Publications SISSA
URI permanente per questa collezione
Sfogliare
Immissioni recenti
1 - 5 di 14827
-
PubblicazioneFrom gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields( 2026)Understanding RNA structural dynamics is essential for elucidating its biological functions, and molecular dynamics (MD) simulations provide an important atomistic complement to experimental approaches. However, the predictive power of MD is fundamentally limited by the accuracy of the underlying empirical force fields (FFs), particularly in capturing the delicate balance of nonbonded interactions. Here, we present a systematic reparameterization strategy that replaces the external gHBfix19 hydrogen-bond (H-bond) correction potential with an equivalent and easy-to-use NBfix Lennard-Jones representation of its main thermodynamic effects within the state-of-the-art OL3 RNA FF. Using a quantitatively converged temperature replica-exchange MD ensemble of the GAGA tetraloop, we employed a reweighting-based optimization protocol to derive NBfix parameters that reproduce the thermodynamic effects of the original gHBfix19 terms. Sequential optimization of the individual gHBfix19 components proved essential to ensure stable and transferable parameter refinement. The resulting fully reformulated NBfix-based variant, termed OL3CP-NBfix19, was validated on a representative set of RNA motifs, including tetranucleotides, A-form duplexes, and tetraloops. Across all tested systems, its performance is comparable to that of the reference gHBfix19 FF. By embedding the H-bond corrections directly into the standard nonbonded framework, the NBfix formulation eliminates external biasing potentials, simplifies practical deployment, and reduces computational overhead. Beyond this specific reparameterization, our results demonstrate a practical workflow for translating targeted H-bond corrections into native FF terms for efficient biomolecular simulations.
-
PubblicazioneRole of injection parameters in jet propagation through realistic binary neutron star merger environments( 2025)After the first multimessenger observation of a binary neutron star (BNS) merger powering a short-duration gamma-ray burst (GRB), GW170817-GRB 170817A, remarkable effort is ongoing to unravel the evolution of the collimated, relativistic outflow (or jet) that was launched during the merger and fed the GRB event, imprinting its angular structure onto the follow-up afterglow signal. Current theoretical models, based on relativistic magnetohydrodynamic (RMHD) simulations, offer detailed insights into the launch and propagation processes that govern jet evolution. Notably, these simulations point out that jet injection parameters, such as luminosity, magnetization, power decay time-scale, and launch time relative to merger, play a crucial role. However, the impact of these parameters is typically investigated within simplified jet propagation environments, lacking a direct connection with a realistic BNS merger aftermath. In this work, we present the first suite of 3-D RMHD simulations exploring the influence of such parameters on the propagation of magnetized incipient GRB jets injected into magnetized environments directly imported from the outcome of a general-relativistic MHD BNS merger simulation. Our results demonstrate that, alongside the injection parameters, the BNS merger environment has a central role in shaping the overall jet evolution. Specifically, under identical jet parameters, the fate of an incipient jet (whether it successfully breaks out or becomes choked) depends strongly on the properties of such an environment. Further quantitative comparison between realistic and simplified environments reveals major differences, emphasizing the importance of incorporating the former for accurate modelling.
-
PubblicazioneApproaching ballistic motion in 3D simulations of gamma-ray burst jets in realistic binary neutron star merger environments( 2025)Context. The concomitant observation of gravitational wave and electromagnetic signals from a binary neutron star (BNS) merger in 2017 confirmed that these events can produce relativistic jets responsible for short gamma-ray bursts (sGRBs). The complex interaction between the jet and the surrounding post-merger environment shapes the angular structure of the outflow, which is then imprinted in the prompt and afterglow sGRB emission. Aims. The outcome of relativistic (magneto)hydrodynamic simulations of jets piercing through post-merger environments is often used as input to compute afterglow signals that can be compared with observations. However, for reliable comparisons, the jet propagation should be followed until nearly ballistic regimes, in which the jet acceleration is essentially over and the angular structure is no longer evolving. This condition is typically reached in 2D simulations, but not in 3D ones. Our goal is to extend a (specific) jet simulation in 3D up to a nearly ballistic phase and analyse the overall dynamical evolution from the jet breakout. Methods. Our work is based on a previous 3D magnetohydrodynamic jet simulation employing a realistic environment imported from a BNS merger simulation, extended here far beyond the evolution time originally covered. After approximately 3 seconds of the jet evolution on the original spherical grid, we remapped the system into a uniform Cartesian grid and reached about 10 seconds without loss of resolution. Results. The specific jet considered here struggled to pierce the dense surroundings, resulting in a rather asymmetrical emerging outflow with a relatively low Lorentz factor. Analysis of the energy conversion processes and corresponding acceleration showed that at the end of our simulation, 98% of the energy is in kinetic form. Moreover, at that time the angular structure is frozen. We thus obtained suitable inputs for computing the afterglow emission. Our procedure is general and applicable to any jet simulation of the same kind.
-
PubblicazioneBlue phosphorene on Au(111): theoretical, spectroscopic and diffraction analysis reveal the role of single Au adatoms( 2024)In investigating the monoatomic layers of P, several stable two-dimensional (2D) allotropes have been theoretically predicted. Among them, single-layer blue phosphorus (BlueP) appears to deliver promising properties. After initial success, where the structure of BlueP triangular patches on Au(111) was conceived on the basis of scanning tunneling microscopy (STM) and density functional theory (DFT), the surface structure model was revisited multiple times with increasing accuracy and insight of theoretical calculations and experimental datasets. Interestingly, the quest for a reliable atomic structure model of BlueP on Au(111) turned out to be very contentious and challenging, particularly considering the possible incorporation of Au atoms in the 2D sheet of P. This article proposes an extended report on theoretical findings that can be extracted from DFT calculations of the orbital projected band structure and employed for an efficient comparison protocol between the calculations and experimental datasets obtained from angle-resolved photoemission spectroscopy (ARPES). The findings, together with experimental and simulated data from STM imaging and surface X-ray diffraction (SXRD), show a clear way to verify the presence and characterize the stabilizing effect of foreign atoms in 2D materials.
-
PubblicazioneB-sure: robustness tests for the detection of the tensor-to-scalar ratio from CMB observations( 2026)Current and future Cosmic Microwave Background (CMB) experiments target the measurement of the B-mode polarised signal, induced by primordial inflationary gravitational waves. Polarised Galactic foregrounds can bias this measurement and cause a false detection. Here we describe a robustness test for the validation of an eventual detection, using scattering transforms as statistical descriptor of component separated CMB maps. The proposed test is able to identify a false detection in ~90% of our simulations, in a realistic configuration.