More is different: 50 years of nuclear BCS

Many of the concepts which are at the basis of the development associated with a quantitative treatment of the variety of phenomena associated with the spontaneous breaking of gauge symmetry in nuclei have been instrumental in connection with novel studies of soft matter, namely of protein evolution and protein folding. Although the route to these subjects and associated development does not necessarily imply the nuclear physics connection, such a connection has proven qualitatively and quantitatively inspiring. In particular to model protein evolution in terms of the alignment of quasispins displaying twenty different projections, one for each of the twenty amino acids occurring in nature, and the associated symmetry breaking in information (sequence) space. Emergent properties of the corresponding phase transition are domain walls which stabilize local elementary structures (LES), few groups of 10-20 aminoacids which become structured already in the denatured state provide the molecular recognition directing protein folding. In fact, their docking is closely related to the transition state of the process. While the two-step, yes or no, folding process, does not provide direct information concerning LES, one can force LES from virtual to become real, observable final state entities. Getting again inspiration from the nuclear case (virtual processes contributing to pair correlations can be forced to become real with the help of a probe which itself changes particle number by two), one would expect that to make real virtual LES, that is segments of the protein which already at an early stage of the folding process flicker in and out of their native conformation, one needs a probe which itself displays a similar behaviour. Peptides displaying a sequence identical to LES are such probes.Comment: Contribution to the Volume 50 years of Nuclear BCS edited by World Scientifi

Direct observation of the glue pairing the halo of the nucleus 11Li

With the help of a unified description of the nuclear structure and of the direct reaction mechanism we show that a recent 1H(11Li,9Li)3H experiment provides, for the first time in nuclear physics, direct evidence of phonon mediated pairing.Comment: 9 pages, 4 figures. Major change

Reading the three-dimensional structure of a protein from its amino acid sequence

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that while linear sequencing of the amino acids specifying a protein is relatively simple to carry out, the determination of the folded-native-conformation can only be done by an elaborate X-ray diffraction analysis performed on crystals of the protein or, if the protein is very small, by nuclear magnetic resonance techniques. Using insight obtained from lattice model simulations of the folding of small proteins (fewer than 100 residues), in particular of the fact that this phenomenon is essentially controlled by conserved contacts among strongly interacting amino acids, which also stabilize local elementary structures formed early in the folding process and leading to the (post-critical) folding core when they assemble together, we have worked out a successful strategy for reading the three-dimensional structure of a notional protein from its amino acid sequence.Comment: misprints eliminated and small mistakes correcte

Difference between stable and exotic nuclei: medium polarization effects

The bare NN-potential, parametrized so as to reproduce the nuclear phase shifts leads to a sizable Cooper pair binding energy in nuclei along the stability valley. It is a much debated matter whether this value accounts for the "empirical" value of the pairing gap or whether a similarly important contribution arises from the exchange of collective vibrations between Cooper pair partners. In keeping with the fact that two-particle transfer reactions are the specific probe of pairing in nuclei, and that exotic halo nuclei like 11Li are extremely polarizable, we find that the recent studied reaction, namely 11Li+p -> 9Li+t, provides direct evidence of phonon mediated pairing in nuclei

Pair-transfer probability in open- and closed-shell Sn isotopes

Approximations made to estimate two-nucleon transfer probabilities in ground-state to ground-state transitions and physical interpretation of these probabilities are discussed. Probabilities are often calculated by approximating both ground states, of the initial nucleus A and of the final nucleus A\pm 2 by the same quasiparticle vacuum. We analyze two improvements of this approach. First, the effect of using two different ground states with average numbers of particles A and A\pm2 is quantified. Second, by using projection techniques, the role of particle number restoration is analyzed. Our analysis shows that the improved treatment plays a role close to magicity, leading to an enhancement of the pair-transfer probability. In mid-shell regions, part of the error made by approximating the initial and final ground states by a single vacuum is compensated by projecting onto good particle number. Surface effects are analyzed by using pairing interactions with a different volume-to-surface mixing. Finally, a simple expression of the pair-transfer probability is given in terms of occupation probabilities in the canonical basis. We show that, in the canonical basis formulation, surface effects which are visible in the transfer probability are related to the fragmentation of single-particle occupancies close to the Fermi energy. This provides a complementary interpretation with respect to the standard quasiparticle representation where surface effects are generated by the integrated radial profiles of the contributing wave functions.Comment: 12 pages, 7 figure

Hiking in the energy landscape in sequence space: a bumpy road to good folders

With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space of sequences. Residues which play a key role in the foldability of the chain and in the stability of the native state are highly conserved, even among the chains belonging to different clusters. If, according to the interaction matrix, some strong attractive interactions are almost degenerate (i.e. they can be realized by more than one type of aminoacid contacts) sequence clusters group into a few super-clusters. Sequences belonging to different super-clusters are dissimilar, displaying very small ($\approx 10$) similarity, and residues in key-sites are, as a rule, not conserved. Similar behavior is observed in the analysis of real protein sequences.Comment: 17 pages 5 figures Corrected typos added auxiliary informatio