Our researchers

Numerous problems encountered in computational biology can be formulated as optimization problems. In this context, optimization of drug release characteristics or dosing schedules for anticancer agents has become a prominent area not only for the development of new drugs, but also for established drugs. However, in complex systems, optimization of drug exposure is not a trivial task and cannot be efficiently addressed through trial-error simulation exercises. Finding a solution to those problems is a challenging task which requires more advanced strategies like optimal control theory. In this work, we perform an optimal control analysis on a previously developed computational model for the testosterone effects of triptorelin in prostate cancer patients with the goal of finding optimal drug-release characteristics. We demonstrate how numerical control optimization of non-linear models can be used to find better therapeutic approaches in order to improve the final outcome of the patients.

Polycrystals of thin colloidal deposits, with thickness controlled by spin-coating speed, exhibit axial symmetry with local 4-fold and 6-fold symmetric structures, termed orientationally correlated polycrystals (OCPs). While spin-coating is a very facile technique for producing large-area colloidal deposits, the axial symmetry prevents us from achieving true long-range order. To obtain true long-range order, we break this axial symmetry by introducing a patterned surface topography and thus eliminate the OCP character. We then examine symmetryindependent methods to quantify order in these disordered colloidal deposits. We find that all the information in the bond-orientational order parameters is well captured by persistent homology analysis methods that only use the centers of the particles as input data. It is expected that these methods will prove useful in characterizing other disordered structures.

Semantic memory is the subsystem of human memory that stores knowledge of concepts or meanings, as opposed to life specific experiences. The organization of concepts within semantic memory can be understood as a semantic network, where the concepts (nodes) are associated (linked) to others depending on perceptions, similarities, etc. Lexical access is the complementary part of this system and allows the retrieval of such organized knowledge. While conceptual information is stored under certain underlying organization (and thus gives rise to a specific topology), it is crucial to have an accurate access to any of the information units, e. g. the concepts, for efficiently retrieving semantic information for real-time need. An example of an information retrieval process occurs in verbal fluency tasks, and it is known to involve two different mechanisms: "clustering", or generating words within a subcategory, and, when a subcategory is exhausted, "switching" to a new subcategory. We extended this approach to random-walking on a network (clustering) in combination to jumping (switching) to any node with certain probability and derived its analytical expression based on Markov chains. Results show that this dual mechanism contributes to optimize the exploration of different network models in terms of the mean first passage time. Additionally, this cognitive inspired dual mechanism opens a new framework to better understand and evaluate exploration, propagation and transport phenomena in other complex systems where switching-like phenomena are feasible.