| 1. |
|
|
| 2. |
- Bauer, Pavol, et al.
(författare)
-
URDME v. 1.2: User's manual
- 2012
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations on structured, cartesian meshes. The underlying algorithm is the next subvolume method, extended to unstructured meshes by obtaining jump coefficients from a finite element formulation of the corresponding macroscopic equation. This manual describes version 1.2 of the software. URDME 1.2 includes support for Comsol Multiphysics 4.1, 4.2, 4.3 as well as the previous version 3.5a. Additionally, support for basic SBML has been added along with the possibility to compile in stand-alone mode.
|
|
| 3. |
|
|
| 4. |
- Drawert, Brian, et al.
(författare)
-
URDME v. 1.1: User's manual
- 2011
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations on structured, cartesian meshes. The underlying algorithm is the next subvolume method (NSM), extended to unstructured meshes by obtaining jump coefficients from the finite element formulation of the corresponding macroscopic equation. This manual describes the changes in the software compared to the previous version, URDME 1.0. Notable changes include support for Comsol Multiphysics 3.5a and a stronger decoupling between core simulation routines and the Matlab interface by making core solvers stand-alone executables. This opens up for more flexible simulation workflows when many realizations of the stochastic process need to be generated.
|
|
| 5. |
- Engblom, Henrik, et al.
(författare)
-
The evaluation of an electrocardiographic myocardial ischemia acuteness score to predict the amount of myocardial salvage achieved by early percutaneous coronary intervention Clinical validation with myocardial perfusion single photon emission computed tomography and cardiac magnetic resonance.
- 2011
-
Ingår i: Journal of Electrocardiology. - : Elsevier BV. - 1532-8430 .- 0022-0736. ; 44, s. 525-532
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The time from symptom onset to reperfusion in acute myocardial infarction (MI) has been shown to be a poor predictor of patient outcome. Acute electrocardiographic (ECG) changes, however, have been shown useful for estimated acuteness of myocardial ischemia using the Anderson-Wilkins ECG ischemia acuteness score (AW-acuteness score). The aim was to study whether acute ischemic ECG changes can predict the amount of salvageable myocardium in patients with acute ST-elevation MI. METHODS: Thirty-eight patients treated with primary percutaneous coronary intervention for first-time ST-elevation MI were retrospectively enrolled. Myocardium at risk (MaR) was determined by myocardial perfusion single photon emission computed tomography acutely or by T2-weighted cardiac magnetic resonance after 1 week, at the same time when final MI size was determined by late gadolinium enhancement. Myocardial salvage was calculated as (MaR - MI size)/MaR and compared with AW-acuteness score and time from symptom onset to primary percutaneous coronary intervention. RESULTS: The AW-acuteness score correlated significantly with salvageable myocardium for right coronary artery (RCA) occlusions (r = -0.57; P = .02) but not for left anterior descending artery (LAD) occlusions (r = -0.04; P = .88). Time from symptom onset did not correlate with the amount of salvageable myocardium (LAD, r = 0.04 and P = .87; RCA, r = -0.40 and P = .13). CONCLUSIONS: There is a moderate correlation between AW-acuteness score and salvageable myocardium in patients with acute RCA occlusion but not in patients with LAD occlusion.
|
|
| 6. |
- Engblom, Stefan, et al.
(författare)
-
Approximations for the moments of nonstationary and state dependent birth–death queues
- 2014
-
Ingår i: Computing Research Repository. ; :1406.6164
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper we propose a new method for approximating the nonstationary moment dynamics of one dimensional Markovian birth-death processes. By expanding the transition probabilities of the Markov process in terms of Poisson-Charlier polynomials, we are able to estimate any moment of the Markov process even though the system of moment equations may not be closed. Using new weighted discrete Sobolev spaces, we derive explicit error bounds of the transition probabilities and new weak a priori estimates for approximating the moments of the Markov processs using a truncated form of the expansion. Using our error bounds and estimates, we are able to show that our approximations converge to the true stochastic process as we add more terms to the expansion and give explicit bounds on the truncation error. As a result, we are the first paper in the queueing literature to provide error bounds and estimates on the performance of a moment closure approximation. Lastly, we perform several numerical experiments for some important models in the queueing theory literature and show that our expansion techniques are accurate at estimating the moment dynamics of these Markov process with only a few terms of the expansion.
|
|
| 7. |
- Engblom, Stefan, et al.
(författare)
-
On diffuse interface modeling and simulation of surfactants in two-phase fluid flow
- 2013
-
Ingår i: Communications in Computational Physics. - : Global Science Press. - 1815-2406 .- 1991-7120. ; 14:4, s. 879-915
-
Tidskriftsartikel (refereegranskat)abstract
- An existing phase-fieldmodel of two immiscible fluids with a single soluble surfactant present is discussed in detail. We analyze the well-posedness of the model and provide strong evidence that it is mathematically ill-posed for a large set of physically relevant parameters. As a consequence, critical modifications to the model are suggested that substantially increase the domain of validity. Carefully designed numerical simulations offer informative demonstrations as to the sharpness of our theoretical results and the qualities of the physical model. A fully coupled hydrodynamic test-case demonstrates the potential to capture also non-trivial effects on the overall flow.
|
|
| 8. |
- Engblom, Stefan
(författare)
-
On the stability of stochastic jump kinetics
- 2014
-
Ingår i: Applied Mathematics. - : Scientific Research Publishing, Inc.. - 2152-7385 .- 2152-7393. ; 5, s. 3217-3239
-
Tidskriftsartikel (refereegranskat)
|
|
| 9. |
|
|
| 10. |
- Engblom, Stefan
(författare)
-
On well-separated sets and fast multipole methods
- 2011
-
Ingår i: Applied Numerical Mathematics. - : Elsevier BV. - 0168-9274 .- 1873-5460. ; 61:10, s. 1096-1102
-
Tidskriftsartikel (refereegranskat)abstract
- The notion of well-separated sets is crucial in fast multipole methods as the main idea is to approximate the interaction between such sets via cluster expansions. We revisit the one-parameter multipole acceptance criterion in a general setting and derive a relative error estimate. This analysis benefits asymmetric versions of the method, where the division of the multipole boxes is more liberal than in conventional codes. Such variants offer a particularly elegant implementation with a balanced multipole tree, a feature which might be very favorable on modern computer architectures.
|
|
