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Absorption and emission in inorganic bipolar solar cells based on low dimensional structures exhibiting the effects of quantum confinement is investigated in the framework of a comprehensive microscopic theory of the optical and electronic…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Flocks of birds, schools of fish, mixtures of motors and cytoskeletal filaments, swimming bacteria and driven granular media are systems of interacting motile units that exhibit collective behaviour. These can all be described as active…
As integrated photonic systems grow in scale and complexity, Photonic Design Automation (PDA) tools and Process Design Kits (PDKs) have become increasingly important for layout and simulation. However, fixed PDKs often fail to meet the…
Photovoltaic energy conversion in photovoltaic cells has been analyzed by the detailed balance approach or by thermodynamic arguments. Here we introduce a network representation to analyze the performance of such systems once a suitable…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Here we introduce and study a photonic analogue of the Kondo model. The model is defined as a far detuned regime of photonic scattering off a three-level emitter in a $\Lambda$-type configuration coupled to a one-dimensional transmission…
This work presents a mathematical model which describes both the genesis and growth of oxygenic photogranules (OPGs) and the related treatment process. The photogranule has been modelled as a free boundary domain with radial symmetry, which…
We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the…
In this paper we consider dynamics of a molecular system subjected to external pumping by a light source. Within a completely quantum mechanical treatment, we derive a general formula, which enables to asses effects of different light…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Mathematical models of population extinction have a variety of applications in such areas as ecology, paleontology and conservation biology. Here we propose and investigate two types of sub-exponential models of population extinction.The…
Learning compact and interpretable representations is a very natural task, which has not been solved satisfactorily even for simple binary datasets. In this paper, we review various ways of composing experts for binary data and argue that…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…