Zobrazeno 1 - 10
of 73
pro vyhledávání: '"Andersen, Jakob L."'
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
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
Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species $X$ catalyzes its own formation. From the perspective of chemical kinetics, autocatalysts show a regime of super-linear growth. Given a chemical reactio
Externí odkaz:
http://arxiv.org/abs/2107.03086
The Kappa biochemistry and the M{\O}D organic chemistry frameworks are amongst the most intensely developed applications of rewriting-based methods in the life sciences to date. A typical feature of these types of rewriting theories is the necessity
Externí odkaz:
http://arxiv.org/abs/2106.02573
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
Akademický článek
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We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to rea
Externí odkaz:
http://arxiv.org/abs/1712.02594
Autor:
Andersen, Jakob L., Merkle, Daniel
The state-of-the-art tools for practical graph canonization are all based on the individualization-refinement paradigm, and their difference is primarily in the choice of heuristics they include and in the actual tool implementation. It is thus not p
Externí odkaz:
http://arxiv.org/abs/1711.08289