Reaction Diffusion Master Equation

Mesoscopic-microscopic hybrid algorithm with automatic partitioning

September 11, 2017September 11, 2017 Stefan Hellander No Comments

We have developed a multiscale method coupling the mesoscopic and microscopic scales. On the mesoscopic scale, systems are modeled as discrete jump processes on a structured or unstructured grid, while on the microscopic scale, molecules are modeled by hard spheres diffusing in continuous space. Microscopic simulations are accurate but computationally expensive. In this paper we…

Multiscale methods, News, publication, Reaction Diffusion Master Equation

Open PhD position

February 5, 2015February 5, 2015 admin No Comments

We are currently hiring a PhD student to work on the project From Single Cells to Tumors – Multiscale Simulation of Stochastic (multi)cellular Systems . Deadline for application: March 15. Instructions for how to apply can be found here: Instructions for application.

Multiscale methods, News, PyURDME, Reaction Diffusion Master Equation

StochSS 1.4: Introducing Spatial Stochastic Modeling and Simulations

September 1, 2014September 1, 2014 admin No Comments

We are excited to announce the release of StochSS 1.4 Version 1.4 includes spatial stochastic simulation capabilities powered by PyURDME (http://www.pyurdme.org/). Details and instructions on how to obtain the code can be found on the Download page Tutorials are available on the Documentation page Linda Petzold and Chandra Krintz – University of California Santa Barbara Per Lotstedt and Andreas Hellander – Uppsala…

News, PyURDME, Reaction Diffusion Master Equation, Software, Stochastic Chemical Kinetics, StochSS

Open PhD student position

June 25, 2014June 25, 2014 admin No Comments

We have an opening for a PhD student in computational systems biology. Interested candidates are encouraged to contact me for more details. Apply to the position here.

Multiscale methods, News, Reaction Diffusion Master Equation

PyURDME 1.0

June 25, 2014June 25, 2014 admin No Comments

After more than a year of development, we are happy to announce the release of PyURDME 1.0.0! PyURDME is a Python module for spatial stochastic simulation model development and simulation. PyURDME is connected to URDME in that is uses a modified version of its core solver. While URDME is mainly designed as an interactive Matlab…

PhD and Postdoc positions

January 17, 2014 admin No Comments

The Center for Applied Mathematics (CIM) in Uppsala are looking for up to 3 PhD students in applied mathematics. Within this call there is an opportunity to joint the group working on the project From cell-cell interactions to embryo development: Multiscale models and simulation in systems biology. This project is a collaboration with Carolina Wählby….

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Hes1, Multiscale methods, News, Reaction Diffusion Master Equation, Stochastic Chemical Kinetics, StochSS, URDME

Spatial Stochastic Simulation of the Hes1 gene regulatory network

January 23, 2013 admin No Comments

Individual mouse embryonic stem cells have been found to exhibit highly variable differentiation responses under the same environmental conditions. Recent experimatal evidence suggest that the noisy cyclic expression of Hes1 and its downstream genes are responsible for this, but the mechanism underlying this variability in expression is not well understood. Together with Mark Chaplain’s group,…

Hes1, News, Reaction Diffusion Master Equation

URDME 1.2 Released

December 18, 2012December 18, 2012 admin No Comments

We are happy to announce the release of URDME 1.2. New features include support for Comsol 4.1, 4.2 and 4.3. We have also added the ability to compile the solvers independently of Matlab libraries. This will greatly simplify deployment of URDME jobs by StochSS down the line. To get URDME 1.2: www.urdme.org Or visit us…

URDME paper in BMC Systems Biology

August 16, 2012August 17, 2012 admin No Comments

Ever since the first version of URDME, a software framework based on our theoretical work on RDME simulations on unstructured meshes, was made public in 2008, we have wanted to write up a journal publication that describes the software. For variuos reasons we have not gotten around to it, until now. The paper, published in…

Reaction Diffusion Master Equation, URDME

On the reaction-diffusion master equation in the microscopic limit

August 16, 2012January 25, 2016 admin No Comments

The RDME will break down in the limit of vanishing voxel sizes, in the sense that contributions from bimolecular reactions will be lost. The problem sets on earlier (for larger voxels), the more diffusion limited the reaction is. This is a problem that has attracted a lot of interest since it was pointed out by…

publication, Reaction Diffusion Master Equation