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Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on(More)
Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of(More)
In a component-based development process the selection of components is an activity that takes place over multiple lifecycle phases that span from requirement specifications through design to implementation and integration. In different phases, different assumptions are valid and different granularity of information is available, which has a consequence(More)
Na(+)/Ca(2+) exchangers (NCXs) are ubiquitous membrane transporters with a key role in Ca(2+) homeostasis and signaling. NCXs mediate the bidirectional translocation of either Na(+) or Ca(2+), and thus can catalyze uphill Ca(2+) transport driven by a Na(+) gradient, or vice versa. In a major breakthrough, a prokaryotic NCX homolog (NCX_Mj) was recently(More)
Metadynamics calculations allow investigating structure, plasticity, and energetics in a variety of biological processes spanning from molecular docking to protein folding. Recent theoretical developments have led to applications to increasingly complex systems and processes stepping up the biological relevance of the problem solved. Here, after summarizing(More)
Metadynamics is a powerful sampling technique that uses a nonequilibrium history-dependent process to reconstruct the free-energy surface as a function of the relevant collective variables s . In Bussi [Phys. Rev. Lett. 96, 090601 (2006)] it is proved that, in a Langevin process, metadynamics provides an unbiased estimate of the free energy F(s) . We here(More)
We discuss the geometrical interpretation of a well-known smoothing operator applied to the Molecular Distance Geometry Problem, and we then describe a heuristic approach based on Variable Neighbourhood Search on the smoothed and original problem. This algorithm often manages to find solutions having higher accuracy than other methods. This is important as(More)
Functional criteria often drive the component selection in the assembly of a software system. Minimal distance strategies are frequently adopted to select the components that require minimal adaptation effort. This type of approach hides to developers the non-functional characteristics of components, although they may play a crucial role to meet the system(More)
The task of scheduling communications between satellites and ground control stations is getting more and more critical since an increasing number of satellites must be controlled by a small set of stations. In such a congested scenario, the current practice, in which experts build handmade schedules, often leaves a large number of communication requests(More)