5,799 research outputs found
Colloidal interactions in two dimensional nematics
The interaction between two disks immersed in a 2D nematic is investigated
(i) analitically using the tensor order parameter formalism for the nematic
configuration around isolated disks and (ii) numerically using finite element
methods with adaptive meshing to minimize the corresponding Landau-de Gennes
free energy. For strong homeotropic anchoring, each disk generates a pair of
defects with one-half topological charge responsible for the 2D quadrupolar
interaction between the disks at large distances. At short distance, the
position of the defects may change, leading to unexpected complex interactions
with the quadrupolar repulsive interactions becoming attractive. This short
range attraction in all directions is still anisotropic. As the distance
between the disks decreases their preferred relative orientation with respect
to the far-field nematic director changes from oblique to perpendicular.Comment: 7 pages, 7 figure
Two triangulations methods based on edge refinement
In this paper two curvature adaptive methods of surface triangulation
are presented. Both methods are based on edge refinement to obtain a
triangulation compatible with the curvature requirements. The first
method applies an incremental and constrained Delaunay triangulation
and uses curvature bounds to determine if an edge of the triangulation
is admissible. The second method uses this function also in the edge
refinement process, i.e. in the computation of the location of a
refining point, and in the re-triangulation needed after the insertion
of this refining point. Results are presented, comparing both
approachesPostprint (published version
Motion of a Janus Particle Very Near a Wall
This article describes the simulated Brownian motion of a sphere comprising hemispheres of unequal zeta potential (i.e., “Janus” particle) very near a wall. The simulation tool was developed and used to assist in the methodology development for applying Total Internal Reflection Microscopy (TIRM) to anisotropic particles. Simulations of the trajectory of a Janus sphere with cap density matching that of the base particle very near a boundary were used to construct 3D potential energy landscapes that were subsequently used to infer particle and solution properties, as would be done in a TIRM measurement. Results showed that the potential energy landscape of a Janus sphere has a transition region at the location of the boundary between the two Janus halves, which depended on the relative zeta potential magnitude. The potential energy landscape was fit to accurately obtain the zeta potential of each hemisphere, particle size, minimum potential energy position and electrolyte concentration, or Debye length. We also determined the appropriate orientation bin size and regimes over which the potential energy landscape should be fit to obtain system properties. Our simulations showed that an experiment may require more than 106 observations to obtain a suitable potential energy landscape as a consequence of the multivariable nature of observations for an anisotropic particle. These results illustrate important considerations for conducting TIRM for anisotropic particles
Packing Characteristics of Different Shaped Proppants for use with Hydrofracing - A Numerical Investigation using 3D FEMDEM
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3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Recent advances in electron microscopy have enabled the imaging of single
cells in 3D at nanometer length scale resolutions. An uncharted frontier for in
silico biology is the ability to simulate cellular processes using these
observed geometries. Enabling such simulations requires watertight meshing of
electron micrograph images into 3D volume meshes, which can then form the basis
of computer simulations of such processes using numerical techniques such as
the Finite Element Method. In this paper, we describe the use of our recently
rewritten mesh processing software, GAMer 2, to bridge the gap between poorly
conditioned meshes generated from segmented micrographs and boundary marked
tetrahedral meshes which are compatible with simulation. We demonstrate the
application of a workflow using GAMer 2 to a series of electron micrographs of
neuronal dendrite morphology explored at three different length scales and show
that the resulting meshes are suitable for finite element simulations. This
work is an important step towards making physical simulations of biological
processes in realistic geometries routine. Innovations in algorithms to
reconstruct and simulate cellular length scale phenomena based on emerging
structural data will enable realistic physical models and advance discovery at
the interface of geometry and cellular processes. We posit that a new frontier
at the intersection of computational technologies and single cell biology is
now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies
available upon reques
Kinetic Solvers with Adaptive Mesh in Phase Space
An Adaptive Mesh in Phase Space (AMPS) methodology has been developed for
solving multi-dimensional kinetic equations by the discrete velocity method. A
Cartesian mesh for both configuration (r) and velocity (v) spaces is produced
using a tree of trees data structure. The mesh in r-space is automatically
generated around embedded boundaries and dynamically adapted to local solution
properties. The mesh in v-space is created on-the-fly for each cell in r-space.
Mappings between neighboring v-space trees implemented for the advection
operator in configuration space. We have developed new algorithms for solving
the full Boltzmann and linear Boltzmann equations with AMPS. Several recent
innovations were used to calculate the discrete Boltzmann collision integral
with dynamically adaptive mesh in velocity space: importance sampling,
multi-point projection method, and the variance reduction method. We have
developed an efficient algorithm for calculating the linear Boltzmann collision
integral for elastic and inelastic collisions in a Lorentz gas. New AMPS
technique has been demonstrated for simulations of hypersonic rarefied gas
flows, ion and electron kinetics in weakly ionized plasma, radiation and light
particle transport through thin films, and electron streaming in
semiconductors. We have shown that AMPS allows minimizing the number of cells
in phase space to reduce computational cost and memory usage for solving
challenging kinetic problems
Dynamics And Surface Forces Experienced By An Anisotropic Colloidal Particle Near A Boundary
Colloidal interactions play an important role in determining the macroscopic properties of different materials. Recent work in this area has focused on the role anisotropic particles play in these materials. This thesis summarizes work conducted on the dynamics and interactions of an anisotropic colloid particle near a solid wall. Specifically, the methodology for conducting Total Internal Reflection Microscopy (TIRM) on anisotropic colloidal systems near a boundary was developed. This new method is called “Scattering Morphology Resolved - TIRM” (SMR-TIRM). Simulations of the Brownian motion of a sphere comprising hemispheres of different composition (i.e. a Janus particle) very near a wall were conducted. Trajectories obtained from these simulations were used to construct 3D potential energy landscapes. Results showed that the potential energy landscape of a Janus sphere has a transition region at the location of the boundary between the two Janus halves, which depended on the relative zeta potential magnitude. In this thesis, an experimental technique for the direct and local measure of cap thickness of a coated Janus particle was summarized. It is found that the cap varied in thickness continuously along the perimeter ofthe particle. To better understand the impact ofthe coating on the dynamics of Janus particle, Brownian dynamics simulations to predict the translational and rotational fluctuations of a Janus sphere with a cap of non-matching density near a boundary was utilized. The simulation results show that the presence of the cap significantly impacts the rotational dynamics of the particle as a consequence of gravitational torque. vi In the last part of this thesis, the SMR-TIRM was used to map scattering from ellipsoid particles. The hypothesis driving this work was that evanescent wave scattering from an ellipsoidal particle depended on both the aspect ratio and orientation. Analysis of the light scattered from the particle showed that both ellipticity and directionality correlated with particle orientation and aspect ratio. In principle, these relationships will allow tracking of the particle’s position and orientation via the scattered light morphology
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