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Alessandra Villa

Senior researcher

About me

Current position: Associate Professor

Main interests: RNA dynamics, RNA riboswitches, gene regulation and nucleic acids, biomolecular simulation of biological/medical relevant processes, development of atomistic and coarse grained models.

Previous research appointments

Polymer theory group, Max Planck Institute for Polymer Research, Mainz, Germany.

Theoretical chemistry group of Prof. Gerhard Stock, Goethe University, Frankfurt am Main, Germany. Molecular dynamics group of Prof. Alan E. Mark, University of Groningen, The Netherlands.  


Research description

My research is focused on understanding the interactions which govern cellular processes. In particular, I am interested in understanding binding and aggregation of biomolecules in medical relevant context. The final aim is to understand the chemistry and the physics of biological processes to successfully develop new synthetic molecules with medical or biotechnological applications.

I use computational chemistry methods and in particular molecular dynamics techniques. Molecular simulations provide a microscopic description of biophysical processes and are performed to verify new hypothesis of binding and/or aggregation mechanisms and to test new molecules or mutations in systems.

Current projects

- Understanding subcellullar processes involved in traumatic brain injuries and dementia

"Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study." Saeedimasine et. al. Scientific Reports 2019 9(1), 8000.

- Non-coding RNA: interactions and dynamics in bacterial riboswitches.

"Loop-loop interaction in adenine-sensing riboswitch: A molecular dynamics study" Allner et al. RNA 2013

- The role of tautomerism and pH in designing triple forming oligonucleotides: a promise tools to modulate gene expression

  "Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies" Hartono et al. ACS Omega 2017, 2(5), 2165-2177.

- Base tautomerism and modification in ribosome. 

"Computational Study of Uracil Tautomeric Forms in the Ribosome: The Case of Uracil and 5-Oxyacetic Acid Uracil in the First Anticodon Position of tRNA." Hartono et al. J. Phys. Chem. B, 2018, 122 (3), pp 1152–1160

Teaching portfolio

Current teaching activities:

- Course coordinator, lecturer and examiner of “‘Applied communication in biomedicine 4”, master program in Biomedicine, Karolinska Institutet (Sweden).

- Course coordinator, designer and lecturer of Doctoral Course: “Principles of nucleic acid structure” (DEVREG program), Karolinska Institutet (Sweden).

- Lecturer of “Molecular Simulation”, master course in Simulation Methods in Medical Engineering, Kungliga Tekniska Högskolan (Sweden).

Pedagogical Qualifications

- University Pedagogy 1 and 2  at Stockholm Univesity, Sweden.

- Pedagogy for doctoral supervisors at Karolinska Institutet, Sweden.




  • 2015 Docent in Biochemistry, Karolinska Institutet, Sweden.
  • 2000 Ph.D. in Physical-Chemistry, University of Milano, Italy.
  • 1998 Master in ’Management of technology’, University of Milano, Italy.
  • 1995 Degree in Chemistry, University of Milano, Italy.  


Academic honours, awards and prizes

Individual Marie Curie Fellowship (2000)

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