Key publications

Asymmetry of wetting and de-wetting on high-friction surfaces originates from the same molecular physics, M Pellegrino, B Hess – Physics of Fluids, 2022,

Scalable Constant pH Molecular Dynamics in GROMACS, Noora Aho, Pavel Buslaev, Anton Jansen, Paul Bauer, Gerrit Groenhof, Berk Hess, Journal of Chemical Theory and Computation 18 (10), 6148-6160,

The accelerated weight histogram method for alchemical free energy calculations, M Lundborg, J Lidmar, B Hess
The Journal of Chemical Physics 154 (20), 204103,

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS, Szilárd Páll, Artem Zhmurov, Paul Bauer, Mark Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl, The Journal of Chemical Physics 153 (13), 134110,

Permeability and ammonia selectivity in aquaporin TIP2; 1: linking structure to function,
V Lindahl, P Gourdon, M Andersson, B HesScientific reports 8 (1), 1-13,

Sequence dependency of canonical base pair opening in the DNA double helix
V Lindahl, A Villa, B Hess
PLoS computational biology 13 (4), e1005463,

I have three, related, main research interests. One is understanding how interactions at the atomistic scale affect processes at larger scales, using molecular simulations. A second is developing algorithms to accelerate sampling of conformational transitions in biomolecules. And the third is developing (parallel) algorithms for molecular simulation. In most research projects in the group these interest come together. One main goal is improving sampling of conformational transitions in biomolecular systems.

Molecular dynamics can provide details on both atomistic time and length scales, which is not possible through experiments. But simulations are costly because of the very short time step. Performance can be improved by improved general algorithms, which my group works on. Moreover, several orders of magnitude of speed-up can be had by accelerated sampling methods.

This enables understanding functional mechanisms of proteins which have not been accessible before. New and improved methods are integrated in the GROMACS molecular simulation package, of which I am a main developers since more than two decades. This is the most popular molecular simulation package world-wide and is used by many groups in both academia and (pharmaceutical) industry.

A second research direction is understanding wetting of surfaces by liquids. This is relevant both in nature, as well as for industry (e.g. microfluidics). Experiments are limited by the wavelength of light, so simulations are the only way to look at processes at interfaces. Here the group has unique competences, which enables the study of sufficiently large system using atomistic detail, providing new insight into molecular processes that control (de)wetting.


Last updated: 2023-02-08

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