Energy Level Quasi-Crossings: Accidental Degeneracies or Signature of Quantum Chaos?

In the field of quantum chaos, the study of energy levels plays an important role. The aim of this review paper is to critically discuss some of the main contributions regarding the connection between classical dynamics, semi-classical quantization and spectral statistics of energy levels. In particular, we analyze in detail degeneracies and quasi-crossings in the eigenvalues of quantum Hamiltonians which are classically non-integrable. Summary: 1. Introduction; 2. Quasi-Crossing and Chaos; 3. Molecular Spectroscopy; 4. Nuclear Models; 4.1 Zirnbauer-Verbaashot-Weidenmuller Model; 4.2 Lipkin-Meshow-Glick Model; 5. Particle Physics and Field Theory; 6. Conclusions.Comment: 26 pages, Latex, 9 figures, to be published in International Journal of Modern Physics

Nonlinear wave interactions in quantum magnetoplasmas

Nonlinear interactions involving electrostatic upper-hybrid (UH), ion-cyclotron (IC), lower-hybrid (LH), and Alfven waves in quantum magnetoplasmas are considered. For this purpose, the quantum hydrodynamical equations are used to derive the governing equations for nonlinearly coupled UH, IC, LH, and Alfven waves. The equations are then Fourier analyzed to obtain nonlinear dispersion relations, which admit both decay and modulational instabilities of the UH waves at quantum scales. The growth rates of the instabilities are presented. They can be useful in applications of our work to diagnostics in laboratory and astrophysical settings.Comment: 15 pages, to appear in Physics of Plasma

Dust ion-acoustic shocks in quantum dusty pair-ion plasmas

The formation of dust ion-acoustic shocks (DIASs) in a four-component quantum plasma whose constituents are electrons, both positive and negative ions and immobile charged dust grains, is studied. The effects of both the dissipation due to kinematic viscosity and the dispersion caused by the charge separation as well as the quantum tunneling due to the Bohm potential are taken into account. The propagation of small but finite amplitude dust ion-acoustic waves (DIAWs) is governed by the Korteweg-de Vries-Burger (KdVB) equation which exhibits both oscillatory and monotonic shocks depending not only on the viscosity parameters, but also on the quantum parameter H (the ratio of the electron plasmon to the electron Fermi energy) and the positive to negative ion density ratio. Large amplitude stationary shocks are recovered for a Mach number exceeding its critical value. Unlike the small amplitude shocks, quite a smaller value of the viscosity parameter, H and the density ratio may lead to the large amplitude monotonic shock strucutres. The results could be of importance in astrophysical and laser produced plasmas.Comment: 15 pages, 5 figure

Heavy-Fermion Instability in Double-Degenerate Plasmas

In this work we study the propagations of normal frequency modes for quantum hydrodynamic (QHD) waves in the linear limit and introduce a new kind of instability in a double-degenerate plasma. Three different regimes, namely, low, intermediate and high magnetic field strengths are considered which span the applicability of the work to a wide variety of environments. Distinct behavior is observed for different regimes, for instance, in the laboratory-scale field regime no frequency-mode instability occurs unlike those of intermediate and high magnetic-field strength regimes. It is also found that the instability of this kind is due to the heavy-fermions which appear below a critical effective-mass parameter ($\mu_{cr}=\sqrt{3}$) and that the responses of the two (lower and upper frequency) modes to fractional effective-mass change in different effective-mass parameter ranges (below and above the critical value) are quite opposite to each other. It is shown that, the heavy-fermion instability due to extremely high magnetic field such as that encountered for a neutron-star crust can lead to confinement of stable propagations in both lower and upper frequency modes to the magnetic poles. Current study can have important implications for linear wave dynamics in both laboratory and astrophysical environments possessing high magnetic fields

DeepREx-WS: A web server for characterising protein–solvent interaction starting from sequence

Protein–solvent interaction provides important features for protein surface engineering when the structure is absent or partially solved. Presently, we can integrate the notion of solvent exposed/buried residues with that of their flexibility and intrinsic disorder to highlight regions where mutations may increase or decrease protein stability in order to modify proteins for biotechnological reasons, while preserving their functional integrity. Here we describe a web server, which provides the unique possibility of integrating knowledge of solvent and non-solvent exposure with that of residue conservation, flexibility and disorder of a protein sequence, for a better understanding of which regions are relevant for protein integrity. The core of the webserver is DeepREx, a novel deep learning-based tool that classifies each residue in the sequence as buried or exposed. DeepREx is trained on a high-quality, non-redundant dataset derived from the Protein Data Bank comprising 2332 monomeric protein chains and benchmarked on a blind test set including 200 protein sequences unrelated with the training set. Results show that DeepREx performs at the state-of-the-art in the field. In turn, the Web Server, DeepREx-WS, supplements the predictions of DeepREx with features that allow a better characterisation of exposed and buried regions: i) residue conservation derived from multiple sequence alignment; ii) local sequence hydrophobicity; iii) residue flexibility computed with MEDUSA; iv) a predictor of secondary structure; v) the presence of disordered regions as derived from MobiDB-Lite3.0. The web server allows browsing, selecting and intersecting the different features. We demonstrate a possible application of the DeepREx-WS for assisting the identification of residues to be variated in protein surface engineering processes

Trees and Shrubs Monitoring Using an Ecological Approach: The Conclusion of the Restoration Project of Borgotrebbia Landfill (Northern Italy)

Plants growth monitoring in restored landfills are poorly available in literature. These data might be of critical importance for the evaluation and improvement of current and future restoration projects. Our study was focused on the plant\u2019s growth monitoring during a Life project (LIFE10 ENV/IT/000400 NEW LIFE), designed to restore a closed landfill (located in Northern Italy) using reconstituted soils. The growth monitoring was conducted on mortality rate, stress symptoms and phenological cycle completion of 10 plant species (trees and shrubs). Data were acquired during the 12 months following the end of the restoration with an ecological approach, using Landolt\u2019s indices and CSR functional strategy. It was observed that the stress-tolerant and the heliphilous ruderal species were the ones that best adapt to the restored environment (dead plants: 0 - 39%; unhealthy plants: 24 - 42%), whereas the most competitive species were the ones with highest mortality (17 - 43%) and stress symptoms (43 - 51%)

Case Report: REL-1017 Reduces Abnormal Clinician Administered Dissociative States Scale Scores in Patients with Major Depressive Disorder

BACKGROUND: Dissociative symptoms may be found in a subset of patients with major depressive disorders (MDD). The Clinician-Administered Dissociative States Scale (CADSS) is a 23-item scale for the measurement of present-state dissociative symptoms with good inter-rater reliability and construct validity that can discriminate patients with dissociative disorders. The total CADSS score is derived by adding the score for each of the 23 items. A score of 4 or more on the CADSS is considered abnormal and clinically meaningful. Uncompetitive N-methyl-d-aspartic acid receptor (NMDAR) channel blockers have been proposed as a treatment for post-traumatic stress disorder (PTSD). REL-1017 is a novel, low potency, NMDAR channel blocker currently in Phase 3 studies for MDD. METHODS: This retrospective case series describes a subset of patients from a double-blind, randomized, placebo-controlled, in-patient 7-day, phase 2 trial of oral, once daily, 25 mg (75 mg loading dose on day 1, first dose) and 50 mg REL-1017 (100 mg loading dose on day 1, first dose) as an adjunctive treatment for MDD. This subset of patients was selected based on abnormal CADSS score at baseline, pre-treatment with the study drug. As part of REL-1017 safety evaluation, the CADSS was administered at four timepoints to all study patients: (a) 30 to 60 minutes pre-treatment at baseline on day 1; (b) 2 hours post-treatment on day 1 (after the first dose of study drug); (c) 2 hours post-treatment on day 7 (after the last dose); and (d) prior to discharge on day 9 (2 days after the last dose). RESULTS: Among the 62 randomized patients, four patients had a CADSS score of at least 4 on day 1 before study drug administration (2 patients in the 25 mg arm [CADSS score 22 and 4]; 1 patient in the 50 mg arm [CADSS score 35]; 1 patient in the placebo arm [CADSS score 6]). Among these 4 patients, starting on day 1, 2 hours post-treatment, the 2 subjects in the 25 mg subgroup (75 mg loading dose) and 1 subject in the 50 mg subgroup (100 mg loading dose) showed a clinically meaningful decrease in their CADSS score, while the single patient in the placebo group showed no change. CADSS scores on Day 1 pre-treatment, day 1 post-treatment, day 7 post last treatment, and on day 9 prior to discharge were 22-2-6-0; 4-0-0-0; 35-14-9-0, and 6-6-n/a-n/a, for the two patients in the 25 mg REL-1017 subgroup, the single patient in the 50 mg REL-1017 subgroup, and the single patient in the placebo group, respectively. CONCLUSIONS: These retrospective case report data potentially signal that REL-1017 may determine rapid and sustained improvement in patients with MDD and concurrent clinically meaningful dissociative symptoms assessed by a CADSS score of 4 or above. Ongoing phase 3 trials with REL-1017 are expected to enroll a total of 1200 outpatients with MDD. These studies will potentially generate additional data that may support the initiation of controlled studies with REL-1017 for the treatment of PTSD. FUNDING: Relmada Therapeutics

CoCoNat: a novel method based on deep learning for coiled-coil prediction

MOTIVATION: Coiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction methods include the precise identification of CCD boundaries, the annotation of the typical heptad repeat pattern along the coiled-coil helices as well as the prediction of the oligomerization state. RESULTS: In this article, we describe CoCoNat, a novel method for predicting coiled-coil helix boundaries, residue-level register annotation, and oligomerization state. Our method encodes sequences with the combination of two state-of-the-art protein language models and implements a three-step deep learning procedure concatenated with a Grammatical-Restrained Hidden Conditional Random Field for CCD identification and refinement. A final neural network predicts the oligomerization state. When tested on a blind test set routinely adopted, CoCoNat obtains a performance superior to the current state-of-the-art both for residue-level and segment-level CCD. CoCoNat significantly outperforms the most recent state-of-the-art methods on register annotation and prediction of oligomerization states. AVAILABILITY AND IMPLEMENTATION: CoCoNat web server is available at https://coconat.biocomp.unibo.it. Standalone version is available on GitHub at https://github.com/BolognaBiocomp/coconat

Spin kinetic theory - quantum kinetic theory in extended phase space

The concept of phase space distribution functions and their evolution is used in the case of en enlarged phase space. In particular, we include the intrinsic spin of particles and present a quantum kinetic evolution equation for a scalar quasi-distribution function. In contrast to the proper Wigner transformation technique, for which we expect the corresponding quasi-distribution function to be a complex matrix, we introduce a spin projection operator for the density matrix in order to obtain the aforementioned scalar quasi-distribution function. There is a close correspondence between this projection operator and the Husimi (or Q) function used extensively in quantum optics. Such a function is based on a Gaussian smearing of a Wigner function, giving a positive definite distribution function. Thus, our approach gives a Wigner-Husimi quasi-distribution function in extended phase space, for which the reduced distribution function on the Bloch sphere is strictly positive. We also discuss the gauge issue and the fluid moment hierarchy based on such a quantum kinetic theory.Comment: 10 pages, to appear in Transport Theory and Statistical Physics, proceedings of Vlasovia III, 200

Antibacterial effects of two synthetic peptides against Enterococcus faecalis biofilms: A preliminary in vitro study

Aim: Current endodontic techniques are unable to fully eradicate intracanal bacteria. Thus, new agents that effectively eliminate endodontic pathogens are needed. The aim of this study was to assess the antibacterial properties of two synthetic peptides, namely KP and L18R, against planktonic cells and biofilms of the endodontic pathogen Enterococcus faecalis. Methodology: KP and L18R bactericidal activity against E. faecalis ATCC 29212 was evaluated by colony forming unit assays and the half maximal effective concentration (EC50) was calculated. The effect of peptides on E. faecalis biofilm formation onto polystyrene plates was also assessed by the crystal violet assay. Confocal laser scanning microscopy (CLSM) analysis was carried out to compare the effects of KP, L18R and a Ca(OH)2 saturated solution in an in vitro model of dental infection consisting in 2-day-old E. faecalis biofilms grown on hydroxyapatite disks. Results: Both KP and L18R showed strong bactericidal activity against planktonic E. faecalis. L18R proved to be 10-folds more ef fective than KP (KP and L18R EC50 values=4.520×10-6 M and 3.624×10-7 M, respectively). Peptides inhibited E. faecalis biofilm formation in a dose-dependent manner and L18R resulted more effectivethan KP. CLSM images showed that Ca(OH)2, KP and L18R remarkably impaired E. faecal is biof i lms pre -grown on hydroxyapatite. Conclusions: KP and L18R effectively inhibited E. faecalis, both in planktonic and biofilm form. L18R demonstrated a more potent antibacterial activity than KP. These preliminary results suggest that antimicrobial peptides may represent a promising new strategy for endodontic infection control