Alessandra Villa

PDC Center for High Performance Computing
KTH Royal Institute of Technology




Alessandra was educated as a chemistry at the University of Milano. After a quantum chemistry, she got a Marie Curie Fellowship to work on biomolecular force fields at Groningen University. Then, she moved to Goethe University and MPI for polymer science in Germany, where her main focus were nucleic acid simulations and coarse grained models, and later, to Sweden (Karolinska Institute) to continue to work nucleic acids.
Her main research interest is to elucidate the molecular interactions that govern cellular processes using biomolecular simulations. A large part of her work focuses on the development of molecular models both at the atomistic and coarse grained levels to better describe how biomolecules interact. She has wide experience both in combining experimental and simulation techniques and in combining molecular models (multiscale apporach) to solve biochemical and biophysical questions.


  • GROMACS development (focus on user-driven development)
  • Multiscale modelling of axonal subcellular components.

Key publications:

  • Axonal subcellullar components
  • Localized Axolemma Deformations Suggest Mechanoporation as Axonal Injury Trigger Montanino et al. Front. Neurol. (2020)
  • Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study Saeedimasine et al. Scientific Reports (2019).
  • Molecular models
  • Magnesium ion-water coordination and exchange in biomolecular simulations O. Allnér et al. J. Chem. Theory Comput. (2012)
  • Dynamics and Structure of Ln(III)-aquo ions: A comparative molecular dynamics study using ab initio based flexible and polarizable model potentials Villa et al. J. Phys. Chem. B (2009).
  • Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation Villa et al. Phys. Chem. Chem. Phys. (2009).
  • A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53a5 and 53a6 Oostenbrink et al. J. Comput. Chem, (2004).
  • Calculation of the free energy of solvation for neutral analogs of amino acid side chains. Villa et al. J. Comput. Chem 2002, 23, 548.
  • Nucleic acid modelling
  • Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids Hartono et al. J. Chem. Inf. Model. (2018).
  • Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies. Hartono et al. ACS Omega (2017)
  • Sequence dependency of canonical base pair opening in the DNA double helix. Lindahl et al. PLoS Comput Biol (2017)
  • Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch, Villa et al. Nucleic Acids Research (2009)


  • 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.