Related papers: InferenceMAP: Mapping of Single-Molecule Dynamics …
Over recent years, super-resolution and single-molecule imaging methods have delivered unprecedented details on the nanoscale organization and dynamics of individual molecules in different contexts. Yet, visualizing single-molecule…
Enzymes have been shown to diffuse faster in the presence of their reactants. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF)…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
Current single molecule methods either rely on fluorescence or lack chemical information. Here we report stimulated Raman photothermal encoded scattering (SRPSCAT) microscopy for quantitative bond-selective imaging of single-biomolecule…
The development and generation of synthetic data are becoming increasingly vital in the field of statistical disclosure control. The PSInference package provides tools to perform exact inferential analysis on singly imputed synthetic data…
Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…
Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…
The advent of single molecule microscopy has revolutionized biological investigations by providing a powerful tool for the study of intercellular and intracellular trafficking processes of protein molecules which was not available before…
We consider the problem of designing synthetic cells to achieve a complex goal (e.g., mimicking the immune system by seeking invaders) in a complex environment (e.g., the circulatory system), where they might have to change their control…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
The Neyman-Scott point process is a widely used point process model which is easily interpretable and easily extendable to include various types of inhomogeneity. The inference for such complex models is then complicated and fast methods,…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Diffusion coefficient measurements are important for many biological and material investigations, such as particle dynamics, kinetics, and size determinations. Amongst current measurement methods, single particle tracking (SPT) offers the…
In Real-Time, Feedback-Driven Single Particle Tracking methods, measurements of the emission intensity from a labeled, nanometer-scale particle are used in a feedback loop to track the motion of the particle as it moves inside its native…
Interacting particle system (IPS) models have proven to be highly successful for describing the spatial movement of organisms. However, it has proven challenging to infer the interaction rules directly from data. In the field of equation…
Single-molecule junctions - nanoscale systems where a molecule is connected to metallic electrodes - offer a unique platform for studying charge, spin and energy transport in non-equilibrium many-body quantum systems, with few parallels in…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…