Zobrazeno 1 - 10
of 200
pro vyhledávání: '"Fontana, Walter"'
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:
Fontana, Walter, Honegger, Philipp
Some time ago we came across a rather unknown and, in our opinion, intriguing paper by Otto R\"ossler on autocatalysis. That the paper is written in German might be one reason for having spent 50 years below the radar despite being of potential inter
Externí odkaz:
http://arxiv.org/abs/2209.04731
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
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically when large
Externí odkaz:
http://arxiv.org/abs/2108.04077
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
Autor:
Ross, Robert J. H., Fontana, Walter
We are concerned with how the implementation of growth determines the expected number of state-changes in a growing self-organizing process. With this problem in mind, we examine two versions of the voter model on a one-dimensional growing lattice. O
Externí odkaz:
http://arxiv.org/abs/2011.05780
Autor:
Abramov, David, Otto, Jasmine, Dubey, Mahika, Artanegara, Cassia, Boutillier, Pierre, Fontana, Walter, Forbes, Angus G.
We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and other compl
Externí odkaz:
http://arxiv.org/abs/1911.04638
Publikováno v:
Proc. Natl. Acad. Sci. U.S.A. 117/6 (2020) 2930-2937
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood as stoich
Externí odkaz:
http://arxiv.org/abs/1907.11533
Publikováno v:
EPTCS 286, 2019, pp. 65-78
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that explains
Externí odkaz:
http://arxiv.org/abs/1901.00592
Autor:
Ross, Robert, Fontana, Walter
We present continuum models that describe the evolution of the position of a random walker on a growing network using four different growth algorithms. Three of these involve a random element, including one in which the motility rate of the random wa
Externí odkaz:
http://arxiv.org/abs/1812.09568