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BACKGROUND In this paper we apply a novel agent-based simulation method in order to model intracellular reactions in detail. The simulations are performed within a virtual cytoskeleton enriched with further crowding elements, which allows the analysis of molecular crowding effects on intracellular diffusion and reaction rates. The cytoskeleton network leads(More)
We investigate a three-dimensional multiscale model of vascular tumour growth, which couples blood flow, angiogenesis, vascular remodelling, nutrient/growth factor transport, movement of, and interactions between, normal and tumour cells, and nutrient-dependent cell cycle dynamics within each cell. In particular, we determine how the domain size, aspect(More)
The transduction of signals depends on the translocation of signaling molecules to specific targets. Undirected diffusion processes play a key role in the bridging of spaces between different cellular compartments. The diffusion of the molecules is, in turn, governed by the intracellular architecture. Molecular crowding and the cytoskeleton decrease(More)
A method is proposed for identification of kinetic parameters when diffusion of substrates is limiting in reactions catalyzed by immobilized enzymes. This method overcomes conventional sequential procedures, which assume immobilization does not affect the conformation of the enzyme and, thus, consider intrinsic and inherent kinetics to be the same. The(More)
Agent-based models are rigorous tools for simulating the interactions of individual entities, such as organisms or molecules within cells and assessing their effects on the dynamic behavior of the system as a whole. In context with bioprocess and biosystems engineering there are several interesting and important applications. This contribution aims at(More)
Angiogenesis marks an important turning point in the growth of solid tumours. Avascular tumours rely on diffusive transport to supply them with the nutrients they need to grow and, as a result, they typically grow to a maximal size of several millimetres in diameter. Growth stops when the rate at which nutrient-starved cells in the tumour centre die(More)
Basic characteristics (efficiency, selectivity, non-equilibrium) of capillary columns with a super-thick layer of stationary liquid phase are investigated. In contrast to traditionally used capillary columns with standard stationary phase thickness of 0.1-0.5 um, some new variables are now established. Firstly, the values of relative retention depend on(More)
New area in capillary gas chromatography (GC) was investigated. Many important analytical tasks can be solved only use very short capillary columns. Variation of chromatographic characteristics of ultra-short capillary columns with column length was originally studied at the conditions of gas-liquid chromatography. The column length varied from 500 to 10(More)
A method for the sensitive and selective determination of glycine in brain tissue has been developed. Small samples of brain tissue were homogenized by sonication in 0.7 N formic acid, and [1,2 13C2,15N]glycine was then added as internal standard. After centrifugation, aliquots of the supernatants were dried and the resulting residues were derivatized in a(More)
Detailed measurements of multiphase flows that prevail in bioreactors tell us that different transport mechanisms are dominating on different observation scales. The consequence in terms of reactor modeling is that the processes on different scales can be treated independently. A three-dimensional, dynamical model is presented that can be used to describe(More)