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When calculating the free-energy of ions permeating membrane proteins, an initial decision to make is how many ions needs to be included in the calculation. This decision is usually based on previous knowledge (both experiments and simulations), and on the intuition of the researcher. But intuition might be wrong… And taking the number of ions wrong might render free-energy profiles that are ...

Computational representation of complex biological processes is becoming an increasingly established approach to complement the experimental analysis and study methods to halt/redirect pathological processes. In this review paper we focus on Epithelial to Mesenchymal transition (EMT), a phenotypic transformation with a pivotal role in cancer progression and metastases formation, and present a ...

Epithelial to Mesenchymal transition (EMT) is an exceedingly complex biological process that plays a key role in cancer progression and metastases formation. To unravel this complexity and isolate specific genetic markers important for this transition, we have developed a computational model recapitulating both single cell and population behaviours. The former was represented with a boolean ...

The selectivity of ion channels to different ion species is crucial for important biological processes, as nerve transmission and muscular contraction. Thanks to the availability of experimental atomic structures of several ion channels, including K⁺-channels, Na⁺-channels and Ca²⁺-channels, it is now possible to investigate the microscopic details of conduction ...

The binding of proteins to DNA controls many cellular events, including gene expression. In order to work properly, DNA binding proteins need to find their target sequences on DNA with high speed and accuracy. The recognition of the specific DNA binding site requires intimate contacts between the protein and the DNA molecule. However, strong atomic interactions between the two molecules are ...

The sinoatrial node (SAN) is the normal pacemaker of the mammalian heart. Over several decades, a large amount of data on the ionic mechanisms underlying the spontaneous electrical activity of SAN pacemaker cells has been obtained, mostly in experiments on single cells isolated from rabbit SAN. This allowed the development of comprehensive mathematical models of the electrical activity of ...