David Knies
I recently joined the Institute for System Dynamics as a PhD student. I'm currently working on a dynamic model of nitrate respiration in E. coli.
SEEK ID: https://fairdomhub.org/people/394
Location:
Germany
ORCID: Not specified
Joined: 24th Jan 2012
Expertise: Not specified
Tools: Matlab, Copasi, Flux balance analysis, Dynamic modelling
Roles
PAL
Their tagsRelated items
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.
The model is described ...
Creators: Michael Ederer, David Knies
Submitter: Michael Ederer
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
DownloadThis ordinary-differential equation model is a spatially lumped model showing the behaviour of oxygen in the three compartments medium, membrane and cytoplasm and its impact on FNR inactivation, hereby showing the effects of different oxygen concentrations, diffusion coefficients and reaction rates. The model was created with the Matlab SimBiology toolbox.
Creator: Samantha Nolan
Submitter: David Knies
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.
Creator: Samantha Nolan
Submitter: David Knies
Model type: Partial differential equations (PDE)
Model format: Mathematica
Environment: Not specified
