86,747 research outputs found
BSP-fields: An Exact Representation of Polygonal Objects by Differentiable Scalar Fields Based on Binary Space Partitioning
The problem considered in this work is to find a dimension independent algorithm for the generation of signed scalar fields exactly representing polygonal objects and satisfying the following requirements: the defining real function takes zero value exactly at the polygonal object boundary; no extra zero-value isosurfaces should be generated; C1 continuity of the function in the entire domain. The proposed algorithms are based on the binary space partitioning (BSP) of the object by the planes passing through the polygonal faces and are independent of the object genus, the number of disjoint components, and holes in the initial polygonal mesh. Several extensions to the basic algorithm are proposed to satisfy the selected optimization criteria. The generated BSP-fields allow for applying techniques of the function-based modeling to already existing legacy objects from CAD and computer animation areas, which is illustrated by several examples
A High-Order Kernel Method for Diffusion and Reaction-Diffusion Equations on Surfaces
In this paper we present a high-order kernel method for numerically solving
diffusion and reaction-diffusion partial differential equations (PDEs) on
smooth, closed surfaces embedded in . For two-dimensional
surfaces embedded in , these types of problems have received
growing interest in biology, chemistry, and computer graphics to model such
things as diffusion of chemicals on biological cells or membranes, pattern
formations in biology, nonlinear chemical oscillators in excitable media, and
texture mappings. Our kernel method is based on radial basis functions (RBFs)
and uses a semi-discrete approach (or the method-of-lines) in which the surface
derivative operators that appear in the PDEs are approximated using
collocation. The method only requires nodes at "scattered" locations on the
surface and the corresponding normal vectors to the surface. Additionally, it
does not rely on any surface-based metrics and avoids any intrinsic coordinate
systems, and thus does not suffer from any coordinate distortions or
singularities. We provide error estimates for the kernel-based approximate
surface derivative operators and numerically study the accuracy and stability
of the method. Applications to different non-linear systems of PDEs that arise
in biology and chemistry are also presented
Probabilistic Solutions to Differential Equations and their Application to Riemannian Statistics
We study a probabilistic numerical method for the solution of both boundary
and initial value problems that returns a joint Gaussian process posterior over
the solution. Such methods have concrete value in the statistics on Riemannian
manifolds, where non-analytic ordinary differential equations are involved in
virtually all computations. The probabilistic formulation permits marginalising
the uncertainty of the numerical solution such that statistics are less
sensitive to inaccuracies. This leads to new Riemannian algorithms for mean
value computations and principal geodesic analysis. Marginalisation also means
results can be less precise than point estimates, enabling a noticeable
speed-up over the state of the art. Our approach is an argument for a wider
point that uncertainty caused by numerical calculations should be tracked
throughout the pipeline of machine learning algorithms.Comment: 11 page (9 page conference paper, plus supplements
Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations
Atomic radii and charges are two major parameters used in implicit solvent
electrostatics and energy calculations. The optimization problem for charges
and radii is under-determined, leading to uncertainty in the values of these
parameters and in the results of solvation energy calculations using these
parameters. This paper presents a new method for quantifying this uncertainty
in implicit solvation calculations of small molecules using surrogate models
based on generalized polynomial chaos (gPC) expansions. There are relatively
few atom types used to specify radii parameters in implicit solvation
calculations; therefore, surrogate models for these low-dimensional spaces
could be constructed using least-squares fitting. However, there are many more
types of atomic charges; therefore, construction of surrogate models for the
charge parameter space requires compressed sensing combined with an iterative
rotation method to enhance problem sparsity. We demonstrate the application of
the method by presenting results for the uncertainties in small molecule
solvation energies based on these approaches. The method presented in this
paper is a promising approach for efficiently quantifying uncertainty in a wide
range of force field parameterization problems, including those beyond
continuum solvation calculations.The intent of this study is to provide a way
for developers of implicit solvent model parameter sets to understand the
sensitivity of their target properties (solvation energy) on underlying choices
for solute radius and charge parameters
- …