Estimation of protein folding probability from equilibrium simulations

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide or protein. The procedure utilizes a structurally homogeneous clustering and does not require any additional simulation. It can be used to detect multiple folding pathways as shown for a three-stranded antiparallel $\beta$-sheet peptide investigated by implicit solvent molecular dynamics simulations.Comment: 7 pages, 4 figures, supplemetary material

New approach of fragment charge correlations in 129Xe+(nat)Sn central collisions

A previous analysis of the charge (Z) correlations in the $\Delta Z-$ plane for Xe+Sn central collisions at 32 MeV/u has shown an enhancement in the production of equally sized fragments (low $\Delta Z$) which was interpreted as an evidence for spinodal decomposition. However the signal is weak and rises the question of the estimation of the uncorrelated yield. After a critical analysis of its robustness, we propose in this paper a new technique to build the uncorrelated yield in the charge correlation function. The application of this method to Xe+Sn central collision data at 32, 39, 45 and 50 MeV/u does not show any particular enhancement of the correlation function in any $\Delta Z$ bin.Comment: 23 pages, 9 figures, revised version with an added figure and minor changes. To appear in Nuclear Physics

Freeze-out volume in multifragmentation - dynamical simulations

Stochastic mean-field simulations for multifragmenting sources at the same excitation energy per nucleon have been performed. The freeze-out volume, a concept which needs to be precisely defined in this dynamical approach, was shown to increase as a function of three parameters: freeze-out instant, fragment multiplicity and system size.Comment: Submitted to Eur. Phys. J. A - march 200

Quantum and statistical fluctuations in dynamical symmetry breaking

Dynamical symmetry breaking in an expanding nuclear system is investigated in semi-classical and quantum framework by employing a collective transport model which is constructed to mimic the collective behavior of expanding systems. It is shown that the fluctuations in collective coordinates during the expansion are developed mainly by the enhancement of the initial fluctuations by the driving force, and that statistical and quantum fluctuations have similar consequences. It is pointed out that the quantal fluctuations may play an important role in the development of instabilities by reducing the time needed to break the symmetry, and the possible role of quantal fluctuations in spinodal decomposition of nuclei is discussed.Comment: 19 Latex pages including 6 figure

Expansion and evaporation of hot nuclei: Comparison between semi-classical and quantal mean-field approaches

We present a general discussion of the mean field dynamics of finite nuclei prepared under extreme conditions of temperature and pressure. We compare the prediction of semi-classical approximation with complete quantum simulations. Many features of the dynamics are carefully studied such as the collective expansion, the evaporation process, the different time-scale... This study points out many quantitative differences between quantum and semi-classical approaches. Part of the differences are related to numerical features inherent in semi-classical simulations but most of them are a direct consequence of the non treatment of nuclei as quantal objects. In particular, we show that because of a too strong damping in semi-classical approaches the expansion of hot nuclei is quenched and the speed of the collective motion reduced.Comment: 41 pages including 14 figure