Alignment-free molecular shape comparison using spectral geometry: the framework

A framework is presented for the calculation of novel alignment-free descriptors of molecular shape. The methods are based on the technique of spectral geometry which has been developed in the field of computer vision where it has shown impressive performance for the comparison of deformable objects such as people and animals. Spectral geometry techniques encode shape by capturing the curvature of the surface of an object into a compact, information-rich representation that is alignment-free while also being invariant to isometric deformations, that is, changes that do not distort distances over the surface. Here, we adapt the technique to the new domain of molecular shape representation. We describe a series of parametrization steps aimed at optimizing the method for this new domain. Our focus here is on demonstrating that the basic approach is able to capture a molecular shape into a compact and information-rich descriptor. We demonstrate improved performance in virtual screening over a more established alignment-free method and impressive performance compared to a more accurate, but much more computationally demanding, alignment-based approach

Gibbs' Paradox according to Gibbs and slightly beyond

The so-called Gibbs paradox is a paradigmatic narrative illustrating the necessity to account for the N! ways of permuting N identical particles when summing over microstates. Yet, there exist some mixing scenarios for which the expected thermodynamic outcome depends on the viewpoint one chooses to justify this combinatorial term. After a brief summary on Gibbs' paradox and what is the standard rationale used to justify its resolution, we will allow ourself to question from a historical standpoint whether the Gibbs paradox has actually anything to do with Gibbs' work. In so doing, we also aim at shedding a new light with regards to some of the theoretical claims surrounding its resolution. We will then turn to the statistical thermodynamics of discrete and continuous mixtures and introduce the notion of composition entropy to characterise these systems. This will enable us to address, in a certain sense, a "curiosity" pointed out by Gibbs in a paper published in 1876. Finally, we will �nish by proposing a connexion between the results we propose and a recent extension of the Landauer bound regarding the minimum amount of heat to be dissipated to reset one bit of memory

Search for Darkonium in e+e- Collisions

Collider searches for dark sectors, new particles interacting only feebly with ordinary matter, have largely focused on identifying signatures of new mediators, leaving much of dark sector structures unexplored. In particular, the existence of dark matter bound states (darkonia) remains to be investigated. This possibility could arise in a simple model in which a dark photon (A0 ) is light enough to generate an attractive force between dark fermions. We report herein a search for a JPC ¼ 1−− darkonium state, the ϒD, produced in the reaction eþe− → γϒD, ϒD → A0 A0 A0 , where the dark photons subsequently decay into pairs of leptons or pions, using 514 fb−1 of data collected with the BABAR detector. No significant signal is observed, and we set bounds on the γ − A0 kinetic mixing as a function of the dark sector coupling constant for 0.001 < mA0 < 3.16 GeV and 0.05 < mϒD < 9.5 GeV.publishedVersio

Drug-resistant tuberculosis transmission and resistance amplification within families

ArticleDrug-resistant tuberculosis is caused by transmission of resistant strains of Mycobacterium tuberculosis and by acquisition of resistance through inadequate treatment. We investigated the clinical and molecular features of the disease in 2 families after drug-resistant tuberculosis was identified in 2 children. The findings demonstrate the potential for resistance to be transmitted and amplified within families

The structure and terahertz dynamics of water confined in nanoscale pools in salt solutions

The behaviour of liquid water below its melting point is of great interest as it may hold clues to the properties of normal liquid water and of water in and on the surfaces of biomolecules. A second critical point, giving rise to a polyamorphic transition between high and low density water, may be hidden in the supercooled region but cannot be observed directly. Here it is shown that water can be locked up in nano-pools or worm-like structures using aqueous LiCl salt solutions and can be studied with terahertz spectroscopies. Very high dynamic range ultrafast femtosecond optical Kerr effect (OKE) spectroscopy is used to study the temperature-dependent behaviour of water in these nano-pools on timescales from 10 fs to 4 ns. These experiments are complemented by temperature-dependent nuclear magnetic resonance (NMR) diffusion measurements, concentration-dependent Fourier-transform infrared (FTIR) measurements, and temperature-dependent rheology. It is found that liquid water in the nanoscale pools undergoes a fragile-to-strong transition at about 220 K associated with a sharp increase in the inhomogeneity of translational dynamics

Evaluation of the current status and knowledge contributions of professional doctorates

The article examines the status and knowledge contributions of professional doctorates (PDs) undertaken by practising professionals who in most cases are not intending to join the academic community. The purpose of these doctorates is usually to research and develop an original contribution to practice through practitioner-research. Giving greater primacy to practice knowledge has caused new developments in doctoral education. The discussion is based upon a research project and an extensive literature review. Internationally, quality assurance agencies have generally embraced more work-related and practice-oriented criteria in doctoral learning. Doctoral learning that seeks to enhance practice and develop benefit to communities and organisations in professional contexts leads to different pedagogic protocols for higher education, for example a differently ordered approach to ethical issues of research, assessment and peer review. More curriculum development and understanding of the wider knowledge contributions of doctorates is needed across higher education and professional communities