A program transformation technique should terminate, return efficient output programs and be efficient itself. These requirements are mutually conflicting, so a balance must be sought between definite termination and possible efficiency. For positive supercompilation [17], ensuring termination requires memoisation of expressions, and these are subsequently used to determine when to perform gene...

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...

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two different co-solvents of water, urea and dimethyl sulphoxide (DMSO), and study unfolding of four different proteins to understand the respective sequence of mel...

The key to efficient on-the-fly reachability analysis based on unfolding is to focus the expansion of the finite prefix towards the desired marking. However, current unfolding strategies typically equate to blind (breadth-first) search. They do not exploit the knowledge of the marking that is sought, merely entertaining the hope that the road to it will be short. This paper investigates directe...

We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe local minima on the path of stretching and releasing. At given force, we find multiple configurations which are separated by energy barriers. A collapsed globul...

Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is slowly varying and exponentially decreases as a function of the force. The time dependencies of the end-to-end distances are also distinct. The time sequence...

Using a statistical mechanical treatment, we study RNA folding energy landscapes. We first validate the theory by showing that, for the RNA molecules we tested having only secondary structures, this treatment (i) predicts about the same native structures as the Zuker method, and (ii) qualitatively predicts the melting curve peaks and shoulders seen in experiments. We then predict thermodynamic ...

A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence, in the conformational search. Pathway prediction, thus gives more insight into the folding process and is a valuable guiding tool to search the conformation space. In this paper, we propose a novel 'unfolding' approach to predict the folding pathway...

Program transformation is an appealing technique which allows to improve run-time efficiency, space-consumption, and more generally to optimize a given program. Essentially, it consists of a sequence of syntactic program manipulations which preserves some kind of semantic equivalence. Unfolding is one of the basic operations which is used by most program transformation systems and which consist...

We study the unfolding of a parallel G-quadruplex from human telomeric DNA by mechanical stretching using steered molecular dynamics (MD) simulation. We find that the force curves and unfolding processes strongly depend on the pulling sites. With pulling sites located on the sugar-phosphate backbone, the force-extension curve shows a single peak and the unfolding proceeds sequentially. Pulling ...