Diffusion Analysis of NAnoscopic Ensembles: A Tracking-Free Diffusivity Analysis for Nanoscopic Ensembles in Biological Samples and Nanotechnology

The rapid development of microscopic techniques over the past decades enables the establishment of single molecule fluorescence imaging as a powerful tool in biological and biomedical sciences. Single molecule fluorescence imaging allows to study the chemical, physicochemical, and biological properties of target molecules or particles by tracking their molecular position in the biological environment and determining their dynamic behavior. However, the precise determination of particle distribution and diffusivities is often challenging due to high molecule/particle densities, fast diffusion, and photobleaching/blinking of the fluorophore. A novel, accurate, and fast statistical analysis tool, Diffusion Analysis of NAnoscopic Ensembles (DANAE), that solves all these obstacles is introduced. DANAE requires no approximations or any a priori input regarding unknown system-inherent parameters, such as background distributions; a requirement that is vitally important when studying the behavior of molecules/particles in living cells. The superiority of DANAE with various data from simulations is demonstrated. As experimental applications of DANAE, membrane receptor diffusion in its natural membrane environment, and cargo mobility/distribution within nanostructured lipid nanoparticles are presented. Finally, the method is extended to two-color channel fluorescence microscopy

Increase of Thermal Resistance Between a Nanostructure and a Surface due to Phonon Multireflections

The thermal resistance between a nanostructure and a half-body is calculated in the framework of particle-phonons physics. The current models approximate the nanostructure as a thermal bath. We prove that the multireflections of heat carriers in the nanostructure significantly increase resistance in contradiction with former predictions. This increase depends on the shape of the nanostructure and the heat carriers mean free path only. We provide a general and simple expression for the contact resistance and examine the specific cases of nanowires and nanoparticles

A simulation-guided fluorescence correlation spectroscopy tool to investigate the protonation dynamics of cytochrome c oxidase

Fluorescence correlation spectroscopy (FCS) is a single molecule based technique to temporally resolve rate-dependent processes by correlating the fluorescence fluctuations of individual molecules traversing through a confocal volume. In addition, chemical processes like protonation or intersystem crossing can be monitored in the sub-microsecond range. FCS thereby provides an excellent tool for investigations of protonation dynamics in proton pumps like cytochrome c oxidase (CcO). To achieve this, the pH- dependent fluorescent dye fluorescein was attached as a protonation probe to the CcO surface via site-specific labeling of single reactive cysteines that are located close to the entry point of a proton input channel (K-pathway). The analysis of protonation dynamics is complicated by overlapping triplet and protonation rates of the fluorophore. A Monte Carlo simulation based algorithm was developed to facilitate discrimination of these temporally overlapping processes thus allowing for improved protonation reaction rate determination. Using this simulation-guided approach we determined precise local proton association and dissociation rates and provide information about protein surface effects, such as proton collecting antennae, on the transport properties of proton transfer channels

Light and pH-induced Changes in Structure and Accessibility of Transmembrane Helix B and Its Immediate Environment in Channelrhodopsin-2

A variant of the cation channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) was selectively labeled at position Cys-79 at the end of the first cytoplasmic loop and the beginning of transmembrane helix B with the fluorescent dye fluorescein (acetamidofluorescein). We utilized (i) time- resolved fluorescence anisotropy experiments to monitor the structural dynamics at the cytoplasmic surface close to the inner gate in the dark and after illumination in the open channel state and (ii) time-resolved fluorescence quenching experiments to observe the solvent accessibility of helix B at pH 6.0 and 7.4. The light-induced increase in final anisotropy for acetamidofluorescein bound to the channel variant with a prolonged conducting state clearly shows that the formation of the open channel state is associated with a large conformational change at the cytoplasmic surface, consistent with an outward tilt of helix B. Furthermore, results from solute accessibility studies of the cytoplasmic end of helix B suggest a pH-dependent structural heterogeneity that appears below pH 7. At pH 7.4 conformational homogeneity was observed, whereas at pH 6.0 two protein fractions exist, including one in which residue 79 is buried. This inaccessible fraction amounts to 66% in nanodiscs and 82% in micelles. Knowledge about pH-dependent structural heterogeneity may be important for CrChR2 applications in optogenetics

Heat transfer between a nano-tip and a surface

We study quasi-ballistic heat transfer through air between a hot nanometer-scale tip and a sample. The hot tip/surface configuration is widely used to perform nonintrusive confined heating. Using a Monte-Carlo simulation, we find that the thermal conductance reaches 0.8 MW.m-2K-1 on the surface under the tip and show the shape of the heat flux density distribution (nanometer-scale thermal spot). These results show that a surface can be efficiently heated locally without contact. The temporal resolution of the heat transfer is a few tens of picoseconds.Comment: 4 page

Nanoscale heat transfer at contact between a hot tip and a substrate

Hot tips are used either for characterizing nanostructures by using scanning thermal microscopes or for local heating to assist data writing. The tip-sample thermal interaction involves conduction at solid-solid contact as well as conduction through the ambient gas and through the water meniscus. We analyze those three heat transfer modes with experimental data and modeling. We conclude that the three modes contribute in a similar manner to the thermal contact conductance but they have distinct contact radii ranging from 30 nm to 1 micron. We also show that any scanning thermal microscope has a 1-3 microns resolution when used in ambient air

Temperature measurement of sub-micrometric ICs by scanning thermal microscopy

Surface temperature measurements were performed with a Scanning Thermal Microscope mounted with a thermoresistive wire probe of micrometrSurface temperature measurements were performed with a Scanning Thermal Microscope mounted with a thermoresistive wire probe of micrometric size. A CMOS device was designed with arrays of resistive lines 0.35µm in width. The array periods are 0.8 µm and 10µm to study the spatial resolution of the SThM. Integrated Circuits with passivation layers of micrometric and nanometric thicknesses were tested. To enhance signal-to-noise ratio, the resistive lines were heated with an AC current. The passivation layer of nanometric thickness allows us to distinguish the lines when the array period is 10μm. The results raise the difficulties of the SThM measurement due to the design and the topography of ICs on one hand and the size of the thermal probe on the other hand.ic size. A CMOS device was designed with arrays of resistive lines 0.35µm in width. The array periods are 0.8 µm and 10µm to study the spatial resolution of the SThM. Integrated Circuits with passivation layers of micrometric and nanometric thicknesses were tested. To enhance signal-to-noise ratio, the resistive lines were heated with an AC current. The passivation layer of nanometric thickness allows us to distinguish the lines when the array period is 10μm. The results raise the difficulties of the SThM measurement due to the design and the topography of ICs on one hand and the size of the thermal probe on the other hand

Effects of spatial dispersion in near-field radiative heat transfer between two parallel metallic surfaces

We study the heat transfer between two parallel metallic semi-infinite media with a gap in the nanometer-scale range. We show that the near-field radiative heat flux saturates at distances smaller than the metal skin depth when using a local dielectric constant and investigate the origin of this effect. The effect of non-local corrections is analysed using the Lindhard-Mermin and Boltzmann-Mermin models. We find that local and non-local models yield the same heat fluxes for gaps larger than 2 nm. Finally, we explain the saturation observed in a recent experiment as a manifestation of the skin depth and show that heat is mainly dissipated by eddy currents in metallic bodies.Comment: Version without figures (8 figures in the complete version

Epidemics on contact networks: a general stochastic approach

Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach is especially well adapted for modelling spreading processes and/or population dynamics. In particular, the generality of our systematic framework and the fact that its assumptions are explicitly stated suggests that it could be used as a common ground for comparing existing epidemics models too complex for direct comparison, such as agent-based computer simulations. We provide many examples for the special cases of susceptible-infectious-susceptible (SIS) and susceptible-infectious-removed (SIR) dynamics (e.g., epidemics propagation) and we observe multiple situations where accurate results may be obtained at low computational cost. Our perspective reveals a subtle balance between the complex requirements of a realistic model and its basic assumptions.Comment: Main document: 16 pages, 7 figures. Electronic Supplementary Material (included): 6 pages, 1 tabl

Near-field induction heating of metallic nanoparticles due to infrared magnetic dipole contribution

We revisit the electromagnetic heat transfer between a metallic nanoparticle and a metallic semi-infinite substrate, commonly studied using the electric dipole approximation. For infrared and microwave frequencies, we find that the magnetic polarizability of the particle is larger than the electric one. We also find that the local density of states in the near field is dominated by the magnetic contribution. As a consequence, the power absorbed by the particle in the near field is due to dissipation by fluctuating eddy currents. These results show that a number of near-field effects involving metallic particles should be affected by the fluctuating magnetic fields.Comment: publi\'e dans Physical Review B 77 (2008), version avant revie