Walter Fontana

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Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the(More)
We develop and test four alternative logics of attachment accumulative advantage, homophily, follow-the-trend, and multiconnectivity to account for both the structure and dynamics of interorganizational collaboration in the field of biotechnology. The commercial field of the life sciences is typified by wide dispersion in the sources of basic knowledge and(More)
Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning. Yet, this same combinatorial explosion makes the traditional modelling paradigm based on systems of differential equations impractical. In contrast, agentbased or(More)
Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from(More)
Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of how a system works in terms of the biomolecules in the system and their possible states and interactions. A set of rules can be as easy to read as a diagrammatic(More)
Given the combinatorial nature of cellular signalling pathways, where biological agents can bind and modify each other in a large number of ways, concurrent or agent-based languages seem particularly suitable for their representation and simulation [1–4]. Graphical modelling languages such as κ [5–8], or the closely related BNG language [9– 14], seem to(More)
We develop an abstract chemistry, implemented in a lambda-calculus-based modeling platform, and argue that the following features are generic to this particular abstraction of chemistry; hence, they would be expected to reappear if "the tape were run twice": (i) hypercycles of self-reproducing objects arise; (ii) if self-replication is inhibited,(More)
ion<lb>Ax ∪ {x : τ ′} e : τ<lb>A λx.e : τ ′ → τ Let<lb>A e : σ Ax ∪ {x : σ} e′ : τ<lb>A (let x = e in e′) : τ The meaning of the Taut-rule is simply that a free variable has the type assigned<lb>to it in the boundary condition. If there is no assignment the expression x is not<lb>typable, and is barred from the universe.<lb>The meaning of rule App is also(More)
We develop and test four alternative logics of attachment accumulative advantage, homophily, follow-the-trend, and multiconnectivity to account for both the structure and dynamics of interorganizational collaboration in the field of biotechnology. The commercial field of the life sciences is typified by wide dispersion in the sources of basic knowledge and(More)