We generalize the unfolding semantics, previously developed for concrete formalisms such as Petri nets and graph grammars, to the abstract setting of (single pushout) rewriting over adhesive categories. The unfolding construction is characterized as a coreflection, i.e. the unfolding functor arises as the right adjoint to the embedding of the category of occurrence grammars into the category of...

PDZ domains are protein-protein interaction modules sharing the same structural arrangement. To discern whether they display common features in their unfolding/misfolding behaviour we have analyzed in this work the unfolding thermodynamics, together with the misfolding kinetics, of the PDZ fold using three archetypical examples: the second and third PDZ domains of the PSD95 protein and the Erbi...

Understanding the folding processes of a protein into its three-dimensional native structure only with its amino-acid sequence information is a long-standing challenge in modern science. Twohundred independent folding simulations (starting from non-native conformations) and twohundred independent unfolding simulations (starting from the folded native structure) are performed using the united-re...

Petri net unfolding prefixes are an important technique for formal verification and synthesis. In this paper we show that the requirement that the adequate order used for truncating a Petri net unfolding must be well-founded is superfluous in many important cases, i.e. it logically follows from other requirements. We give a complete analysis when this is the case. These results concern the very...

Loop scheduling is an important problem in parallel processing. The retiming technique reorganizes an iteration; the unfolding technique schedules several iterations together. We combine these two techniques to obtain a static schedule with a reduced average computation time per iteration. We first prove that the order of retiming and unfolding is immaterial for scheduling a data-flow graph (DF...

The mechanism by which proteins are denatured by urea is still not well understood, especially on the atomic scale where these interactions occur in vivo. In this study, the structure of the peptide GPG has been investigated in aqueous urea solutions in order to understand the combination of roles that both urea and water play in protein unfolding. Using a combination of neutron diffraction enh...

Four methods are compared to drive the unfolding of a protein: (1) high temperature (T-run), (2) high pressure (P-run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F-run, radial force driven unfolding), and (4) by weak coupling of the difference between the temperature of the radially outward moving at...

Heat capacity (Cp) is one of several major thermodynamic quantities commonly measured in proteins. With more than half a dozen definitions, it is the hardest of these quantities to understand in physical terms, but the richest in insight. There are many ramifications of observed Cp changes: The sign distinguishes apolar from polar solvation. It imparts a temperature (T) dependence to entropy an...

Hydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms (for example, piezophiles). Increase in hydrostatic pressure, much like increase in temperature, perturbs the thermodynamic equilibrium between native and unfolded states of proteins. Experimentally, it has been observed that increase in hydrostatic ...