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Thomas Soddemann

Publications and source records attributed to Thomas Soddemann.

3 recordsLinked to original sources

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein-structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at www.migenas.org (click 'Start Toolkit').

Animals↗

Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations.

We discuss dissipative particle dynamics as a thermostat to molecular dynamics, and highlight some of its virtues: (i) universal applicability irrespective of the interatomic potential; (ii) correct and unscreened reproduction of hydrodynamic correlations; (iii) stabilization of the numerical integration of the equations of motion; and (iv) the avoidance of a profile bias in boundary-driven nonequilibrium simulations of shear flow. Numerical results on a repulsive Lennard-Jones fluid illustrate our arguments.

Journal Article↗

Nonequilibrium molecular dynamics simulation of shear-induced alignment of amphiphilic model systems.

We study the shear-induced alignment transition from transverse to the shear plane to parallel and perpendicular in a lamellar or smectics system. A recently proposed simple continuum model for amphiphiles is studied by large-scale nonequilibrium molecular dynamics simulation. We find a shear-rate dependence of the alignment transition under shear flow, parallel at low and perpendicular alignment at high shear rates. To identify the alignment and degree of order of these shear-induced orientations by scattering, a 3D analysis of the scattering data is needed.

Journal Article↗