Simone Furini

PhD (Bioengineering), Alma Mater Studiorum – Università di Bologna, Italy. (2008)

M.E. (Electronical Engineering), Alma Mater Studiorum- Università di Bologna, Italy (2003)

Assistant Professor at the Department of Medical Biotechnologies University of Siena, Italy. 2009-Present

Visiting fellow at the Department of Physical Chemistry, University of Pannonia, Veszprém, Hungary, 2016

Visiting fellow at the Department of Chemistry, King’s College London, UK, 2013

Post-doctoral researcher; Alma Mater Studiorum- Università di Bologna, Italy. 2008

The aim of my research activity is how to include atomic and molecular details in numerical simulations of biological systems. The current research projects span a broad set of topics, including conduction across biological membranes, protein-DNA interactions, and mathematical modelling of regulatory gene networks.

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 lipid 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. The common ground of my research activities about ion channels is how to relate the atomic structure of these membrane proteins to their functional characteristics. To this aim, I adopt different simulation approaches, ranging from continuum models of electrodiffusion, to Brownian dynamics, and full atomistic simulations. The pros and cons of these strategies (more details = higher computational cost) asks for a combined usage of mathematical models at different scales. How to link atomic simulations with coarse models, and finally to experimental data, is a fundamental part of my research.

Regulatory Gene Networks. Synthetic biology aims to adopt the principles of engineering to the design of synthetic devices based on biological systems. The rational design of biological systems necessarily requires a quantitative understanding of the processes governing their dynamics. The aim of my research activity in the field is to simulate the behavior of gene regulatory networks by deterministic and stochastic modelling in order to understand how engineering principles could be applied to the design of gene networks with well-defined functional features.

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