Lack of self-averaging in neutral evolution of proteins

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.     

Soft Constraint Logic Programming and Generalized Shortest Path Problems

In this paper we study the relationship between Constraint Programming (CP) and Shortest Path (SP) problems. In particular, we show that classical, multicriteria, partially ordered, and modality-based SP problems can be naturally modeled and solved within the Soft Constraint Logic Programming (SCLP) framework, where logic programming is coupled with soft constraints. In this way we provide this large class of SP problems with a high-level and declarative linguistic support whose semantics takes care of both finding the cost of the shortest path(s) and also of actually finding the path(s). On the other hand, some efficient algorithms for certain classes of SP problems can be exploited to provide some classes of SCLP programs with an efficient way to compute their semantics.     

13C NMR examination of some N-thioaroylmorpholine–bromine adducts

The ¹³C NMR chemical shifts of three N-thioaroylmorpholine–bromine adducts, previously used as synthetic intermediates, are compared and discussed in the light of the corresponding shifts of the parent thioamides and suitable model compounds. Chemical shift changes are interpreted in terms of the electronic perturbation resulting from bromine coordination at sulphur.     

Thermal transformations and stability of organometallic materials with electrical and optical properties: the case of polycrystalline cis-[Ir(CO)2Cl(C5H5N)

In this paper the solid-state transformations under heating of cis-[Ir(CO)2Cl(C5H5N)] are discussed. The complexity of the transformations was revealed by integrating infrared spectroscopy, conventional and bidimensional X-ray diffraction, thermal analysis, and hot stage optical microscopy. During heating anisotropic expansion of the lattice along the Ir-Ir stacking takes place. Then cis-[Ir(CO)2Cl(C5H5N)] undergoes an irreversible solid-solid phase transition to a lattice of higher symmetry followed by a reversible transition into the amorphous phase. Under proper cooling a partial recrystallization takes place. Experiments in the presence of oxygen must be carried out in short time periods to avoid oxidation from Ir(I) to Ir(III).     

On the use of the theory of dynamical systems for transient problems

This paper is a preliminary work to address the problem of dynamical systems with parameters varying in time. An idea to predict their behavior is proposed. These systems are called transient systems, and are distinguished from steady systems in which parameters are constant. In particular, in steady systems the excitation is either constant (e.g., nought) or periodic with amplitude, frequency, and phase angle which do not vary in time. We apply our method to systems, which are subjected to a transient excitation that is neither constant nor periodic. The effect of switching-off and full-transient forces is investigated. The former can be representative of switching-off procedures in machines; the latter can represent earthquake vibrations, wind gusts, etc., acting on a mechanical system. This class of transient systems can be seen as the evolution of an ordinary steady system into another ordinary steady system, for both of which the classical theory of dynamical systems holds. The evolution from a steady system to the other is driven by a transient force, which is regarded as a map between the two steady systems.     

Non-linear dynamics of a mechanical system with a frictional unilateral constraint

We analyze the dynamics of a two-dimensional system constituted by two masses subjected to elastic, gravitational and viscous forces and constrained by a moving frictional mono-lateral surface. The model exhibits a time-varying dynamics capable of reproducing the hopping phenomenon, an unwanted phenomenon observed in many applications such as the motion of a robotic arm on a surface or that of a wiper on a windscreen. The system dynamics, besides being affected by geometrical non-linearities, has a non-smooth nature due to the impact and friction laws involved in the model. The complexity of the resulting equations and of the transition conditions require the problem to be solved numerically. Various periodic motions are found and the effect of varying the system parameters, in particular the friction coefficient, is investigated. Finally, simulations are used to gain some insight the behavior of the windscreen wiper.     

Application of the anionic homologous Fries‐rearrangement to the synthesis of 3‐alkylbenzofuran‐2(3H)‐ones

We have developed an effective organometallic‐based procedure allowing the employment of 2‐methylphenols as easily available starting materials in the synthesis of 3‐alkylbenzofuran‐2(3H)‐ones. The first step of this protocol, an anionic homologous Fries‐rearrangement, afforded 2‐(2‐ tert ‐butyldimethylsilyloxyaryl)acetamides, which were selectively metalated and monoalkylated at the benzylic position. Acidic work‐up of crude products afforded the desired heterocycles in satisfactory overall yields. Copyright © 2008 John Wiley & Sons, Ltd.