A5061308439- Lipid Membrane Structure and Behavior
- DNA and Nucleic Acid Chemistry
- Quasicrystal Structures and Properties
- Electrostatics and Colloid Interactions
- Spectroscopy and Quantum Chemical Studies
- Nanopore and Nanochannel Transport Studies
- Force Microscopy Techniques and Applications
- Advanced Combinatorial Mathematics
- Theoretical and Computational Physics
- Mathematical Dynamics and Fractals
- Bacteriophages and microbial interactions
- Diffusion and Search Dynamics
- Advanced biosensing and bioanalysis techniques
- Advanced Fluorescence Microscopy Techniques
- Protein Structure and Dynamics
- Archaeology and Rock Art Studies
- Sphingolipid Metabolism and Signaling
- Stochastic processes and statistical mechanics
- RNA Interference and Gene Delivery
- Material Dynamics and Properties
- Micro and Nano Robotics
- Tuberculosis Research and Epidemiology
- Receptor Mechanisms and Signaling
- Advanced Thermodynamics and Statistical Mechanics
- Advanced Mathematical Identities
Université Toulouse III - Paul Sabatier
2015-2024
Laboratoire de Physique Théorique
2015-2024
Centre National de la Recherche Scientifique
2015-2024
Université de Toulouse
2014-2024
Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes
2012-2021
Laboratoire de Biotechnologie de l'Environnement
2015
Laser & Plasma Technologies (United States)
2011
Institut de Pharmacologie et de Biologie Structurale
2008
Laboratoire de Chimie et Physique Quantiques
2000-2004
Université Paris Cité
1997-1998
Using high-throughput tethered particle motion single-molecule experiments, the double-stranded DNA persistence length, Lp, is measured in solutions with Na+ and Mg2+ ions of various ionic strengths, I. Several theoretical equations for Lp(I) are fitted to experimental data, but no decisive theory found which fits all Lp values two ion valencies. Properly extracted from trajectory using simulations, varies 30 55 nm, comparable previous results. For Na+-only case, an increasing concave...
Even though the persistence length $L_P$ of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength $I$ lacks consensual description. Using high-throughput single-molecule technique statistical physics modeling, we measure presence monovalent (Li$^+$, Na$^+$, K$^+$) divalent (Mg$^{2+}$, Ca$^{2+}$) metallic alkyl ammonium ions, over large range 0.5 mM $\leq I\leq 5$ M. We show that linear Debye-H\"uckel-type theories do not describe even...
Phthiocerol dimycocerosate (DIM) is a major virulence factor of the pathogen Mycobacterium tuberculosis (Mtb). While this lipid promotes entry Mtb into macrophages, which occurs via phagocytosis, its molecular mechanism action unknown. Here, we combined biophysical, cell biology, and modeling approaches to reveal DIM on macrophage membranes leading first step infection. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry showed that molecules are...
T-cell cytotoxic function relies on the cooperation between highly specific but poorly adhesive receptor (TCR) and integrin LFA-1. How LFA-1-mediated adhesion may scale with TCR stimulation strength is ill-defined. Here, we show that LFA-1 conformation activation scales to calibrate human cytotoxicity. Super-resolution microscopy analysis reveals >1000 nanoclusters provide a discretized platform at immunological synapse translate engagement density of ligand ICAM-1 into graded adhesion....
Mycobacterium tuberculosis ( Mtb ) is the causative agent of (TB), a disease that claims ~1.6 million lives annually. The current treatment regime long and expensive, missed doses contribute to drug resistance. Therefore, development new anti-TB drugs remains one highest public health priorities. has evolved complex cell envelope represents formidable barrier antibiotics. envelop consists four distinct layers enriched for specific lipids glycans. Although outer membrane, comprised mycolic...
We propose a variant of the algorithm by [R. Simson, E. D. Sheets, and K. Jacobson, Biophys. 69, 989 (1995)]. Their was developed to detect transient confinement zones in experimental single-particle tracking trajectories diffusing membrane proteins or lipids. show that our is able wider class confining potential shapes than Simson et al. Furthermore, it enables not only temporary but also jumps between zones. Jumps are predicted skeleton fence picket models. In case mu-opioid receptors,...
T lymphocyte cytotoxicity relies on a synaptic ring of function-associated antigen 1 (LFA-1), which permits polarized delivery lytic granules. How LFA-1 organization is controlled by underlying actin cytoskeleton dynamics poorly understood. Here, we explored the contribution regulator WASP to topography using combination microscopy modalities. We uncover that reduced Wiskott-Aldrich syndrome patient-derived CD8+ lymphocytes lacking associated with activation, unstable synapse, and delayed...
The issue of the nucleation and slow closure mechanisms non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics Brownian simulations. A minimal mesoscopic model used where double helix made two interacting bead-spring rotating strands with a prescribed torsional modulus duplex state. We demonstrate that timescales for (respectively, closure) an approximately 10 base-pair bubble, agreement experiments, are associated crossing free-energy...
We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes vesicles undergoing phase separation.
A physical scenario accounting for the existence of size-limited submicrometric domains in cell membranes is proposed. It based on numerical investigation counterpart, lipidic where proteins are diffusing, recently discovered cluster phases colloidal suspensions. I demonstrate that interactions between proteins, namely, short-range attraction and longer-range repulsion, make possible stable small clusters. The consequences explored terms membrane organization diffusion properties. connection...
It has recently been proposed that proteins embedded in lipidic biomembranes can spontaneously self-organize into stable small clusters, or membrane nanodomains, due to the competition between short-range attractive and longer-range repulsive forces proteins, specific these systems. In this paper, we carry on our investigation, by Monte Carlo simulations, of different aspects cluster phases biomembranes. First, compare long-range potentials (including notably three-body terms) demonstrate...
The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting idea, different biophysical studies have found an unexpected increase in flexibility molecules with various sequences a function temperature, would be consistent formation growing number denatured sequences. Here, we take...
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a the double helix axis, either intrinsic sequence or induced by binding proteins. Developing method measure bend angles that does not perturb conformation itself DNA-protein complex challenging task. Here, we propose joint theory-experiment high-throughput approach rigorously such using Tethered Particle Motion (TPM) technique. By carefully modeling TPM...
Initiation of transposition requires formation a synaptic complex between both transposon ends and the transposase (Tpase), enzyme which catalyses DNA cleavage strand transfer ensures mobility. We have used single-molecule approach, tethered particle motion (TPM), to observe binding Tpase derivative, OrfAB[149], amputated for its C-terminal catalytic domain, molecules carrying one or two IS911 ends. Binding OrfAB[149] single end provoked small shortening DNA. This is consistent with bend...
Statistical DNA models available in the literature are often effective where base-pair state only (unbroken or broken) is considered. Because of a decrease by factor 30 bending rigidity sequence broken bonds, bubble, compared to double stranded state, inclusion molecular conformational degrees freedom more general mesoscopic model needed. In this paper we do so presenting one-dimensional Ising model, which describes internal states, coupled discrete wormlike chain describing configurations...
A statistical model of homopolymer DNA, coupling internal base-pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature DNA length the fraction denaturation bubbles their correlation deduced. transition emerges naturally when fluctuations are integrated out driven by difference in bending (entropy dominated) free energy between broken unbroken segments. Conformational properties such as...
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion a particle probe tethered to surface single molecule and detecting its amplitude movement. We discuss in this context time resolution TPM, which strongly depends on particle-DNA complex relaxation time, i.e. characteristic it takes explore configuration space diffusion. By comparing theory, simulations experiments,...
Up-down asymmetric inclusions impose a local, spontaneous curvature to an elastic membrane. When several of them are inserted in same membrane, they feel effective forces mediated by the both and entropic nature. Following approach initiated Dommersnes Fournier vanishing tension case [Eur. Phys. J. B 12, 9 (1999)], also using pseudo-analytical micellization theory, we derive statistical mechanics inclusion assemblies when subject additional short-range, attractive interaction. Our main...
The tilings of rhombi in two dimensions and rhomboedra three are studied when they constrained by fixed boundary conditions. We establish a link between those conditions free or periodic ones: the entropy is written as functional integral which treated via saddle-point method. can exhibit dominant states statistical ensemble show that display strong structural inhomogeneity caused boundary. This responsible for difference ones. method uses representation membranes embedded higher-dimensional...