University of Paderborn

About: University of Paderborn is a education organization based out in Paderborn, Nordrhein-Westfalen, Germany. It is known for research contribution in the topics: Control reconfiguration & Software. The organization has 6684 authors who have published 16929 publications receiving 323154 citations.

Toward Theoretical Analyis of Long-Range Proton Transfer Kinetics in Biomolecular Pumps†

Abstract: Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.

Fluctuating emg signals: Investigating long-term effects of pattern matching algorithms

Abstract: In this paper, we investigate the behavior of state-of-the-art pattern matching algorithms when applied to electromyographic data recorded during 21 days. To this end, we compare the five classification techniques k-nearest-neighbor, linear discriminant analysis, decision trees, artificial neural networks and support vector machines. We provide all classifiers with features extracted from electromyographic signals taken from forearm muscle contractions, and try to recognize ten different hand movements. The major result of our investigation is that the classification accuracy of initially trained pattern matching algorithms might degrade on subsequent data indicating variations in the electromyographic signals over time.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems

Abstract: The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.