Mario Medugno

We propose in this paper an integrated optical electromagnetic field sensor suitable for sensing in the Fresnel region over a wide frequency range (ELF to UHF band). This device yields minimal coupling with critical radiating structures, and enables their near-field monitoring. The principle of the optical sensor is described and technologies and applications of this interferometric device are discussed.

A procedure for fabrication of photomasks on photographic films with minimum feature achievable of about 20 μm, which are particularly suitable for the fast prototyping of microfluidic devices, has been improved. We used a commercial photographic enlarger in reverse mode obtaining 10:1 reduction factor with error less than 1%. Masks have been characterized by optical transmission measurement and contact profilometry: the exposed region completely absorbs light in the wavelength region explored, while the non-exposed region is transparent from 350 nm on; the average film thickness is of 410 nm and its roughness is about 120 nm. A PDMS microfluidic device has been realized and tested in order to prove the effectiveness of designed photomasks used with the common UV light box.

We propose a low cost electronic circuit based on a microcontroller unit (MCU), suitable for electrochemical control in several systems requiring fluid detection and discrimination. We describe the hardware and software design of the smart fluid sensor implementing the necessary programmed logic, signal generation and processing. Testing application to devices and systems over different dimensional scales as in microfluidic devices and in power plants are discussed.

Optical devices have the potential for large scale integration and can be successfully used in mission critical environments; in particular optical probes interacting with electric fields can be used in several electromagnetic compatibility (EMC) and industrial, scientifical and medical (ISM) applications. We describe an electro-optical device based on a LiNbO₃ Mach-Zehnder integrated interferometer which has, with respect to standard metallic probes, a very reduced coupling effect on the electromagnetic field to be measured. The probe is mainly made by non conductive materials, making such device suitable for experimental measurement of electromagnetic fields in near field region (or Fresnel's one) of transmitting antennas or in their reactive zone. Here no simple theory is available in order to evaluate the fields and mutual coupling between antennas and standard probes strongly affect the measurements: the optical probe avoids the coupling of the fields with metallic structures and the loss of antenna calibration which typically yield measurement errors. The probe has been tested in the ELF and VHF bands as shown in the Figures below. The device characterization is discussed and its performance is optimised by an electro-optical device mathematic model.

We consider a model of the origin of genetic code organization incorporating the biosynthetic relationships between amino acids and their physicochemical properties. We study the behavior of the genetic code in the set of codes subject both to biosynthetic constraints and to the constraint that the biosynthetic classes of amino acids must occupy only their own codon domain, as observed in the genetic code. Therefore, this set contains the smallest number of elements ever analyzed in similar studies. Under these conditions and if, as predicted by physicochemical postulates, the amino acid properties played a fundamental role in genetic code organization, it can be expected that the code must display an extremely high level of optimization. This prediction is not supported by our analysis, which indicates, for instance, a minimization percentage of only 80%. These observations can therefore be more easily explained by the coevolution theory of genetic code origin, which postulates a role that is important but not fundamental for the amino acid properties in the structuring of the code. We have also investigated the shape of the optimization landscape that might have arisen during genetic code origin. Here, too, the results seem to favor the coevolution theory because, for instance, the fact that only a few amino acid exchanges would have been sufficient to transform the genetic code (which is not a local minimum) into a much better optimized code, and that such exchanges did not actually take place, seems to suggest that, for instance, the reduction of translation errors was not the main adaptive theme structuring the genetic code.

A paper (Amirnovin R, J Mol Evol 44:473–476, 1997) seems to undermine the validity of the coevolution theory of genetic code origin by shedding doubt on the connection between the biosynthetic relationships between amino acids and the organization of the genetic code, at a time when the literature on the topic takes this for granted. However, as a few papers cite this paper as evidence against the coevolution theory, and to cast aside all doubt on the subject, we have decided to reanalyze the statistical bases on which this theory is founded. We come to the following conclusions: (1) the methods used in the above referred paper contain certain mistakes, and (2) the statistical foundations on which the coevolution theory is based are extremely robust. We have done this by critically appraising Amirnovin's paper and suggesting an alternative method based on the generation of random codes which, along with the method reported in the literature, allows us to evaluate the significance, in the genetic code, of different sets of amino acid pairs in biosynthetic relationships. In particular, by using this method and after building up a certain set of amino acid pairs reflecting the expectations of the coevolution theory, we show that the presence of this set in the genetic code would be obtained, purely by chance, with a probability of 6 × 10⁻⁵. This observation seems to provide particularly strong support to the coevolution theory.

We have assumed that the coevolution theory of genetic code origin (Wong JT, Proc Natl Acad Sci USA 72:1909–1912, 1975) is essentially correct. This theory makes it possible to identify at least 10 evolutionary stages through which genetic code organization might have passed prior to reaching its current form. The calculation of the minimization level of all these evolutionary stages leads to the following conclusions. (1) The minimization percentages increased linearly with the number of amino acids codified in the codes of the various evolutionary stages when only the sense changes are considered in the analysis. This seems to favor the physicochemical theory of genetic code origin even if, as discussed in the paper, this observation is also compatible with the coevolution theory. (2) For the first seven evolutionary stages of the genetic code, this trend is less clear and indeed is inverted when we consider the global optimisation of the codes due to both sense changes and synonymous changes. This inverse correlation between minimization percentages and the number of amino acids codified in the codes of the intermediate stages seems to favor neither the physicochemical nor the stereochemical theories of genetic code origin, as it is in the early and intermediate stages of code development that these theories would expect minimization to have played a crucial role, and this does not seem to be the case. However, these results are in agreement with the coevolution theory, which attributes a role to the physicochemical properties of amino acids that, while important, is nevertheless subordinate to the mechanism which concedes codons from the precursor amino acids to the product amino acids as the primary factor determining the evolutionary structuring of the genetic code. The results are therefore discussed in the context of the various theories proposed to explain genetic code origin.

Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code.