4,218 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
Electrokinetic and hydrodynamic properties of charged-particles systems: From small electrolyte ions to large colloids
Dynamic processes in dispersions of charged spherical particles are of
importance both in fundamental science, and in technical and bio-medical
applications. There exists a large variety of charged-particles systems,
ranging from nanometer-sized electrolyte ions to micron-sized charge-stabilized
colloids. We review recent advances in theoretical methods for the calculation
of linear transport coefficients in concentrated particulate systems, with the
focus on hydrodynamic interactions and electrokinetic effects. Considered
transport properties are the dispersion viscosity, self- and collective
diffusion coefficients, sedimentation coefficients, and electrophoretic
mobilities and conductivities of ionic particle species in an external electric
field. Advances by our group are also discussed, including a novel
mode-coupling-theory method for conduction-diffusion and viscoelastic
properties of strong electrolyte solutions. Furthermore, results are presented
for dispersions of solvent-permeable particles, and particles with non-zero
hydrodynamic surface slip. The concentration-dependent swelling of ionic
microgels is discussed, as well as a far-reaching dynamic scaling behavior
relating colloidal long- to short-time dynamics
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