Related papers: An Analysis of Surface Relaxation in the Surface C…
The regular Cauchy--Born method is a useful and efficient tool for analyzing bulk properties of materials in the absence of defects. However, the method normally fails to capture surface effects, which are essential to determining material…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
We describe a two-level method for computing a function whose zero-level set is the surface reconstructed from given points scattered over the surface and associated with surface normal vectors. The function is defined as a linear…
Cell blebs are protrusions of the cell membrane and can be instrumental for cell migration. We derive a continuum model for the mechanical and geometrical aspects of the onset of blebbing in terms of a force balance. It is abstract and…
The accurate and efficient simulation of Partial Differential Equations (PDEs) in and around arbitrarily defined geometries is critical for many application domains. Immersed boundary methods (IBMs) alleviate the usually laborious and…
A thin plate or slab, prepared so that opposite faces have different surface stresses, will bend as a result of the stress difference. We have developed a classical molecular dynamics (MD) formulation where (similar in spirit to…
Earlier, normalization conditions for the columns of the PCM (Polarized Continuum Model) were determined and a method of enlarged surface meshes was developed. We developed similar methods for the COSMO (COnductor like Screening MOdel).…
The shifted boundary method (SBM) is an approximate domain method for boundary value problems, in the broader class of unfitted/embedded/immersed methods. It has proven to be quite efficient in handling problems with complex geometries,…
We provide a basic method of Smoothed Particle Hydrodynamics (SPH) to simulate liquid droplet with surface tension in three dimensions. Liquid droplet is a simple case for surface tension modeling. Surface tension works only on fluid…
Simulations of SiC crystal growth using molecular dynamics (MD) have become popular in recent years. They, however, simulate very fast deposition rates, to reduce computational costs. Therefore, they are more akin to surface sputtering,…
The most essential concept in concurrent multiscale methods involving atomistic-continuum coupling is how to define the relation between atomistic and continuum regions. A well-known coupling method that has been frequently employed in…
This paper proposes improvements to the physically-based surface triangulation method, bubble meshing. The method simulates physical bubbles to automatically generate mesh vertices, resulting in high-quality Delaunay triangles. Despite its…
We extend the recently introduced divergence-conforming immersed boundary (DCIB) method [1] to fluid-structure interaction (FSI) problems involving closed co-dimension one solids. We focus on capsules and vesicles, whose discretization is…
This paper proposes a new approach to address the problem of unmeasured confounding in spatial designs. Spatial confounding occurs when some confounding variables are unobserved and not included in the model, leading to distorted…
Defined mathematically as critical points of surface area subject to a volume constraint, constant mean curvatures (CMC) surfaces are idealizations of interfaces occurring between two immiscible fluids. Their behavior elucidates phenomena…
This paper introduces the scaled boundary cubature (SBC) scheme for accurate and efficient integration of functions over polygons and two-dimensional regions bounded by parametric curves. Over two-dimensional domains, the SBC method reduces…
In this paper, we investigate the effect of boundary surface roughness on numerical simulations of incompressible fluid flow past a cylinder in two and three spatial dimensions furnished with slip boundary conditions. The governing…
Supervised machine learning approaches require the formulation of a loss functional to be minimized in the training phase. Sequential data are ubiquitous across many fields of research, and are often treated with Euclidean distance-based…
The structural relaxation of amorphous materials is described as arising from the superposition of elementary processes with varying activation energies. We show that it is possible to obtain the kinetic parameters of these processes from…
Verifying the correctness of Bayesian computation is challenging. This is especially true for complex models that are common in practice, as these require sophisticated model implementations and algorithms. In this paper we introduce…