A method for molecular dynamics on curved surfaces

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focussed on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to combine standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface, in which such interactions can be taken into account. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates allowing for the reuse of many other standard tools without modifications, including parallelisation through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, confined Brownian motion is obtained, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: (i) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes and (ii) the self-assembly of a coarse-grained virus capsid protein model.Comment: 30 pages, 5 figure

Confinement without boundaries: Anisotropic diffusion on the surface of a cylinder

Densely packed systems of thermal particles in curved geometries are frequently encountered in biological and microfluidic systems. In 2D systems, at sufficiently high surface coverage, diffusive motion is widely known to be strongly affected by physical confinement, e.g., by the walls. In this Letter, we explore the effects of confinement by shape, not rigid boundaries, on the diffusion of particles by confining them to the surface of a cylinder. We find that both the magnitude and the directionality of lateral diffusion is strongly influenced by the radius of the cylinder. An anisotropy between diffusion in the longitudinal and circumferential direction of the cylinder develops. We demonstrate that the origin of this effect lies in the fact that screw-like packings of mono- and oligodisperse discs on the surface of a cylinder induce preferential collective motions in the circumferential direction, but also show that even in polydisperse systems lacking such order an intrinsic finite size confinement effect increases diffusivity in the circumferential direction

Left-wing populist discourse in Belgium: The effect of the rise of the Parti du Travail de Belgique on mainstream parties

Since 2009, the rise of the most important Belgian Francophone left-wing populist party, i.e. the Parti du Travail de Belgique (PTB), has been increasingly seen as a challenge for mainstream parties. Given the lack of research on Belgium within the field of political left-populist discourse, this paper analyses the effect of the growing popularity of the left-populist party on mainstream parties’ discourse. To investigate this issue, a discourse analysis has been conducted following the Modified Spatial Theory which argues that, when triggered, mainstream parties choose between three different strategies (accommodative, dismissive, or adversarial) to respond to the rise of populism. The findings show that, the rise of the PTB has had more effect on the Socialist Party’s discourse, which has accommodated and converged with the PTB on several typically populist issues, while the other two mainstream parties have rather dismissed and tried to discredit the political discourse of the PTB

Impact of Interaction Range and Curvature on Crystal Growth of Particles Confined to Spherical Surfaces

When colloidal particles form a crystal phase on a spherical template, their packing is governed by the effective interaction between them and the elastic strain of bending the growing crystal. For example, if growth commences under appropriate conditions, and the circular crystal that forms reaches a critical size, growth continues by incorporation of defects to alleviate elastic strain. Recently it was found experimentally that, if defect formation is somehow not possible, the crystal instead continues growing in ribbons that protrude from the original crystal. Here we report on computer simulations in which we observe both the formation of ribbons at short interaction ranges and packings that incorporate defects if the interaction is longer-ranged. The ribbons only form above some critical crystal size, below which the nucleus is roughly spherically shaped. We find that the scaling of the critical crystal size differs slightly from the one proposed by the Manoharan group, and reason this is because the actual process is a two-step heterogeneous nucleation of ribbons on top of roughly circular crystals.Comment: 24 pages, 11 figure

Introduction

This introduction sets out the purpose of the volume as well as its societal relevance and summarizes the different approaches used by the authors.&nbsp

A relax-and- fix heuristic for the three-dimensional bin-packing model with transportation constraints

peer reviewe

Three dimensional Bin Packing Problem applied to air transport

Packing boxes into containers is a daily process in many di erent elds and especially in transport. However, the particular case of air transport brings some new constraints such as the stability or the fragility of the cargo. The distribution of the weight has also to be considered. Moreover, this special case also brings some data such as the dimensions of the possible containers, called Unit Load Devices. This paper is concerned with the formulation of the three dimensional palletization which includes the main constraints met in the air cargo industry. It proposes a integer linear program for this combinatorial optimization problem

Huge decreases in the risk of breast cancer relapse over the last three decades

Introduction The aim of this study was to evaluate local and systemic breast cancer control by comparing the risk of relapse in breast cancer patients in 2003–2004 with that in 1972–1979 and in 1980–1986. Methods About 8,570 women diagnosed with invasive breast cancer in 2003–2004 were selected from the population-based Netherlands Cancer Registry and compared with 133 patients treated in 1972–1979 and 174 in 1980–1986. Five-year risk of relapse was calculated by the Kaplan–Meier method. Cox-proportional hazard models were applied to adjust for tumour size, nodal status and age at diagnosis. Results Patients diagnosed in 2003–2004 had smaller tumours and a less advanced nodal stage than patients diagnosed in 1972–1986. In 1972–1979, 1980–1986 and 2003–2004, treatment included mastectomy in 94%, 72% and 47%; postmastectomy radiotherapy in 75%, 70% and 30%; chemotherapy in 9%, 14% and 37% and hormonal therapy in 3%, 3% and 42% of patients, respectively. Five-year risk of locoregional and distant recurrence decreased from 37% and 34% to 15%, respectively. The 5-year risk of second primary breast cancer did not differ and was 1%, 4% and 2%, respectively. The improved relapse-free survival in patients diagnosed in 2003–2004 as compared with 1972–1979 hardly changed after adjustment (HR = 0.38, 95% CI = 0.28–0.52). Conclusion Over the last decades, local breast cancer therapies have become less rigorous, whereas systemic therapy use has increased. Simultaneously, the risk of breast cancer relapse has tremendously decreased. Future novel therapies may lead to such small additional decreases in relapse rates, while the long-term side effects in breast cancer survivors will increas

Des options politico-stratégiques pour le développement professionnel des enseignants universitaires

Le texte qui suit est un résumé des témoignages d’experts de quatre institutions universitaires. Tout au long de ce numéro, ont été présentés et analysés différents dispositifs développés dans les universités pour permettre et soutenir le développement professionnel des enseignants-chercheurs, particulièrement au sein de structures institutionnelles spécifiques (centres de pédagogie universitaire, par exemple). Ces dispositifs sont variés : des formations instituées, des modalités diverses d’..