4,736 research outputs found
A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver
In this paper, we present a GPU-accelerated direct-sum boundary integral
method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a
well-posed boundary integral formulation is used to ensure the fast convergence
of Krylov subspace based linear algebraic solver such as the GMRES. The
molecular surfaces are discretized with flat triangles and centroid
collocation. To speed up our method, we take advantage of the parallel nature
of the boundary integral formulation and parallelize the schemes within CUDA
shared memory architecture on GPU. The schemes use only
size-of-double device memory for a biomolecule with triangular surface
elements and partial charges. Numerical tests of these schemes show
well-maintained accuracy and fast convergence. The GPU implementation using one
GPU card (Nvidia Tesla M2070) achieves 120-150X speed-up to the implementation
using one CPU (Intel L5640 2.27GHz). With our approach, solving PB equations on
well-discretized molecular surfaces with up to 300,000 boundary elements will
take less than about 10 minutes, hence our approach is particularly suitable
for fast electrostatics computations on small to medium biomolecules
Triangulation of uniform particle systems: its application to the implicit surface texturing
Particle systems, as originally presented by Witkin and Heckbert [32], offer an elegant solution to sample implicit
surfaces of arbitrary genus, while providing an extremely regular distribution of samples over the surface. In this
paper, we present an ef cient technique that uses particle systems to rapidly generate a triangular mesh over an
implicit surface, where each triangle is almost equilateral. The major advantage of such a triangulation is that
it minimizes the deformations between the mesh and the underlying implicit surface. We exploit this property
by using few triangular texture samples mapped in a non-periodic fashion as presented by Neyret and Cani [16].
The result is a pattern-based texturing method that maps homogeneous non-periodic textures to arbitrary implicit
surfaces, with almost no deformation
Finite element methods for surface PDEs
In this article we consider finite element methods for approximating the solution of partial differential equations on surfaces. We focus on surface finite elements on triangulated surfaces, implicit surface methods using level set descriptions of the surface, unfitted finite element methods and diffuse interface methods. In order to formulate the methods we present the necessary geometric analysis and, in the context of evolving surfaces, the necessary transport formulae. A wide variety of equations and applications are covered. Some ideas of the numerical analysis are presented along with illustrative numerical examples
The century of the incomplete revolution: searching for general relativistic quantum field theory
In fundamental physics, this has been the century of quantum mechanics and
general relativity. It has also been the century of the long search for a
conceptual framework capable of embracing the astonishing features of the world
that have been revealed by these two ``first pieces of a conceptual
revolution''. I discuss the general requirements on the mathematics and some
specific developments towards the construction of such a framework. Examples of
covariant constructions of (simple) generally relativistic quantum field
theories have been obtained as topological quantum field theories, in
nonperturbative zero-dimensional string theory and its higher dimensional
generalizations, and as spin foam models. A canonical construction of a general
relativistic quantum field theory is provided by loop quantum gravity.
Remarkably, all these diverse approaches have turn out to be related,
suggesting an intriguing general picture of general relativistic quantum
physics.Comment: To appear in the Journal of Mathematical Physics 2000 Special Issu
Improvements to the APBS biomolecular solvation software suite
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
understanding solvation and electrostatics in biomedical applications: accurate
and efficient models for biomolecular solvation and electrostatics, robust and
scalable software for applying those theories to biomolecular systems, and
mechanisms for sharing and analyzing biomolecular electrostatics data in the
scientific community. To address new research applications and advancing
computational capabilities, we have continually updated APBS and its suite of
accompanying software since its release in 2001. In this manuscript, we discuss
the models and capabilities that have recently been implemented within the APBS
software package including: a Poisson-Boltzmann analytical and a
semi-analytical solver, an optimized boundary element solver, a geometry-based
geometric flow solvation model, a graph theory based algorithm for determining
p values, and an improved web-based visualization tool for viewing
electrostatics
Dynamical Optimal Transport on Discrete Surfaces
We propose a technique for interpolating between probability distributions on
discrete surfaces, based on the theory of optimal transport. Unlike previous
attempts that use linear programming, our method is based on a dynamical
formulation of quadratic optimal transport proposed for flat domains by Benamou
and Brenier [2000], adapted to discrete surfaces. Our structure-preserving
construction yields a Riemannian metric on the (finite-dimensional) space of
probability distributions on a discrete surface, which translates the so-called
Otto calculus to discrete language. From a practical perspective, our technique
provides a smooth interpolation between distributions on discrete surfaces with
less diffusion than state-of-the-art algorithms involving entropic
regularization. Beyond interpolation, we show how our discrete notion of
optimal transport extends to other tasks, such as distribution-valued Dirichlet
problems and time integration of gradient flows
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