443 citations
- National Institutes of HealthUS7 papers
- Rush UniversityUS5 papers
- University of ChicagoUS5 papers
- University of KansasUS5 papers
- Johns Hopkins UniversityUS4 papers
- Massachusetts Institute of TechnologyUS4 papers
- Northwestern UniversityUS4 papers
- RWTH Aachen UniversityDE4 papers
- Tel Aviv UniversityIL4 papers
- University College LondonGB4 papers
- University of Bari Aldo MoroIT4 papers
- University of PannoniaHU4 papers
4 papers · 1 filter
Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering
Chris Gaiteri, Mingming Chen, Boleslaw Szymanski +9
Biological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological compone…
Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory
Jaydeep P. Bardhan, Matthew G. Knepley
We present two open-source (BSD) implementations of ellipsoidal harmonic expansions for solving problems of potential theory using separation of variables. Ellipsoidal harmonics ar…
Mathematical Analysis of the BIBEE Approximation for Molecular Solvation: Exact Results for Spherical Inclusions
Jaydeep P. Bardhan, Matthew G. Knepley
We analyze the mathematically rigorous BIBEE (boundary-integral based electrostatics estimation) approximation of the mixed-dielectric continuum model of molecular electrostatics,…
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley +2
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved…