Berk Hess

Associate Professor of Biophysics
Department of Applied Physics
KTH Royal Institute of Technology

Email: berk.hess@scilifelab.se

Biography

Berk graduated for the university in Groningen in the Netherlands in 2002, where he did his PhD under the supervision of Herman Berendsen. After a post-doc at the Max-Planck institute for polymer research in Mainz (Germany), he moved to Stockholm University in 2009. Since 2011 he is Associate Professor at KTH.

The center theme in his research is understanding how interactions at the molecular scale affect events at larger scale, both in macromolecules, such as proteins, as well as in wetting. A large part of his research focuses on methods for accelerating sampling, through general, parallel molecular dynamics method improvement as well as accelerated sampling of conformational transitions. All methods are freely available through the GROMACS molecular simulation package, of which Berk is a main developer since more than two decades.

Projects:

Publications

  • Riemann metric approach to optimal sampling of multidimensional free-energy landscapes
    V. Lindahl, J. Lidmar and B. Hess
    Phys. Rev. E, 98, 023312 (2018)
  • Molecular origin of contact line friction in dynamic wetting
    P. Johansson and B. Hess
    Phys. Rev. Fluids, 3, 074201 (2018)
  • Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
    V. Lindahl, P. Gourdon, M. Andersson and B. Hess
    Scientific Reports, 8, 2995 (2018)
  • Sequence dependency of canonical base pair opening in the DNA double helix
    V. Lindahl, J. Lidmar and B. Hess
    PLOS Computational Biology, 13 (4), e1005463 (2017)
  • The GROMACS portable high-performance CPU SIMD layer
    M. Abraham, S. Pall, R. Schulz, T. Murtola, B. Hess and E. Lindahl
    ACM Proceedings for EASC2016, accepted (2016)
  • Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation
    C. L. Wennberg, T. Murtola, S. Pall, M. J. Abraham, B. Hess and E. Lindahl
    J. Chem. Theory Comput., 9, 5737-5746 (2015)
  • Water-substrate physico-chemistry in wetting dynamics
    P. Johansson, A. Carlson and B. Hess
    J. Fluid Mech., 781, 696-711 (2015)
  • GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
    M. J. Abraham, T Murtola, R. Schulz, S. Pall, J. C. Smith, B. Hess and E. Lindahl
    SoftwareX, 1, 19-25 (2015)
  • Chapter in Solving Software Challenges for Exascale (Lecture Notes in Computer Science), Springer International Publishing, 3-27 (2015)
    S. Pall, M. J. Abraham, C. Kutzner, B. Hess and E. Lindahl
    Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
    \hlink{http://dx.doi.org/10.1007/978-3-319-15976-8_1
  • Accelerated weight histogram method for exploring free energy landscapes
    V. Lindahl, J. Lidmar and B. Hess
    J. Chem. Phys. 141, 044110 (2014)
  • Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties
    C. Wennberg, T. Murtola, B. Hess and E. Lindahl
    J. Chem. Theory Comput., 9, 3527-3537 (2013)
  • A flexible algorithm for calculating pair interactions on SIMD architectures
    S. Pall and B. Hess
    Comput. Phys. Commun., 184, 2641–2650 (2013)
  • Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions
    P. M. Kasson, B. Hess and E. Lindahl
    Chem. Phys. Lip., 169, 106-112 (2013)
  • GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
    S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and E. Lindahl
    Bioinformatics, 29, 845 (2013)
  • The Free Energy Barrier for Arginine Gating Charge Translation Is Altered by Mutations in the Voltage Sensor Domain
    C. S. Schwaiger, S. I. Brojesson, B. Hess, B. Wallner, F. Elinder and E. Lindahl
    PLOS ONE, 7, e45880 (2012)
  • SHAKE parallelization
    R. Elber, A. P. Ruymgaart and B. Hess
    Eur. Phys. J. Spec. Top. 200, 211 (2011)
  • Ion pairing in aqueous electrolyte solutions with biologically relevant anions
    P. Ganguly, P. Schravendijk, B. Hess and N. F. A. van der Vegt
    J. Phys. Chem. B 115 3734 (2011)
  • GROMACS – The road ahead
    B. Hess and D. van der Spoel
    Comp. Molec. Sci. 1, 211 (2011)
  • 3(10)-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State
    C. S. Schwaiger, P. Bjelkmar, B. Hess and E. Lindahl
    Biophys J. 100, 1446 (2011)
  • Algorithm improvements for molecular dynamics simulations
    P. Larsson, B. Hess and E. Lindahl
    Comp. Molec. Sci. 1, 93 (2011)
  • Driving Forces for Adsorption of Amphiphilic Peptides to the Air-Water Interface
    O. Engin, A. Villa, M. Sayar and B. Hess
    J. Phys. Chem. B 114, 11093 (2010)
  • Chain packing in polycarbonate glasses
    D. Steuber, T. Y. Yu, B. Hess, K. Kremer, R. D. O’Connor and J. Schaefer
    J. Chem. Phys. 132, 104901 (2010)
  • Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
    P. Bjelkmar, P. Larsson, M. A. Cuendet, B. Hess and E. Lindahl
    J. Chem. Theory Comput. 6, 459 (2010)
  • Cation specific binding with protein surface charges
    B. Hess and N. A. F. van der Vegt
    Proc. Natl. Acad. Sci. USA 106, 13296 (2009)
  • Dynamics and Structure of Ln(III)-aqua ions: A comparative molecular dynamics study using ab initio based fexible and polarizable model potentials
    A. Villa, B. Hess and H. Saint-Martin
    J. Phys. Chem. B 113, 7270 (2009)
  • Interaction of water with N,N’-1,2-ethanediyl-bis(6-hydroxy-hexanamide) crystals: A simulation study
    B. Hess, J. A. W. Harings, S. Rastogi and N. F. A. van der Vegt
    J. Phys. Chem. B 113, 627 (2009)
  • Predictive modeling of phenol chemical potentials in molten bisphenol-A-polycarbonate over a broad temperature range
    B. Hess and N. F. A. van der Vegt
    Macromolecules 41, 7281 (2008)
  • Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties
    L. M. Ghiringhelli, B. Hess, N. F. A. van der Vegt and L. Delle Site
    JACS 130, 13460 (2008)
  • Modeling Solubilities of Additives in Polymer Microstructures: Single Step Perturbation Method based on a Soft Cavity Reference State
    T. Ozal, C. Peter, B. Hess and N. van der Vegt
    Macromolecules 41, 5055 (2008)
  • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    B. Hess, C. Kutzner, D. van der Spoel and E. Lindahl
    J. Chem. Theory Comput. 4, 435 (2008)
  • Fast growth thermodynamic integration: calculating excess chemical potentials of additive molecules in polymer microstructures
    B. Hess, C. Peter, T. Ozal and N. van der Vegt
    Marcomolecules 41, 2283 (2008)
  • P-LINCS: A parallel linear constraint solver for molecular simulation
    B. Hess
    J. Chem. Theory Comput. 4, 116 (2008)
  • Solvent-averaged potentials for alkali-, earth alkali- and alkylammonium halide aqueous solutions
    B. Hess and N. van der Vegt
    J. Chem. Phys. 127, 234508 (2007)
  • Stability of Hydrophobically Modified Poly(p-phenylene)sulfonate Bundles as Observed by Molecular Dynamics Simulation
    B. Hess, M Sayar and C. Holm
    Macromolecules 40, 1703 (2007)
  • Density functional study of ion hydration for the alkali metal ions (Li+,Na+,K+) and the halide ions (F-,Br-,Cl-)
    C. Krekeler, B. Hess and L. Delle Site
    J. Phys. Chem. 125, 54305 (2006)
  • Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models
    B. Hess and N. F. A. van der Vegt
    J. Phys. Chem. B 110, 17616 (2006)
  • Osmotic coefficients of atomistic NaCl (aq) force-fields
    B. Hess, C. Holm and N. van der Vegt
    J. Chem. Phys. 124, 164509 (2006)
  • Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate
    B. Hess, S. Leon, N. van der Vegt and K. Kremer
    Soft Matter 2, 409 (2006)
  • Modeling Multibody Effects in Ionic Solutions with a Concentration Dependent Dielectric Permittivity
    B. Hess, C. Holm and N. van der Vegt
    Phys. Rev. Lett. 96, 147801 (2006)
  • Reproducible polypeptide folding and structure prediction using molecular dynamics simulations
    M. Seibert, A. Patriksson, B. Hess and D. van der Spoel
    J. Mol. Biol. 354, 173 (2005)
  • GROMACS: Fast, Flexible, and Free
    D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen
    J. Comput. Chem. 26, 1701 (2005)
  • A molecular dynamics study of dislocation nucleation from a crack tip
    B. Hess, B.J. Thijsse and E. van der Giessen
    Phys. Rev B 71 054111 (2005)
  • An application of flexible constraints in Monte Carlo simulations of the isobaric – isothermal ensemble of liquid water and ice Ih
    H. Saint-Martin, B. Hess and H.J.C. Berendsen
    J. Chem. Phys. 120, 11133-11143 (2004)
  • Photoactivation of the Photoactive Yellow Protein: Why photon absorption triggers a trans-to-cis isomerization of the chromophore in the Protein
    G. Groenhof, M. Bouxin-Cademartory, B. Hess, S.P. de Visser, H.J.C. Berendsen, M. Olivucci, A.E. Mark and M.A. Robb
    J. Am. Chem. Soc. 126, 4228-4233 (2004)
  • Orientation restraints in molecular dynamics simulations. using time and ensemble averaging
    B. Hess and R.M. Scheek
    J. Magn. Res. 164, 19-27 (2003)
  • Evaluation and analysis of channel models: simulations of alamethicin
    D.P. Tieleman, B. Hess and M.S.P. Sansom.
    Biophys. J. 83, 2393-2407 (2002)
  • Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water.
    B. Hess, H. Saint-Martin and H.J.C. Berendsen
    J. Chem. Phys. 116, 9602-9610 (2002)
  • Convergence of sampling in protein simulations
    B. Hess
    Phys. Rev. E 65, 031910 (2002)
  • Determining the shear viscosity of model liquids from molecular dynamics simulations
    B. Hess
    J. Chem. Phys. 116, 209-217 (2002)
  • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    E. Lindahl, B. Hess and D. van der Spoel
    J. Mol. Mod. 7, 306-317 (2001)
  • Further investigation on the validity of Stokes-Einstein behaviour at the molecular level
    R. Walser, B. Hess, A.E. Mark and W.F. van Gunsteren
    Chem. Phys. Lett. 334, 337-342 (2001)
  • Similarities between principal components of protein dynamics and random diffusion
    B. Hess
    Phys. Rev. E 62, 8438-8448 (2000)
  • Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
    A. K. Feenstra, B. Hess, and H.J.C. Berendsen
    J. Comp. Chem. 20, 786-798 (1999)
  • LINCS: A linear constraint solver for molecular simulations
    B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije
    J. Comp. Chem. 18, 1463-1472 (1997)