Luca Tubiana, PhD

E-Mail: luca.tubiana@univie.ac.at
Computational Physics

Project: "ABM" - In Silico automated tumor targeting screening methodology for applications to the CD47 receptor

Automated Bio-Marker: Nano-medicine, which uses hard or soft nano-particles that attach selectively to tumours, is one of the most promising fields for cancer imaging and treatment. A major challenge for progress in this field is the development of Anti-Cancer Drugs (ACDs) which are able to target directly the tumour cells, without affecting healthy cells. ACDs are identified mainly through large and expensive trial-and-error screenings, with limited help from computational modelling. In collaboration with Prof. I. Coluzza, I am developing Automated Bio-Marker, a novel computational protocol to design protein ligands that can be used as coating for drug-delivery vehicles to cancer cells. The computational design protocol adopted in this project is based on Caterpillar, a coarse-grained model recently introduced by Prof. Coluzza and on advanced stochastic techniques to explore the phase space of ligands. Using these instruments allows for control over the ligand-receptor binding affinity without affecting the selectivity. This project focuses in particular on CD47, a signal regulatory protein alpha receptor (SIRPa) present in many cancers such as ovarian, breast, colon, bladder, glioblastoma, hepatocellular carcinoma, and prostate.

Physics of Viruses: Viruses are subcellular agents that infect organisms in order to reproduce themselves. While viruses can not reproduce autonomously, they are subject to several evolutionary pressures and are arguably among the simplest systems on which evolution can be studied. Most viruses encode their genes on RNA genomes, often single-stranded (ssRNA). The simplest of such single-stranded RNA viruses are constituted by a single molecule of RNA surrounded by a protective protein shell, called viral capsid. In several cases, these viruses reproduce themselves through a spontaneous self-assembly process in which the protein of the capsid attach to the RNA genome. Viral ssRNAs often have physical properties which facilitate the formation of the virus, suggesting that their genome encodes not only for viral proteins, but also for its own physical properties. Using statistical mechanics and computational methods I am investigating the evolutionary relationship between the physical properties viral ssRNA and its functional and genetic properties.

Topological entanglement in polymers: Long polymers, as well as compact polymers, are found to be knotted with high probability. The presence of knots affects polymers' physical properties and has deep effects on the functional properties of biopolymers like dsDNA or proteins. Recent studies also suggested that tight knots may be manipulated for nanotechnological applications. Using computational methods I am investigating the equilibrium and dynamical properties of knots in various polymeric systems, focussing in particular on the possible strategies to manipulate them in experimentally reproducible setups.

Publications

  • Raffaello Potestio, Luca Tubiana. Discretized knot motion on a tensioned fiber induced by transverse waves. Soft Matter, 12(3):669-673, 2016.

  • Saeed Najafi, Rudolf Podgornik, Raffaello Potestio, Luca Tubiana. Role of bending energy and knot chirality in knot distribution and their effective interaction along stretched semiflexible polymers. Polymers, 8(10) 347, 2016.

  • Saeed Najafi, Luca Tubiana, Rudolf Podgornik, Raffaello Potestio. Chirality modifies the interaction between knots. Europhysics Letters, 114(5) 2015.

  • Luca Tubiana, Anže Lošdorfer Božič, Cristian Micheletti, and Rudolf Podgornik. Synonymous mutations reduce genome compactness in icosahedral ssrna viruses. Biophysical journal, 108(1):194-202, 2015.

  • Marco Di Stefano, Luca Tubiana, Massimiliano Di Ventra, and Cristian Micheletti. Driving knots on dna with ac/dc electric fields: topological friction and memory effects. Soft Matter, 10:6491-6498, 2014.

  • Luca Tubiana. Computational study on the progressive factorization of composite polymer knots into separated prime components. Physical Review E, 89(5):052602, 2014.

  • Luca Tubiana, Angelo Rosa, Filippo Fragiacomo, and Cristian Micheletti. Spontaneous knotting and unknotting of flexible linear polymers: equilibrium and kinetic aspects. Macromolecules, 46(9):3669-3678, 2013.

  • Luca Tubiana, Enzo Orlandini, and Cristian Micheletti. Multiscale entanglement in ring polymers under spherical confinement. Physical review letters, 107(18):188302, 2011.

  • Luca Tubiana, Enzo Orlandini, and Cristian Micheletti. Probing the entanglement and locating knots in ring polymers: A comparative study of different arc closure schemes. Progress of Theoretical Physics Supplement, 191:192-204, 2011.

  • Angelo Rosa, Enzo Orlandini, Luca Tubiana, and Cristian Micheletti. Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology. Macromolecules, 44(21):8668-8680, 2011.

  • Davide Marenduzzo, Enzo Orlandini, Andrzej Stasiak, De Witt Sumners, Luca Tubiana, and Cristian Micheletti. Dna-dna interactions in bacteriophage capsids are responsible for the observed dna knotting. Proceedings of the National Academy of Sciences, 106(52):22269-22274, 2009.