@inproceedings {INPROC-2018-52,
author = {Nehzat Emamy and Pascal Litty and Thomas Klotz and Miriam Mehl and Oliver R{\"o}hrle},
title = {{POD-DEIM model order reduction of the Monodomain Reaction-Diffusion Sub-Model of the Neuro-Muscular System}},
booktitle = {IUTAM Symposium on Model Order Reduction of Coupled Systems; Stuttgart, Germany, May 22-25, 2018: MORCOS 2018},
editor = {J. Fehr and B. Haasdonk},
publisher = {Springer},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {1--14},
type = {Konferenz-Beitrag},
month = {Mai},
year = {2018},
isbn = {879-3-030-21012-0},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {We apply POD-DEIM model order reduction to a 0D/1D model used to simulate the
propagation of action potentials through the myocardium or along skeletal
muscle fibers. This corresponding system of ODEs (reaction) and PDEs
(diffusion) is called the monodomain equation. 0D sets of ODEs describing the
ionic currents flowing across the cell membrane are coupled along muscle fibers
through a \$1\$D diffusion process for the transmembrane potential. Due to the
strong coupling of the transmembrane potential and other state variables
describing the behavior of the membrane, a total reduction strategy including
all degrees of freedom turns out to be more efficient than a reduction of only
the transmembrane potential. The total reduction approach is four orders of
magnitude more accurate than partial reduction and shows a faster convergence
in the number of POD modes with respect to the mesh refinement. A speedup of
\$2.7\$ is achieved for a 1D mesh with \$320\$ nodes. Considering the DEIM
approximation in combination with the total reduction, the nonlinear functions
corresponding to the ionic state variables are also approximated in addition to
the nonlinear ionic current in the monodomain equation. We observe that the
same number of DEIM interpolation points as the number of POD modes is the
optimal choice regarding stability, accuracy and runtime for the current
POD-DEIM approach.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-52&engl=0}
}
@inproceedings {INPROC-2018-51,
author = {Nehzat Emamy and Pascal Litty and Thomas Klotz and Miriam Mehl and Oliver R{\"o}hrle},
title = {{POD-DEIM model order reduction for the Monodomain reaction-dissusion equation in neuro-muscular system}},
booktitle = {Proceedings of 6th European Conference on Computational Mechanics (Solids, Structures and Coupled Problems) (ECCM 6) and the 7th European Conference on Computational Fluid Dynamics (ECFD 7); Glasgow, UK, June 11-15, 2018},
editor = {Roger Owen and Ren{\'e} de Borst and Jason Reese and Chris Pearce},
publisher = {International Center for Numerical Methods in Engineerin (CIMNE)},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {2514--2524},
type = {Konferenz-Beitrag},
month = {Juni},
year = {2018},
isbn = {978-84-947311-6-7},
language = {Englisch},
cr-category = {A General Literature,
G Mathematics of Computing,
E Data},
ee = {ftp://ftp.informatik.uni-stuttgart.de/pub/library/ncstrl.ustuttgart_fi/INPROC-2018-51/INPROC-2018-51.pdf},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {We apply the POD-DEIM model order reduction to the propagation of the
transmembrane potential along \$1\$D muscle fibers. This propagation is
represented using the monodomain partial differential equation. The monodomain
equation, which is a reaction-diffusion equation, is coupled through its
reaction term with a set of ordinary differential equations, which provide the
ionic current across the cell membrane. Due to the strong coupling of the
transmembrane potential and ionic state variables, we reduce them all together
proposing a total reduction strategy. We compare the current strategy with the
conventional strategy of reducing the transmembrane potential. Considering the
current approach, the discrete system matrix is slightly modified to adjust for
the size. However, size of the precomputed reduced system matrix remains the
same, which means the same computational cost. The current approach appears to
be four orders of magnitude more accurate considering the equivalent number of
modes on the same grid in comparison to the conventional approach. Moreover, it
shows a faster convergence in the number of POD modes with respect to the grid
refinement. Using the DEIM approximation of nonlinear functions in combination
with the total reduction, the nonlinear functions corresponding to the ionic
state variables are also approximated besides the nonlinear ionic current in
the monodomain equation. For the current POD-DEIM approach, it appears that the
same number of DEIM interpolation points as the number of POD modes is the
optimal choice regarding stability, accuracy and runtime.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2018-51&engl=0}
}
@inproceedings {INPROC-2017-73,
author = {Nehzat Emamy and Maria Luk{\'a}\&\#269;ov{\'a}-Medvid’ov{\'a} and Stefanie Stalter and Peter Virnau and Leonid Yelash},
title = {{Reduced-order hybrid multiscale method combining the Molecular Dynamics and the Discontinuous-Galerkin method}},
booktitle = {Proceedings of VII International Conference on Computational Methods for Coupled Problems in Science and Engineering (Coupled Problems 2017)},
address = {Rhodes Island, Greece},
publisher = {ECCOMAS},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {62--76},
type = {Konferenz-Beitrag},
month = {Juni},
year = {2017},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2017-73&engl=0}
}
@inproceedings {INPROC-2015-63,
author = {Nehzat Emamy and Martin Karcher and Roozbeh Mousavi and Martin Oberlack},
title = {{A high-order fully coupled electro-fluid-dynamics solver for multiphase flow simulations}},
booktitle = {VI International Conference on Computational Methods for Coupled Problems in Science and Engineering},
address = {San Servolo Island, Venice, Greece},
publisher = {ECCOMAS},
institution = {Universit{\"a}t Stuttgart, Fakult{\"a}t Informatik, Elektrotechnik und Informationstechnik, Germany},
pages = {753--759},
type = {Konferenz-Beitrag},
month = {Mai},
year = {2015},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=INPROC-2015-63&engl=0}
}
@article {ART-2018-08,
author = {Chris P. Bradley and Nehzat Emamy and Thomas Ertl and Dominik G{\"o}ddeke and Andreas Hessenthaler and Thomas Klotz and Aaron Kr{\"a}mer and Michael Krone and Benjamin Maier and Miriam Mehl and Tobias Rau and Oliver R{\"o}hrle},
title = {{Enabling Detailed, Biophysics-Based Skeletal Muscle Models on HPC Systems}},
journal = {Frontiers in Physiology},
publisher = {frontiers},
volume = {9},
pages = {816--816},
type = {Artikel in Zeitschrift},
month = {Juli},
year = {2018},
doi = {10.3389/fphys.2018.00816},
language = {Englisch},
cr-category = {G.0 Mathematics of Computing General},
ee = {https://www.frontiersin.org/article/10.3389/fphys.2018.00816},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2018-08&engl=0}
}
@article {ART-2018-03,
author = {Stefanie Stalter and Leonid Yelash and Nehzat Emamy and Antonia Statt and Martin Hanke and Luk{\'a}\&\#269 and Maria Ov{\'a}-Medvid’ov{\'a} and Peter Virnau},
title = {{Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats}},
journal = {Computer Physics Communications},
publisher = {Elsevier},
volume = {224},
pages = {198--208},
type = {Artikel in Zeitschrift},
month = {M{\"a}rz},
year = {2018},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {Heterogeneous multiscale methods (HMM) combine molecular accuracy of
particle-based simulations with the computational efficiency of continuum
descriptions to model flow in soft matter liquids. In these schemes, molecular
simulations typically pose a computational bottleneck, which we investigate in
detail in this study. We find that it is preferable to simulate many small
systems as opposed to a few large systems, and that a choice of a simple
isokinetic thermostat is typically sufficient while thermostats such as
Lowe{\^a}€“Andersen allow for simulations at elevated viscosity. We discuss
suitable choices for time steps and finite-size effects which arise in the
limit of very small simulation boxes. We also argue that if colloidal systems
are considered as opposed to atomistic systems, the gap between microscopic and
macroscopic simulations regarding time and length scales is significantly
smaller. We propose a novel reduced-order technique for the coupling to the
macroscopic solver, which allows us to approximate a non-linear stress{\^a}€“strain
relation efficiently and thus further reduce computational effort of
microscopic simulations.},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2018-03&engl=0}
}
@article {ART-2017-18,
author = {Zahra Niroobakhsh and Nehzat Emamy and Roozbeh Mousavi and Florian Kummer and Martin Oberlack},
title = {{Numerical investigation of laminar vortex shedding applying a discontinuous Galerkin Finite Element method}},
journal = {Progress in Computational Fluid Dynamics, An International Journal (PCFD)},
publisher = {Inderscience Publishers},
volume = {17},
number = {3},
pages = {131--140},
type = {Artikel in Zeitschrift},
month = {M{\"a}rz},
year = {2017},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2017-18&engl=0}
}
@article {ART-2017-17,
author = {Nehzat Emamy and Florian Kummer and Markus Mrosek and Martin Karcher and Martin Oberlack},
title = {{Implicit-explicit and explicit projection schemes for the unsteady incompressible Navier-Stokes equations using a high-order dG method}},
journal = {Computers \& Fluids},
publisher = {Elsevier},
volume = {154},
pages = {285--295},
type = {Artikel in Zeitschrift},
month = {September},
year = {2017},
language = {Englisch},
cr-category = {I.6.0 Simulation and Modeling General},
department = {Universit{\"a}t Stuttgart, Institut f{\"u}r Parallele und Verteilte Systeme, Simulation gro{\ss}er Systeme},
abstract = {},
url = {http://www2.informatik.uni-stuttgart.de/cgi-bin/NCSTRL/NCSTRL_view.pl?id=ART-2017-17&engl=0}
}