The research in the group focuses on mathematical modelling of biological processes at the molecular and cellular level. We are based in the Department of Medical Biotechnologies of the University of Siena

Research Topics

Ion Channels

Ion channels are membrane proteins that regulate the passage of ions across cell membranes. At a first glance, they could be described as hydrophilic pores that span the hydrophobic core of cell membranes. But ion channels are fairly complicated pores: they select the permeable ion species, and they open and close in response to chemical/physical stimuli. The human genome codes for hundreds of ion channels, and these proteins are crucial for several biological processes, including muscular contraction, signaling in the nervous system, and cellular homeostasis. We are interested in understanding how ions move across ion channels, and how similar ion species, as K+ and Na+, are selected with high efficiency. To this aim, we adopt different simulation approaches, ranging from continuum models of electrodiffusion, to Brownian dynamics, and full atomistic simulations.

Synthetic Biology

Synthetic biology aims to adopt the principles of engineering to the design of novel functions in biological systems. The potential applications of synthetic biology are numerous, from the controlled release of drugs, to energy production, and environmental sensing. However, its full potential is still unexpressed, largely because of the lack of accurate tools for the efficient design of synthetic devices. The rational design of biological systems necessarily requires a quantitative understanding of the processes governing their dynamics. In this context, our aim is to simulate the behaviours of gene regulatory networks by deterministic and stochastic modelling, in order to identify basic principles that could be useful for the design of synthetic devices.

Protein-DNA Interactions

At the finest detail, any regulatory role exerted by proteins on gene expression is the result of atomic interactions with the DNA molecule. This basic observation alone justifies the wide interest in protein-DNA interactions among the scientific community. On the top of its biological implications, the binding of proteins to DNA is also an interesting physical process by itself. Proteins are able to find their binding sites on the DNA at high speed and with exquisite selectivity. Considering the overwhelming number of non-specific sequences along a typical DNA molecule, which might differ from the target sequence by as little as 1 base pair, this is an extraordinary functional characteristic. How protein moves along the DNA sequence, and how they recognise the presence of a target sequence once they encounter it, are the questions that drive our research activities in the field.