F. E. Mackay

Modelling defect-bonded chains produced by colloidal particles in a cholesteric liquid crystal

We use a Landau-de Gennes free-energy model to investigate interactions generated by spherical particles with strong planar anchoring immersed in a cholesteric liquid crystal. With a pitch of ~1.5 times the particle diameter, the +1 boojums present for a particle in a nematic split into four +1/2 defects leading to defect lines in the bulk around the particle which look like handles emerging from its surface. When multiple particles are present, handles from adjacent particles join together, forming a defect bond between them. We present results for defect-bonded chains, and investigate the energies associated with this bonding.

Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid ☆

Abstract Long-range hydrodynamic interactions have been implemented into the open-source molecular dynamics package, LAMMPS, though the creation of a fix, lb_fluid. These interactions are treated by interpolating the MD particle density onto a discrete lattice, which is then coupled to the fluid. A thermal lattice-Boltzmann algorithm is used to model the fluid, which includes mass and momentum conserving noise, providing a thermostat for both the particles and the fluid. Program summary Program title: fix_lb_fluid Catalogue identifier: AEPH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPH_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public license No. of lines in distributed program, including test data, etc.: 439446 No. of bytes in distributed program, including test data, etc.: 9579863 Distribution format: tar.gz Programming language: C++. Computer: All. Operating system: All. Has the code been vectorized or parallelized?: Yes. Parallelized using MPI directives. RAM: Depends on the problem Supplementary material: The data file for the “confined_colloid” example can be downloaded here. Classification: 7.7. External routines: LAMMPS [1] ( http://lammps.sandia.gov ) Nature of problem: The inclusion of long-range hydrodynamic effects into molecular dynamics simulations requires the presence of an explicit solvent. Currently, the only option for incorporating such a solvent into a LAMMPS [1] simulation is the explicit inclusion of each of the individual solvent molecules. This is obviously quite computationally intensive, and for large system sizes can quickly become impractical. Solution method: As an alternative, we have implemented a coarse-grained model for the fluid, simplifying the problem, while retaining the solvent degrees of freedom. We use a thermal lattice-Boltzmann model for the fluid, which is coupled to the molecular dynamics particles at each fluid time step [2,3]. Restrictions: While LAMMPS supports non-orthogonal simulation boxes, this particular fix can only be performed using a three-dimensional, orthogonal simulation domain. In addition, this fix allows for external walls in the z -direction ( x – y plane) only; the simulation domain is always assumed to be periodic along the x and y directions. However, immersed boundaries can be added anywhere by the user. Running time: The run time for fix_lb_fluid varies from minutes to days depending on the system size, the number of lattice mesh points, and the number of processors used. References: [1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117 (1995) 1–19. [2] S.T.T. Ollila, C. Denniston, M. Karttunen, T. Ala-Nissila, J. Chem. Phys. 134 (2011) 064902. [3] F.E. Mackay, C. Denniston, J. Comput. Phys. 237 (2013) 289.

Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces

We propose a new method for coupling both point and composite MD particles to a lattice-Boltzmann fluid. This coupling is implemented through the use of conservative forces, calculated by assuming elastic collisions between the particles and the fluid, thereby eliminating the need for any adjustable coupling constants. With the implementation of a mass and momentum conserving thermal lattice-Boltzmann method, the fluid acts as a heat bath for the MD particles without the need for external Langevin noise. We demonstrate the effectiveness of this method using a variety of simple, well known flow problems. In addition, by studying the velocity autocorrelation function, we are able to validate the fluctuation-dissipation theorem for the algorithm.

USING OPTICAL/NEAR-INFRARED INTERFEROMETRIC POLARIMETRY TO PLACE CONSTRAINTS ON THE DISKS SURROUNDING Be STARS

We present predictions for the normalized Stokes visibilities of a Be star disk, as would be measured by an interferometric polarimeter. Using both a simple geometric model for the disk as well as a more complex radiative transfer model, we investigate, in detail, the effect of each of the model parameters on the resultant normalized Stokes visibilities. We find normalized visibility amplitudes for the total star and disk system of ~10–2-10–3 at shorter baselines, and ~10–3-10–4 at longer baselines, requiring, at small and moderate baselines, an accuracy for interferometric polarization observations better than ~10–3-10–4, including all random and systematic errors. Provided this level of accuracy is attainable, we find that the Stokes Q visibility may be important both for the removal of model degeneracies present when considering the intensity alone, as well as for providing an estimate of the inclination angle of the disk.

Locally stable diamond colloidal crystal formed in a cholesteric liquid crystal

We use a Landau de Gennes free energy approach to model a diamond colloidal crystal immersed in a cholesteric liquid crystal. The pitch in our cholesteric is chosen in order to give rise to the most energetically favourable colloid-defect structure, commensurate with the diamond lattice. This structure corresponds to defect lines travelling along symmetry axes in the diamond crystal. By adding noise to the liquid crystal phase we are able to measure the phonon spectrum of our colloidal crystal, which we find to be consistent with a locally stable configuration. Therefore, although it may not correspond to the global minimum energy structure, once formed our diamond lattice should be stable against thermal fluctuations.

Deformable vesicles interacting in a nematic liquid crystal

Using a lattice-Boltzmann algorithm, we investigate the behavior of 2D deformable vesicles immersed in a nematic liquid crystal. We represent our particles using a bead-spring model, with both linear and angular springs, and assume homeotropic anchoring of the liquid crystal at the particle surface. The resulting liquid crystal defects and distortions lead to a non-uniform pressure exerted on the particle surface, accompanied by a deformation of its shape. We present the resulting equilibrium shapes for a range of surface elasticities, and investigate the interactions between pairs of vesicles.

Halting the hallmarks: a cellular automaton model of early cancer growth inhibition

Cancer treatment is a fragmented and varied process, as “cancer” is really hundreds of different diseases. The “hallmarks of cancer” proposed by Hanahan and Weinberg (Cell 100(1):57–70, 2000) are a framework for viewing cancer within a common set of underlying principles—ten properties that are common to almost all cancers, allowing them to grow uncontrollably and ravage the body. We used a cellular automaton model of tumour growth paired with lattice Boltzmann methods modelling oxygen flow to simulate combination drugs targeted at knocking out pairs of hallmarks. We found that knocking out some pairs of cancer-enabling hallmarks did not prevent tumour formation, while other pairs significantly prevent tumour growth (

Investigating the continuum linear polarization of Be stars

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