58 citations · 112 across the 14 of their papers we have counts for
17 papers
Translation of a 1971 paper by Otto Rössler with added margin notes and a commentary
Walter Fontana, Philipp Honegger
Some time ago we came across a rather unknown and, in our opinion, intriguing paper by Otto Rössler on autocatalysis. That the paper is written in German might be one reason for ha…
Representing catalytic mechanisms with rule composition
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
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 tra…
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…
Modeling random walkers on growing random networks
Robert Ross, Walter Fontana
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 ran…
A random walker's view of networks whose growth it shapes
Robert J. H. Ross, Charlotte Strandkvist, Walter Fontana
We study a simple model in which the growth of a network is determined by the location of one or more random walkers. Depending on walker speed, the model generates a spectrum of s…
Compressibility of random walker trajectories on growing networks
Robert J. H. Ross, Charlotte Strandkvist, Walter Fontana
We find that the simple coupling of network growth to the position of a random walker on the network generates a traveling wave in the probability distribution of nodes visited by…
Embodying probabilistic inference in biochemical circuits
Yarden Katz, Michael Springer, Walter Fontana
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference…
Dynamic Influence Networks for Rule-based Models
Angus G. Forbes, Andrew Burks, Kristine Lee +4
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-…
A knowledge representation meta-model for rule-based modelling of signalling networks
Adrien Basso-Blandin, Walter Fontana, Russ Harmer
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts…
Non-equilibrium phase transitions in biomolecular signal transduction
Eric Smith, Supriya Krishnamurthy, Walter Fontana +1
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of pr…
The stochastic behavior of a molecular switching circuit with feedback
Supriya Krishnamurthy, Eric Smith, David Krakauer +1
Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. Th…
Chance and Necessity in Evolution: Lessons from RNA
Peter Schuster, Walter Fontana
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (…