Friday, 26 Feb 2021

Topics related by tag: Computational models

Microenvironmental signals control hybrid EMT phenotypes

Multidisciplinary approaches prove to be helpful to investigate microenvironmental signals driving cancer cell molecular phenotype. Epithelial to Mesenchymal transition (EMT) has a pivotal role in cancer progression and metastasis formation. Coupling in silico and in vitro analyses, this manuscript gains an insight in the signal transduction cascades driven by a stiff ...

A Scaffold Simulator to study of cancer cell survival and 3D spatial distribution (SALSA)

3D cell cultures are becoming increasingly common in-vitro approaches to study cell behaviour in more accurate and realistic settings. The experimental study of these systems, however, is complicated by the lack of non-destructive methods for the quantification of relevant properties like cell density and spatial distribution. Computational simulations can be used to ...

Computational models of Epithelial to Mesenchymal Transition

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 ...

Computational model of cell phenotype decision making

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 ...

Molecular Dynamics simulations reveal how K+-channels might conduct K+ ions at high speed

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 ...

Molecular Dynamics simulations can analyze how protein might move along DNA sequences

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 ...

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Modelling the electrical activity of a cardiac pacemaker cell

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 ...

Mathematical models predict the behavior of modular synthetic gene circuits

Most of synthetic circuits developed have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to ...

Quantification of fluorescent protein markers in single bacterial cell

The evaluation of phenotypic variability within an isogenic population of bacterial cells, requires the quantification of gene expression at single cell level. Flow cytometers and microscopy set-ups equipped with microfluidic devices and incubation chambers are instruments capable of evaluating the level of specific proteins in individual cells. However they are ...