Zobrazeno 1 - 10
of 113
pro vyhledávání: '"Krasny, Robert"'
An integral equation method is presented for the 1D steady-state Poisson-Nernst-Planck equations modeling ion transport through membrane channels. The differential equations are recast as integral equations using Green's 3rd identity yielding a fixed
Externí odkaz:
http://arxiv.org/abs/2304.04371
The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solut
Externí odkaz:
http://arxiv.org/abs/2109.09772
We present the barycentric Lagrange dual tree traversal (BLDTT) fast summation method for particle interactions. The scheme replaces well-separated particle-particle interactions by adaptively chosen particle-cluster, cluster-particle, and cluster-cl
Externí odkaz:
http://arxiv.org/abs/2012.06925
Autor:
Wilson, Leighton, Krasny, Robert
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is often taken
Externí odkaz:
http://arxiv.org/abs/2010.10570
We present an MPI + OpenACC implementation of the kernel-independent barycentric Lagrange treecode (BLTC) for fast summation of particle interactions on GPUs. The distributed memory parallelization uses recursive coordinate bisection for domain decom
Externí odkaz:
http://arxiv.org/abs/2003.01836
We present a real-space computational method called treecode-accelerated Green Iteration (TAGI) for all-electron Kohn-Sham Density Functional Theory. TAGI is based on a reformulation of the Kohn-Sham equations in which the eigenvalue problem in diffe
Externí odkaz:
http://arxiv.org/abs/2003.01833
Publikováno v:
Commun. Comput. Phys., 28 (2020), pp. 1415-1436
A kernel-independent treecode (KITC) is presented for fast summation of particle interactions. The method employs barycentric Lagrange interpolation at Chebyshev points to approximate well-separated particle-cluster interactions. The KITC requires on
Externí odkaz:
http://arxiv.org/abs/1902.02250
Publikováno v:
Adv. Appl. Math. Mech., 11 (4) (2019), pp. 737-756
The Stokeslet and stresslet kernels are commonly used in boundary element simulations and singularity methods for slow viscous flow. Evaluating the velocity induced by a collection of Stokeslets and stresslets by direct summation requires $O(N^2)$ op
Externí odkaz:
http://arxiv.org/abs/1811.12498
Autor:
Jurrus, Elizabeth, Engel, Dave, Star, Keith, Monson, Kyle, Brandi, Juan, Felberg, Lisa E., Brookes, David H., Wilson, Leighton, Chen, Jiahui, Liles, Karina, Chun, Minju, Li, Peter, Gohara, David W., Dolinsky, Todd, Konecny, Robert, Koes, David R., Nielsen, Jens Erik, Head-Gordon, Teresa, Geng, Weihua, Krasny, Robert, Wei, Guo Wei, Holst, Michael J., McCammon, J. Andrew, Baker, Nathan A.
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 a
Externí odkaz:
http://arxiv.org/abs/1707.00027
Publikováno v:
In Computer Physics Communications August 2021 265
