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1

Composing Scalable Nonlinear Algebraic Solvers

Brune, Peter R., Knepley, Matthew G., Smith, Barry F., Tu, Xuemin

Journal:

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

2

Optimal, scalable forward models for computing gravity anomalies

Dave A. May, Matthew G. Knepley

Journal:

Geophysical Journal International

Year:

2011

Language:

english

File:

PDF, 487 KB

english, 2011

3

Efficient Mesh Management in Firedrake Using PETSc DMPlex

Lange, Michael, Mitchell, Lawrence, Knepley, Matthew G., Gorman, Gerard J.

Journal:

SIAM Journal on Scientific Computing

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

4

An implicit discontinuous Galerkin method for modeling acute edema and resuscitation in the small intestine

Thompson, Travis B, Riviere, Beatrice M, Knepley, Matthew G

Journal:

Mathematical Medicine and Biology

Year:

2019

Language:

english

File:

PDF, 9.63 MB

english, 2019

5

An Analysis of the Child Behavior Checklist Anxiety Problems Scale’s Predictive Capabilities

Knepley, Mark J., Kendall, Philip C., Carper, Matthew M.

Journal:

Journal of Psychopathology and Behavioral Assessment

Year:

2019

Language:

english

File:

PDF, 454 KB

english, 2019

6

PetFMM—A dynamically load-balancing parallel fast multipole library

Felipe A. Cruz, Matthew G. Knepley, L. A. Barba

Journal:

International Journal for Numerical Methods in Engineering

Year:

2011

Language:

english

File:

PDF, 1.54 MB

english, 2011

7

PetRBF — A parallel O(N) algorithm for radial basis function interpolation with Gaussians

Rio Yokota, L.A. Barba, Matthew G. Knepley

Journal:

Computer Methods in Applied Mechanics and Engineering

Year:

2010

Language:

english

File:

PDF, 772 KB

english, 2010

8

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L.A. Barba, Tsuyoshi Hamada

Journal:

Computer Physics Communications

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

9

PyClaw: Accessible, Extensible, Scalable Tools for Wave Propagation Problems

Ketcheson, David I., Mandli, Kyle, Ahmadia, Aron J., Alghamdi, Amal, de Luna, Manuel Quezada, Parsani, Matteo, Knepley, Matthew G., Emmett, Matthew

Journal:

SIAM Journal on Scientific Computing

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

10

Optimizing the Evaluation of Finite Element Matrices

Kirby, Robert C., Knepley, Matthew, Logg, Anders, Scott, L. Ridgway

Journal:

SIAM Journal on Scientific Computing

Year:

2005

Language:

english

File:

PDF, 204 KB

english, 2005

11

An efficient algorithm for classical density functional theory in three dimensions: Ionic solutions

Knepley, Matthew G., Karpeev, Dmitry A., Davidovits, Seth, Eisenberg, Robert S., Gillespie, Dirk

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 519 KB

english, 2010

12

Finite Element Integration on GPUs

Knepley, Matthew G., Terrel, Andy R.

Journal:

ACM Transactions on Mathematical Software

Year:

2013

Language:

english

File:

PDF, 742 KB

english, 2013

13

Energetics of Calcium Selectivity: A Three-Dimensional Classical Density Functional Theory Approach

Knepley, Matthew G., Karpeev, Dmitry A., Eisenberg, Robert S., Gillespie, Dirk

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 77 KB

english, 2009

14

[IEEE 2012 11th International Symposium on Parallel and Distributed Computing (ISPDC) - Munich, Germany (2012.06.25-2012.06.29)] 2012 11th International Symposium on Parallel and Distributed Computing - Composable Linear Solvers for Multiphysics

Brown, Jed, Knepley, Matthew G., May, David A., McInnes, Lois Curfman, Smith, Barry

Year:

2012

Language:

english

File:

PDF, 195 KB

english, 2012

15

Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and Graded Meshes

Brune, Peter R., Knepley, Matthew G., Scott, L. Ridgway

Journal:

SIAM Journal on Scientific Computing

Year:

2013

Language:

english

File:

PDF, 1.41 MB

english, 2013

16

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

Bardhan, Jaydeep P., Knepley, Matthew G., Anitescu, Mihai

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.26 MB

english, 2009

17

Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions

Bardhan, Jaydeep P., Knepley, Matthew G.

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 369 KB

english, 2011

18

Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

Bardhan, Jaydeep P., Knepley, Matthew G.

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 182 KB

english, 2014

19

Run-Time Extensibility and Librarization of Simulation Software

Brown, Jed, Knepley, Matthew G., Smith, Barry F.

Journal:

Computing in Science & Engineering

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

20

Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a Hydration-Shell Poisson-Boltzmann Model

Bardhan, Jaydeep P., Knepley, Matthew G.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 41 KB

english, 2016

21

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface

Tabrizi, Amirhossein Molavi, Knepley, Matthew G., Bardhan, Jaydeep P.

Journal:

Molecular Physics

Year:

2016

Language:

english

File:

PDF, 705 KB

english, 2016

22

A stochastic performance model for pipelined Krylov methods

Morgan, Hannah, Knepley, Matthew G., Sanan, Patrick, Scott, L. Ridgway

Journal:

Concurrency and Computation: Practice and Experience

Year:

2016

Language:

english

File:

PDF, 647 KB

english, 2016

23

[ACM Press the Platform for Advanced Scientific Computing Conference - Lausanne, Switzerland (2016.06.08-2016.06.10)] Proceedings of the Platform for Advanced Scientific Computing Conference on ZZZ - PASC '16 - Extreme-Scale Multigrid Components within PETSc

May, Dave A., Sanan, Patrick, Rupp, Karl, Knepley, Matthew G., Smith, Barry F.

Year:

2016

Language:

english

File:

PDF, 1013 KB

english, 2016

24

Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators

Bardhan, Jaydeep P., Knepley, Matthew G., Brune, Peter

Journal:

Molecular Based Mathematical Biology

Year:

2015

Language:

english

File:

PDF, 666 KB

english, 2015

25

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

Molavi Tabrizi, Amirhossein, Goossens, Spencer, Mehdizadeh Rahimi, Ali, Knepley, Matthew, Bardhan, Jaydeep P.

Journal:

The Journal of Chemical Physics

Year:

2017

Language:

english

File:

PDF, 692 KB

english, 2017

26

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent

Molavi Tabrizi, Amirhossein, Goossens, Spencer, Mehdizadeh Rahimi, Ali, Cooper, Christopher D., Knepley, Matthew G., Bardhan, Jaydeep P.

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.88 MB

english, 2017

27

Landau Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures

Adams, Mark F., Hirvijoki, Eero, Knepley, Matthew G., Brown, Jed, Isaac, Tobin, Mills, Richard

Journal:

SIAM Journal on Scientific Computing

Year:

2017

Language:

english

File:

PDF, 2.41 MB

english, 2017

28

Mesh Algorithms for PDE with Sieve I: Mesh Distribution

Knepley, Matthew G., Karpeev, Dmitry A.

Journal:

Scientific Programming

Year:

2009

Language:

english

File:

PDF, 2.84 MB

english, 2009

29

A hybridizable discontinuous Galerkin method for two-phase flow in heterogeneous porous media

Fabien, Maurice S., Knepley, Matthew G., Riviere, Beatrice M.

Journal:

International Journal for Numerical Methods in Engineering

Year:

2018

Language:

english

File:

PDF, 952 KB

english, 2018

30

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Kreienkamp, Amelia B., Liu, Lucy Y., Minkara, Mona S., Knepley, Matthew G., Bardhan, Jaydeep P., Radhakrishnan, Mala L.

Journal:

Molecular Based Mathematical Biology

Year:

2013

Language:

english

File:

PDF, 4.36 MB

english, 2013

31

Solvation thermodynamics of neutral and charged solutes using the solvation-layer interface condition continuum dielectric model

Mehdizadeh Rahimi, Ali, Molavi Tabrizi, Amirhossein, Goossens, Spencer, Knepley, Matthew G., Bardhan, Jaydeep P.

Journal:

International Journal of Quantum Chemistry

Year:

2018

Language:

english

File:

PDF, 1.98 MB

english, 2018

32

Modular and flexible spectral-element waveform modelling in two and three dimensions

Afanasiev, Michael, Boehm, Christian, van Driel, Martin, Krischer, Lion, Rietmann, Max, May, Dave A, Knepley, Matthew G, Fichtner, Andreas

Journal:

Geophysical Journal International

Year:

2019

Language:

english

File:

PDF, 6.26 MB

english, 2019

33

Manycore Parallel Computing for a Hybridizable Discontinuous Galerkin Nested Multigrid Method

Fabien, Maurice S., Knepley, Matthew G., Mills, Richard T., Rivière, Béatrice M.

Journal:

SIAM Journal on Scientific Computing

Year:

2019

Language:

english

File:

PDF, 489 KB

english, 2019

34

Families of Interior Penalty Hybridizable discontinuous Galerkin methods for second order elliptic problems

Fabien, Maurice S., Knepley, Matthew G., Riviere, Beatrice M.

Journal:

Journal of Numerical Mathematics

Year:

2019

Language:

english

File:

PDF, 507 KB

english, 2019

35

Families of Interior Penalty Hybridizable discontinuous Galerkin methods for second order elliptic problems

Fabien, Maurice S., Knepley, Matthew G., Riviere, Beatrice M.

Journal:

Journal of Numerical Mathematics

Year:

2019

File:

PDF, 507 KB

2019

36

A high order hybridizable discontinuous Galerkin method for incompressible miscible displacement in heterogeneous media

Fabien, Maurice S., Knepley, Matthew, Riviere, Beatrice

Journal:

Results in Applied Mathematics

Year:

2020

File:

PDF, 3.24 MB

2020

37

Understanding performance variability in standard and pipelined parallel Krylov solvers

Morgan, Hannah, Sanan, Patrick, Knepley, Matthew, Mills, Richard Tran

Journal:

International Journal of High Performance Computing Applications

Year:

2020

File:

PDF, 1.30 MB

2020