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R. A. Broglia

Publications and source records attributed to R. A. Broglia.

At least 37 records · Page 2Linked to original sources
arXiv2011

Study of the transition from pairing vibrational to pairing rotational regimes between magic numbers N=50 and N=82, with two-nucleon transfer

Absolute values of two-particle transfer cross sections along the Sn-isotopic chain from closed shell to closed shell (100Sn,132Sn) are calculated taking properly into account nuclear correlations, as well as the successive, simultaneous and non-orthogonality contributions to the differential cross sections. The results are compared with systematic, homogeneous bombarding conditions (p, t) data. The observed agreement, almost within statistical errors and without free parameters, testify to the fact that theory is able to be quantitative in its predictions.

nucl-th↗
arXiv2010

Linear response of light deformed nuclei investigated by self-consistent quasiparticle random-phase-approximation

We present a calculation of the properties of vibrational states in deformed, axially--symmetric even--even nuclei, within the framework of a fully self--consistent Quasparticle Random Phase Approximation (QRPA). The same Skyrme energy density and density-dependent pairing functionals are used to calculate the mean field and the residual interaction in the particle-hole and particle-particle channels. We have tested our software in the case of spherical nuclei against fully self consistent calculations published in the literature, finding excellent agreement. We investigate the consequences of neglecting the spin-orbit and Coulomb residual interactions in QRPA. Furthermore we discuss the improvement obtained in the QRPA result associated with the removal of spurious modes. Isoscalar and isovector responses in the deformed ${}^{24-26}$Mg, $^{34}$Mg isotopes are presented and compared to experimental findings.

nucl-th↗
arXiv2010

Finite-size effects and collective vibrations in the inner crust of neutron stars

We study the linear response of the inner crust of neutron stars within the Random Phase Approximation, employing a Skyrme-type interaction as effective interaction. We adopt the Wigner-Seitz approximation, and consider a single unit cell of the Coulomb lattice which constitutes the inner crust, with a nucleus at its center, surrounded by a sea of free neutrons. With the use of an appropriate operator, it is possible to analyze in detail the properties of the vibrations of the surface of the nucleus and their interaction with the modes of the sea of free neutrons, and to investigate the role of shell effects and of resonant states.

nucl-th↗
arXiv2010

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.

nucl-th↗
arXiv2009

Fragmentation of the photoabsorption strength in neutral and charged metal microclusters

The line shape of the plasma resonance in both neutral and charged small sodium clusters is calculated. The overall properties of the multipeak structure observed in the photoabsorption cross section of spherical Na_8 and Na_20 neutral clusters can be understood in terms of Landau damping. Quantal configurations are shown to play an important role. In the case of charged Na_9+ and Na_21^+ clusters a single peak is predicted that carries most of the oscillator strength.

cond-mat.mes-hall↗
arXiv2009

Atomic-detailed milestones along the folding trajectory of protein G

The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the folding of proteins. Making use of a biasing algorithm, based on the principle of the ratchet-and-pawl, we have been able to calculate eight folding trajectories (to an RMSD between 1.2A and 2.5A) of the B1 domain of protein G in explicit solvent without the need of high-performance computing. The simulations show that in the denatured state there is a complex network of cause-effect relationships among contacts, which results in a rather hierarchical folding mechanism. The network displays few local and nonlocal native contacts which are cause of most of the others, in agreement with the NOE signals obtained in mildly-denatured conditions. Also nonnative contacts play an active role in the folding kinetics. The set of conformations corresponding to the transition state display phi-values with a correlation coefficient of 0.69 with the experimental ones. They are structurally quite homogeneous and topologically native-like, although some of the side chains and most of the hydrogen bonds are not in place.

q-bio.BM↗
arXiv2009

PLUMED: a portable plugin for free-energy calculations with molecular dynamics

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 the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.

physics.comp-ph↗
arXiv2008

Microscopic calculation and LDA of the spatial dependence of the pairing field with bare and induced interactions

The bare nucleon-nucleon interaction is essential for the production of pair correlations in nuclei, but an important contribution also arises from the induced interaction resulting from the exchange of collective vibrations between nucleons moving in time reversal states close to the Fermi energy. The pairing field resulting from the summed interaction is strongly peaked at the nuclear surface. It is possible to reproduce the detailed spatial dependence of this field using a Local Density Approximation (LDA) and a contact interaction, with parameters which are quite different from those commonly used in more phenomenological approaches.

nucl-th↗
arXiv2008

Medium polarization and finite size effects on the superfluidity of the inner crust of neutron stars

The 1S0 pairing gap associated with the inner crust of a neutron star is calculated, taking into account the coexistence of the nuclear lattice with the sea of free neutrons (finite size effects), as well as medium polarization effects associated with the exchange of density and spin fluctuations. Both effects are found to be important and to lead to an overall quenching of the pairing gap. This result, whose quantitative value is dependent on the effective interaction used to generate the single-particle levels, is a consequence of the balance between the attractive (repulsive) induced interaction arising from the exchange of density (spin) modes, balance which in turn is influenced by the presence of the protons and depends on the single-particle structure of the system.

nucl-th↗
arXiv2008

Vortex-nucleus interaction in the inner crust of neutron stars

The structure of a vortex in the inner crust of neutron stars is calculated within the framework of quantum mean field theory taking into account the interaction with the nuclei composing the Coulomb lattice. Making use of the results obtained with different nuclear interactions, the pinning energy, relevant in the study of glitches, is worked out. Quantal size and density dependent effects are found to be important.

astro-ph↗
arXiv2007

Metadynamic sampling of the free energy landscapes of proteins coupled with a Monte Carlo algorithm

Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing understanding on the general principles underlying the mechanism of protein folding. We show that it is possible to couple metadynamics and Monte Carlo algorithms to obtain the free energy of model proteins in a way which is computationally very economical.

cond-mat.stat-mech↗
arXiv2007

Exploring the Protein G Helix Free Energy Surface by Solute Tempering Metadynamics

The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling with an affordable computational effort. From the sampled free-energy surface we are able to reproduce a number of experimental observations, such as the fact that the lowest minimum corresponds to a globular conformation displaying some degree of beta-structure, that the helical state is metastable and involves only 65% of the chain. The calculations also show that the system populates consistently a pi-helix state and that the hydrophobic staple motif is present only in the free-energy minimum associated with the helices, and contributes to their stabilization. The use of metadynamics coupled with solute tempering results then particularly suitable to provide the thermodynamics of a short peptide, and its computational efficiency is promising to deal with larger proteins.

q-bio.BM↗
arXiv2007

Use of the Metropolis algorithm to simulate the dynamics of protein chains

The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of 1 degree on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.

q-bio.OT↗
arXiv2006

Medium polarization isotopic effects on nuclear binding energies

There exist several effective interactions whose parameters are fitted to force mean field predictions to reproduce experimental findings of finite nuclei and calculated properties of infinite nuclear matter. Exploiting this tecnique one can give a good description of nuclear binding energies. We present evidence that further progress can be made by taking into account medium polarization effects associated with surface and pairing vibrations.

nucl-th↗
arXiv2006

Quantum calculation of vortices in the inner crust of neutron stars

We study, within a quantum mechanical framework based on self-consistent mean field theory, the interaction between a vortex and a nucleus immersed in a sea of free neutrons, a scenario representative of the inner crust of neutron stars. Quantal finite size effects force the vortex core outside the nucleus, influencing vortex pinning in an important way.

nucl-th↗
arXiv2005

What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model

The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences, characterized by a low native energy, display three main thermodynamical phases, namely a coil-like phase, an unfolded globule and a folded phase (plus other two phases, namely frozen and random coil, populated only at extremes temperatures). Interestingly, the unfolded globule has some regions already structured. Poorly designed sequences, on the other hand, display a wide transition from the random coil to a frozen state. The comparison with the analytic theory of heteropolymers is discussed.

q-bio.BM↗