David van der Spoel


David van der Spoel
Protein Folding Laboratory

Uppsala University

davidvanderspoel-virus

Research interests

The research in the protein folding laboratory is focused on developing modeling software and methods for use in biology and medicine. High performance computing resources are used to study molecular liquids as a proxy for biomolecules. Quantum chemistry is used to study small molecules and to collect data needed to improve models. Applications focus on 1) RNA structure and dynamics in the context of viral genomes, 2) binding of small molecules to proteins in order to study the effect of pollutant molecules on living organisms and 3) atmospheric chemistry. Further work has been performed recently on carbon sequestration and storage, involving either proteins or ionic liquids, and on antibiotic peptides.

Group members

Nina Fischer, Ph.D. Post doc
Gadzikano Munyuki, Ph.D. Post doc
Mohammad Ghahremanpour, M.Sc. Ph.D. student
Jin Zhang, M.Sc. visiting Ph.D. student
Paul J. van Maaren, M.Sc., visiting researcher
Anders Gärdenäs, programmer

Key publications

  • Carl Caleman, Jochen S. Hub, Paul J. van Maaren and David van der Spoel: Atomistic Simulation of Ion Solvation in Water Explain Surface Preference of Halides Proc. Natl. Acad. Sci. U.S.A. 108 pp. 6838-6842 (2011)
  • Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel: Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Compressibility, Expansion Coefficient and Dielectric Constant J. Chem. Theor. Comput. 8 pp. 61-74 (2012)
  • Daniel S.D. Larsson, Lars Liljas and David van der Spoel: Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations PLoS Comput. Biol. 8 pp. e1002502 (2012)
  • Sander Pronk, Szilard Pall, Roland Schulz, Per Larsson, Par Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl: GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 pp. 845-854 (2013)
  • Sergio Manzetti, Roos van der Spoel and David van der Spoel: Chemical properties, environmental fate and degradation of seven classes of pollutants Chem. Res. Toxicol. 27 pp. 713-737 (2014)

External homepage

http://folding.bmc.uu.se

Contact

spoel@xray.bmc.uu.se