Zobrazeno 1 - 10
of 138
pro vyhledávání: '"Fagerberg Rolf"'
Autor:
Pal, Adittya, Fagerberg, Rolf, Andersen, Jakob Lykke, Flamm, Christoph, Dittrich, Peter, Merkle, Daniel
Finding pathways that optimize the formation of a particular target molecule in a chemical reaction network is a key problem in many settings, including reactor systems. Reaction networks are mathematically well represented as hypergraphs, a modeling
Externí odkaz:
http://arxiv.org/abs/2411.15900
Autor:
Andersen, Jakob L., Davoodi, Akbar, Fagerberg, Rolf, Flamm, Christoph, Fontana, Walter, Kolčák, Juri, Laurent, Christophe V. F. P., Merkle, Daniel, Nøjgaard, Nikolai
The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic systems with a large variety of applications. We introduce a novel method of
Externí odkaz:
http://arxiv.org/abs/2404.02692
Autor:
Andersen, Jakob L., Banke, Sissel, Fagerberg, Rolf, Flamm, Christoph, Merkle, Daniel, Stadler, Peter F.
The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pat
Externí odkaz:
http://arxiv.org/abs/2309.10629
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the chemical struct
Externí odkaz:
http://arxiv.org/abs/2308.12735
Autor:
Andersen, Jakob L., Fagerberg, Rolf, Flamm, Christoph, Fontana, Walter, Kolčák, Juri, Laurent, Christophe V. F. P., Merkle, Daniel, Nøjgaard, Nikolai
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a rule for mod
Externí odkaz:
http://arxiv.org/abs/2201.04515
Autor:
Andersen, Jakob L., Fagerberg, Rolf, Kolčák, Juri, Laurent, Christophe V. F. P., Merkle, Daniel, Nøjgaard, Nikolai
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made feasible via t
Externí odkaz:
http://arxiv.org/abs/2201.04360
Autor:
Andersen, Jakob L., Fagerberg, Rolf, Flamm, Christoph, Fontana, Walter, Kolčák, Juraj, Laurent, Christophe V. F. P., Merkle, Daniel, Nøjaard, Nikolai
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this complex problem
Externí odkaz:
http://arxiv.org/abs/2102.03292
The fragile complexity of a comparison-based algorithm is $f(n)$ if each input element participates in $O(f(n))$ comparisons. In this paper, we explore the fragile complexity of algorithms adaptive to various restrictions on the input, i.e., algorith
Externí odkaz:
http://arxiv.org/abs/2102.00338
Publikováno v:
BMC Bioinformatics, Vol 7, Iss 1, p 29 (2006)
Abstract Background The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n3) algorithm upon which all existing implementations are based.
Externí odkaz:
https://doaj.org/article/4990b600708a44df90d4d07ae961704d
Autor:
Afshani, Peyman, Fagerberg, Rolf, Hammer, David, Jacob, Riko, Kostitsyna, Irina, Meyer, Ulrich, Penschuck, Manuel, Sitchinava, Nodari
We initiate a study of algorithms with a focus on the computational complexity of individual elements, and introduce the fragile complexity of comparison-based algorithms as the maximal number of comparisons any individual element takes part in. We g
Externí odkaz:
http://arxiv.org/abs/1901.02857