabilize the DNA duplex nanostructure. These findings are important for designing functional DNA nanostructures and predicting the local DNA structure.
NATURE NANOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Soeren Doose
Summary: Single-molecule localization microscopy has become an important tool in biomedical research. The LOCAN Python library provides well-defined data structures and analysis methods for analyzing localization data in a script or computable notebook.
Article
Optics
Lei Chen, Qian Liu, Keng C. Chou
Summary: Single-molecule localization microscopy allows visualization of cellular structures at the nanometer scale, but analyzing point cloud images presents challenges. Existing cluster identification algorithms require users to input cutoff thresholds based on distance or density, leading to user-dependent cluster assignment. We present a cluster identification algorithm mimicking human vision and requiring no input parameters, which produces visually satisfactory assignments. This algorithm was tested on identifying fusion protein clusters of the Nipah virus and extended to analyze three-dimensional point clouds.
Article
Chemistry, Physical
K. Basnayake, D. Holcman
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Physics, Multidisciplinary
Suney Toste, David Holcman
Summary: This study derives asymptotic formulas for the mean exit time of the fastest Brownian particle among N identical ones to an absorbing boundary under various initial distributions. The results show a continuous algebraic decay law for the mean exit time, differing from classical Weibull or Gumbel results. Formulas are derived for 1-dimensional and 2-dimensional cases, compared with stochastic simulations, and a discussion on applications in cell biology involving long-tail initial distributions is provided.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Biochemistry & Molecular Biology
Andrea Papale, David Holcman
Summary: The stability of chromatin loops inside the nucleus is dependent on the balance between binding and unbinding events, with the number of cross-linkers playing a key role. The time scale of loop stability can vary from minutes to the entire cell cycle lifetime as the number of cross-linkers increases.
Article
Biology
A. Tricot, I. M. Sokolov, D. Holcman
Summary: The distribution of voltage in sub-micron cellular domains is poorly understood, especially in terms of maintaining electro-neutrality. Through studying the voltage distribution in a generic domain, it was found that long-range voltage drop changes may have significance in neuronal microcompartments and the activation of voltage-gated channels on the surface membrane.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
U. Dobramysl, D. Holcman
Summary: A computational approach is developed to locate the source of a steady-state gradient of diffusing particles, with a fast numerical scheme accelerating simulation time without computing Brownian trajectories explicitly. Results show that analytical formulae and numerical simulation agree on a large range of parameters for reconstructing the source location, while also investigating the uncertainties and window configurations' influence on source reconstruction. Possible applications for cell navigation in biology are discussed as well.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Multidisciplinary Sciences
Kanishka Basnayake, David Mazaud, Lilia Kushnireva, Alexis Bemelmans, Nathalie Rouach, Eduard Korkotian, David Holcman
Summary: The study reveals that replenishment of dendritic spines involves store-operated calcium entry pathway. Key conditions for replenishment without depletion include small amplitude and slow timescale of calcium influx, as well as close proximity between the spine apparatus and plasma membranes. The nanoscale organization of dendritic spines separates replenishment from depletion.
Article
Engineering, Biomedical
Matteo Dora, David Holcman
Summary: This paper proposes a new wavelet-based method for removing artifacts from single-channel EEGs. The method adaptively attenuates artifacts of different nature through data-driven renormalization of wavelet components and demonstrates superior performances on different kinds of artifacts and signal-to-noise levels. The proposed method provides a valuable tool to remove artifacts in real-time EEG applications with few electrodes, such as monitoring in special care units.
IEEE TRANSACTIONS ON NEURAL SYSTEMS AND REHABILITATION ENGINEERING
(2022)
Article
Multidisciplinary Sciences
F. Paquin-Lefebvre, D. Holcman
Summary: This study investigates the diffusion behavior of Brownian particles injected on the surface of a bounded domain, analyzing the distribution of concentration between different windows. The solution is obtained using Green's function techniques and second-order asymptotic analysis, with the results depending on factors such as influx amplitude, diffusion properties, and the geometrical organization of the windows.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Biochemical Research Methods
Lou Zonca, David Holcman
Summary: This study investigates how connected neuronal networks contribute to the emergence of the alpha-band, finding that the alpha-band is generated by network behavior near the attractor of the Up-state. By modeling the interaction of excitatory and inhibitory networks, the study shows that short-term plasticity in well-connected neuronal networks can explain the emergence and fragmentation of the alpha-band.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Mathematics, Applied
Lou Zonca, David Holcman
Summary: This study examines the exit time of two-dimensional dynamical systems perturbed by small noise, revealing that the maximum of the probability density function of trajectories is not located at the point attractor and that exiting the basin of attraction does not guarantee full escape. By applying these results to neuronal networks, the study sheds light on bursting events and explains the non-Poissonian long interburst durations observed in neuronal dynamics.
JOURNAL OF NONLINEAR SCIENCE
(2022)
Review
Physics, Condensed Matter
S. Toste, D. Holcman
Summary: The article investigates the switching behavior of stochastic particles between two states and estimates the fastest arrival time through solving Fokker-Planck equations. The results reveal that the fastest particle avoids switching when the switching rates are low, but it switches twice when the diffusion in state 2 is much faster than in state 1.
EUROPEAN PHYSICAL JOURNAL B
(2022)
Article
Mathematics, Applied
Matteo Dora, Stephane Jaffard, David Holcman
Summary: Wavelet quantile normalization (WQN) is a nonparametric algorithm designed to remove transient artifacts from single-channel EEG in real-time while preserving the continuity of monitoring. The algorithm regularizes the signal by transporting the wavelet coefficient distributions of artifacted epochs into a reference distribution. The WQN algorithm preserves the distribution of wavelet coefficients compared to classical wavelet thresholding methods.
APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS
(2022)
Review
Physics, Multidisciplinary
Ulrich Dobramysl, David Holcman
Summary: Computational methods are powerful and complementary in applied sciences like biology, exploring the gap between molecular and cellular scales. Recent progress includes diffusion modeling, asymptotic analysis, hybrid methods, and simulations for cell sensing and guidance via external gradients. The focus is on reconstructing point source location, estimating uncertainty in source reconstruction, and discussing the impact of window configurations on source position recovery.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Article
Multidisciplinary Sciences
Jurgen Reingruber, Andrea Papale, Stephane Ruckly, Jean-Francois Timsit, David Holcman
Summary: Before vaccines, countries used social restrictions to prevent healthcare system saturation and regain control over COVID-19. Computational approaches are key to efficiently control a pandemic. This study develops a data-driven computational framework to control the pandemic with non-pharmaceutical interventions, using a compartmental model and recalibration based on new data.
Article
Physics, Fluids & Plasmas
F. Paquin-Lefebvre, S. Toste, D. Holcman
Summary: This article introduces the redundancy principle and its application in studying rare events. The authors propose a criterion based on splitting probabilities to estimate large n and obtain explicit computations, which are compared with stochastic simulations. They also provide examples of extreme trajectories with killing in dimension 2 and suggest that optimal trajectories should avoid penetrating inside the killing region for large n. Finally, some applications to cell biology are discussed.