CO2 packing polymorphism under confinement in cylindrical nanopores

We investigate the effect of cylindrical nano-confinement on the phase behaviour of a rigid model of carbon dioxide using both molecular dynamics and well tempered metadynamics. To this aim we study a simplified pore model across a parameter space comprising pore diameter, CO2-pore wall potential and CO2 density. In order to systematically identify ordering events within the pore model we devise a generally applicable approach based on the analysis of the distribution of intermolecular orientations. Our simulations suggest that, while confinement in nano-pores inhibits the formation of known crystal structures, it induces a remarkable variety of ordered packings unrelated to their bulk counterparts, and favours the establishment of short range order in the fluid phase. We summarise our findings by proposing a qualitative phase diagram for this model

Lattice gas cellular automata model for rippling and aggregation in myxobacteria

A lattice-gas cellular automaton (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2-3 minutes, a minimum response time of up to 1 minute and no maximum oscillation period best reproduce rippling in the experiments of {\it Myxoccoccus xanthus}. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented

Two-dimensional array of magnetic particles: The role of an interaction cutoff

Based on theoretical results and simulations, in two-dimensional arrangements of a dense dipolar particle system, there are two relevant local dipole arrangements: (1) a ferromagnetic state with dipoles organized in a triangular lattice, and (2) an anti-ferromagnetic state with dipoles organized in a square lattice. In order to accelerate simulation algorithms we search for the possibility of cutting off the interaction potential. Simulations on a dipolar two-line system lead to the observation that the ferromagnetic state is much more sensitive to the interaction cutoff $R$ than the corresponding anti-ferromagnetic state. For $R \gtrsim 8$ (measured in particle diameters) there is no substantial change in the energetical balance of the ferromagnetic and anti-ferromagnetic state and the ferromagnetic state slightly dominates over the anti-ferromagnetic state, while the situation is changed rapidly for lower interaction cutoff values, leading to the disappearance of the ferromagnetic ground state. We studied the effect of bending ferromagnetic and anti-ferromagnetic two-line systems and we observed that the cutoff has a major impact on the energetical balance of the ferromagnetic and anti-ferromagnetic state for $R \lesssim 4$. Based on our results we argue that $R \approx 5$ is a reasonable choice for dipole-dipole interaction cutoff in two-dimensional dipolar hard sphere systems, if one is interested in local ordering.Comment: 8 page

Fast, Scalable, and Interactive Software for Landau-de Gennes Numerical Modeling of Nematic Topological Defects

Numerical modeling of nematic liquid crystals using the tensorial Landau-de Gennes (LdG) theory provides detailed insights into the structure and energetics of the enormous variety of possible topological defect configurations that may arise when the liquid crystal is in contact with colloidal inclusions or structured boundaries. However, these methods can be computationally expensive, making it challenging to predict (meta)stable configurations involving several colloidal particles, and they are often restricted to system sizes well below the experimental scale. Here we present an open-source software package that exploits the embarrassingly parallel structure of the lattice discretization of the LdG approach. Our implementation, combining CUDA/C++ and OpenMPI, allows users to accelerate simulations using both CPU and GPU resources in either single- or multiple-core configurations. We make use of an efficient minimization algorithm, the Fast Inertial Relaxation Engine (FIRE) method, that is well-suited to large-scale parallelization, requiring little additional memory or computational cost while offering performance competitive with other commonly used methods. In multi-core operation we are able to scale simulations up to supra-micron length scales of experimental relevance, and in single-core operation the simulation package includes a user-friendly GUI environment for rapid prototyping of interfacial features and the multifarious defect states they can promote. To demonstrate this software package, we examine in detail the competition between curvilinear disclinations and point-like hedgehog defects as size scale, material properties, and geometric features are varied. We also study the effects of an interface patterned with an array of topological point-defects.Comment: 16 pages, 6 figures, 1 youtube link. The full catastroph

Optimized coupling of cold atoms into a fiber using a blue-detuned hollow-beam funnel

We theoretically investigate the process of coupling cold atoms into the core of a hollow-core photonic-crystal optical fiber using a blue-detuned Laguerre-Gaussian beam. In contrast to the use of a red-detuned Gaussian beam to couple the atoms, the blue-detuned hollow-beam can confine cold atoms to the darkest regions of the beam thereby minimizing shifts in the internal states and making the guide highly robust to heating effects. This single optical beam is used as both a funnel and guide to maximize the number of atoms into the fiber. In the proposed experiment, Rb atoms are loaded into a magneto-optical trap (MOT) above a vertically-oriented optical fiber. We observe a gravito-optical trapping effect for atoms with high orbital momentum around the trap axis, which prevents atoms from coupling to the fiber: these atoms lack the kinetic energy to escape the potential and are thus trapped in the laser funnel indefinitely. We find that by reducing the dipolar force to the point at which the trapping effect just vanishes, it is possible to optimize the coupling of atoms into the fiber. Our simulations predict that by using a low-power (2.5 mW) and far-detuned (300 GHz) Laguerre-Gaussian beam with a 20-{\mu}m radius core hollow-fiber it is possible to couple 11% of the atoms from a MOT 9 mm away from the fiber. When MOT is positioned further away, coupling efficiencies over 50% can be achieved with larger core fibers.Comment: 11 pages, 12 figures, 1 tabl

Solid-State Effects on the Optical Excitation of Push-Pull Molecular J-Aggregates by First-Principles Simulations

J-aggregates are a class of low-dimensional molecular crystals which display enhanced interaction with light. These systems show interesting optical properties as an intense and narrow red-shifted absorption peak (J-band) with respect to the spectrum of the corresponding monomer. The need to theoretically investigate optical excitations in J-aggregates is twofold: a thorough first-principles description is still missing and a renewed interest is rising recently in understanding the nature of the J-band, in particular regarding the collective mechanisms involved in its formation. In this work, we investigate the electronic and optical properties of a J-aggregate molecular crystal made of ordered arrangements of organic push-pull chromophores. By using a time dependent density functional theory approach, we assess the role of the molecular packing in the enhancement and red shift of the J-band along with the effects of confinement in the optical absorption, when moving from bulk to low-dimensional crystal structures. We simulate the optical absorption of different configurations (i.e., monomer, dimers, a polymer chain, and a monolayer sheet) extracted from the bulk crystal. By analyzing the induced charge density associated with the J-band, we conclude that it is a longitudinal excitation, delocalized along parallel linear chains and that its overall red shift results from competing coupling mechanisms, some giving red shift and others giving blue shift, which derive from both coupling between transition densities and renormalization of the single-particle energy levels.Comment: This is the published version of the work, distributed under the terms of the ACS AuthorChoice licence https://pubs.acs.org/page/policy/authorchoice_termsofuse.htm