Related papers: A New Analytical Method for Computing Solvent Acce…
Currently, the area of geometric modeling and the construction of 3D models based on point clouds from laser sensors is actively developing. One of the basic tasks of geometric modeling is the reconstruction of a surface from a cloud of…
This article presents a new and efficient alternative to well established algorithms for molecular geometry optimization. The new approach exploits the approximate decoupling of molecular energetics in a curvilinear internal coordinate…
Real-space refinement of atomic models in macromolecular crystallography or in cryo electron microscopy fits a model to a map obtained experimentally. This requires generating model maps of a limited resolution which moreover may vary from…
An elementary, albeit higher dimensional, argument is used to compute the area under the power function curve between 0 and 1.
A numerical method based on smoothed particle hydrodynamics with adaptive spatial resolution (SPH-ASR) was developed for simulating free surface flows. This method can reduce the computational demands while maintaining the numerical…
We present a novel algorithm to compute multi-scale curvature fields on triangle meshes. Our algorithm is based on finding robust mean curvatures using the ball neighborhood, where the radius of a ball corresponds to the scale of the…
We introduce a numerical method for reconstructing a multidimensional surface using the gradient of the surface measured at some values of the coordinates. The method consists of defining a multidimensional spline function and minimizing…
This paper describes an interdisciplinary approach to geometry modeling of geospatial boundaries. The objective is to extract surfaces from irregular spatial patterns using differential geometry and obtain coherent directional predictions…
Fluid-Structure Interaction (FSI) is a crucial problem in ocean engineering. The smoothed particle hydrodynamics (SPH) method has been employed recently for FSI problems in light of its Lagrangian nature and its advantage in handling…
We formulate a simple solvation potential based on a coarsed-grain representation of amino acids with two spheres modeling the $C_\alpha$ atom and an effective side-chain centroid. The potential relies on a new method for estimating the…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
Particle-based shape modeling (PSM) is a family of approaches that automatically quantifies shape variability across anatomical cohorts by positioning particles (pseudo landmarks) on shape surfaces in a consistent configuration. Recent…
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…
Computing a quasi-developable strip surface bounded by design curves finds wide industrial applications. Existing methods compute discrete surfaces composed of developable lines connecting sampling points on input curves which are not…
Nielsen, et al. [1, 2] proposed a view of quantum computation where determining optimal algorithms is equivalent to extremizing a geodesic length or cost functional. This view of optimization is highly suggestive of an action principle of…
The parameterization of open and closed anatomical surfaces is of fundamental importance in many biomedical applications. Spherical harmonics, a set of basis functions defined on the unit sphere, are widely used for anatomical shape…
First principles calculations based on density functional theory are having an incerasing impact on our understanding of molecule-surface interactions. For example, calculations of the multi-dimensional potential energy surface have…
The goal of this paper is to exhibit and analyze an algorithm that takes a given closed orientable hyperbolic surface and outputs an explicit Dirichlet domain. The input is a fundamental polygon with side pairings. While grounded in…
We present a simple, accurate method for computing singular or nearly singular integrals on a smooth, closed surface, such as layer potentials for harmonic functions evaluated at points on or near the surface. The integral is computed with…
We present an amelioration of current known algorithms for optimal spectral partitioning problems. The idea is to use the advantage of a representation using density functions while decreasing the computational time. This is done by…