Software Development

Biomolecular simulations rely on many software tools. These tools need continuous improvement and implementation of new methods and technologies in order to enhance the quality and accuracy of the simulations. Additionally management tools are required to ensure  a reliable infrastructure.

Vienna Soil-Organic-Matter Modeler

Soil organic matter (SOM) is abundant in the environment and plays an important role in a number of biogeochemical processes including plant growth, the distribution of nutrients, the environmental fate of pollutants and carbon storage. SOM is composed of small flexible molecules forming supramolecular structures that interact through weak interactions. Despite the great importance of understanding behavior of such molecules at the atomic level, computational modeling, a premier high-resolution technique providing great level of details has been surprising little employed to study such substances. To fill this gap, we have developed the Vienna Soil Organic Matter Modeler that creates condensed phase models of SOM corresponding to realistic, experimentally available samples with varying compositions. These models can be further used in combination with MD simulations for modeling of desired processes and properties of SOM, for example, sorption properties of selected pollutant compounds depend on the composition and conditions of SOM or structure and interactions of SOM molecules at the microscopic level.

A. Sündermann, R. Solc, D. Tunega, G. Haberhauer, M.H. Gerzabek, C. Oostenbrink
Vienna Soil Organic Matter Modeler - Generating condensed-phase models of humic substances
J. Mol. Graph. Model. 62 (2015) 243 - 261
doi: 10.1016/j.jmgm.2015.10.007

D. Petrov, D. Tunega, M.H. Gerzabek, C. Oostenbrink
Molecular dynamics simulations of the standard Leonardite humic acid: microscopic analysis of the structure and dynamics
Env. Sci. Techn. (2017) online
doi: 10.1021/acs.est.7b00266

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