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Bauer, Pavol
Publications (10 of 13) Show all publications
Lindén, J., Bauer, P., Engblom, S. & Jonsson, B. (2019). Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores. ACM Transactions on Modeling and Computer Simulation, 29(2), 11:1-25, Article ID 11.
Open this publication in new window or tab >>Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores
2019 (English)In: ACM Transactions on Modeling and Computer Simulation, ISSN 1049-3301, E-ISSN 1558-1195, Vol. 29, no 2, p. 11:1-25, article id 11Article in journal (Refereed) Published
National Category
Computer Sciences
Identifiers
urn:nbn:se:uu:diva-342180 (URN)10.1145/3301500 (DOI)000468031300004 ()
Projects
UPMARC
Available from: 2019-04-02 Created: 2018-02-19 Last updated: 2019-06-18Bibliographically approved
Lindén, J., Bauer, P., Engblom, S. & Jonsson, B. (2018). Fine-grained local dynamic load balancing in PDES. In: Proc. 6th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation: . Paper presented at SIGSIM-PADS 2018 (pp. 201-212). New York: ACM Press
Open this publication in new window or tab >>Fine-grained local dynamic load balancing in PDES
2018 (English)In: Proc. 6th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2018, p. 201-212Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
New York: ACM Press, 2018
National Category
Computer Sciences
Identifiers
urn:nbn:se:uu:diva-342174 (URN)10.1145/3200921.3200928 (DOI)978-1-4503-5092-1 (ISBN)
Conference
SIGSIM-PADS 2018
Projects
UPMARC
Available from: 2018-05-14 Created: 2018-02-19 Last updated: 2018-11-12Bibliographically approved
Bauer, P., Engblom, S., Mikulovic, S. & Senek, A. (2018). Multiscale modelling via split-step methods in neural firing. Mathematical and Computer Modelling of Dynamical Systems, 24, 426-445
Open this publication in new window or tab >>Multiscale modelling via split-step methods in neural firing
2018 (English)In: Mathematical and Computer Modelling of Dynamical Systems, ISSN 1387-3954, E-ISSN 1744-5051, Vol. 24, p. 426-445Article in journal (Refereed) Published
National Category
Computational Mathematics Neurosciences
Identifiers
urn:nbn:se:uu:diva-332008 (URN)10.1080/13873954.2018.1488740 (DOI)000440605300005 ()
Projects
UPMARCeSSENCE
Available from: 2018-08-01 Created: 2017-10-22 Last updated: 2018-11-19Bibliographically approved
Mikulovic, S., Restrepo, C. E., Siwani, S., Bauer, P., Johann, S. P., Tort, A. B. L., . . . Leão, R. N. (2018). Ventral hippocampal OLM cells control type 2 theta oscillations and response to predator odor. Nature Communications, 9, 3638:1-15, Article ID 3638.
Open this publication in new window or tab >>Ventral hippocampal OLM cells control type 2 theta oscillations and response to predator odor
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2018 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, p. 3638:1-15, article id 3638Article in journal (Refereed) Published
National Category
Neurosciences Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-364241 (URN)10.1038/s41467-018-05907-w (DOI)000444014100013 ()30194386 (PubMedID)
Projects
eSSENCE
Available from: 2018-09-07 Created: 2018-10-29 Last updated: 2018-10-30Bibliographically approved
Lindén, J., Bauer, P., Engblom, S. & Jonsson, B. (2017). Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems. In: Proc. 5th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation: . Paper presented at SIGSIM-PADS 2017 (pp. 53-64). New York: ACM Press
Open this publication in new window or tab >>Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems
2017 (English)In: Proc. 5th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2017, p. 53-64Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
New York: ACM Press, 2017
National Category
Computer Sciences
Identifiers
urn:nbn:se:uu:diva-328367 (URN)10.1145/3064911.3064916 (DOI)978-1-4503-4489-0 (ISBN)
Conference
SIGSIM-PADS 2017
Projects
UPMARC
Available from: 2017-05-16 Created: 2017-08-22 Last updated: 2018-11-12Bibliographically approved
Bauer, P. (2017). Parallelism in Event-Based Computations with Applications in Biology. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Parallelism in Event-Based Computations with Applications in Biology
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Event-based models find frequent usage in fields such as computational physics and biology as they may contain both continuous and discrete state variables and may incorporate both deterministic and stochastic state transitions. If the state transitions are stochastic, computer-generated random numbers are used to obtain the model solution. This type of event-based computations is also known as Monte-Carlo simulation.

In this thesis, I study different approaches to execute event-based computations on parallel computers. This ultimately allows users to retrieve their simulation results in a fraction of the original computation time. As system sizes grow continuously or models have to be simulated at longer time scales, this is a necessary approach for current computational tasks.

More specifically, I propose several ways to asynchronously simulate such models on parallel shared-memory computers, for example using parallel discrete-event simulation or task-based computing. The particular event-based models studied herein find applications in systems biology, computational epidemiology and computational neuroscience.

In the presented studies, the proposed methods allow for high efficiency of the parallel simulation, typically scaling well with the number of used computer cores. As the scaling typically depends on individual model properties, the studies also investigate which quantities have the greatest impact on the simulation performance.

Finally, the presented studies include other insights into event-based computations, such as methods how to estimate parameter sensitivity in stochastic models and how to simulate models that include both deterministic and stochastic state transitions.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. p. 48
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1586
Keywords
Event-based computations, Parallel algorithms, Discrete-event simulation, Monte-Carlo methods, Systems biology.
National Category
Other Computer and Information Science Computational Mathematics
Research subject
Scientific Computing
Identifiers
urn:nbn:se:uu:diva-332009 (URN)978-91-513-0125-9 (ISBN)
Public defence
2017-12-11, 2347, ITC, Lägerhyddsvägen 2, Uppsala, 10:15 (English)
Opponent
Supervisors
Projects
UPMARC
Available from: 2017-11-30 Created: 2017-10-22 Last updated: 2018-03-07
Widgren, S., Engblom, S., Bauer, P., Frössling, J., Emanuelson, U. & Lindberg, A. (2016). Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle. Veterinary research (Print), 47, 81:1-17, Article ID 81.
Open this publication in new window or tab >>Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle
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2016 (English)In: Veterinary research (Print), ISSN 0928-4249, E-ISSN 1297-9716, Vol. 47, p. 81:1-17, article id 81Article in journal (Refereed) Published
National Category
Computer Sciences Veterinary Science
Identifiers
urn:nbn:se:uu:diva-300846 (URN)10.1186/s13567-016-0366-5 (DOI)000381350100001 ()27515697 (PubMedID)
Projects
UPMARCeSSENCE
Available from: 2016-08-11 Created: 2016-08-15 Last updated: 2018-11-12Bibliographically approved
Bauer, P., Engblom, S. & Widgren, S. (2016). Fast event-based epidemiological simulations on national scales. The international journal of high performance computing applications, 30, 438-453
Open this publication in new window or tab >>Fast event-based epidemiological simulations on national scales
2016 (English)In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, p. 438-453Article in journal (Refereed) Published
National Category
Computer Sciences Computational Mathematics
Identifiers
urn:nbn:se:uu:diva-264751 (URN)10.1177/1094342016635723 (DOI)000387763100005 ()
Projects
UPMARCeSSENCE
Available from: 2016-04-11 Created: 2015-10-16 Last updated: 2018-11-12Bibliographically approved
Patra, K., Lyons, D. J., Bauer, P., Hilscher, M. M., Sharma, S., Leão, R. N. & Kullander, K. (2015). A role for solute carrier family 10 member 4, or vesicular aminergic-associated transporter, in structural remodelling and transmitter release at the mouse neuromuscular junction.. European Journal of Neuroscience, 41(3), 316-327
Open this publication in new window or tab >>A role for solute carrier family 10 member 4, or vesicular aminergic-associated transporter, in structural remodelling and transmitter release at the mouse neuromuscular junction.
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2015 (English)In: European Journal of Neuroscience, ISSN 0953-816X, E-ISSN 1460-9568, Vol. 41, no 3, p. 316-327Article in journal (Refereed) Published
Abstract [en]

The solute carrier and presynaptic vesicle protein solute carrier family 10 member 4, or vesicular aminergic-associated transporter (VAAT), was recently proven to have a modulatory role in central cholinergic signalling. It is currently unknown whether VAAT also affects peripheral cholinergic synapses. Here we demonstrated a regulatory role for the presynaptic vesicle protein VAAT in neuromuscular junction (NMJ) development and function. NMJs lacking VAAT had fewer branch points, whereas endplates showed an increased number of islands. Whereas the amplitude of spontaneous miniature endplate potentials in VAAT-deficient NMJs was decreased, the amplitude of evoked endplate potentials and the size of the readily releasable pool of vesicles were both increased. Moreover, VAAT-deficient NMJs displayed aberrant short-term synaptic plasticity with enhanced synaptic depression in response to high-frequency stimulation. Finally, the transcript levels of cholinergic receptor subunits in VAAT-deficient muscles were increased, indicating a compensatory postsynaptic sensitization. Our results suggested that VAAT modulates NMJ transmission efficiency and, as such, may represent a novel target for treatment of disorders affecting motor neurons.

National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-239636 (URN)10.1111/ejn.12790 (DOI)000349150000004 ()25410831 (PubMedID)
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2014-12-29 Created: 2014-12-29 Last updated: 2018-01-11Bibliographically approved
Bauer, P., Lindén, J., Engblom, S. & Jonsson, B. (2015). Efficient inter-process synchronization for parallel discrete event simulation on multicores. In: Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation: . Paper presented at SIGSIM-PADS 2015 (pp. 183-194). New York: ACM Press
Open this publication in new window or tab >>Efficient inter-process synchronization for parallel discrete event simulation on multicores
2015 (English)In: Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2015, p. 183-194Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
New York: ACM Press, 2015
National Category
Computer Sciences
Identifiers
urn:nbn:se:uu:diva-260199 (URN)10.1145/2769458.2769476 (DOI)978-1-4503-3583-6 (ISBN)
Conference
SIGSIM-PADS 2015
Projects
UPMARC
Available from: 2015-06-10 Created: 2015-08-17 Last updated: 2018-11-12Bibliographically approved
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