2 citations · 3 across the 3 of their papers we have counts for
12 papers
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth +1
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 amo…
Graph Transformation for Enzymatic Mechanisms
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
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 e…
Balancing conservative and disruptive growth in the voter model
Robert J. H. Ross, Walter Fontana
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 t…
RuleVis: Constructing Patterns and Rules for Rule-Based Models
David Abramov, Jasmine Otto, Mahika Dubey +4
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 simulat…
Combinatorial protein-protein interactions on a polymerizing scaffold
Andrés Ortiz-Muñoz, Héctor F. Medina-Abarca, Walter Fontana
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to pol…
Interactions between Causal Structures in Graph Rewriting Systems
Ioana Cristescu, Walter Fontana, Jean Krivine
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal…