A comparison of neighbor search algorithms for large rigid molecules

Fast determination of neighboring atoms is an essential step in molecular dynamics simulations or Monte Carlo computations, and there exists a variety of algorithms to efficiently compute neighbor lists. However, most of these algorithms are general, and not specifically designed for a given type of application. As a result, although their average performance is satisfactory, they might be inappropriate in some specific application domains. In this article, we study the case of detecting neighbors between large rigid molecules, which has applications in, e.g., rigid body molecular docking, Monte Carlo simulations of molecular self-assembly or diffusion, and rigid body molecular dynamics simulations. More precisely, we compare the traditional grid-based algorithm to a series of hierarchy-based algorithms that use bounding volumes to rapidly eliminate large groups of irrelevant pairs of atoms during the neighbor search. We compare the performance of these algorithms based on several parameters: the size of the molecules, the average distance between them, the cutoff distance, as well as the type of bounding volume used in the culling hierarchy (AABB, OBB, wrapped, or layered spheres). We demonstrate that for relatively large systems (> 100,000 atoms) the algorithm based on the hierarchy of wrapped spheres shows the best results and the traditional grid-based algorithm gives the worst timings. For small systems, however, the grid-based algorithm and the one based on the wrapped sphere hierarchy are beneficial.     

Specific detection of Campylobacter jejuni using the bacteriophage NCTC 12673 receptor binding protein as a probe

Campylobacter jejuni is found in the intestines of poultry, cattle, swine, wild birds and pet animals and is the major cause of foodborne gastroenteritis in developed countries. We report the use of the receptor binding protein (RBP) of Campylobacter bacteriophage NCTC 12673 for the specific capture of Campylobacter jejuni bacteria using RBP-derivatized capturing surfaces. The Gp48 RBP was expressed as a glutathione S-transferase-Gp48 (GST-Gp48) fusion protein and immobilized onto surface plasmon resonance (SPR) surfaces using glutathione self-assembled monolayers (GSH SAM). Bovine serum albumin (BSA) was used to block any non-specific binding. Glutathione SAM leads to an oriented attachment of the protein, resulting in a two- to three-fold improvement of bacterial capture when compared to dithiobis(succinimidyl propionate) (DTSP) SAM-based unoriented attachment. The specificity of recognition was confirmed using Salmonella enterica subsp. enterica serovar Typhimurium as a negative control, which indeed showed negligible binding. The detection limit of the RBP-derivatized SPR surfaces was found to be 10(2) cfu/ml. Finally, GST-Gp48 was also immobilized onto magnetic beads that were successfully used to capture and pre-concentrate the host pathogen from suspension.     

Nilmanifolds with a calibrated G2-structure

We introduce obstructions to the existence of a calibrated G₂-structure on a Lie algebra g of dimension seven, not necessarily nilpotent. In particular, we prove that if there is a Lie algebra epimorphism from g to a six-dimensional Lie algebra h with kernel contained in the center of g, then h has a symplectic form. As a consequence, we obtain a classification of the nilpotent Lie algebras that admit a calibrated G₂-structure.     

Influence of the aspect ratio on boiling flows in rectangular mini-channels

This article presents experiments conducted with two single rectangular mini-channels of same hydraulic diameter (1.4 mm) and different aspect ratios for conditions of horizontal boiling flow. The Forane® 365 HX used was subcooled (ΔT_sub = 15 °C) for all the boiling curves presented in the paper. Local heat transfer coefficients were measured for heat flux ranging from 25 to 62 kW m⁻² and mass flux from 200 kg m⁻² s⁻¹ to 400 kg m⁻² s⁻¹. The boiling flows were observed with two different cameras (depending on the flow velocity) through a visualization window. The flow patterns in the two channels were compared for similar conditions. The results show that the boiling heat transfer coefficient and the pressure drop values are different for the two single mini-channels. For low heat flux condition, the channel with lowest aspect ratio (H/W = 0.143) has a higher heat transfer coefficient. On the other hand, for high heat flux condition, the opposite situation occurs, namely the heat transfer coefficient becomes higher for the channel with highest aspect ratio (H/W = 0.43). This is probably due to the earlier onset of dryout in the channel with lowest aspect ratio. For the two cases of heating, the pressure drop for the two-phase flow remains lower for the channel with lowest aspect ratio. These results show that the aspect ratio plays a substantial role for boiling flows in rectangular channels. As for single-phase flows, the heat transfer characteristics are significantly influenced (even though the hydraulic diameter remains the same) by this parameter.     

Development and characterisation of an XeCl excimer laser-generated soft-X-ray plasma source and its applications

Summary A large-aperture, long-pulse XeCl excimer laser has been used to generate a soft-X-ray plasma source. Several laser optical configurations have been employed to optimise X-ray emission, including positive-branch unstable resonators and injection by seeding the gain region of the laser with a small commercial excimer laser, resulting in power densities in the range 10¹²–10¹⁴ W cm⁻². The characteristics of the plasma source for each different laser configuration and for different target materials are investigated. The most suitable source conditions (spectral energy distribution, time duration, etc.) for specific applications are discussed. Supported by the Royal Society, UK. Supported by INFM, Italy.     

Biosystem response to soft-X-rays irradiation: non-monotonic effects in the relevant biological parameters of yeast cells

Summary Soft-X-rays irradiation of yeast cells allows selective interference with different cellular structures. The monitoring of different physical parameters leads to substantial variations in the response to X-rays showing that monotonicity should not be taken for granted. Also at INFM (Istituto Nazionale di Fisica della Materia).