Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank

We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein-ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 A), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.Peer reviewe

Enhanced Production of Neutron-Rich Rare Isotopes in Peripheral Collisions at Fermi Energies

A large enhancement in the production of neutron-rich projectile residues is observed in the reactions of a 25 MeV/nucleon 86Kr beam with the neutron rich 124Sn and 64Ni targets relative to the predictions of the EPAX parametrization of high-energy fragmentation, as well as relative to the reaction with the less neutron-rich 112Sn target. The data demonstrate the significant effect of the target neutron-to-proton ratio (N/Z) in peripheral collisions at Fermi energies. A hybrid model based on a deep-inelastic transfer code (DIT) followed by a statistical de-excitation code appears to account for part of the observed large cross sections. The DIT simulation indicates that the production of the neutron-rich nuclides in these reactions is associated with peripheral nucleon exchange. In such peripheral encounters, the neutron skins of the neutron-rich 124Sn and 64Ni target nuclei may play an important role. From a practical viewpoint, such reactions between massive neutron-rich nuclei offer a novel and attractive synthetic avenue to access extremely neutron-rich rare isotopes towards the neutron-drip line.Comment: 4 pages, 3 figures, submitted to Phys. Rev. Let

Electrical model of an NMOS body biased structure in triple-well technology under photoelectric laser stimulation

International audience— This study is driven by the need to optimize failure analysis methodologies based on laser/silicon interactions with an integrated circuit using a triple-well process. It is therefore mandatory to understand the behavior of elementary devices to laser illumination, in order to model and predict the behavior of more complex circuits. This paper presents measurements of the photoelectric currents induced by a pulsed-laser on an NMOS transistor in triple-well Psubstrate/DeepNwell/Pwell structure dedicated to low power body biasing techniques. This evaluation compares the triple-well structure to a classical Psubstrate-only structure of an NMOS transistor. It reveals the possible activation change of the bipolar transistors. Based on these experimental measurements, an electrical model is proposed that makes it possible to simulate the effects induced by photoelectric laser stimulation

SIGMA and XTE observations of the soft X-ray transient XTEJ1755-324

We present observations of the X-ray transient XTEJ1755-324 performed during summer 1997 with the XTE satellite and with the SIGMA hard X-ray telescope onboard the GRANAT observatory. The source was first detected in soft X-rays with XTE on July 25 1997 with a rather soft X-ray spectrum and its outburst was monitored in soft X-rays up to November 1997. On September 16 it was first detected in hard X-rays by the French soft gamma ray telescope SIGMA during a Galactic Center observation. The flux was stronger on September 16 and 17 reaching a level of about 110 mCrab in the 40-80 keV energy band. On the same days the photon index of the spectrum was determined to be alpha =-2.3 +/- 0.9 (1 sigma error) while the 40-150 keV luminosity was about 8 x 10^{36} erg/s for a distance of 8.5 kpc. SIGMA and XTE results on this source indicate that this source had an ultrasoft-like state during its main outburst and a harder secondary outburst in September. These characteristics make the source similar to X-Nova Muscae 1991, a well known black hole candidate.Comment: 19 pages LaTeX, 6 Postscript figures included, Accepted by Astrophysical Journa

Discovery of the Vanadium Isotopes

Twenty-four vanadium isotopes have so far been observed; the discovery of these isotopes is discussed. For each isotope a brief summary of the first refereed publication, including the production and identification method, is presented.Comment: to be published in At. Data. Nucl. Data Table

Laser Fault Injection into SRAM cells: Picosecond versus Nanosecond pulses

International audience—Laser fault injection into SRAM cells is a widely used technique to perform fault attacks. In previous works, Roscian and Sarafianos studied the relations between the layout of the cell, its different laser-sensitive areas and their associated fault model using 50 ns duration laser pulses. In this paper, we report similar experiments carried out using shorter laser pulses (30 ps duration instead of 50 ns). Laser-sensitive areas that did not appear at 50 ns were observed. Additionally, these experiments confirmed the validity of the bit-set/bit-reset fault model over the bit-flip one. We also propose an upgrade of the simulation model they used to take into account laser pulses in the picosecond range. Finally, we performed additional laser fault injection experiments on the RAM memory of a microcontroller to validate the previous results

Proton drip-line nuclei in Relativistic Hartree-Bogoliubov theory

Ground-state properties of spherical even-even nuclei $14\leq Z \leq 28$ and $N=18,20,22$ are described in the framework of Relativistic Hartree Bogoliubov (RHB) theory. The model uses the NL3 effective interaction in the mean-field Lagrangian, and describes pairing correlations by the pairing part of the finite range Gogny interaction D1S. Binding energies, two-proton separation energies, and proton $rms$ radii that result from fully self-consistent RHB solutions are compared with experimental data. The model predicts the location of the proton drip-line. The isospin dependence of the effective spin-orbit potential is discussed, as well as pairing properties that result from the finite range interaction in the $pp$ channel.Comment: 12 pages, RevTex, 10 p.s figures, submitted to Phys. Rev.

GOHTAM: a website for ‘Genomic Origin of Horizontal Transfers, Alignment and Metagenomics’

Motivation: This website allows the detection of horizontal transfers based on a combination of parametric methods and proposes an origin by researching neighbors in a bank of genomic signatures. This bank is also used to research an origin to DNA fragments from metagenomics studies