Biomedical subjects

Bernd Hartke

Publications and source records attributed to Bernd Hartke.

5 recordsLinked to original sources

PubMed2006

Fingerprints of delocalized transition states in quantum dynamics.

Reactions with delocalized transition states (plateau reactions) can be characterized statically by their energy profile along the reaction path, where they exhibit a broad, flat region instead of one or several well-defined saddle points on the potential energy surface. Employing our new, highly flexible quantum dynamics code to perform two-dimensional and effective four-dimensional quantum wave packet propagations on ab initio based model potentials, we show that plateau reactions can also be discerned from the other standard reaction types by their dynamics.

Journal Article↗

PubMed2006

Propagation with distributed Gaussians as a sparse, adaptive basis for higher-dimensional quantum dynamics.

A simple quantum wavepacket propagation algorithm is presented, designed to produce a very compact, non-direct product representation in higher-dimensional cases. Instead of moving basis functions around, localized basis functions at pre-defined centers are added to and deleted from the representation, generating an active basis function set strictly localized to the region where the moving wavepacket has significantly non-zero values. Simple one-dimensional examples prove this property, as well as the ability of the algorithm to accommodate splitting and rejoining of an arbitrary number of wavefunction pieces, and tunnelling through potential energy barriers. It is argued that future applications to higher-dimensional examples will be less expensive than with traditional direct-product bases, since making the basis adaptive has a lower scaling than the elementary steps necessary for any propagation algorithm itself.

Algorithms↗

PubMed2006

Larger water clusters with edges and corners on their way to ice: structural trends elucidated with an improved parallel evolutionary algorithm.

For the difficult task of finding global minimum energy structures for molecular clusters of nontrivial size, we present a highly efficient parallel implementation of an evolutionary algorithm. By completely abandoning the traditional concept of generations and by replacing it with a less rigid pool concept, we have managed to eliminate serial bottlenecks completely and can operate the algorithm efficiently on an arbitrary number of parallel processes. Nevertheless, our new algorithm still realizes all of the main features of our old, successful implementation. First tests of the new algorithm are shown for the highly demanding problem of water clusters modeled by a potential with flexible, polarizable monomers (TTM2-F). For this problem, our new algorithm not only reproduces all of the global minima proposed previously in considerably less CPU time but also leads to improved proposals in several cases. These, in turn, qualitatively change our earlier predictions concerning the transitions from all-surface structures to cages with a single interior molecule, and from one to two interior molecules. Furthermore, we compare preliminary results up to n = 105 with locally optimized cuts from several ice modifications. This comparison indicates that relaxed ice structures may start to be competitive already at cluster sizes above n = 90.

Journal Article↗

PubMed2005

Towards protein folding with evolutionary techniques.

We present design details and first tests of a new evolutionary algorithm approach to ab initio protein folding. It does not focus on dihedral angles exclusively, but mainly operates on introduction, extension, break-up, and destruction of secondary structure elements, given as correlated dihedral angle values. In first test applications to polyalanines (up to 60 residues) and random primary sequences (up to 40 residues), we demonstrate that this use of prior knowledge is well balanced: On the one hand, it ensures quick introduction of secondary structure elements if they are favorable for a given primary sequence, but still allows for efficient location of pure random coil solutions without enforcing any secondary structure elements, if folds of this type are preferred by the given primary sequence. Furthermore, the algorithm is clearly able to pack several secondary structure elements into favorable tertiary structure arrangements, although no part of the algorithm is explicitly designed to do this. In first test examples on real-life peptides between 21 and 44 residues from the Protein Data Bank, the quality of the results depends on the force field used (as expected); nevertheless, we can show that the algorithm is able to find structures in good agreement with the targets easily and consistently, if the force field allows for that.

Algorithms↗

PubMed2002

Dodecahedral clathrate structures and magic numbers in alkali cation microhydration clusters.

Using global geometry optimization based on our specialized version of Genetic Algorithms, we have examined the global and most important local minimum energy structures of water microsolvation clusters of potassium and cesium cations within the common TIP4P/OPLS model. Together with our earlier results on the corresponding sodium case, this work constitutes a first step towards a theoretical elucidation of "magic numbers" of solvating molecules and proposed special structures occurring in these systems. In particular, the actual role of dodecahedral cage structures is examined. Within the present model, they do not occur in sodium microsolvation, in agreement with the absence of the magic number 20 for this system. For potassium and cesium microsolvation, dodecahedral cages do occur but their actual structures are far from ideal and their importance appears to be overrated. We offer simple explanations for structural features and trends, and for magic numbers smaller than 20.

Journal Article↗