Related papers: Single particle algorithms to reveal cellular nano…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Biomolecules exhibit dynamic conformations critical to their functions, yet observing these processes at the single-molecule level under native conditions remains a formidable challenge. While surface immobilization has been widely used to…
In numerous systems in biophysics and related fields, scientists measure (with very smart methods) individual molecules (e.g. biopolymers (proteins, DNA, RNA, etc), nano - crystals, ion channels), aiming at finding a model from the data.…
Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state…
Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions. Many biological processes unfold along continuous trajectories, yet it remains challenging to extract smooth, low-dimensional…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano…
The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…
The condensation of biomolecules into biomolecular condensates via liquid-liquid phase separation (LLPS) is a ubiquitous mechanism that drives cellular organization. To enable these functions, biomolecules have evolved to drive LLPS and…
Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted…
For over three decades, scanning probe microscopy (SPM) has been a key method for exploring material structures and functionalities at nanometer and often atomic scales in ambient, liquid, and vacuum environments. Historically, SPM…
The study of moving particles (e.g. molecules, virus, vesicles, organelles, or whole cells) is crucial to decipher a plethora of cellular mechanisms within physiological and pathological conditions. Powerful live-imaging approaches enable…
Local interactions drive emergent collective behavior, which pervades biological and social complex systems. But uncovering the interactions that produce a desired behavior remains a core challenge. In this paper, we present EvoSOPS, an…
The nanoscale interaction between single emitters and plasmonic structures is traditionally studied by relying on near-perfect, deterministic, nanoscale-control. This approach is ultra-low throughput thus rendering systematic studies…
Nanoscale chromatin domains, variously termed nucleosome clutches, nanodomains, or packing domains, have emerged as fundamental architectural units of the mammalian genome during interphase and mitosis. Unlike cohesin-dependent loops or…
This work exploits the zeptoliter sensing volume of electrolyte-filled nanopores to determine, simultaneously and in real time, the approximate shape, volume, charge, rotational diffusion coefficient, and dipole moment of individual…
The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…