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BPS 2020
Contributed by Chiara Bartolucci
Modeling the electrical activity of human induced pluripotent stem cell-derived cardiomyocytes
Contributed by Michelangelo Paci
Free-energy profiles and number of permeation ions
Contributed by Simone FuriniWhen 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 ...
Concentration gradients in simulations with PBC
Contributed by Simone Furini
Selectivity in bacterial Na+ channels
Contributed by Simone Furini
Microenvironmental signals control hybrid EMT phenotypes
Contributed by Emanuele Giordano
A Scaffold Simulator to study of cancer cell survival and 3D spatial distribution (SALSA)
Contributed by Marilisa Cortesi
Computational models of Epithelial to Mesenchymal Transition
Contributed by Marilisa CortesiComputational 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 ...
Computational model of cell phenotype decision making
Contributed by Marilisa CortesiEpithelial 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 ...
Semi-Automatic Analysis of Invasion and Migration Transwell Assays (I-AbACUS)
Contributed by Marilisa CortesiTranswell assays are another common experimental approach for the quantification of migration and invasion (see also Automatic quantification of (cancer) cell invasiveness). This method relies on a semi-permeable membrane and a layer of Matrigel coating to simulate ...
Molecular Dynamics simulations reveal how K+-channels might conduct K+ ions at high speed
Contributed by Simone FuriniThe 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 ...
Molecular Dynamics simulations can analyze how protein might move along DNA sequences
Contributed by Simone FuriniThe 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 ...
