Siegfried Höfinger

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Scientific applications do frequently suffer from limited compute performance. In this article, we investigate the suitability of specialized computer chips to overcome this limitation. An enhanced Poisson Boltzmann program is ported to the graphics processing unit and the application specific integrated circuit MDGRAPE-3 and resulting execution times are(More)
A parallel version of an optimization algorithm for arbitrary functions of arbitrary dimension N has been developed and tested on an IBM-Regatta HPC system equipped with 16 CPUs of Power4 type, each with 1.3 GHz clock frequency. The optimization algorithm follows a simplex-like stochastic search technique aimed at quasi-complete sampling of all the local(More)
Electron transfer is a fundamental process that can be studied with the help of computer simulation. The underlying quantum mechanical description renders the problem a computationally intensive application. In this study, we probe the graphics processing unit (GPU) for suitability to this type of problem. Time-critical components are identified via(More)
The accurate description of solvation effects is highly desirable in numerous computational chemistry applications. One widely used methodology treats the solvent as a uniform continuum ("implicit solvation"), and describes its net interaction with the solute by solving the Poisson-Boltzmann (PB) equation using the Boundary Element Method (BEM). These(More)
Four different force fields are examined for dynamic characteristics using cholesterol as a case study. The extent to which various types of internal degrees of freedom become thermodynamically relevant is evaluated by means of principal component analysis. More complex degrees of freedom (angle bending, dihedral rotations) show a trend towards force field(More)
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but our results are also of interest to finite difference techniques of Poisson Boltzmann calculations. At first, we(More)
We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters are determined by comparison to experimental data as well as high-level quantum mechanical reference calculations. The(More)
A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form the basis of free energy perturbation calculations that consider the onset and growth of a repulsive sphere. This(More)