Nucleosomes in the chromatin

Molecular dynamics at T=310 K MD of the tri-nucleosome complex in ionized water. Above: the starting configuration. Below: final configuration after 300 ns of MD. The DNA is in blue, histones silver, ions indicated by points.

Radiation environment on Mars surface

Topography MAP from Mars Global Surveyor, Mars Orbiter Laser Altimeter (MOLA). Copyright: NASA.
Radiation spectra at the surface of Mars at Oxia Planum as induced by GCR impacting protons and α-particles during solar minimum (January 2009) (solid lines) and close to solar maximum during the declining phase of solar cycle 23 (early October 2003) (circles): downward and upward contributions, separated for particle type. GCR, Galactic Cosmic Rays. (Monte Carlo simulation with dMEREM, SpenVis, GEANT4).

DNA damage and repair

The interrogation complex hOGG1/DNA after 500 ns of MD equilibration at T=310K in TIP3P water with 0.1M NaCl. As observed in the experimental configuration, OGG1 (color ribbons) grabs the DNA (white) containing the 8-oxoG at two distinct sites: the purple region holds the 8-oxoG and everts the whole nucleotide into extra-helical conformation (white spheres); the green region holds DNA at the distance of about one-half turn.

DNA aptamers to detect cancer cells

EpCAM is heavily expressed on the surface of cancer cells. (b) Schematic representation of the device used for the molecular recognition of EpCAM on a target cell. The molecular dynamics simulations of EpCAM (purple) interacting with the DNA aptamer ("aptasensor") immobilised on the Au surface, allow to interpret the variation of tunnel current from the redox species attached to one end of the DNA. (c) AFM image (10×10 μm) and AFM cross section of the nanopillars to immobilise cancer cells. (d) Schematic representation of the typical current-voltage cyclic voltammetry of redox-labelled aptasensors.

The big paper on 3 nucleosomes is out!

Just appeared in Journal of Molecular Biology:

Nucleosome Array Deformation in Chromatin is Sustained by Bending, Twisting and Kinking of Linker DNA, F. Cleri, S. Giordano, R. Blossey (J. Mol. Biol. 435, 128263 (2023))

New papers on statistical mechanics appeared in 2023

Our team has just published two new papers on very special stat-mech themes:

On the one-dimensional transition state theory and the relation between statistical and deterministic oscillation frequencies of anharmonic energy wells S. Giordano, F. Cleri. R Blossey (Ann. der Phys. 535, 00294, 2023)

Infinite ergodicity in generalized geometric Brownian motions with nonlinear drift S. Giordano, F. Cleri. R Blossey (Phys. Rev. E 107, 044111, 2023)

New PhD student

Congratulations to Safwen Ghediri, new PhD student who joined our group in June, to work on the ANR project DYPROSOME!

Detection of cancer cells: two new papers on biosensors & bioelectronics

Last papers from the IEMN-IBL-LIMMS collaboration:

Redox-labelled electrochemical aptasensors with nanosupported cancer cells 

Single-Cell Electrochemical Aptasensor Array

New paper appeared in eLife, March 2022

Check out our last paper just published in eLife, last part of M. Tomezak's PhD:

The out-of-field dose in radiation therapy induces delayed tumorigenesis by senescence evasion

Welcome our new PhD student Parvathy!

Congratulations to Parvathy Sarma who joined our group February 2022 to work on the SENEXIMEX project, on radiation-induced cell senescence! Welcome Parvathy, we wish you a productive PhD work!

 

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