Computational Biophysics
We use numerical models to understand the building blocks of life
Research
The Computational Biophysics group is an interdisciplinary team of scientists from different backgrounds but all with experience in computational modelling of biological systems and statistical mechanics. Our research focuses on the applications of statistical mechanics to soft-matter and complex biological systems. Our goal is to build simple models of natural complex systems, such as proteins, and in doing so learn their fundamental function and copy them into artificial systems.
Protein Design
With computer simulations we study what allows proteins to use just about 20 building blocks to assemble the most variable and complex structures in nature. Proteins are also sophisticated molecular machines, that can walk push pull and even trap molecules and other proteins. An important goal of our work is to understand the function of specific proteins and design new molecular machines.
We study how soft-nanopores can are capable of promoting the refolding of misfolded proteins and/or disassembly of protein aggregates. By forcing protein solutions through polymer grafted nano-pores with a fluid flow, the protein aggregates break apart and unfold, affording a second chance at folding properly.
Optimization of immobilized enzymes
Using computer simulations we study and optimise the immobilisation strategy of enzymes on surfaces.
Bionic Proteins
This research project aims at design new polymer materials with tuneable self-assembling properties. Learning from proteins we want our materials to be made by a simple set of reusable building blocks.
Differential Protein Annotation (DiPA)
Protein Functional regions result from an evolutionary process leading to specific patterns of amino acids tailored to the activity of the biomolecule. The identification of residues directly responsible for functionality has been obtained with large scale mutation experiments where the effect on the protein function is tested against each alteration. We have developed a tool to identify such regions without any knowledge of the biological role of the protein.
Protein Aggregation
How easly proteins aggregate? and what is the role of water? We try to answer such quetions with our computational models. We show how in protein mixtures each component is capable of maintaining its folded state at densities greater than the one at which they would precipitate in single-species solutions.
Hepatitis Virus
The main entry pathway of the hepatitis virus in human cells involves the interaction with the CD81 tretraspannin receptor. We study the pH response of the system. We found a new pH-sensing mechanism based on water solvation that induces large scale protein conformational changes.
The protein corona is a fouling layer that forms on nano-particles injected in the body. The corona drastically limits the efficacity of nanomedicine devices. In our group we have developed a new PEG based coating that drastically reduces the formation of the fouling layer.
Sars-CoV-2
The COVID-19 pandemic made clear the vulnerability of our society towards viral infections. We work at developing quick drug design and repurposing methods to promply respond to current and future threats.
Viral Sensing
Explores a new method for the highly sensitive detection of the SARS-CoV-2 spike protein, which could be useful in diagnosing COVID-19