Stefan Engblom

Morphological Stability for in silico Models of Avascular Tumors

Blom, Erik; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2024

• DOI for Morphological Stability for in silico Models of Avascular Tumors
• Download full text (pdf) of Morphological Stability for in silico Models of Avascular Tumors

Bayesian Monitoring of COVID-19 in Sweden

Marin, Robin; Runvik, Håkan; Medvedev, Alexander; Engblom, Stefan

Part of Epidemics, 2023

• DOI for Bayesian Monitoring of COVID-19 in Sweden
• Download full text (pdf) of Bayesian Monitoring of COVID-19 in Sweden

Bayesian inference in epidemics: linear noise analysis

Bronstein, Samuel; Engblom, Stefan; Marin, Robin

Part of Mathematical Biosciences and Engineering, p. 4128-4152, 2023

• DOI for Bayesian inference in epidemics: linear noise analysis
• Download full text (pdf) of Bayesian inference in epidemics: linear noise analysis

App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden

Kennedy, Beatrice; Fitipaldi, Hugo; Hammar, Ulf; Maziarz, Marlena et al.

Part of Nature Communications, 2022

• DOI for App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden
• Download full text (pdf) of App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden

Robust and integrative Bayesian neural networks for likelihood-free parameter inference

Wrede, Fredrik; Eriksson, Robin; Jiang, Richard; Petzold, Linda et al.

Part of 2022 International Joint Conference on Neural Networks (IJCNN), p. 1-10, 2022

• DOI for Robust and integrative Bayesian neural networks for likelihood-free parameter inference

Distributed and Adaptive Fast Multipole Method in Three Dimensions

Bull, Jonathan R.; Engblom, Stefan

Part of Communications in Computational Physics, p. 959-984, 2021

• DOI for Distributed and Adaptive Fast Multipole Method in Three Dimensions

Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline

Liu, Jing; Engblom, Stefan; Nettelblad, Carl

Part of Journal of the Optical Society of America A, p. 1673-1686, 2020

• DOI for Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline

Bayesian epidemiological modeling over high-resolution network data

Engblom, Stefan; Eriksson, Robin; Widgren, Stefan

Part of Epidemics, 2020

• DOI for Bayesian epidemiological modeling over high-resolution network data
• Download full text (pdf) of Bayesian epidemiological modeling over high-resolution network data

Supervised classification methods for flash X-ray single particle diffraction imaging

Liu, Jing; van der Schot, Gijs; Engblom, Stefan

Part of Optics Express, p. 3884-3899, 2019

• DOI for Supervised classification methods for flash X-ray single particle diffraction imaging

SimInf: An R package for data-driven stochastic disease spread simulations

Widgren, Stefan; Bauer, Pavol; Eriksson, Robin; Engblom, Stefan

Part of Journal of Statistical Software, p. 1-42, 2019

• DOI for SimInf: An R package for data-driven stochastic disease spread simulations

Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores

Lindén, Jonatan; Bauer, Pavol; Engblom, Stefan; Jonsson, Bengt

Part of ACM Transactions on Modeling and Computer Simulation, 2019

• DOI for Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores

Stochastic simulation of pattern formation in growing tissue: A multilevel approach

Engblom, Stefan

Part of Bulletin of Mathematical Biology, p. 3010-3023, 2019

• DOI for Stochastic simulation of pattern formation in growing tissue: A multilevel approach

Assessing uncertainties in x-ray single-particle three-dimensional reconstruction

Liu, Jing; Engblom, Stefan; Nettelblad, Carl

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2018

• DOI for Assessing uncertainties in x-ray single-particle three-dimensional reconstruction

A general high order two-dimensional panel method

Goude, Anders; Engblom, Stefan

Part of Applied Mathematical Modelling, p. 1-17, 2018

• DOI for A general high order two-dimensional panel method

Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time

Engblom, Stefan; Wilson, Daniel B.; Baker, Ruth E.

Part of Royal Society Open Science, 2018

• DOI for Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time

Fine-grained local dynamic load balancing in PDES

Lindén, Jonatan; Bauer, Pavol; Engblom, Stefan; Jonsson, Bengt

Part of Proc. 6th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, p. 201-212, 2018

• DOI for Fine-grained local dynamic load balancing in PDES

Multiscale modelling via split-step methods in neural firing

Bauer, Pavol; Engblom, Stefan; Mikulovic, Sanja; Senek, Aleksandar

Part of Mathematical and Computer Modelling of Dynamical Systems, p. 426-445, 2018

• DOI for Multiscale modelling via split-step methods in neural firing

Mesoscopic modeling of random walk and reactions in crowded media

Engblom, Stefan; Lötstedt, Per; Meinecke, Lina

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2018

• DOI for Mesoscopic modeling of random walk and reactions in crowded media

Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics

Chevallier, Augustin; Engblom, Stefan

Part of SIAM Journal on Numerical Analysis, p. 469-498, 2018

• DOI for Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics

Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control

Widgren, Stefan; Engblom, Stefan; Emanuelson, Ulf; Lindberg, Ann

Part of Veterinary research (Print), 2018

• DOI for Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control

Stability and strong convergence for spatial stochastic kinetics

Engblom, Stefan

Part of Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, p. 109-125, Springer, 2017

• DOI for Stability and strong convergence for spatial stochastic kinetics

Vascular sprouts induce local attraction of proangiogenic neutrophils

Christoffersson, Gustaf; Lomei, Jalal; O'Callaghan, Paul; Kreuger, Johan et al.

Part of Journal of Leukocyte Biology, p. 741-751, 2017

• DOI for Vascular sprouts induce local attraction of proangiogenic neutrophils

Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems

Lindén, Jonatan; Bauer, Pavol; Engblom, Stefan; Jonsson, Bengt

Part of Proc. 5th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, p. 53-64, 2017

• DOI for Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems

Data-driven computational disease spread modeling: from measurement to parametrization and control

Engblom, Stefan; Widgren, Stefan

Part of Disease Modelling and Public Health, p. 305-328, Elsevier, 2017

• DOI for Data-driven computational disease spread modeling: from measurement to parametrization and control

Analysis and design of jump coefficients in discrete stochastic diffusion models

Meinecke, Lina; Engblom, Stefan; Hellander, Andreas; Lötstedt, Per

Part of SIAM Journal on Scientific Computing, 2016

• DOI for Analysis and design of jump coefficients in discrete stochastic diffusion models
• Download full text (pdf) of Analysis and design of jump coefficients in discrete stochastic diffusion models

Preconditioned Metropolis sampling as a strategy to improve efficiency in posterior exploration

Engblom, Stefan; Sunkara, Vikram

p. 89-94, 2016

• DOI for Preconditioned Metropolis sampling as a strategy to improve efficiency in posterior exploration

Mesoscopic modeling of stochastic reaction–diffusion kinetics in the subdiffusive regime

Blanc, Emilie; Engblom, Stefan; Hellander, Andreas; Lötstedt, Per

Part of Multiscale Modeling & simulation, p. 668-707, 2016

• DOI for Mesoscopic modeling of stochastic reaction–diffusion kinetics in the subdiffusive regime

Fast Matlab compatible sparse assembly on multicore computers

Engblom, Stefan; Lukarski, Dimitar

Part of Parallel Computing, p. 1-17, 2016

• DOI for Fast Matlab compatible sparse assembly on multicore computers

Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle

Widgren, Stefan; Engblom, Stefan; Bauer, Pavol; Frössling, Jenny et al.

Part of Veterinary research (Print), 2016

• DOI for Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle

Fast event-based epidemiological simulations on national scales

Bauer, Pavol; Engblom, Stefan; Widgren, Stefan

Part of The international journal of high performance computing applications, p. 438-453, 2016

• DOI for Fast event-based epidemiological simulations on national scales

Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks

Milias-Argeitis, Andreas; Engblom, Stefan; Bauer, Pavol; Khammash, Mustafa

Part of Journal of the Royal Society Interface, 2015

• DOI for Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks
• Download full text (pdf) of Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks

Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Ekeberg, Tomas; Engblom, Stefan; Liu, Jing

Part of The international journal of high performance computing applications, p. 233-243, 2015

• DOI for Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters
• Download full text (pdf) of Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Strong convergence for split-step methods in stochastic jump kinetics

Engblom, Stefan

Part of SIAM Journal on Numerical Analysis, p. 2655-2676, 2015

• DOI for Strong convergence for split-step methods in stochastic jump kinetics
• Download full text (pdf) of Strong convergence for split-step methods in stochastic jump kinetics

Efficient inter-process synchronization for parallel discrete event simulation on multicores

Bauer, Pavol; Lindén, Jonatan; Engblom, Stefan; Jonsson, Bengt

Part of Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, p. 183-194, 2015

• DOI for Efficient inter-process synchronization for parallel discrete event simulation on multicores

X-ray laser imaging of biomolecules using multiple GPUs

Engblom, Stefan; Liu, Jing

Part of Parallel Processing and Applied Mathematics, p. 480-489, 2014

• DOI for X-ray laser imaging of biomolecules using multiple GPUs

Dynamic autotuning of adaptive fast multipole methods on hybrid multicore CPU and GPU systems

Holm, Marcus; Engblom, Stefan; Goude, Anders; Holmgren, Sverker

Part of SIAM Journal on Scientific Computing, 2014

• DOI for Dynamic autotuning of adaptive fast multipole methods on hybrid multicore CPU and GPU systems

On the stability of stochastic jump kinetics

Engblom, Stefan

Part of Applied Mathematics, p. 3217-3239, 2014

• DOI for On the stability of stochastic jump kinetics

On diffuse interface modeling and simulation of surfactants in two-phase fluid flow

Engblom, Stefan; Do-Quang, Minh; Amberg, Gustav; Tornberg, Anna-Karin

Part of Communications in Computational Physics, p. 879-915, 2013

• DOI for On diffuse interface modeling and simulation of surfactants in two-phase fluid flow

Adaptive fast multipole methods on the GPU

Goude, Anders; Engblom, Stefan

Part of Journal of Supercomputing, p. 897-918, 2013

• DOI for Adaptive fast multipole methods on the GPU

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

Part of BMC Systems Biology, 2012

• DOI for URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Adaptive fast multipole methods on the GPU

Goude, Anders; Engblom, Stefan

2012

• Download full text (pdf) of Adaptive fast multipole methods on the GPU

On well-separated sets and fast multipole methods

Engblom, Stefan

Part of Applied Numerical Mathematics, p. 1096-1102, 2011

• DOI for On well-separated sets and fast multipole methods

Analytical solutions for a single blade in vertical axis turbine motion in two dimensions

Deglaire, Paul; Engblom, Stefan; Ågren, Olov; Bernhoff, Hans

Part of European journal of mechanics. B, Fluids, p. 506-520, 2009

• DOI for Analytical solutions for a single blade in vertical axis turbine motion in two dimensions

Galerkin spectral method applied to the chemical master equation

Engblom, Stefan

Part of Communications in Computational Physics, p. 871-896, 2009

Spectral approximation of solutions to the chemical master equation

Engblom, Stefan

Part of Journal of Computational and Applied Mathematics, p. 208-221, 2009

• DOI for Spectral approximation of solutions to the chemical master equation

Parallel in time simulation of multiscale stochastic chemical kinetics

Engblom, Stefan

Part of Multiscale Modeling & simulation, p. 46-68, 2009

• DOI for Parallel in time simulation of multiscale stochastic chemical kinetics

Simulation of stochastic reaction-diffusion processes on unstructured meshes

Engblom, Stefan; Ferm, Lars; Hellander, Andreas; Lötstedt, Per

Part of SIAM Journal on Scientific Computing, p. 1774-1797, 2009

• DOI for Simulation of stochastic reaction-diffusion processes on unstructured meshes

Numerical Solution Methods in Stochastic Chemical Kinetics

Engblom, Stefan

2008

• Download full text (pdf) of Numerical Solution Methods in Stochastic Chemical Kinetics

Computing the moments of high dimensional solutions of the master equation

Engblom, Stefan

Part of Applied Mathematics and Computation, p. 498-515, 2006

• DOI for Computing the moments of high dimensional solutions of the master equation

Numerical methods for the chemical master equation

Engblom, Stefan

2006

• Download full text (pdf) of Numerical methods for the chemical master equation

Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Nordman, Alfred T.; Engblom, Stefan; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 5435-5447, 2026

• DOI for Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Bayesian three-point water models

Nordman, Alfred T.; Engblom, Stefan; Van der Spoel, David

Part of npj Computational Materials, 2025

• DOI for Bayesian three-point water models
• Download full text (pdf) of Bayesian three-point water models

Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach

Menz, Gesina; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2025

• DOI for Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach
• Download full text (pdf) of Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach

Modeling the hallmarks of avascular tumors

Blom, Erik; Engblom, Stefan; Menz, Gesina

2025

• DOI for Modeling the hallmarks of avascular tumors

Morphological Stability for in silico Models of Avascular Tumors

Blom, Erik; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2024

• DOI for Morphological Stability for in silico Models of Avascular Tumors
• Download full text (pdf) of Morphological Stability for in silico Models of Avascular Tumors

Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Nordman, Alfred T.; Engblom, Stefan; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 5435-5447, 2026

• DOI for Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Bayesian three-point water models

Nordman, Alfred T.; Engblom, Stefan; Van der Spoel, David

Part of npj Computational Materials, 2025

• DOI for Bayesian three-point water models
• Download full text (pdf) of Bayesian three-point water models

Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach

Menz, Gesina; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2025

• DOI for Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach
• Download full text (pdf) of Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach

Morphological Stability for in silico Models of Avascular Tumors

Blom, Erik; Engblom, Stefan

Part of Bulletin of Mathematical Biology, 2024

• DOI for Morphological Stability for in silico Models of Avascular Tumors
• Download full text (pdf) of Morphological Stability for in silico Models of Avascular Tumors

Bayesian Monitoring of COVID-19 in Sweden

Marin, Robin; Runvik, Håkan; Medvedev, Alexander; Engblom, Stefan

Part of Epidemics, 2023

• DOI for Bayesian Monitoring of COVID-19 in Sweden
• Download full text (pdf) of Bayesian Monitoring of COVID-19 in Sweden

Bayesian inference in epidemics: linear noise analysis

Bronstein, Samuel; Engblom, Stefan; Marin, Robin

Part of Mathematical Biosciences and Engineering, p. 4128-4152, 2023

• DOI for Bayesian inference in epidemics: linear noise analysis
• Download full text (pdf) of Bayesian inference in epidemics: linear noise analysis

App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden

Kennedy, Beatrice; Fitipaldi, Hugo; Hammar, Ulf; Maziarz, Marlena et al.

Part of Nature Communications, 2022

• DOI for App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden
• Download full text (pdf) of App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden

Distributed and Adaptive Fast Multipole Method in Three Dimensions

Bull, Jonathan R.; Engblom, Stefan

Part of Communications in Computational Physics, p. 959-984, 2021

• DOI for Distributed and Adaptive Fast Multipole Method in Three Dimensions

Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline

Liu, Jing; Engblom, Stefan; Nettelblad, Carl

Part of Journal of the Optical Society of America A, p. 1673-1686, 2020

• DOI for Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline

Bayesian epidemiological modeling over high-resolution network data

Engblom, Stefan; Eriksson, Robin; Widgren, Stefan

Part of Epidemics, 2020

• DOI for Bayesian epidemiological modeling over high-resolution network data
• Download full text (pdf) of Bayesian epidemiological modeling over high-resolution network data

Supervised classification methods for flash X-ray single particle diffraction imaging

Liu, Jing; van der Schot, Gijs; Engblom, Stefan

Part of Optics Express, p. 3884-3899, 2019

• DOI for Supervised classification methods for flash X-ray single particle diffraction imaging

SimInf: An R package for data-driven stochastic disease spread simulations

Widgren, Stefan; Bauer, Pavol; Eriksson, Robin; Engblom, Stefan

Part of Journal of Statistical Software, p. 1-42, 2019

• DOI for SimInf: An R package for data-driven stochastic disease spread simulations

Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores

Lindén, Jonatan; Bauer, Pavol; Engblom, Stefan; Jonsson, Bengt

Part of ACM Transactions on Modeling and Computer Simulation, 2019

• DOI for Exposing inter-process information for efficient PDES of spatial stochastic systems on multicores

Stochastic simulation of pattern formation in growing tissue: A multilevel approach

Engblom, Stefan

Part of Bulletin of Mathematical Biology, p. 3010-3023, 2019

• DOI for Stochastic simulation of pattern formation in growing tissue: A multilevel approach

Temporal upscaling in micromagnetism via heterogeneous multiscale methods

Arjmand, Doghonay; Engblom, Stefan; Kreiss, Gunilla

Part of Journal of Computational and Applied Mathematics, p. 99-113, 2019

• DOI for Temporal upscaling in micromagnetism via heterogeneous multiscale methods

Assessing uncertainties in x-ray single-particle three-dimensional reconstruction

Liu, Jing; Engblom, Stefan; Nettelblad, Carl

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2018

• DOI for Assessing uncertainties in x-ray single-particle three-dimensional reconstruction

A general high order two-dimensional panel method

Goude, Anders; Engblom, Stefan

Part of Applied Mathematical Modelling, p. 1-17, 2018

• DOI for A general high order two-dimensional panel method

Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time

Engblom, Stefan; Wilson, Daniel B.; Baker, Ruth E.

Part of Royal Society Open Science, 2018

• DOI for Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time

Multiscale modelling via split-step methods in neural firing

Bauer, Pavol; Engblom, Stefan; Mikulovic, Sanja; Senek, Aleksandar

Part of Mathematical and Computer Modelling of Dynamical Systems, p. 426-445, 2018

• DOI for Multiscale modelling via split-step methods in neural firing

Mesoscopic modeling of random walk and reactions in crowded media

Engblom, Stefan; Lötstedt, Per; Meinecke, Lina

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2018

• DOI for Mesoscopic modeling of random walk and reactions in crowded media

Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics

Chevallier, Augustin; Engblom, Stefan

Part of SIAM Journal on Numerical Analysis, p. 469-498, 2018

• DOI for Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics

Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control

Widgren, Stefan; Engblom, Stefan; Emanuelson, Ulf; Lindberg, Ann

Part of Veterinary research (Print), 2018

• DOI for Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control

Vascular sprouts induce local attraction of proangiogenic neutrophils

Christoffersson, Gustaf; Lomei, Jalal; O'Callaghan, Paul; Kreuger, Johan et al.

Part of Journal of Leukocyte Biology, p. 741-751, 2017

• DOI for Vascular sprouts induce local attraction of proangiogenic neutrophils

Analysis and design of jump coefficients in discrete stochastic diffusion models

Meinecke, Lina; Engblom, Stefan; Hellander, Andreas; Lötstedt, Per

Part of SIAM Journal on Scientific Computing, 2016

• DOI for Analysis and design of jump coefficients in discrete stochastic diffusion models
• Download full text (pdf) of Analysis and design of jump coefficients in discrete stochastic diffusion models

Mesoscopic modeling of stochastic reaction–diffusion kinetics in the subdiffusive regime

Blanc, Emilie; Engblom, Stefan; Hellander, Andreas; Lötstedt, Per

Part of Multiscale Modeling & simulation, p. 668-707, 2016

• DOI for Mesoscopic modeling of stochastic reaction–diffusion kinetics in the subdiffusive regime

Fast Matlab compatible sparse assembly on multicore computers

Engblom, Stefan; Lukarski, Dimitar

Part of Parallel Computing, p. 1-17, 2016

• DOI for Fast Matlab compatible sparse assembly on multicore computers

Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle

Widgren, Stefan; Engblom, Stefan; Bauer, Pavol; Frössling, Jenny et al.

Part of Veterinary research (Print), 2016

• DOI for Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle

Fast event-based epidemiological simulations on national scales

Bauer, Pavol; Engblom, Stefan; Widgren, Stefan

Part of The international journal of high performance computing applications, p. 438-453, 2016

• DOI for Fast event-based epidemiological simulations on national scales

Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks

Milias-Argeitis, Andreas; Engblom, Stefan; Bauer, Pavol; Khammash, Mustafa

Part of Journal of the Royal Society Interface, 2015

• DOI for Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks
• Download full text (pdf) of Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks

Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Ekeberg, Tomas; Engblom, Stefan; Liu, Jing

Part of The international journal of high performance computing applications, p. 233-243, 2015

• DOI for Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters
• Download full text (pdf) of Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Strong convergence for split-step methods in stochastic jump kinetics

Engblom, Stefan

Part of SIAM Journal on Numerical Analysis, p. 2655-2676, 2015

• DOI for Strong convergence for split-step methods in stochastic jump kinetics
• Download full text (pdf) of Strong convergence for split-step methods in stochastic jump kinetics

Approximations for the moments of nonstationary and state dependent birth–death queues

Engblom, Stefan; Pender, Jamol

Part of Computing Research Repository, 2014

• DOI for Approximations for the moments of nonstationary and state dependent birth–death queues

Dynamic autotuning of adaptive fast multipole methods on hybrid multicore CPU and GPU systems

Holm, Marcus; Engblom, Stefan; Goude, Anders; Holmgren, Sverker

Part of SIAM Journal on Scientific Computing, 2014

• DOI for Dynamic autotuning of adaptive fast multipole methods on hybrid multicore CPU and GPU systems

On the stability of stochastic jump kinetics

Engblom, Stefan

Part of Applied Mathematics, p. 3217-3239, 2014

• DOI for On the stability of stochastic jump kinetics

On diffuse interface modeling and simulation of surfactants in two-phase fluid flow

Engblom, Stefan; Do-Quang, Minh; Amberg, Gustav; Tornberg, Anna-Karin

Part of Communications in Computational Physics, p. 879-915, 2013

• DOI for On diffuse interface modeling and simulation of surfactants in two-phase fluid flow

Adaptive fast multipole methods on the GPU

Goude, Anders; Engblom, Stefan

Part of Journal of Supercomputing, p. 897-918, 2013

• DOI for Adaptive fast multipole methods on the GPU

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

Part of BMC Systems Biology, 2012

• DOI for URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

On well-separated sets and fast multipole methods

Engblom, Stefan

Part of Applied Numerical Mathematics, p. 1096-1102, 2011

• DOI for On well-separated sets and fast multipole methods

Analytical solutions for a single blade in vertical axis turbine motion in two dimensions

Deglaire, Paul; Engblom, Stefan; Ågren, Olov; Bernhoff, Hans

Part of European journal of mechanics. B, Fluids, p. 506-520, 2009

• DOI for Analytical solutions for a single blade in vertical axis turbine motion in two dimensions

Galerkin spectral method applied to the chemical master equation

Engblom, Stefan

Part of Communications in Computational Physics, p. 871-896, 2009

Spectral approximation of solutions to the chemical master equation

Engblom, Stefan

Part of Journal of Computational and Applied Mathematics, p. 208-221, 2009

• DOI for Spectral approximation of solutions to the chemical master equation

Parallel in time simulation of multiscale stochastic chemical kinetics

Engblom, Stefan

Part of Multiscale Modeling & simulation, p. 46-68, 2009

• DOI for Parallel in time simulation of multiscale stochastic chemical kinetics

Simulation of stochastic reaction-diffusion processes on unstructured meshes

Engblom, Stefan; Ferm, Lars; Hellander, Andreas; Lötstedt, Per

Part of SIAM Journal on Scientific Computing, p. 1774-1797, 2009

• DOI for Simulation of stochastic reaction-diffusion processes on unstructured meshes

Computing the moments of high dimensional solutions of the master equation

Engblom, Stefan

Part of Applied Mathematics and Computation, p. 498-515, 2006

• DOI for Computing the moments of high dimensional solutions of the master equation

Multiscale simulation of stochastic reaction–diffusion networks

Engblom, Stefan; Hellander, Andreas; Lötstedt, Per

Part of Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, p. 55-79, Springer, 2017

• DOI for Multiscale simulation of stochastic reaction–diffusion networks

Stability and strong convergence for spatial stochastic kinetics

Engblom, Stefan

Part of Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, p. 109-125, Springer, 2017

• DOI for Stability and strong convergence for spatial stochastic kinetics

Data-driven computational disease spread modeling: from measurement to parametrization and control

Engblom, Stefan; Widgren, Stefan

Part of Disease Modelling and Public Health, p. 305-328, Elsevier, 2017

• DOI for Data-driven computational disease spread modeling: from measurement to parametrization and control

Numerical Solution Methods in Stochastic Chemical Kinetics

Engblom, Stefan

2008

• Download full text (pdf) of Numerical Solution Methods in Stochastic Chemical Kinetics

Numerical methods for the chemical master equation

Engblom, Stefan

2006

• Download full text (pdf) of Numerical methods for the chemical master equation

Robust and integrative Bayesian neural networks for likelihood-free parameter inference

Wrede, Fredrik; Eriksson, Robin; Jiang, Richard; Petzold, Linda et al.

Part of 2022 International Joint Conference on Neural Networks (IJCNN), p. 1-10, 2022

• DOI for Robust and integrative Bayesian neural networks for likelihood-free parameter inference

Towards Confident Bayesian Parameter Estimation in Stochastic Chemical Kinetics

Engblom, Stefan; Eriksson, Robin; Vilanova, Pedro

Part of Numerical Mathematics and Advanced Applications ENUMATH 2019, p. 373-380, 2021

• DOI for Towards Confident Bayesian Parameter Estimation in Stochastic Chemical Kinetics

Initialization of a Disease Transmission Model

Runvik, Håkan; Medvedev, Alexander; Eriksson, Robin; Engblom, Stefan

Part of IFAC PapersOnline, p. 839-844, 2020

• DOI for Initialization of a Disease Transmission Model
• Download full text (pdf) of Initialization of a Disease Transmission Model

SimInf for spatio-temporal data-driven modeling of African swine fever in Swedish wildboar

Widgren, Stefan; Rosendal, Thomas; Engblom, Stefan; Ståhl, Karl

Part of GeoVet 2019, 2019

• DOI for SimInf for spatio-temporal data-driven modeling of African swine fever in Swedish wildboar

Fine-grained local dynamic load balancing in PDES

Lindén, Jonatan; Bauer, Pavol; Engblom, Stefan; Jonsson, Bengt

Part of Proc. 6th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, p. 201-212, 2018

• DOI for Fine-grained local dynamic load balancing in PDES

Towards Bayesian parametrization of national scale epidemics

Eriksson, Robin; Engblom, Stefan; Widgren, Stefan

Part of MATHMOD 2018 Extended Abstracts, p. 65-66, 2018

• DOI for Towards Bayesian parametrization of national scale epidemics

Multiscale stochastic neuron modeling – with applications in deep brain stimulation

Senek, Aleksandar; Engblom, Stefan

Part of Proc. Summer Simulation Multiconference, 2017

• DOI for Multiscale stochastic neuron modeling – with applications in deep brain stimulation

Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems

Lindén, Jonatan; Bauer, Pavol; Engblom, Stefan; Jonsson, Bengt

Part of Proc. 5th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, p. 53-64, 2017

• DOI for Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems

Preconditioned Metropolis sampling as a strategy to improve efficiency in posterior exploration

Engblom, Stefan; Sunkara, Vikram

p. 89-94, 2016

• DOI for Preconditioned Metropolis sampling as a strategy to improve efficiency in posterior exploration

A direct solver for the advection–diffusion equation using Green's functions and low-rank approximation

Bull, Jonathan; Engblom, Stefan; Holmgren, Sverker

Part of Proc. 7th ECCOMAS Congress, p. 7302-7316, 2016

• DOI for A direct solver for the advection–diffusion equation using Green's functions and low-rank approximation

Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics

Bauer, Pavol; Engblom, Stefan

Part of Numerical Mathematics and Advanced Applications, p. 519-527, 2015

• DOI for Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics

Efficient inter-process synchronization for parallel discrete event simulation on multicores

Bauer, Pavol; Lindén, Jonatan; Engblom, Stefan; Jonsson, Bengt

Part of Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, p. 183-194, 2015

• DOI for Efficient inter-process synchronization for parallel discrete event simulation on multicores

X-ray laser imaging of biomolecules using multiple GPUs

Engblom, Stefan; Liu, Jing

Part of Parallel Processing and Applied Mathematics, p. 480-489, 2014

• DOI for X-ray laser imaging of biomolecules using multiple GPUs

The well-posedness of diffuse interface modeling of surfactants in two-phase fluid flow

Do-Quang, Minh; Engblom, Stefan; Tornberg, Anna-Karin; Amberg, Gustav

Part of Wetting and Evaporation, p. 80-81, 2013

Stable and accurate wave simulations in complex geometries and discontinuous media

Mattsson, Ken; Almquist, Martin; Engblom, Stefan

Part of Proc. 11th International Conference on Mathematical and Numerical Aspects of Waves, p. 201-202, 2013

Time-parallel simulation of stochastic chemical kinetics

Engblom, Stefan

Part of Numerical Analysis and Applied Mathematics, p. 174-177, 2008

• DOI for Time-parallel simulation of stochastic chemical kinetics

Modeling the hallmarks of avascular tumors

Blom, Erik; Engblom, Stefan; Menz, Gesina

2025

• DOI for Modeling the hallmarks of avascular tumors

Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Nordman, Alfred T.; Engblom, Stefan; van der Spoel, David

Adaptive fast multipole methods on the GPU

Goude, Anders; Engblom, Stefan

2012

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On the stability of stochastic jump kinetics

Engblom, Stefan

2012

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Simulation of stochastic reaction-diffusion processes on unstructured meshes

Engblom, Stefan; Ferm, Lars; Hellander, Andreas; Lötstedt, Per

2008

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Parallel in time simulation of multiscale stochastic chemical kinetics

Engblom, Stefan

2008

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A discrete spectral method for the chemical master equation

Engblom, Stefan

2008

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Gaussian quadratures with respect to discrete measures

Engblom, Stefan

2006

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Computing the moments of high dimensional solutions of the master equation

Engblom, Stefan

2005

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